quasitools: test-data/mutation

annotate test-data/mutation_db.tsv @ 2:a7093d5933a8 draft

planemo upload for repository https://github.com/phac-nml/quasitools commit de4309426401ce655435d6867b05c3673b9d086f

author	nml
date	Mon, 26 Mar 2018 14:23:30 -0400
parents	71976cfc9022
children

rev	line source
0 71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	1 #Gene Wildtype Position Mutation Category Surveillance Comment
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	2 PR L 10 F PIMinor No L10F is a common nonpolymorphic, PI-selected accessory mutation associated with reduced susceptibility to each of the PIs except ATV, SQV, and TPV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	3 PR L 10 I PIMinor No L10I/V are polymorphic, PI-selected accessory mutations that reduce PI susceptibility or increase the replication of viruses with other PI-resistance mutations.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	4 PR L 10 V PIMinor No L10I/V are polymorphic, PI-selected accessory mutations that reduce PI susceptibility or increase the replication of viruses with other PI-resistance mutations.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	5 PR L 10 R PIMinor No L10R/Y are rare, nonpolymorphic PI-selected accessory mutations. Their effects on PI susceptibility have not been well studied.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	6 PR L 10 Y PIMinor No L10R/Y are rare, nonpolymorphic PI-selected accessory mutations. Their effects on PI susceptibility have not been well studied.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	7 PR V 11 I PIMinor No V11I is a minimally polymorphic PI-resistance accessory mutation that is often selected in patients receiving DRV. It is associated with minimal reductions in DRV and FPV susceptibility. It is included in the Tibotec GSS for DRV. V11L is a nonpolymorphic accessory PI-resistance mutation that is also associated with minimal reductions in DRV and FPV susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	8 PR V 11 L PIMinor No V11I is a minimally polymorphic PI-resistance accessory mutation that is often selected in patients receiving DRV. It is associated with minimal reductions in DRV and FPV susceptibility. It is included in the Tibotec GSS for DRV. V11L is a nonpolymorphic accessory PI-resistance mutation that is also associated with minimal reductions in DRV and FPV susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	9 PR K 20 R Other No K20R is a highly polymorphic, PI-selected accessory mutation that improves HIV-1 replication fitness in viruses with other PI-resistance mutations.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	10 PR K 20 I PIMinor No K20I is the consensus amino acid in subtype G and CRF02_AG. In subtypes B and C, K20I is a PI-selected mutation that appears to reduce NFV susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	11 PR K 20 T PIMinor No K20T is a nonpolymorphic accessory PI-selected mutation that is associated with reduced susceptibility to each of the PIs except SQV and TPV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	12 PR K 20 M PIMinor No K20M/V are rare, relatively nonpolymorphic PI-selected mutations that have not been well studied.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	13 PR K 20 V PIMinor No K20M/V are rare, relatively nonpolymorphic PI-selected mutations that have not been well studied.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	14 PR L 23 I PIMinor Yes L23I is an uncommon nonpolymorphic mutation selected primarily by NFV. It causes low/intermediate-level resistance to NFV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	15 PR L 24 I PIMinor Yes L24I is a nonpolymorphic mutation selected by IDV and, less often, LPV. It reduces susceptibility to FPV, IDV, LPV, SQV, ATV and NFV. It increases susceptibility to TPV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	16 PR L 24 F PIMinor No L24F is an uncommon nonpolymorphic PI-selected mutation that appears to have a susceptibility profile similar to L24I. L24M is a rare nonpolymorphic PI-selected mutation that has not been well studied.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	17 PR L 24 M PIMinor No L24F is an uncommon nonpolymorphic PI-selected mutation that appears to have a susceptibility profile similar to L24I. L24M is a rare nonpolymorphic PI-selected mutation that has not been well studied.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	18 PR D 30 N PIMajor Yes D30N is a nonpolymorphic substrate-cleft mutation that causes high-level resistance to NFV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	19 PR V 32 I PIMajor Yes V32I is a nonpolymorphic substrate-cleft mutation associated with reduced susceptibility to each PI except SQV. It is included in the Tibotec DRV GSS.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	20 PR L 33 F PIMinor No L33F is a relatively nonpolymorphic accessory mutation selected by DRV, FPV, LPV, NFV and TPV. In combination with other PI-resistance mutations, L33F is associated with reduced susceptibility to these PIs. It is included in the Tibotec DRV GSS.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	21 PR L 33 I PIMinor No L33I is a relatively nonpolymorphic PI-selected mutation that appears to have minimal, if any, effects on PI susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	22 PR L 33 V Other No L33V is a polymorphism that does not appear to be selected by PIs or to be associated with reduced PI susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	23 PR E 35 G PIMinor No E35G is a relatively nonpolymorphic PI-selected mutation that is weakly associated with reduced NFV and TPV susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	24 PR K 43 T PIMinor No K43T is a nonpolymorphic PI-selected accessory mutation that, in combination with other PI-resistance mutations, is associated with reduced susceptibility to most PIs. It is also part of the GSS for TPV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	25 PR M 46 I PIMajor Yes M46I/L are nonpolymorphic PI-selected mutations that reduce susceptibility to IDV, NFV, FPV, LPV and ATV when present with other mutations. M46L also reduces susceptibility to TPV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	26 PR M 46 L PIMajor Yes M46I/L are nonpolymorphic PI-selected mutations that reduce susceptibility to IDV, NFV, FPV, LPV and ATV when present with other mutations. M46L also reduces susceptibility to TPV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	27 PR M 46 V PIMinor No M46I/L are nonpolymorphic PI-selected mutations that reduce susceptibility to IDV, NFV, FPV, LPV and ATV when present with other mutations. M46L also reduces susceptibility to TPV. M46V is a rare nonpolymorphic PI-selected mutation that has not been well studied.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	28 PR I 47 V PIMajor Yes I47V is a nonpolymorphic mutation selected by IDV, FPV, LPV and DRV. It is associated with reduced susceptibility to each of the PIs except SQV and ATV. I47V is included in the Tibotec DRV GSS.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	29 PR I 47 A PIMajor Yes I47A is a nonpolymorphic mutation selected by LPV. It usually occurs in combination with V32I and it confers high-level resistance to LPV and FPV and low/intermediate-resistance to the remaining PIs except ATV and SQV. It increases susceptibility to SQV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	30 PR G 48 V PIMajor Yes G48V is a nonpolymorphic substrate-cleft mutation selected by SQV and, less often, by IDV and LPV. It confers high-level resistance to SQV, intermediate-level resistance to ATV, and low-level resistance to NFV, IDV and LPV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	31 PR G 48 M PIMajor Yes G48V is a nonpolymorphic substrate-cleft mutation selected by SQV and, less often, by IDV and LPV. It confers high-level resistance to SQV, intermediate-level resistance to ATV, and low-level resistance to NFV, IDV and LPV. G48M is a 2-base pair nonpolymorphic mutation selected in patients who have received multiple PIs. It causes high-level resistance to SQV, intermediate-level resistance to ATV and NFV and low-level resistance to IDV and LPV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	32 PR G 48 A PIMajor No G48V causes high-level resistance to SQV, intermediate-level resistance to ATV and NFV, and low-level resistance to IDV and LPV. G48M is a less common mutation that appears to have similar effects on PI susceptibility. G48A/S/T/Q are rare nonpolymorphic PI-selected mutations that occur in patients who have received multiple PIs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	33 PR G 48 S PIMajor No G48V causes high-level resistance to SQV, intermediate-level resistance to ATV and NFV, and low-level resistance to IDV and LPV. G48M is a less common mutation that appears to have similar effects on PI susceptibility. G48A/S/T/Q are rare nonpolymorphic PI-selected mutations that occur in patients who have received multiple PIs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	34 PR G 48 T PIMajor No G48V causes high-level resistance to SQV, intermediate-level resistance to ATV and NFV, and low-level resistance to IDV and LPV. G48M is a less common mutation that appears to have similar effects on PI susceptibility. G48A/S/T/Q are rare nonpolymorphic PI-selected mutations that occur in patients who have received multiple PIs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	35 PR G 48 Q PIMajor No G48V causes high-level resistance to SQV, intermediate-level resistance to ATV and NFV, and low-level resistance to IDV and LPV. G48M is a less common mutation that appears to have similar effects on PI susceptibility. G48A/S/T/Q are rare nonpolymorphic PI-selected mutations that occur in patients who have received multiple PIs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	36 PR G 48 L PIMajor No G48V causes high-level resistance to SQV, intermediate-level resistance to ATV and NFV, and low-level resistance to IDV and LPV. G48M is a less common mutation that appears to have similar effects on PI susceptibility. G48A/S/T/Q are rare nonpolymorphic PI-selected mutations that occur in patients who have received multiple PIs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	37 PR I 50 L PIMajor Yes I50L is a nonpolymorphic substrate-cleft mutation selected by ATV. It causes intermediate/high-level resistance to ATV and increases susceptibility to the remaining PIs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	38 PR I 50 V PIMajor Yes I50V is a nonpolymorphic substrate-cleft mutation selected by FPV, LPV and DRV. It reduces susceptibility to these PIs and increases susceptibility to TPVI50V is included in the Tibotec DRV GSS.