From 1fc2e82e396a925c2bc878840825d3fea7f63c71 Mon Sep 17 00:00:00 2001 From: immasushiroll Date: Fri, 12 Jun 2026 16:57:56 -0400 Subject: [PATCH 1/5] bunch of comments --- scripts/json2csv.py | 5 + scripts/timing.py | 4 + sierralocal/data/HIVDB_10.2.xml | 4408 ++ sierralocal/data/mutation-type-pairs_hiv1.csv | 44 +- sierralocal/data/rx-all_subtype-all.csv | 46739 +++++++++------- sierralocal/jsonwriter.py | 6 + sierralocal/nucaminohook.py | 33 +- sierralocal/updater.py | 3 + 8 files changed, 29433 insertions(+), 21809 deletions(-) create mode 100644 sierralocal/data/HIVDB_10.2.xml diff --git a/scripts/json2csv.py b/scripts/json2csv.py index 6837bb7..ef8a53a 100644 --- a/scripts/json2csv.py +++ b/scripts/json2csv.py @@ -1,3 +1,8 @@ +""" +Convert JSON generated from Sierra processor into CSV format, retaining +only drug-specific resistance scores. +""" + import json import csv import argparse diff --git a/scripts/timing.py b/scripts/timing.py index 2068aaf..df2bebf 100644 --- a/scripts/timing.py +++ b/scripts/timing.py @@ -1,3 +1,7 @@ +""" +Script to compare sierralocal and sierrapy runtimes on a sample of 10 files. +""" + import subprocess from sierralocal import main import os diff --git a/sierralocal/data/HIVDB_10.2.xml b/sierralocal/data/HIVDB_10.2.xml new file mode 100644 index 0000000..4a98f13 --- /dev/null +++ b/sierralocal/data/HIVDB_10.2.xml @@ -0,0 +1,4408 @@ + + + + HIVDB + 10.2 + 2026-04-26 + + + CA + CAI + + + PR + PI + + + RT + NRTI,NNRTI + + + IN + INSTI + + + 1 + Susceptible + S + + + 2 + Potential Low-Level Resistance + S + + + 3 + Low-Level Resistance + I + + + 4 + Intermediate Resistance + I + + + 5 + High-Level Resistance + R + + + NRTI + ABC,AZT,D4T,DDI,FTC,3TC,TDF,ISL + + + NNRTI + DOR,EFV,ETR,NVP,RPV,DPV + + + PI + ATV/r,DRV/r,FPV/r,IDV/r,LPV/r,NFV,SQV/r,TPV/r + + + INSTI + BIC,CAB,DTG,EVG,RAL + + + CAI + LEN + + 1, 10 TO 14 => 2, 15 TO 29 => 3, 30 TO 59 => 4, 60 TO INF => 5)]]> + 1 + + + + + + 1 + + + + + + 1 + + + + + 1000-fold reduced LEN susceptibility. It has an RC of 1%-6%. It occurred in 6 patients in the CAPELLA study usually in combination with other mutations.]]> + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + 1000 reduced LEN susceptibility.]]> + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + 10-fold reduced susceptibility to RAL but has minimal if any effect on susceptibility to CAB, DTG, and BIC. F121C is an extremely rare mutation. Preliminary data suggests it may confers high level phenotypic resistance to RAL, EVG, and possibly CAB. $listMutsIn{121(NOT CY)} is an unusual mutation at this position.]]> + 1 + + + + + + 1 + + + + + 10-fold reduced susceptibility to RAL but has minimal if any effect on susceptibility to CAB, DTG, and BIC.]]> + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + 10-fold while reducing DTG, BIC, and CAB by about 1.5-fold. N155S/T are extremely rare nonpolymorphic mutations that reduce RAL and EVG susceptibility about 5-fold and greater than 30-fold respectively but have little effect on CAB, DTG, and BIC. $listMutsIn{155(NOT HST)} is an unusual mutation at this position.]]> + 1 + + + + + 10-fold while reducing DTG, BIC, and CAB by about 1.5-fold.]]> + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + =10-fold but do not appear to reduce susceptibility to other INSTIs. $listMutsIn{92(NOT GQV)} is an unusual mutation at this position.]]> + 1 + + + + + =10-fold but do not appear to reduce susceptibility to other INSTIs.]]> + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + + + + + 1 + + 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210W => 5, + MAX(215F => 10, 215Y => 10), + 65RN AND 151M => 10, + 77L AND 116Y AND 151ML => 15, + 74V AND 184IV => 15, + 115F AND 184IV => 15, + 41L AND 215FY => 10, + 210W AND 215FY => 10, + 41L AND 210W => 5, + 41L AND 210W AND 215FY => 15, + 41L AND 44AD AND 210W AND 215FY => 5, + 40F AND 41L AND 210W AND 215FY => 5, + 41L AND 67EGNHST AND 215FY => 5, + 67EGNHST AND 215FY AND 219ENQRW => 5, + 67EGNHST AND 70R AND 219ENQRW => 10, + 41L AND 184VI AND 215FY => 10, + 67EGNHST AND 70R AND 184VI AND 219ENQRW => 10 +)]]> + + + + + + + + + AZT + zidovudine + + 15, + 62V => 5, + 65R => -10, + MAX(67E => 15, 67G => 15, 67H => 15, 67N => 15, 67S => 15, 67T => 15, 67d => 30), + MAX(69G => 5, 69i => 60), + 70R => 30, + MAX(75I => 5, 75A => 10, 75M => 10, 75S => 10, 75T => 10), + 77L => 5, + 116Y => 10, + MAX(151L => 30, 151M => 60), + MAX(184I => -10, 184V => -10), + 210W => 15, + MAX(215F => 60, 215Y => 60, 215A => 10, 215C => 10, 215D => 10, 215E => 10, 215I => 20, 215L => 10, 215N => 10, 215S => 10, 215V => 20), + 65RN AND 151M => 10, + 77L AND 116Y AND 151ML => 15, + MAX(41L AND 215FY => 10, 41L AND 215ACDEILNSV => 10), + MAX(210W AND 215FY => 10, 210W AND 215ACDEILNSV => 10), + 41L AND 210W => 10, + 41L AND 44AD AND 210W AND 215FY => 5, + 40F AND 41L AND 210W AND 215FY => 5, + 41L AND 67EGNHST AND 215FY => 5, + 67EGNHST AND 215FY AND 219ENQRW => 5, + 67EGNHST AND 70R AND 219ENQRW => 15, + MAX(219E => 10, 219N => 10, 219Q => 10, 219R => 10, 219W => 10), + 151M AND 184IV => 10 +)]]> + + + + + + + + + D4T + stavudine + + 15, + 62V => 5, + MAX(65E => 10, 65N => 30, 65R => 60), + MAX(67E => 10, 67G => 10, 67H => 10, 67N => 15, 67S => 10, 67T => 10, 67d => 30), + 68d => 30, + MAX(69G => 10, 69i => 60, 69d => 30, 69D => 10), + MAX(70E => 15, 70G => 15, 70N => 15, 70Q => 15, 70R => 15, 70S => 15, 70T => 15, 70d => 30), + MAX(75I => 5, 75A => 30, 75M => 30, 75S => 30, 75T => 60), + 77L => 10, + 116Y => 10, + MAX(151L => 30, 151M => 60), + MAX(184I => -10, 184V => -10), + 210W => 15, + MAX(215F => 40, 215Y => 40, 215A => 20, 215C => 20, 215D => 20, 215E => 20, 215I => 20, 215L => 20, 215N => 20, 215S => 20, 215V => 20), + MAX(41L AND 215FY => 10, 41L AND 215ACDEILNSV => 5), + MAX(210W AND 215FY => 10, 210W AND 215ACDEILNSV => 5), + 41L AND 210W => 10, + 41L AND 44AD AND 210W AND 215FY => 5, + 40F AND 41L AND 210W AND 215FY => 5, + MAX(219E => 10, 219N => 10, 219Q => 10, 219R => 10, 219W => 10), + 151M AND 184IV => 10, + 41L AND 67EGN AND 215FY => 5, + 67EGN AND 215FY AND 219ENQR => 5, + 67EGN AND 70R AND 219ENQR => 10, + 70R AND 215FY => 5, + 77L AND 116Y AND 151M => 10, + 70EGNQST AND 184IV => 10 +)]]> + + + + + + + + + DDI + didanosine + + 10, + 62V => 5, + MAX(65E => 10, 65N => 30, 65R => 60), + MAX(67E => 5, 67G => 5, 67H => 5, 67N => 5, 67S => 5, 67T => 5, 67d => 30), + 68d => 30, + MAX(69G => 10, 69i => 60, 69d => 30, 69D => 30), + MAX(70E => 15, 70G => 15, 70N => 15, 70Q => 15, 70R => 10, 70S => 15, 70T => 15, 70d => 30), + MAX(74I => 60, 74V => 60), + MAX(75I => 5, 75A => 15, 75M => 15, 75S => 15, 75T => 30), + 77L => 10, + 116Y => 10, + MAX(151L => 30, 151M => 60), + MAX(184I => 10, 184V => 10), + 210W => 10, + MAX(215F => 15, 215Y => 15, 215A => 10, 215C => 10, 215D => 10, 215E => 10, 215I => 10, 215L => 10, 215N => 10, 215S => 10, 215V => 10), + MAX(41L AND 215FY => 10, 41L AND 215ACDEILNSV => 5), + MAX(210W AND 215FY => 10, 210W AND 215ACDEILNSV => 5), + 41L AND 210W => 10, + 41L AND 44AD AND 210W AND 215FY => 5, + 40F AND 41L AND 210W AND 215FY => 5, + MAX(219E => 5, 219N => 5, 219Q => 5, 219R => 5, 219W => 5), + 41L AND 67EGN AND 215FY => 5, + 67EGN AND 215FY AND 219ENQR => 5, + 67EGN AND 70R AND 219ENQR => 10, + 70R AND 215FY => 5, + 77L AND 116Y AND 151M => 10 +)]]> + + + + + + + + + FTC + emtricitabine + + 15, 65R => 15), + 67d => 15, + 68d => 15, + MAX(69i => 30, 69d => 15), + MAX(70E => 10, 70G => 10, 70N => 10, 70Q => 10, 70S => 10, 70T => 10, 70d => 10), + 75I => 5, + 77L => 5, + 116Y => 5, + MAX(151L => 10, 151M => 15), + MAX(184I => 60, 184V => 60), + 65RN AND 151M => 10, + 77L AND 116Y AND 151ML => 15, + 41L AND 210W AND 215FY => 15, + 67EGNHST AND 70R AND 219ENQRW => 10 +)]]> + + + + + + + + + 3TC + lamivudine + + 15, 65R => 15), + 67d => 15, + 68d => 15, + MAX(69i => 30, 69d => 15), + MAX(70E => 10, 70G => 10, 70N => 10, 70Q => 10, 70S => 10, 70T => 10, 70d => 10), + 75I => 5, + 77L => 5, + 116Y => 5, + MAX(151L => 10, 151M => 15), + MAX(184I => 60, 184V => 60), + 65RN AND 151M => 10, + 77L AND 116Y AND 151ML => 15, + 41L AND 210W AND 215FY => 15, + 67EGNHST AND 70R AND 219ENQRW => 10 +)]]> + + + + + + + + + TDF + tenofovir + + 5, + 62V => 5, + MAX(65E => 10, 65N => 30, 65R => 45), + MAX(67E => 5, 67G => 5, 67H => 5, 67N => 5, 67S => 5, 67T => 5, 67d => 15), + 68d => 15, + MAX(69G => 5, 69i => 60, 69d => 15), + MAX(70E => 15, 70G => 15, 70N => 15, 70Q => 15, 70R => 5, 70S => 15, 70T => 15, 70d => 15), + 74I => 5, + 75I => 5, + 77L => 5, + 115F => 15, + 116Y => 5, + MAX(151L => 10, 151M => 15), + MAX(184I => -10, 184V => -10), + 210W => 5, + MAX(215F => 10, 215Y => 10), + 65RN AND 151M => 10, + 77L AND 116Y AND 151ML => 15, + 41L AND 215FY => 10, + 210W AND 215FY => 10, + 41L AND 210W => 5, + 41L AND 210W AND 215FY => 15, + 41L AND 44AD AND 210W AND 215FY => 5, + 40F AND 41L AND 210W AND 215FY => 5, + 41L AND 67EGNHST AND 215FY => 5, + 67EGNHST AND 215FY AND 219ENQRW => 5, + 67EGNHST AND 70R AND 219ENQRW => 10, + 70EGNQST AND 184IV => 10, + 65R AND 151M AND 184IV => 10, + 65R AND 68GN => 5, + 62V AND 65R => 5, + 69i AND 184VI => 10 +)]]> + + + + + + + + + ISL + islatravir + + 5, + 65R => -10, + 69i => 60, + 70R => 5, + MAX(74I => -5, 74V => -5), + 75I => -5, + 151M => -10, + MAX(184I => 30, 184V => 30), + 210W => 5, + MAX(215F => 10, 215Y => 10), + 41L AND 215FY => 5, + 210W AND 215FY => 5, + 41L AND 210W => 5, + 41L AND 210W AND 215FY => 5, + 41L AND 67EGNHST AND 215FY => 5, + 67EGNHST AND 215FY AND 219ENQRW => 5, + 67EGNHST AND 70R AND 219ENQRW => 5, + 41L AND 184VI AND 215FY => 10, + 114S => 15, + 114S AND 184IV => 15 +)]]> + + + + + + + + + DOR + doravirine + + 10, + MAX(100I => 10, 100V => 5), + MAX(101E => 5, 101P => 5), + MAX(106A => 60, 106I => 5, 106L => 30, 106M => 30), + 108I => 5, + 179F => 5, + MAX(181C => 5, 181I => 10, 181V => 10), + MAX(188F => 30, 188L => 60), + MAX(190C => 10, 190E => 60, 190Q => 30, 190S => 10, 190T => 10, 190V => 10), + 221Y => 5, + 225H => 10, + MAX(227C => 60, 227I => 45, 227L => 60, 227V => 45, 227Y => 15), + 230L => 60, + 234I => 45, + 236L => 5, + 318F => 60, + 98G AND 234I => 15, + 100I AND 103N => 20, + 103N AND 181C => 5, + 103N AND 225H => 20, + 106I AND 181C => 10, + 106I AND 190S => 10, + MAX(106I AND 227CLIVY => 15, 106A AND 227CL => 15), + 108I AND 181C => 10, + 108I AND 234I => 15, + 181CIV AND 190ACSTV => 10, + 181CIV AND 221Y => 10, + 98G AND 106I => 5, + 98G AND 190ASC => 5, + 98G AND 181CIV => 10, + 101E AND 181C => 5, + MAX(101E AND 190A => 5, 101E AND 190S => 5), + 106I AND 234I => 15, + 106I AND 221Y => 5, + 98G AND 227CL => 15 +)]]> + + + + + + + + + EFV + efavirenz + + 10, + MAX(100I => 45, 100V => 15), + MAX(101E => 15, 101P => 60, 101H => 10), + MAX(106A => 45, 106I => 5, 106L => 10, 106M => 60), + 108I => 10, + MAX(138K => 10, 138G => 10, 138Q => 10, 138R => 10), + MAX(179F => 10, 179D => 10, 179E => 10, 179L => 10), + MAX(181C => 30, 181I => 30, 181V => 30, 181F => 15, 181G => 15, 181S => 15), + MAX(188F => 60, 188L => 60, 188C => 30, 188H => 30), + MAX(190C => 60, 190E => 60, 190Q => 60, 190S => 60, 190T => 60, 190V => 60, 190A => 45), + 221Y => 10, + 225H => 45, + MAX(227C => 45, 227I => 10, 227L => 15, 227V => 10), + MAX(230I => 10, 230L => 45), + 318F => 10, + 98G AND 234I => 5, + MAX(106I AND 227CLIVY => 10, 106A AND 227CL => 15), + 98G AND 181CIV => 5, + 101E AND 181C => 5, + 98G AND 227CL => 15, + MAX(103H => 60, 103N => 60, 103S => 45, 103T => 15), + MAX(238N => 10, 238T => 30), + 103R AND 179D => 20 +)]]> + + + + + + + + + ETR + etravirine + + 10, + MAX(100I => 30, 100V => 10), + MAX(101E => 10, 101P => 45, 101H => 10), + 106I => 5, + MAX(138K => 10, 138G => 10, 138Q => 10, 138R => 10, 138A => 10), + MAX(179F => 15, 179D => 10, 179E => 10, 179L => 10), + MAX(181C => 30, 181I => 60, 181V => 60, 181F => 15, 181G => 15, 181S => 15), + 188L => 15, + MAX(190C => 10, 190E => 45, 190Q => 45, 190S => 10, 190T => 10, 190V => 10, 190A => 10), + 221Y => 10, + 227C => 30, + 230L => 30, + 98G AND 234I => 5, + 106I AND 227CLIVY => 10, + 181CIV AND 190ACSTV => 10, + 98G AND 181CIV => 5, + 101E AND 181C => 5, + MAX(101E AND 190A => 5, 101E AND 190S => 5), + 98G AND 227CL => 15, + 101E AND 188L => 5, + MAX(179F AND 181C => 15, 179T AND 181C => 10) +)]]> + + + + + + + + + NVP + nevirapine + + 30, + MAX(100I => 60, 100V => 30), + MAX(101E => 30, 101P => 60, 101H => 15), + MAX(106A => 60, 106I => 5, 106L => 30, 106M => 60), + 108I => 15, + MAX(138K => 10, 138G => 10, 138Q => 10, 138R => 10), + MAX(179F => 15, 179D => 10, 179E => 10, 179L => 10), + MAX(181C => 60, 181I => 60, 181V => 60, 181F => 60, 181G => 60, 181S => 60), + MAX(188F => 60, 188L => 60, 188C => 60, 188H => 60), + MAX(190C => 60, 190E => 60, 190Q => 60, 190S => 60, 190T => 60, 190V => 60, 190A => 60), + 221Y => 15, + 225H => 45, + MAX(227C => 45, 227I => 30, 227L => 30, 227V => 30, 227Y => 10), + MAX(230I => 30, 230L => 60), + 318F => 30, + 98G AND 234I => 5, + 106I AND 227CLIVY => 10, + 98G AND 227CL => 15, + MAX(103H => 60, 103N => 60, 103S => 60, 103T => 60), + MAX(238N => 10, 238T => 30), + 103R AND 179D => 20, + 348I => 15 +)]]> + + + + + + + + + RPV + rilpivirine + + 15, + MAX(100I => 45, 100V => 15), + MAX(101E => 45, 101P => 60, 101H => 10), + MAX(106A => 5, 106I => 5), + 108I => 5, + MAX(138K => 45, 138G => 20, 138Q => 20, 138R => 20, 138A => 10), + MAX(179F => 15, 179D => 10, 179E => 10, 179L => 10), + MAX(181C => 45, 181I => 60, 181V => 60, 181F => 30, 181G => 30, 181S => 30), + MAX(188F => 30, 188L => 60), + MAX(190C => 10, 190E => 60, 190Q => 45, 190S => 15, 190T => 10, 190V => 10, 190A => 15), + 221Y => 10, + MAX(227C => 45, 227L => 5, 227Y => 15), + MAX(230I => 30, 230L => 60), + 98G AND 234I => 5, + 100I AND 103N => 15, + 106I AND 181C => 10, + MAX(106I AND 227CLIVY => 15, 106A AND 227CL => 10), + 181CIV AND 190ACSTV => 10, + 181CIV AND 221Y => 10, + 98G AND 106I => 5, + 98G AND 190ASC => 5, + 98G AND 181CIV => 5, + 98G AND 227CL => 15, + 103R AND 179D => 15, + MAX(179F AND 181C => 15, 179T AND 181C => 10), + 101E AND 184I => 15, + 138K AND 184I => 15, + 90I => 5 +)]]> + + + + + + + + + DPV + dapirivine + + 30, + MAX(100I => 60, 100V => 15), + MAX(101E => 45, 101P => 60, 101H => 10), + MAX(106A => 5, 106I => 5, 106M => 10), + 108I => 5, + MAX(138K => 45, 138G => 20, 138Q => 20, 138R => 20, 138A => 15), + MAX(179F => 15, 179D => 10, 179E => 10, 179L => 15), + MAX(181C => 60, 181I => 60, 181V => 60, 181F => 30, 181G => 30, 181S => 30), + MAX(188F => 30, 188L => 60, 188C => 5, 188H => 5), + MAX(190C => 10, 190E => 60, 190Q => 45, 190S => 15, 190T => 10, 190V => 10, 190A => 15), + 221Y => 15, + 225H => 10, + MAX(227C => 60, 227L => 10, 227Y => 10), + MAX(230I => 30, 230L => 60), + 90I => 5 +)]]> + + + + + + + + + ATV/r + atazanavir/r + + 5, + 20T => 5, + MAX(24F => 5, 24I => 10, 24M => 5), + 32I => 15, + 33F => 5, + MAX(46I => 10, 46L => 10, 46V => 5), + 47V => 10, + MAX(48A => 10, 48L => 10, 48M => 30, 48Q => 10, 48S => 10, 48T => 10, 48V => 30), + 50L => 60, + MAX(53L => 10, 53Y => 5), + MAX(54A => 15, 54L => 15, 54M => 15, 54S => 15, 54T => 15, 54V => 15), + MAX(73A => 10, 73C => 10, 73D => 5, 73S => 10, 73T => 10, 73V => 5), + 74P => 10, + MAX(82A => 15, 82C => 15, 82F => 15, 82L => 10, 82M => 10, 82S => 30, 82T => 30), + 83D => 10, + MAX(84A => 60, 84C => 45, 84V => 60), + MAX(88D => 10, 88G => 15, 88S => 60, 88T => 15), + 89T => 5, + 90M => 20, + 32I AND 47AV => 5, + 32I AND 54LM => 5, + 46IL AND 84V AND 90M => 5, + 46ILV AND 82ACFLMST => 10, + 46ILV AND 90M => 10, + 47AV AND 54LM => 5, + 53L AND 90M => 10, + 54ALMSTV AND 82ACFLMST => 10, + 54ALMSTV AND 90M => 10, + 73ACSTV AND 90M => 10, + 82ACFLMST AND 90M => 10 +)]]> + + + + + + + + + DRV/r + darunavir/r + + 5, + 32I => 15, + 33F => 5, + MAX(47A => 10, 47V => 10), + MAX(50L => -10, 50V => 20), + MAX(54L => 20, 54M => 20), + 74P => 5, + 76V => 20, + 82F => 15, + MAX(84A => 30, 84C => 15, 84V => 15), + 88S => -5, + 89V => 5, + 32I AND 47AV => 5, + 32I AND 54LM => 5, + 47AV AND 54LM => 5, + 11IL AND 32I => 5, + 11IL AND 54LM => 5, + 32I AND 76V => 5, + 32I AND 84V => 5, + 32I AND 89V => 5, + 47AV AND 84V => 5, + 54LM AND 84V => 5, + 54LM AND 89V => 5 +)]]> + + + + + + + + + FPV/r + fosamprenavir/r + + 15, + 20T => 5, + MAX(24F => 5, 24I => 10, 24M => 5), + 32I => 30, + 33F => 10, + MAX(46I => 10, 46L => 10, 46V => 10), + MAX(47A => 60, 47V => 35), + MAX(50L => -5, 50V => 60), + MAX(54A => 10, 54L => 60, 54M => 60, 54S => 10, 54T => 10, 54V => 10), + MAX(73A => 10, 73C => 10, 73D => 5, 73S => 10, 73T => 10, 73V => 5), + 74P => 10, + 76V => 60, + MAX(82A => 15, 82C => 15, 82F => 30, 82L => 15, 82M => 15, 82S => 15, 82T => 15), + MAX(84A => 60, 84C => 60, 84V => 60), + 88S => -10, + 89V => 10, + 90M => 20, + 32I AND 47AV => 5, + 32I AND 54LM => 5, + 46IL AND 84V AND 90M => 5, + 46ILV AND 82ACFLMST => 10, + 46ILV AND 90M => 10, + 47AV AND 54LM => 5, + 53L AND 90M => 10, + 54ALMSTV AND 82ACFLMST => 10, + 54ALMSTV AND 90M => 10, + 73ACSTV AND 90M => 10, + 82ACFLMST AND 90M => 10, + 11IL AND 32I => 5, + 11IL AND 54LM => 5, + 32I AND 76V => 5, + 32I AND 84V => 5, + 32I AND 89V => 5, + 47AV AND 84V => 5, + 54LM AND 84V => 5, + 54LM AND 89V => 5, + 46ILV AND 76V => 10 +)]]> + + + + + + + + + IDV/r + indinavir/r + + 10, + 20T => 5, + MAX(24F => 5, 24I => 15, 24M => 5), + 32I => 15, + 33F => 5, + MAX(46I => 10, 46L => 10, 46V => 10), + MAX(47A => 15, 47V => 15), + MAX(48A => 10, 48L => 10, 48M => 10, 48Q => 10, 48S => 10, 48T => 10, 48V => 10), + 50L => -5, + MAX(54A => 15, 54L => 10, 54M => 15, 54S => 15, 54T => 15, 54V => 15), + MAX(73A => 15, 73C => 15, 73D => 5, 73S => 15, 73T => 15, 73V => 5), + 74P => 10, + 76V => 30, + MAX(82A => 30, 82C => 15, 82F => 30, 82L => 10, 82M => 30, 82S => 30, 82T => 30), + 83D => 10, + MAX(84A => 60, 84C => 60, 84V => 60), + 88S => 15, + 89V => 5, + 90M => 30, + 32I AND 47AV => 5, + 32I AND 54LM => 5, + 46IL AND 84V AND 90M => 5, + 46ILV AND 82ACFLMST => 10, + 46ILV AND 90M => 10, + 47AV AND 54LM => 5, + 53L AND 90M => 10, + 54ALMSTV AND 82ACFLMST => 10, + 54ALMSTV AND 90M => 10, + 73ACSTV AND 90M => 10, + 82ACFLMST AND 90M => 10, + 11IL AND 32I => 5, + 11IL AND 54LM => 5, + 32I AND 76V => 5, + 32I AND 84V => 5, + 32I AND 89V => 5, + 47AV AND 84V => 5, + 54LM AND 84V => 5, + 54LM AND 89V => 5, + 46ILV AND 76V => 10 +)]]> + + + + + + + + + LPV/r + lopinavir/r + + 5, + MAX(24F => 5, 24I => 10, 24M => 5), + 32I => 15, + 33F => 5, + MAX(46I => 10, 46L => 10, 46V => 5), + MAX(47A => 60, 47V => 15), + MAX(48A => 10, 48L => 10, 48M => 10, 48Q => 10, 48S => 10, 48T => 10, 48V => 10), + MAX(50L => -10, 50V => 30), + MAX(54A => 15, 54L => 20, 54M => 20, 54S => 15, 54T => 15, 54V => 15), + MAX(73A => 5, 73C => 5, 73D => 5, 73S => 5, 73T => 5, 73V => 5), + 74P => 5, + 76V => 30, + MAX(82A => 30, 82C => 15, 82F => 30, 82L => 10, 82M => 25, 82S => 30, 82T => 30), + MAX(84A => 60, 84C => 10, 84V => 30), + 90M => 10, + 32I AND 47AV => 5, + 32I AND 54LM => 5, + 46IL AND 84V AND 90M => 5, + 46ILV AND 82ACFLMST => 10, + 46ILV AND 90M => 5, + 47AV AND 54LM => 5, + 54ALMSTV AND 82ACFLMST => 10, + 54ALMSTV AND 90M => 5, + 82ACFLMST AND 90M => 5, + 11IL AND 32I => 5, + 11IL AND 54LM => 5, + 32I AND 76V => 5, + 32I AND 84V => 5, + 32I AND 89V => 5, + 47AV AND 84V => 5, + 54LM AND 84V => 5, + 54LM AND 89V => 5, + 46ILV AND 76V => 10 +)]]> + + + + + + + + + NFV + nelfinavir + + 15, + 20T => 15, + 23I => 15, + MAX(24F => 10, 24I => 10, 24M => 10), + 30N => 60, + 32I => 15, + 33F => 10, + 43T => 10, + MAX(46I => 30, 46L => 20, 46V => 20), + MAX(47A => 30, 47V => 20), + MAX(48A => 30, 48L => 30, 48M => 30, 48Q => 30, 48S => 30, 48T => 30, 48V => 30), + 50V => 15, + 53L => 10, + MAX(54A => 20, 54L => 20, 54M => 20, 54S => 20, 54T => 20, 54V => 20), + 58E => 