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	39 PR F 53 L PIMinor Yes F53L is a nonpolymorphic mutation selected primarily by SQV, IDV, ATV, and LPV. It reduces susceptibility primarily to ATV, SQV, and NFV. F53Y is a rare nonpolymorphic PI-selected mutation that has not been well studied.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	40 PR F 53 Y PIMinor Yes F53L is a nonpolymorphic mutation selected primarily by SQV, IDV, ATV, and LPV. It reduces susceptibility primarily to ATV, SQV, and NFV. F53Y is a rare nonpolymorphic PI-selected mutation that has not been well studied.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	41 PR I 54 V PIMajor Yes I54V is a nonpolymorphic mutation selected primarily by IDV and LPV. It reduces susceptibility to each of the PIs except DRV. It synergistically reduces PI susceptibility when present in combination with V82 mutations.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	42 PR I 54 T PIMajor Yes I54A/T/S are nonpolymorphic PI-selected mutations that occur almost exclusively in patients who have received multiple PIs. I54A/T/S are associated with reduced susceptibility to each of the PIs except DRV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	43 PR I 54 A PIMajor Yes I54A/T/S are nonpolymorphic PI-selected mutations that occur almost exclusively in patients who have received multiple PIs. I54A/T/S are associated with reduced susceptibility to each of the PIs except DRV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	44 PR I 54 S PIMajor Yes I54A/T/S are nonpolymorphic PI-selected mutations that occur almost exclusively in patients who have received multiple PIs. I54A/T/S are associated with reduced susceptibility to each of the PIs except DRV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	45 PR I 54 L PIMajor Yes I54L is a nonpolymorphic mutation selected by FPV, LPV and DRV. It reduces susceptibility to these PIs and possibly to ATV, IDV, NFV and SQV. It increases susceptibility to TPV. It is in the Tibotec DRV GSS.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	46 PR I 54 M PIMajor Yes I54M is a nonpolymorphic mutation selected by FPV, LPV and DRV. It reduces susceptibility to each of the PIs. It is in the Tibotec DRV GSS.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	47 PR Q 58 E PIMinor No Q58E is a nonpolymorphic accessory PI-selected mutation associated with reduced susceptibility to TPV and possibly other PIs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	48 PR A 71 T PIMinor No A71T/V are polymorphisms that occur in 2-3% of untreated persons. They increase in prevalence in persons receiving PIs. A71I/L are nonpolymorphic mutations that occur in viruses with multiple PI-resistance mutations.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	49 PR A 71 V PIMinor No A71T/V are polymorphisms that occur in 2-3% of untreated persons. They increase in prevalence in persons receiving PIs. A71I/L are nonpolymorphic mutations that occur in viruses with multiple PI-resistance mutations.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	50 PR A 71 I PIMinor No A71T/V are polymorphisms that occur in 2-3% of untreated persons. They increase in prevalence in persons receiving PIs. A71I/L are nonpolymorphic mutations that occur in viruses with multiple PI-resistance mutations.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	51 PR A 71 L PIMinor No A71T/V are polymorphisms that occur in 2-3% of untreated persons. They increase in prevalence in persons receiving PIs. A71I/L are nonpolymorphic mutations that occur in viruses with multiple PI-resistance mutations.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	52 PR G 73 S PIMinor Yes G73S/T/C/A are nonpolymorphic mutations that are selected primarily by ATV, IDV, NFV and SQV. They are associated with reduced susceptibility to these PIs and possibly to DRV, FPV and LPV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	53 PR G 73 T PIMinor Yes G73S/T/C/A are nonpolymorphic mutations that are selected primarily by ATV, IDV, NFV and SQV. They are associated with reduced susceptibility to these PIs and possibly to DRV, FPV and LPV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	54 PR G 73 C PIMinor Yes G73S/T/C/A are nonpolymorphic mutations that are selected primarily by ATV, IDV, NFV and SQV. They are associated with reduced susceptibility to these PIs and possibly to DRV, FPV and LPV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	55 PR G 73 A PIMinor Yes G73S/T/C/A are nonpolymorphic mutations that are selected primarily by ATV, IDV, NFV and SQV. They are associated with reduced susceptibility to these PIs and possibly to DRV, FPV and LPV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	56 PR G 73 V PIMinor No G73V is a nonpolymorphic PI-selected mutation that has not been well studied.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	57 PR T 74 P PIMinor No T74P is a nonpolymorphic PI-selected accessory mutation that occurs primarily in viruses from patients who have received multiple PIs. It is associated with reduced susceptibility to each of the PIs. It is included in the Boehringer-Ingelheim TPV and Tibotec DRV GSS.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	58 PR T 74 S PIMinor No T74S is a polymorphic mutation weakly selected by most PIs and associated with low-level resistance to NFV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	59 PR L 76 V PIMajor Yes L76V is a nonpolymorphic mutation selected by IDV, LPV and DRV. It reduces susceptibility to these PIs and to FPV. It increases susceptibility to ATV, SQV and TPV. L76V is included in the Tibotec DRV GSS.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	60 PR V 82 A PIMajor Yes V82A is a nonpolymorphic substrate-cleft mutation selected primarily by IDV and LPV. It reduces susceptibility to these PIs and causes cross-resistance to ATV and NFV. When it occurs in combination with additional PI-resistance mutations it is also associated with reduced susceptibility to SQV and FPV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	61 PR V 82 C PIMajor Yes V82C is an uncommon nonpolymorphic 2-base-pair substrate-cleft mutation that develops in viruses with multiple PI-resistance mutations from patients who received multiple PIs. Its effects on PI susceptibility have not been well studied.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	62 PR V 82 F PIMajor Yes V82F is a nonpolymorphic substrate-cleft mutation selected primarily in patients who have received multiple PIs. It causes reduced susceptibility to DRV, FPV, IDV, LPV and NFV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	63 PR V 82 I Other No V82I is a highly polymorphic substrate-cleft mutation that is not selected by PIs. It is the consensus amino acid in subtype G viruses.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	64 PR V 82 L PIMajor Yes V82L is an uncommon nonpolymorphic substrate-cleft mutation selected by TPV. It reduces TPV susceptibility but its effects on other PIs have not been well studied.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	65 PR V 82 M PIMajor Yes In most subtypes, V82M is a 2-base-pair substrate-cleft mutation that develops in viruses with multiple PI-resistance mutations from patients who received multiple PIs. In subtype G, V82M is a 1-base-pair mutation. V82M reduces susceptibility to IDV, LPV and possibly other PIs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	66 PR V 82 T PIMajor Yes V82T is a nonpolymorphic substrate-cleft mutation selected in patients who received IDV, TPV, or multiple PIs. It reduces susceptibility to these PIs and to ATV, LPV, and NFV. V82T is included in the Boehringer-Ingelheim TPV GSS. V82S is a nonpolymorphic mutation that appears to have a resistance profile similar to V82T.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	67 PR V 82 S PIMajor Yes V82T is a nonpolymorphic substrate-cleft mutation selected in patients who received IDV, TPV, or multiple PIs. It reduces susceptibility to these PIs and to ATV, LPV, and NFV. V82T is included in the Boehringer-Ingelheim TPV GSS. V82S is a nonpolymorphic mutation that appears to have a resistance profile similar to V82T.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	68 PR N 83 D PIMinor Yes N83D is a nonpolymorphic mutation selected primarily in patients who have received multiple PIs. It is associated with reduced susceptibility to ATV, IDV, NFV, SQV and TPV. It is included in the Boehringer-Ingelheim GSS for TPV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	69 PR I 84 V PIMajor Yes I84V is a nonpolymorphic substrate-cleft mutation selected by each of the PIs. It causes high-level resistance to ATV, FPV, IDV, NFV and SQV, intermediate-level resistance to LPV and TPV, and low-level resistance to DRV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	70 PR I 84 A PIMajor Yes I84A is a rare nonpolymorphic PI-selected substrate-cleft mutation associated with high-level resistance to each of the PIs. I84C is a rare nonpolymorphic PI-selected mutation associated with varying degrees of reduced susceptibility to each of the PIs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	71 PR I 84 C PIMajor Yes I84A is a rare nonpolymorphic PI-selected substrate-cleft mutation associated with high-level resistance to each of the PIs. I84C is a rare nonpolymorphic PI-selected mutation associated with varying degrees of reduced susceptibility to each of the PIs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	72 PR I 85 V Other Yes I85V is a nonpolymorphic PI-selected mutation. It has minimal, if any, effects on PI susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	73 PR N 88 D PIMinor Yes N88D is selected by NFV. In combination with D30N, it synergistically reduces susceptibility to NFV. It may also be associated with reduced susceptibility to ATV and SQV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	74 PR N 88 S PIMajor Yes N88S is a nonpolymorphic mutation selected by NFV and ATV. It causes high-level resistance to NFV and ATV and low-level resistance to IDV and SQV. It increases susceptibility to FPV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	75 PR N 88 T PIMajor No N88G/T are extremely rare nonpolymorphic PI-selected mutations that reduce susceptibility to NFV and ATV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	76 PR N 88 G PIMajor No N88G/T are extremely rare nonpolymorphic PI-selected mutations that reduce susceptibility to NFV and ATV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	77 PR L 89 V PIMinor No L89V is a nonpolymorphic accessory mutation selected by IDV, NFV, FPV, LPV and DRV. It reduces susceptibility to these PIs. L89V is included in the Tibotec DRV GSS (de Meyer 2008).
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	78 PR L 89 I Other No L89T/I are nonpolymorphic PI-selected mutation of uncertain phenotypic and clinical significance.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	79 PR L 89 T Other No L89T/I are nonpolymorphic PI-selected mutation of uncertain phenotypic and clinical significance.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	80 PR L 89 M Other No L89M is a common polymorphism that is not associated with reduced PI susceptibility. It is the consensus amino acid in most non-B subtypes.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	81 PR L 90 M PIMajor Yes L90M is a nonpolymorphic mutation selected primarily by SQV, NFV, IDV and LPV. It reduces susceptibility to each of the PIs except TPV and DRV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	82 RT E 40 F NRTI No E40F is a nonpolymorphic mutation selected by AZT and d4T. It usually occurs in combination with M41L, L210W and T215Y. In this context it is associated with reduced susceptibility to each of the NRTIs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	83 RT M 41 L NRTI Yes M41L is a TAM that usually occurs with T215Y. Together, M41L and T215Y confer high-level resistance to AZT and d4T and intermediate-level resistance to ddI, ABC and TDF. However, viruses with M41L + T215Y + M184V will exhibit intermediate-level resistance to AZT and d4T and low-level resistance to TDF.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	84 RT M 41 I Other No M41I is usually an artifact resulting from APOBEC3G-mediated hypermutation.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	85 RT E 44 A Other No E44A/D are minimally polymorphic accessory NRTI-resistance mutations that usually occur with multiple TAMs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	86 RT E 44 D Other No E44A/D are minimally polymorphic accessory NRTI-resistance mutations that usually occur with multiple TAMs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	87 RT A 62 V NRTI No A62V is an accessory mutation that often occurs in combination with the multinucleoside resistance mutations K65R or Q151M-. Alone it does not reduce NRTI susceptibility. A62V is widespread in subtype A viruses in former Soviet Union countries but is otherwise nonpolymorphic.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	88 RT K 65 R NRTI Yes K65R causes intermediate/high-level resistance to TDF, ddI, ABC and d4T (2 to 3-fold reduced susceptibility) and low to intermediate-level resistance to 3TC and FTC (5 to 7-fold reduced susceptibility). K65R increases susceptibility to AZT.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	89 RT K 65 N NRTI No K65R causes intermediate/high-level resistance to TDF, ddI, ABC and d4T (2 to 3-fold reduced susceptibility) and low to intermediate-level resistance to 3TC and FTC (5 to 7-fold reduced susceptibility). K65R increases susceptibility to AZT. K65N is a rare mutation with effects on NRTI susceptibility that are similar but weaker to those of K65R.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	90 RT K 65 E NRTI No K65R causes intermediate/high-level resistance to TDF, ddI, ABC and d4T (2 to 3-fold reduced susceptibility) and low to intermediate-level resistance to 3TC and FTC (5 to 7-fold reduced susceptibility). K65R increases susceptibility to AZT. K65E is an extremely rare NRTI-selected mutation with markedly reduced replication fitness.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	91 RT D 67 N NRTI Yes D67N is a nonpolymorphic TAM associated with low-level resistance to AZT and d4T. When present with other TAMs, it reduces susceptibility to ABC, TDF and ddI.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	92 RT D 67 E NRTI Yes D67N is a nonpolymorphic TAM associated with low-level resistance to AZT and d4T. When present with other TAMs, it reduces susceptibility to ABC, TDF and ddI. D67G/E/S/T/H are nonpolymorphic NRTI-selected mutations that also generally occur in viruses with multiple TAMs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	93 RT D 67 G NRTI Yes D67N is a nonpolymorphic TAM associated with low-level resistance to AZT and d4T. When present with other TAMs, it reduces susceptibility to ABC, TDF and ddI. D67G/E/S/T/H are nonpolymorphic NRTI-selected mutations that also generally occur in viruses with multiple TAMs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	94 RT D 67 S NRTI No D67N is a nonpolymorphic TAM associated with low-level resistance to AZT and d4T. When present with other TAMs, it reduces susceptibility to ABC, TDF and ddI. D67G/E/S/T/H are nonpolymorphic NRTI-selected mutations that also generally occur in viruses with multiple TAMs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	95 RT D 67 T NRTI No D67N is a nonpolymorphic TAM associated with low-level resistance to AZT and d4T. When present with other TAMs, it reduces susceptibility to ABC, TDF and ddI. D67G/E/S/T/H are nonpolymorphic NRTI-selected mutations that also generally occur in viruses with multiple TAMs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	96 RT D 67 Q NRTI No D67N is a nonpolymorphic TAM associated with low-level resistance to AZT and d4T. When present with other TAMs, it reduces susceptibility to ABC, TDF and ddI. D67G/E/S/T/H are nonpolymorphic NRTI-selected mutations that also generally occur in viruses with multiple TAMs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	97 RT D 67 H NRTI No D67N is a nonpolymorphic TAM associated with low-level resistance to AZT and d4T. When present with other TAMs, it reduces susceptibility to ABC, TDF and ddI. D67G/E/S/T/H are nonpolymorphic NRTI-selected mutations that also generally occur in viruses with multiple TAMs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	98 RT T 69 D NRTI Yes T69D is a nonpolymorphic mutation that reduces susceptibility to ddI and possibly d4T.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	99 RT T 69 G NRTI No T69G is a rare polymorphic mutation that usually occurs in viruses with a deletion at codon 67 and multiple NRTI-resistance mutations. It is associated with reduced susceptibility to ddI, d4T, ABC and possibly TDF.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	100 RT T 69 N NRTI No T69N is a relatively non-polymorphic mutation weakly selected in patients receiving NRTIs. Their effects on NRTI susceptibility have not been well studied.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	101 RT T 69 S Other No T69S/A/I/E are relatively non-polymorphic mutations weakly selected in patients receiving NRTIs. Their effects on NRTI susceptibility have not been well studied.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	102 RT T 69 A Other No T69S/A/I/E are relatively non-polymorphic mutations weakly selected in patients receiving NRTIs. Their effects on NRTI susceptibility have not been well studied.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	103 RT T 69 I Other No T69S/A/I/E are relatively non-polymorphic mutations weakly selected in patients receiving NRTIs. Their effects on NRTI susceptibility have not been well studied.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	104 RT T 69 E Other No T69S/A/I/E are relatively non-polymorphic mutations weakly selected in patients receiving NRTIs. Their effects on NRTI susceptibility have not been well studied.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	105 RT K 70 R NRTI Yes K70R causes intermediate-level resistance to AZT and possibly low-level resistance to d4T and TDF.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	106 RT K 70 E NRTI Yes K70E/G cause low/intermediate-level resistance (2 to 3-fold reduced susceptibility) to TDF, ABC, DDI and possibly 3TC and FTC. K70E increases susceptibility to AZT.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	107 RT K 70 G NRTI No K70E/G cause low/intermediate-level resistance (2 to 3-fold reduced susceptibility) to TDF, ABC, DDI and possibly 3TC and FTC. K70E increases susceptibility to AZT.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	108 RT K 70 Q NRTI No K70R causes intermediate-level resistance to AZT and possibly low-level resistance to d4T and TDF. K70E/G cause low/intermediate-level resistance (2 to 3-fold reduced susceptibility) to TDF, ABC, DDI and possibly 3TC and FTC. K70E increases susceptibility to AZT. K70Q/N/S/T are rare nonpolymorphic NRTI-selected mutations that appear to have resistance profiles similar to K70E/G.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	109 RT K 70 N NRTI No K70R causes intermediate-level resistance to AZT and possibly low-level resistance to d4T and TDF. K70E/G cause low/intermediate-level resistance (2 to 3-fold reduced susceptibility) to TDF, ABC, DDI and possibly 3TC and FTC. K70E increases susceptibility to AZT. K70Q/N/S/T are rare nonpolymorphic NRTI-selected mutations that appear to have resistance profiles similar to K70E/G.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	110 RT K 70 S NRTI No K70R causes intermediate-level resistance to AZT and possibly low-level resistance to d4T and TDF. K70E/G cause low/intermediate-level resistance (2 to 3-fold reduced susceptibility) to TDF, ABC, DDI and possibly 3TC and FTC. K70E increases susceptibility to AZT. K70Q/N/S/T are rare nonpolymorphic NRTI-selected mutations that appear to have resistance profiles similar to K70E/G.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	111 RT K 70 T NRTI No K70R causes intermediate-level resistance to AZT and possibly low-level resistance to d4T and TDF. K70E/G cause low/intermediate-level resistance (2 to 3-fold reduced susceptibility) to TDF, ABC, DDI and possibly 3TC and FTC. K70E increases susceptibility to AZT. K70Q/N/S/T are rare nonpolymorphic NRTI-selected mutations that appear to have resistance profiles similar to K70E/G.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	112 RT L 74 I NRTI Yes L74V/I cause high-level resistance to ddI and intermediate-level resistance to ABC. L74V increases susceptibility to AZT and TDF, but this increase is of uncertain clinical significance.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	113 RT L 74 V NRTI Yes L74V/I cause high-level resistance to ddI and intermediate-level resistance to ABC. L74V increases susceptibility to AZT and TDF, but this increase is of uncertain clinical significance.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	114 RT V 75 I NRTI No V75I is a relatively nonpolymorphic accessory mutation that usually occurs in combination with the multi-nucleoside resistance mutations F77L, F116Y and Q151M. V75I occasionally occurs alone and in this context its clinical significance is unknown.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	115 RT V 75 T NRTI Yes V75T causes high-level d4T resistance and intermediate-level ddI resistance.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	116 RT V 75 M NRTI Yes V75M appears to cause intermediate-level d4T resistance and low-level ddI resistance.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	117 RT V 75 S NRTI Yes V75S/A/L are nonpolymorphic mutations that appear to reduce susceptibility to d4T and ddI.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	118 RT V 75 A NRTI Yes V75S/A/L are nonpolymorphic mutations that appear to reduce susceptibility to d4T and ddI.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	119 RT V 75 L NRTI No V75S/A/L are nonpolymorphic mutations that appear to reduce susceptibility to d4T and ddI.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	120 RT F 77 L NRTI Yes F77L usually occurs in combination with the multinucleoside resistance mutations F116Y and Q151M.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	121 RT Y 115 F NRTI Yes Y115F causes intermediate-level resistance to ABC and low-level resistance to TDF.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	122 RT F 116 Y NRTI Yes F116Y usually occurs in combination with the multinucleoside resistance mutations F77L and Q151M.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	123 RT V 118 I Other No V118I is a polymorphic accessory NRTI-resistance mutation that occurs in combination with multiple TAMs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	124 RT Q 151 M NRTI Yes Q151M causes intermediate/high-level resistance to AZT, ddI, d4T and ABC and low-level resistance to TDF, 3TC and FTC. In combination with mutations at the associated positions 62, 75, 77, and 116, Q151M confers high-level resistance to AZT, ddI, d4T and ABC and intermediate-level resistance to TDF, 3TC and FTC.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	125 RT Q 151 L NRTI No Q151M causes intermediate/high-level resistance to AZT, ddI, d4T and ABC and low-level resistance to TDF, 3TC and FTC. In combination with mutations at the associated positions 75, 77, and 116, Q151M confers high-level resistance to AZT, ddI, d4T and ABC and intermediate-level resistance to TDF, 3TC and FTC. Q151L is an extremely rare transitional mutation that may precede the emergence of the Q151M.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	126 RT M 184 V NRTI Yes M184V/I cause high-level resistance to 3TC and FTC and low-level resistance to ddI and ABC. However, M184V/I are not contraindications to continued treatment with 3TC or FTC because they increase susceptibility to AZT, TDF and d4T and are associated with clinically significant reductions in HIV-1 replication. In combination with K101E or E138K, M184I synergistically reduces RPV susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	127 RT M 184 I NRTI Yes M184V/I cause high-level resistance to 3TC and FTC and low-level resistance to ddI and ABC. However, M184V/I are not contraindications to continued treatment with 3TC or FTC because they increase susceptibility to AZT, TDF and d4T and are associated with clinically significant reductions in HIV-1 replication. In combination with K101E or E138K, M184I synergistically reduces RPV susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	128 RT L 210 W NRTI Yes L210W usually occurs in combination with M41L and T215Y. The combination of M41, L210W and T215Y causes high-level resistance to AZT and d4T and intermediate to high-level resistance to ddI, ABC and TDF.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	129 RT L 210 F Other No L210F/S are rare mutations not associated with NRTI-resistance.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	130 RT L 210 S Other No L210F/S are rare mutations not associated with NRTI-resistance.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	131 RT T 215 Y NRTI Yes T215Y is a TAM which causes intermediate/high-level resistance to AZT and d4T and low-level resistance to ABC, ddI, and TDF.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	132 RT T 215 F NRTI Yes T215F is a TAM that causes intermediate/high-level resistance to AZT and d4T and low-level resistance to ABC, ddI and TDF. Compared with T215Y, T215F occurs more commonly with the Type II TAMs (D67N, K70R, and/or K219E) and in this context, it affects susceptibility to TDF, ABC, and ddI less markedly than T215Y.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	133 RT T 215 S NRTI Yes T215Y/F cause intermediate/high-level resistance to AZT and d4T and low-level resistance to ABC, ddI and TDF. T215S/C/D/E/I/V/N/A/L do not reduce NRTI susceptibility but arise from viruses that once contained T215Y/F. The presence of one of these revertant mutations suggests the possibility that the patient may have once harbored a majority virus population with T215Y/F.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	134 RT T 215 C NRTI Yes T215Y/F cause intermediate/high-level resistance to AZT and d4T and low-level resistance to ABC, ddI and TDF. T215S/C/D/E/I/V/N/A/L do not reduce NRTI susceptibility but arise from viruses that once contained T215Y/F. The presence of one of these revertant mutations suggests the possibility that the patient may have once harbored a majority virus population with T215Y/F.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	135 RT T 215 D NRTI Yes T215Y/F cause intermediate/high-level resistance to AZT and d4T and low-level resistance to ABC, ddI and TDF. T215S/C/D/E/I/V/N/A/L do not reduce NRTI susceptibility but arise from viruses that once contained T215Y/F. The presence of one of these revertant mutations suggests the possibility that the patient may have once harbored a majority virus population with T215Y/F.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	136 RT T 215 E NRTI Yes T215Y/F cause intermediate/high-level resistance to AZT and d4T and low-level resistance to ABC, ddI and TDF. T215S/C/D/E/I/V/N/A/L do not reduce NRTI susceptibility but arise from viruses that once contained T215Y/F. The presence of one of these revertant mutations suggests the possibility that the patient may have once harbored a majority virus population with T215Y/F.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	137 RT T 215 I NRTI Yes T215Y/F cause intermediate/high-level resistance to AZT and d4T and low-level resistance to ABC, ddI and TDF. T215S/C/D/E/I/V/N/A/L do not reduce NRTI susceptibility but arise from viruses that once contained T215Y/F. The presence of one of these revertant mutations suggests the possibility that the patient may have once harbored a majority virus population with T215Y/F.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	138 RT T 215 V NRTI Yes T215Y/F cause intermediate/high-level resistance to AZT and d4T and low-level resistance to ABC, ddI and TDF. T215S/C/D/E/I/V/N/A/L do not reduce NRTI susceptibility but arise from viruses that once contained T215Y/F. The presence of one of these revertant mutations suggests the possibility that the patient may have once harbored a majority virus population with T215Y/F.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	139 RT T 215 A NRTI No T215Y/F cause intermediate/high-level resistance to AZT and d4T and low-level resistance to ABC, ddI and TDF. T215S/C/D/E/I/V/N/A/L do not reduce NRTI susceptibility but arise from viruses that once contained T215Y/F. The presence of one of these revertant mutations suggests the possibility that the patient may have once harbored a majority virus population with T215Y/F.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	140 RT T 215 L NRTI No T215Y/F cause intermediate/high-level resistance to AZT and d4T and low-level resistance to ABC, ddI and TDF. T215S/C/D/E/I/V/N/A/L do not reduce NRTI susceptibility but arise from viruses that once contained T215Y/F. The presence of one of these revertant mutations suggests the possibility that the patient may have once harbored a majority virus population with T215Y/F.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	141 RT T 215 N NRTI No T215Y/F cause intermediate/high-level resistance to AZT and d4T and low-level resistance to ABC, ddI and TDF. T215S/C/D/E/I/V/N/A/L do not reduce NRTI susceptibility but arise from viruses that once contained T215Y/F. The presence of one of these revertant mutations suggests the possibility that the patient may have once harbored a majority virus population with T215Y/F.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	142 RT K 219 Q NRTI Yes K219Q/E are accessory TAMS associated with reduced susceptibility to AZT and possibly d4T.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	143 RT K 219 E NRTI Yes K219Q/E are accessory TAMS associated with reduced susceptibility to AZT and possibly d4T.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	144 RT K 219 N NRTI Yes K219N/R are accessory TAMS that usually occur in combination with multiple other TAMs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	145 RT K 219 R NRTI Yes K219N/R are accessory TAMS that usually occur in combination with multiple other TAMs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	146 RT K 219 W NRTI No K219W is an uncommon NRTI-selected mutation
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	147 RT K 66 d NRTI No Amino acid deletions (d) between codons 66 to 71 are rare and usually occur in combination with multiple TAMs, the Q151M mutation complex, or K65R. Deletions at position 67 are more often associated with multiple TAMs. Deletions at position 69 are more often associated with either the Q151M complex or K65R.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	148 RT D 67 d NRTI No Amino acid deletions (d) between codons 66 to 71 are rare and usually occur in combination with multiple TAMs, the Q151M mutation complex, or K65R. Deletions at position 67 are more often associated with multiple TAMs. Deletions at position 69 are more often associated with either the Q151M complex or K65R.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	149 RT S 68 d NRTI No Amino acid deletions (d) between codons 66 to 71 are rare and usually occur in combination with multiple TAMs, the Q151M mutation complex, or K65R. Deletions at position 67 are more often associated with multiple TAMs. Deletions at position 69 are more often associated with either the Q151M complex or K65R.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	150 RT T 69 d NRTI No Amino acid deletions (d) between codons 66 to 71 are rare and usually occur in combination with multiple TAMs, the Q151M mutation complex, or K65R. Deletions at position 67 are more often associated with multiple TAMs. Deletions at position 69 are more often associated with either the Q151M complex or K65R.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	151 RT K 70 d NRTI No Amino acid deletions (d) between codons 66 to 71 are rare and usually occur in combination with multiple TAMs, the Q151M mutation complex, or K65R. Deletions at position 67 are more often associated with multiple TAMs. Deletions at position 69 are more often associated with either the Q151M complex or K65R.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	152 RT W 71 d NRTI No Amino acid deletions (d) between codons 66 to 71 are rare and usually occur in combination with multiple TAMs, the Q151M mutation complex, or K65R. Deletions at position 67 are more often associated with multiple TAMs. Deletions at position 69 are more often associated with either the Q151M complex or K65R.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	153 RT K 66 i NRTI No Double amino acid insertions between codons 66 to 71 most often align to codon 69 and occur in less than 1% of heavily treated persons. Together with TAMs, they confer high-level resistance to AZT, d4T, ddI, ABC and TDF and intermediate/high-level resistance to 3TC and FTC.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	154 RT D 67 i NRTI No Double amino acid insertions between codons 66 to 71 most often align to codon 69 and occur in less than 1% of heavily treated persons. Together with TAMs, they confer high-level resistance to AZT, d4T, ddI, ABC and TDF and intermediate/high-level resistance to 3TC and FTC.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	155 RT S 68 i NRTI No Double amino acid insertions between codons 66 to 71 most often align to codon 69 and occur in less than 1% of heavily treated persons. Together with TAMs, they confer high-level resistance to AZT, d4T, ddI, ABC and TDF and intermediate/high-level resistance to 3TC and FTC.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	156 RT T 69 i NRTI Yes Double amino acid insertions between codons 66 to 71 most often align to codon 69 and occur in less than 1% of heavily treated persons. Together with TAMs, they confer high-level resistance to AZT, d4T, ddI, ABC and TDF and intermediate/high-level resistance to 3TC and FTC.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	157 RT K 70 i NRTI No Double amino acid insertions between codons 66 to 71 most often align to codon 69 and occur in less than 1% of heavily treated persons. Together with TAMs, they confer high-level resistance to AZT, d4T, ddI, ABC and TDF and intermediate/high-level resistance to 3TC and FTC.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	158 RT W 71 i NRTI No Double amino acid insertions between codons 66 to 71 most often align to codon 69 and occur in less than 1% of heavily treated persons. Together with TAMs, they confer high-level resistance to AZT, d4T, ddI, ABC and TDF and intermediate/high-level resistance to 3TC and FTC.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	159 RT V 90 I NNRTI No V90I is a polymorphic accessory mutation that is weakly selected in patients by each of the NNRTIs. It has a weight of 1.0 in the Tibotec ETR genotypic susceptibility score but is associated with minimal, if any, detectable reduction in NNRTI susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	160 RT A 98 G NNRTI No A98G is a nonpolymorphic accessory mutation that reduces NVP susceptibility by ~5-fold and EFV susceptibility by about 3-fold. It has a weight of 1.0 in the Tibotec ETR genotypic susceptibility score.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	161 RT L 100 I NNRTI Yes L100I is a nonpolymorphic mutation that usually occurs in combination with K103N. In this setting it causes high-level resistance to NVP and EFV (>50-fold reduced susceptibility), high-level resistance to RPV (>10-fold reduced susceptibility) and intermediate-level resistance to ETR (~5-fold reduced susceptibility). It has a weight of 2.5 in the Tibotec ETR genotypic susceptibility score.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	162 RT L 100 V NNRTI No L100V is an extremely rare nonpolymorphic mutation associated with 5 to 10-fold reduced susceptibility to NVP and EFV. It may also reduce susceptibility to ETR and RPV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	163 RT K 101 P NNRTI Yes K101P is a nonpolymorphic mutation that causes high-level resistance (>50-fold reduced susceptibility) to NVP, EFV and RPV and intermediate resistance (~5-fold reduced susceptibility) to ETR. It has a weight of 2.5 in the Tibotec ETR genotypic susceptibility score.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	164 RT K 101 E NNRTI Yes K101E is a nonpolymorphic mutation that causes intermediate resistance to NVP (~5-fold reduced susceptibility) and low-level resistance (~2-fold reduced susceptibility) to EFV, ETR and RPV. It has a weight of 1.0 in the Tibotec ETR genotypic susceptibility score. In combination with M184I it reduces RPV susceptibility by about 5-fold.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	165 RT K 101 H NNRTI No K101H is a nonpolymorphic accessory NNRTI-resistance mutation selected by NVP, EFV and ETR. When present with other NNRTI-resistance mutations, K101H further reduces susceptibility to these NNRTIs. It has a weight of 1.0 in the Tibotec ETR genotypic susceptibility score.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	166 RT K 101 N Other No K101N/A/T are uncommon nonpolymorphic NNRTI-selected mutation of uncertain phenotypic and clinical significance.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	167 RT K 101 Q Other No K101Q is a relatively nonpolymorphic mutation that is weakly selected in patients receiving NVP and EFV. It is of uncertain phenotypic and clinical significance.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	168 RT K 101 R Other No K101R is an uncommon polymorphism that is not associated with reduced NNRTI susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	169 RT K 103 N NNRTI Yes K103N is a nonpolymorphic mutation that causes high-level resistance to NVP (~50-fold reduced susceptibility) and EFV (~20-fold reduced susceptibility).
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	170 RT K 103 S NNRTI Yes K103S is a nonpolymorphic mutation that causes intermediate/high-level resistance to NVP and low/intermediate-level resistance to EFV. Because K103S is a 2-bp change from the wildtype K, patients with K103S may be more likely to harbor K103N (which is just a 1-bp change from wildtype).
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	171 RT K 103 T NNRTI No K103T is an extremely rare nonpolymorphic mutation that appears to cause intermediate/high-level resistance to NVP (~10-fold reduction in susceptibility), but it has little if any effect on EFV susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	172 RT K 103 H NNRTI No K103H is a rare nonpolymorphic mutation that causes high-level resistance (~20-fold reduction in susceptibility) to NVP and EFV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	173 RT K 103 R Other No K103R is a polymorphic mutation that by alone has no effect on NNRTI susceptibility. However, in combination with V179D (and possibly V179E), it reduces NVP and EFV susceptibility about 15-fold.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	174 RT K 103 E NNRTI No K103E/Q are rare mutations that have not been associated with reduced susceptibility to the current NNRTIs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	175 RT K 103 Q NNRTI No K103E/Q are rare mutations that have not been associated with reduced susceptibility to the current NNRTIs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	176 RT V 106 A NNRTI Yes V106A is a nonpolymorphic mutation that causes high-level resistance to NVP (~50-fold reduced susceptibility) and intermediate-level resistance to EFV (~5-fold reduction in susceptibility). Together, V106A and F227L cause high-level resistance to both NVP and EFV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	177 RT V 106 M NNRTI Yes V106M is a nonpolymorphic mutation that causes high-level resistance (>30-fold reduced susceptibility) to NVP and EFV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	178 RT V 106 I NNRTI No V106I is a polymorphic NNRTI-selected accessory mutation. It has a weight of 1.5 in the Tibotec ETR genotypic susceptibility score. It has minimal, if any, effect on NNRTI susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	179 RT V 108 I NNRTI No V108I is a relatively nonpolymorphic accessory mutation selected in patients receiving NVP, EFV and ETR. It causes low-level resistance (~2-fold reduction in susceptibility) to NVP and EFV. It does not appear to reduce susceptibility to ETR or RPV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	180 RT I 132 M Other No I132M is an extremely rare nonpolymorphic mutation that reduces NVP and EFV susceptibility in biochemical assays. I132L is a more common, nonpolymorphic NNRTI-selected mutation that has not been well studied.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	181 RT I 132 L Other No I132M is an extremely rare nonpolymorphic mutation that reduces NVP and EFV susceptibility in biochemical assays. I132L is a more common, nonpolymorphic NNRTI-selected mutation that has not been well studied.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	182 RT E 138 K NNRTI No E138K is a nonpolymorphic mutation selected in a high proportion of patients receiving RPV. Alone it causes low-level RPV resistance (2 to 3-fold reduced susceptibility). However, in combination with the NRTI-resistance mutation M184I it appears sufficient to cause virological failure on an RPV-containing regimen. E138K causes low-level cross-resistance to ETR but minimal, if any, cross-resistance to NVP and EFV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	183 RT E 138 A NNRTI No E138A is a common polymorphic accessory mutation weakly selected in patients receiving ETR and RPV. It reduces ETR and RPV susceptibility ~2-fold. It has a weight of 1.5 in the Tibotec ETR genotypic susceptibility score.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	184 RT E 138 G NNRTI No E138Q/G are nonpolymorphic accessory mutations frequently selected in patients receiving ETR and RPV and occasionally in patients receiving NVP and EFV. E138Q/G are associated with 2 to 3-fold reduced susceptibility to ETR and RPV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	185 RT E 138 Q NNRTI No E138Q/G are nonpolymorphic accessory mutations frequently selected in patients receiving ETR and RPV and occasionally in patients receiving NVP and EFV. E138Q/G are associated with 2 to 3-fold reduced susceptibility to ETR and RPV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	186 RT E 138 R NNRTI No E138R is a rare nonpolymorphic accessory mutation selected in vitro by RPV. It is associated with 2 to 3-fold reduced susceptibility to ETR and RPV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	187 RT V 179 D NNRTI No V179D is a polymorphic accessory mutation selected in patients receiving EFV. It reduces NVP and EFV susceptibility by 2 to 5-fold and ETR and RPV susceptibility ~2-fold. The combination of V179D and K103R act synergistically to reduce NVP and EFV susceptibility >10-fold. V179D has a weight of 1.0 in the Tibotec ETR GSS. V179E is a nonpolymorphic mutation infrequently selected by NVP and EFV. V179E appears to be similar to V179D in its effects on NNRTIs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	188 RT V 179 E NNRTI No V179D is a polymorphic accessory mutation selected in patients receiving EFV. It reduces NVP and EFV susceptibility by 2 to 5-fold and ETR and RPV susceptibility ~2-fold. The combination of V179D and K103R act synergistically to reduce NVP and EFV susceptibility >10-fold. V179D has a weight of 1.0 in the Tibotec ETR GSS. V179E is a nonpolymorphic mutation infrequently selected by NVP and EFV. V179E appears to be similar to V179D in its effects on NNRTIs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	189 RT V 179 F NNRTI Yes V179F is a nonpolymorphic mutation frequently selected in patients receiving ETR. It nearly always occurs in combination with Y181C. Alone V179F has little effect on NNRTI susceptibility. In combination with Y181C, however, it is associated with high-level ETR and RPV resistance (>10-fold reduced susceptibility). It has a weight of 1.5 in the Tibotec ETR GSS.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	190 RT V 179 T NNRTI No V179T is a rare nonpolymorphic mutation infrequently selected in patients receiving NNRTIs. It is associated with minimal reductions in ETR and RPV susceptibility. It has a weight of 1.0 in the Tibotec ETR GSS.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	191 RT V 179 L NNRTI No V179L is a rare nonpolymorphic mutation infrequently selected in patients receiving NVP, EFV and RPV. Its effects on NNRTI susceptibility have not been well studied. It is listed as an RPV-associated drug-resistance mutation in the RPV package insert.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	192 RT V 179 I Other No V179I is a polymorphic mutation that is frequently selected in patients receiving ETR and RPV. It has little, if any, effect on NNRTI susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	193 RT Y 181 C NNRTI Yes Y181C is a nonpolymorphic mutation selected in patients receiving NVP, ETR and RPV. It reduces susceptibility to NVP, ETR, RPV, and EFV by >50-fold, 5-fold, 3-fold, and 2-fold, respectively. Although Y181C itself reduces EFV susceptibility by only 2-fold, it is associated with a reduced response to an EFV-containing regimen because viruses with this mutation often harbor additional minority variant NNRTI-resistance mutations. Y181C has a weight of 2.5 in the Tibotec ETR GSS.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	194 RT Y 181 I NNRTI Yes Y181I/V are 2-base pair nonpolymorphic mutations selected by NVP and ETR. Y181I/V cause high-level resistance to NVP (>50-fold reduced susceptibility) and to ETR and RVP (10 to 15-fold reduced susceptibility). Y181I/V each have a weight of 3.0 in the Tibotec ETR genotypic susceptibility score.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	195 RT Y 181 V NNRTI Yes Y181I/V are 2-base pair nonpolymorphic mutations selected by NVP and ETR. Y181I/V cause high-level resistance to NVP (>50-fold reduced susceptibility) and to ETR and RVP (10 to 15-fold reduced susceptibility). Y181I/V each have a weight of 3.0 in the Tibotec ETR genotypic susceptibility score.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	196 RT Y 181 F NNRTI No Y181F/S/G are rare nonpolymorphic NNRTI-associated mutations that are usually present as part of an electrophoretic mixture. They are likely to represent transitional mutations between Y and I or V.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	197 RT Y 181 S NNRTI No Y181F/S/G are rare nonpolymorphic NNRTI-associated mutations that are usually present as part of an electrophoretic mixture. They are likely to represent transitional mutations between Y and I or V.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	198 RT Y 181 G NNRTI No Y181F/S/G are rare nonpolymorphic NNRTI-associated mutations that are usually present as part of an electrophoretic mixture. They are likely to represent transitional mutations between Y and I or V.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	199 RT Y 188 C NNRTI Yes Y188C is a nonpolymorphic mutation selected in patients receiving NVP and EFV. It confers high-level resistance to NVP (>50-fold reduced susceptibility) and EFV (~20-fold reduced susceptibility).
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	200 RT Y 188 H NNRTI Yes Y188H is a nonpolymorphic mutation selected in patients receiving NVP and EFV. It causes about 5 to 10-fold reduced susceptibility to NVP and EFV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	201 RT Y 188 L NNRTI Yes Y188L is a nonpolymorphic mutation that causes high-level resistance (>50-fold reduced susceptibility) to NVP and EFV and intermediate/high-level resistance (5-fold reduced susceptibility) to RPV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	202 RT Y 188 F NNRTI No Y188F is a rare nonpolymorphic NNRTI-associated mutations that is usually present as part of an electrophoretic mixture. It appears to represent a transitional mutation between Y and L.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	203 RT G 190 A NNRTI Yes G190A is a nonpolymorphic mutation that causes high-level resistance to NVP (>50-fold reduced susceptibility) and intermediate resistance to EFV (5 to 10-fold reduced susceptibility). It has a weight of 1.0 in the Tibotec ETR GSS but does not appear to be selected by ETR or RPV or to reduce their in vitro susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	204 RT G 190 S NNRTI Yes G190S is a nonpolymorphic mutation that causes high-level resistance to NVP and EFV (>50-fold reduced susceptibility). It has a weight of 1.5 in the Tibotec ETR genotypic susceptibility score but does not appear to be selected by ETR or RPV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	205 RT G 190 E NNRTI Yes G190E/Q are nonpolymorphic mutations that cause high-level resistance to NVP and EFV (>50-fold reduced susceptibility). Both mutations also appear to be associated with high-level resistance (>10-fold reduced susceptibility) to RPV and ETR.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	206 RT G 190 Q NNRTI No G190E/Q are nonpolymorphic mutations that cause high-level resistance to NVP and EFV (>50-fold reduced susceptibility). Both mutations also appear to be associated with high-level resistance (>10-fold reduced susceptibility) to RPV and ETR.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	207 RT G 190 C NNRTI No G190C/T/V are rare nonpolymorphic mutations that cause high-level resistance to NVP and EFV (>50-fold reduced susceptibility). Their effects on ETR and RPV susceptibility are not known.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	208 RT G 190 T NNRTI No G190C/T/V are rare nonpolymorphic mutations that cause high-level resistance to NVP and EFV (>50-fold reduced susceptibility). Their effects on ETR and RPV susceptibility are not known.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	209 RT G 190 V NNRTI No G190C/T/V are rare nonpolymorphic mutations that cause high-level resistance to NVP and EFV (>50-fold reduced susceptibility). Their effects on ETR and RPV susceptibility are not known.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	210 RT H 221 Y NNRTI No H221Y is a nonpolymorphic accessory NNRTI-selected mutation that frequently occurs in combination with Y181C. Alone it has minimal detectable effects on NNRTI susceptibility. It is frequently selected in patients receiving RPV (Rimsky 2012, Tibotec 2012).
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	211 RT P 225 H NNRTI Yes P225H is a nonpolymorphic EFV-selected mutation that usually occurs in combination with K103N. The combination of P225H and K103N causes a >50-fold reduction in EFV susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	212 RT F 227 C NNRTI No F227C is an extremely rare nonpolymorphic mutation selected in patients receiving RPV and in vitro by ETR and RPV. It usually occurs in combination with other NNRTI-resistance mutations and in this context it is associated with high-level resistance to each of the NNRTIs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	213 RT F 227 L NNRTI No F227L is a nonpolymorphic mutation that usually occurs in combination with V106A. In this setting it is associated with high-level resistance to NVP and EFV.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	214 RT M 230 L NNRTI Yes M230L is an uncommon nonpolymorphic mutation selected in patients receiving EFV, NVP, and RPV. It causes intermediate to high-level resistance to each of the NNRTIs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	215 RT M 230 I NNRTI No M230I is an extremely rare mutation selected in vitro by RPV. Its effects on NNRTI susceptibility have not been well studied.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	216 RT P 236 L NNRTI No P236L is a nonpolymorphic mutation that causes high-level DLV resistance but does not reduce susceptibility to any other NNRTIs.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	217 RT K 238 T NNRTI No K238T is a nonpolymorphic mutation selected in patients receiving NVP and EFV. It usually occurs in combination with K103N. It reduces susceptibility to NVP and EFV by about 5-fold. It may also reduce susceptibility to ETR and RPV. K238N is a nonpolymorphic accessory mutation that is also selected by NVP and EFV. It appears to have minimal, if any, effects on NNRTI susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	218 RT K 238 N NNRTI No K238T is a nonpolymorphic mutation selected in patients receiving NVP and EFV. It usually occurs in combination with K103N. It reduces susceptibility to NVP and EFV by about 5-fold. It may also reduce susceptibility to ETR and RPV. K238N is a nonpolymorphic accessory mutation that is also selected by NVP and EFV. It appears to have minimal, if any, effects on NNRTI susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	219 RT K 238 R Other No K238R is a common polymorphism that does not reduce NNRTI susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	220 RT Y 318 F NNRTI No Y318F is an uncommon mutation that causes intermediate-level NVP resistance and potentially low-level EFV resistance.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	221 RT N 348 I NNRTI No N348I is a nonpolymorphic accessory mutation selected by the NRTIs AZT and d4T and by NVP and EFV. Alone it reduces AZT and NVP susceptibility by about 3-fold and EFV susceptibility by 2-fold.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	222 IN H 51 Y Accessory No H51Y is an uncommon nonpolymorphic accessory mutation selected in patients receiving RAL and EVG. It is also selected in vitro by EVG and DTG. Alone, H51Y reduces EVG susceptibility 2 to 3-fold. It does not reduce RAL or DTG susceptibility. However, the combination of H51Y and R263K is associated with ~5-fold reduced DTG susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	223 IN T 66 A Major Yes T66A is a nonpolymorphic mutation selected in patients receiving EVG and RAL, usually occurring in combination with other INI-resistance mutations. It reduces EVG susceptibility by ~10-fold. It does not appear to reduce RAL or DTG susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	224 IN T 66 K Major Yes T66K is a nonpolymorphic mutation selected in patients receiving EVG. It is associated with 40 to 80-fold reduced EVG susceptibility, 10 to 20-fold reduced RAL susceptibility and 2-fold reduced DTG susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	225 IN T 66 I Major Yes T66I is a nonpolymorphic mutation selected in patients receiving EVG. T66I decreases EVG susceptibility by ~15-fold but does not reduce RAL or DTG susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	226 IN L 68 V Accessory No L68V is a polymorphic accessory mutation reported in patients receiving EVG. It may synergistically reduce EVG susceptibility in combination with E92Q.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	227 IN L 74 M Accessory No L74M is a polymorphic accessory mutation selected in patients receiving RAL, EVG, and DTG. Alone, it does not reduce INI susceptibility. But when it occurs in combination with other INI-resistance mutations, L74M contributes to reduced RAL, EVG, and DTG susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	228 IN E 92 Q Major Yes E92Q is a common nonpolymorphic mutation selected in patients receiving RAL and EVG. It reduces RAL susceptibility by 5 to 10-fold and EVG susceptibility by ~30-fold. It is the most common INI-resistance mutation associated with virological failure on an EVG-containing regimen. It is selected in vitro by DTG and reduces DTG susceptibility by ~1.5-fold.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	229 IN E 92 V Major No E92V is a nonpolymorphic mutation selected in vitro by the investigational INI GS-9160. It reduces RAL susceptibility by 10-fold and EVG susceptibility by 40-fold.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	230 IN E 92 G Major No E92G is a nonpolymorphic mutation selected in patients receiving EVG. It reduces EVG susceptibility ~10-fold. It does not reduce RAL or DTG susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	231 IN Q 95 K Accessory No Q95K is a nonpolymorphic accessory INI-resistance mutation selected in patients receiving RAL and in vitro by EVG. Alone, it has little if any effect on INI susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	232 IN T 97 A Accessory No T97A is a polymorphic accessory INI-resistance mutation that, depending on subtype, occurs in 1% to 5% of viruses from untreated persons. It is selected by RAL and EVG. Alone, it has minimal if any effect on INI susceptibility but in combination with Y143C/R it markedly reduces RAL susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	233 IN H 114 Y Accessory No H114Y is an extremely rare nonpolymorphic mutation selected in vitro by EVG. It does not appear to be associated with significantly reduced INI susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	234 IN G 118 R Major No G118R is an extremely rare nonpolymorphic mutation that has been selected by RAL in a patient with a CRF02_AG virus. When G118R occurred in combination with L74M in this virus, RAL susceptibility was reduced by ~10-fold and EVG susceptibility by ~3-fold. G118R has been selected in vitro by DTG and reported to reduce DTG susceptibility by 3-fold in a biochemical assay.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	235 IN F 121 Y Major Yes F121Y is a nonpolymorphic mutation that is selected in vitro by RAL and EVG. It has been observed in one patient receiving RAL. It reduces susceptibility to RAL by about 5-fold and to EVG by about 10-fold. It does not appear to reduce DTG susceptibility. $listMutsIn{121(NOT Y)} is an unusual mutation at this position.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	236 IN A 128 T Accessory No A128T is a nonpolymorphic mutation selected in vitro by EVG. It does not appear to reduce INI susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	237 IN E 138 K Accessory No E138K/A are nonpolymorphic accessory resistance mutations selected in patients receiving RAL, EVG, and DTG. They usually occur in combination with Q148 mutations. Alone they do not reduce INI susceptibility. However they are associated with >100-fold reduction in RAL and EVG susceptibility and up to 10-fold reduced DTG susceptibility when they occur in combination with Q148 mutations.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	238 IN E 138 A Accessory No E138K/A are nonpolymorphic accessory resistance mutations selected in patients receiving RAL, EVG, and DTG. They usually occur in combination with Q148 mutations. Alone they do not reduce INI susceptibility. However they are associated with >100-fold reduction in RAL and EVG susceptibility and up to 10-fold reduced DTG susceptibility when they occur in combination with Q148 mutations.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	239 IN E 138 D Other No E138D is a polymorphism that occurs in 1% to 2% of viruses from INI-naive patients. It does not appear to be selected by INIs or to reduce INI susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	240 IN G 140 S Accessory Yes G140S/A/C are nonpolymorphic mutations that usually occur with Q148 mutations in patients receiving RAL or EVG. Alone, they do not reduce INI susceptibility. However, in combination with Q148 mutations they are associated with a >100-fold reduction in RAL and EVG susceptibility and up to 10-fold reduction DTG susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	241 IN G 140 A Accessory Yes G140S/A/C are nonpolymorphic mutations that usually occur with Q148 mutations in patients receiving RAL or EVG. Alone, they do not reduce INI susceptibility. However, in combination with Q148 mutations they are associated with a >100-fold reduction in RAL and EVG susceptibility and up to 10-fold reduction DTG susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	242 IN G 140 C Accessory Yes G140S/A/C are nonpolymorphic mutations that usually occur with Q148 mutations in patients receiving RAL or EVG. Alone, they do not reduce INI susceptibility. However, in combination with Q148 mutations they are associated with a >100-fold reduction in RAL and EVG susceptibility and up to 10-fold reduction DTG susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	243 IN Y 143 C Major Yes Y143C/R are nonpolymorphic mutations selected by RAL. Alone, Y143C and Y143R reduce RAL susceptibility by ~5 and 20-fold, respectively, but in combination with T97A or other accessory mutations they reduce RAL susceptibility >100-fold. Alone, Y143C/R have minimal effects on EVG susceptibility. However, they are associated with 10 to 20-fold reduced EVG susceptibility when they occur in combination with greater or equal than 2 accessory INI-resistance mutations (such as L74M, T97A, G163R, and S230R). Y143 mutations do not reduce DTG susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	244 IN Y 143 R Major Yes Y143C/R are nonpolymorphic mutations selected by RAL. Alone, Y143C and Y143R reduce RAL susceptibility by ~5 and 20-fold, respectively, but in combination with T97A or other accessory mutations they reduce RAL susceptibility >100-fold. Alone, Y143C/R have minimal effects on EVG susceptibility. However, they are associated with 10 to 20-fold reduced EVG susceptibility when they occur in combination with greater or equal than 2 accessory INI-resistance mutations (such as L74M, T97A, G163R, and S230R). Y143 mutations do not reduce DTG susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	245 IN Y 143 H Major Yes Y143C/R are nonpolymorphic mutations selected by RAL. Alone, Y143C and Y143R reduce RAL susceptibility by ~5 and 20-fold, respectively, but in combination with T97A or other accessory mutations they reduce RAL susceptibility >100-fold. Y143H is a less-common mutation at this position. It is likely a transitional mutation between the wildtype Y and the 2-base pair mutant R.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	246 IN Y 143 K Major No Y143K/G/S/A are extremely rare mutations that reduce RAL susceptibility by 5 to 10-fold.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	247 IN Y 143 G Major No Y143K/G/S/A are extremely rare mutations that reduce RAL susceptibility by 5 to 10-fold.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	248 IN Y 143 S Major No Y143K/G/S/A are extremely rare mutations that reduce RAL susceptibility by 5 to 10-fold.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	249 IN Y 143 A Major No Y143K/G/S/A are extremely rare mutations that reduce RAL susceptibility by 5 to 10-fold.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	250 IN P 145 S Major No P145S is a rare nonpolymorphic mutation that has been selected in vitro by EVG and rarely in patients receiving EVG. It causes high-level resistance to EVG but not to RAL or DTG.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	251 IN Q 146 P Major No Q146P is a rare nonpolymorphic mutation that has been selected in vitro by EVG. It reduces EVG susceptibility by ~10-fold.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	252 IN S 147 G Major Yes S147G is a nonpolymorphic mutation selected in patients receiving EVG. It reduces EVG susceptibility 5 to 10-fold. It does not reduce RAL or DTG susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	253 IN Q 148 H Major Yes Q148H/K/R are nonpolymorphic mutations selected by RAL and EVG. Alone, Q148H reduces RAL and EVG susceptibility 5 to 10-fold. Q148R/K reduce RAL and EVG susceptibility 30 to 100-fold. When Q148H/K/R occur in combination with G140S/A or E138K/A, they reduce RAL and EVG susceptibility >100-fold. Alone, Q148H/K/R have minimal effects on DTG susceptibility. In combination with E138K/A +/- G140S/A/C they cause >10-fold reduced susceptibility to DTG.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	254 IN Q 148 K Major Yes Q148H/K/R are nonpolymorphic mutations selected by RAL and EVG. Alone, Q148H reduces RAL and EVG susceptibility 5 to 10-fold. Q148R/K reduce RAL and EVG susceptibility 30 to 100-fold. When Q148H/K/R occur in combination with G140S/A or E138K/A, they reduce RAL and EVG susceptibility >100-fold. Alone, Q148H/K/R have minimal effects on DTG susceptibility. In combination with E138K/A +/- G140S/A/C they cause >10-fold reduced susceptibility to DTG.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	255 IN Q 148 R Major Yes Q148H/K/R are nonpolymorphic mutations selected by RAL and EVG. Alone, Q148H reduces RAL and EVG susceptibility 5 to 10-fold. Q148R/K reduce RAL and EVG susceptibility 30 to 100-fold. When Q148H/K/R occur in combination with G140S/A or E138K/A, they reduce RAL and EVG susceptibility >100-fold. Alone, Q148H/K/R have minimal effects on DTG susceptibility. In combination with E138K/A +/- G140S/A/C they cause >10-fold reduced susceptibility to DTG.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	256 IN V 151 A Accessory No V151A is an extremely rare nonpolymorphic mutation selected in vitro by an investigational INI. It has been reported to reduce susceptibility to RAL by 4-fold and to EVG by 12-fold.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	257 IN V 151 I Accessory No V151I is a polymorphic mutation selected in patients receiving RAL and in vitro by EVG. It appears to have little or no effect on INI susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	258 IN V 151 L Major No V151L is an extremely rare nonpolymorphic mutation selected in vitro by early investigational INIs but not in patients receiving current INIs. It reduces susceptibility to RAL, EVG, and DTG by ~10, ~40, and 3-fold, respectively.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	259 IN S 153 Y Accessory No S153Y/F are extremely rare nonpolymorphic mutations selected in vitro by EVG (S153Y) and DTG (S153Y/F). S153Y/F reduce RAL and DTG susceptibility by ~2-fold and EVG susceptibility by ~4-fold.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	260 IN S 153 F Accessory No S153Y/F are extremely rare nonpolymorphic mutations selected in vitro by EVG (S153Y) and DTG (S153Y/F). S153Y/F reduce RAL and DTG susceptibility by ~2-fold and EVG susceptibility by ~4-fold.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	261 IN N 155 H Major Yes N155H is a nonpolymorphic mutation selected in patients receiving RAL and EVG. Alone, it reduces RAL susceptibility ~15-fold and EVG susceptibility ~30-fold. Susceptibility is further reduced when N155H occurs in combination with E92Q and other primary or accessory INI-resistance mutations. N155H has been selected by DTG in RAL-experienced patients but does not reduce DTG susceptibility by itself.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	262 IN N 155 S Major Yes N155H is a nonpolymorphic mutation selected in patients receiving RAL and EVG. Alone, it reduces RAL susceptibility ~15-fold and EVG susceptibility ~30-fold. Susceptibility is further reduced when N155H occurs in combination with E92Q and other primary or accessory INI-resistance mutations. N155H has been selected by DTG in RAL-experienced patients but does not reduce DTG susceptibility by itself. N155S/T are rare nonpolymorphic mutations selected in vitro by investigational INIs. N155S/T reduce RAL and EVG susceptibility somewhat less effectively than N155H
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	263 IN N 155 T Major No N155H is a nonpolymorphic mutation selected in patients receiving RAL and EVG. Alone, it reduces RAL susceptibility ~15-fold and EVG susceptibility ~30-fold. Susceptibility is further reduced when N155H occurs in combination with E92Q and other primary or accessory INI-resistance mutations. N155H has been selected by DTG in RAL-experienced patients but does not reduce DTG susceptibility by itself. N155S/T are rare nonpolymorphic mutations selected in vitro by investigational INIs. N155S/T reduce RAL and EVG susceptibility somewhat less effectively than N155H
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	264 IN E 157 Q Accessory No E157Q is a polymorphic accessory mutation that is weakly selected in patients receiving RAL. It is selected in vitro by EVG. E157Q reduces RAL susceptibility by about 5-fold and EVG susceptibility by about 2-fold.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	265 IN G 163 R Accessory No G163R/K are nonpolymorphic mutations in all subtypes except subtype F. They are commonly selected in patients receiving RAL. Their effect on INI susceptibility has not been well studied.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	266 IN G 163 K Accessory No G163R/K are nonpolymorphic mutations in all subtypes except subtype F. They are commonly selected in patients receiving RAL. Their effect on INI susceptibility has not been well studied.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	267 IN S 230 R Accessory No S230R is a nonpolymorphic accessory mutation selected in vitro and in vivo by RAL and in vitro by EVG. It appears to have minimal, if any, effect on INI susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	268 IN S 230 N Other No S230N is a polymorphism that is not associated with reduced INI susceptibility.
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f nml parents: diff changeset	269 IN R 263 K Accessory No R263K is a nonpolymorphic mutation selected in patients receiving RAL and DTG and in vitro by EVG and DTG. It reduces RAL, DTG, and EVG susceptibility about 2-fold, 2-fold, and 3 to 5-fold, respectively.

Mercurial > repos > nml > quasitools

annotate test-data/mutation_db.tsv @ 2:a7093d5933a8 draft