10, + MAX(73A => 15, 73C => 15, 73D => 10, 73S => 15, 73T => 15, 73V => 10), + 74P => 20, + 76V => 10, + MAX(82A => 30, 82C => 30, 82F => 30, 82L => 10, 82M => 30, 82S => 30, 82T => 30), + 83D => 15, + MAX(84A => 60, 84C => 60, 84V => 60), + MAX(88D => 60, 88G => 30, 88S => 60, 88T => 30), + 89V => 10, + 90M => 60, + 32I AND 47AV => 5, + 32I AND 54LM => 5, + 46IL AND 84V AND 90M => 5, + 46ILV AND 82ACFLMST => 10, + 46ILV AND 90M => 10, + 47AV AND 54LM => 5, + 53L AND 90M => 10, + 54ALMSTV AND 82ACFLMST => 10, + 54ALMSTV AND 90M => 10, + 73ACSTV AND 90M => 10, + 82ACFLMST AND 90M => 10, + 11IL AND 32I => 5, + 11IL AND 54LM => 5, + 32I AND 76V => 5, + 32I AND 84V => 5, + 32I AND 89V => 5, + 47AV AND 84V => 5, + 54LM AND 84V => 5, + 54LM AND 89V => 5, + 46ILV AND 76V => 10 +)]]> + + + + + + + + + SQV/r + saquinavir/r + + 5, + MAX(24F => 5, 24I => 10, 24M => 5), + 33F => 5, + MAX(46I => 10, 46L => 10, 46V => 5), + MAX(48A => 60, 48L => 60, 48M => 60, 48Q => 60, 48S => 60, 48T => 60, 48V => 60), + MAX(50L => -5, 50V => 15), + 53L => 15, + MAX(54A => 15, 54L => 15, 54M => 15, 54S => 15, 54T => 15, 54V => 15), + MAX(73A => 15, 73C => 15, 73D => 10, 73S => 15, 73T => 15, 73V => 10), + 74P => 10, + MAX(82A => 15, 82C => 15, 82F => 10, 82L => 10, 82M => 15, 82S => 15, 82T => 15), + 83D => 10, + MAX(84A => 60, 84C => 60, 84V => 60), + MAX(88D => 10, 88S => 15), + 90M => 45, + 46IL AND 84V AND 90M => 5, + 46ILV AND 82ACFLMST => 10, + 46ILV AND 90M => 5, + 53L AND 90M => 10, + 54ALMSTV AND 82ACFLMST => 10, + 54ALMSTV AND 90M => 10, + 73ACSTV AND 90M => 10, + 82ACFLMST AND 90M => 10 +)]]> + + + + + + + + + TPV/r + tipranavir/r + + -5, + 32I => 5, + 33F => 10, + 43T => 10, + MAX(46I => 5, 46L => 10, 46V => 5), + MAX(47A => 30, 47V => 30), + MAX(50L => -5, 50V => -5), + MAX(54A => 20, 54L => -10, 54M => 20, 54S => 20, 54T => 20, 54V => 20), + 58E => 15, + 74P => 25, + 76V => -5, + MAX(82C => 10, 82L => 45, 82M => 10, 82S => 30, 82T => 45), + 83D => 25, + MAX(84A => 60, 84C => 30, 84V => 30), + 46IL AND 84V AND 90M => 5 +)]]> + + + + + + + + + BIC + bictegravir + + 10, + MAX(66A => 5, 66I => 5, 66K => 15), + MAX(74F => 5, 74M => 5), + 92Q => 10, + 118R => 45, + MAX(121C => 15, 121Y => 10), + MAX(138A => 10, 138K => 10, 138T => 10), + MAX(140A => 10, 140C => 10, 140R => 10, 140S => 10), + MAX(146I => 5, 146L => 5, 146P => 5, 146R => 5), + 147G => 10, + MAX(148H => 25, 148K => 30, 148R => 25), + 149A => 5, + 151L => 15, + MAX(153F => 15, 153Y => 15), + 155H => 10, + 230R => 10, + 263K => 30, + 49G AND 263K => 10, + 66I AND 118R => 5, + 74F AND 75I => 10, + MAX(74I AND 118R => 5, 74FM AND 118R => 10), + MAX(74I AND 148HKR => 5, 74FM AND 148HKR => 15), + 74I AND 155H => 5, + 75A AND 118R => 10, + 75A AND 148HKR => 5, + 118R AND 138AKT => 10, + 122N AND 148HKR => 5, + 138AKT AND 140ACS => 10, + 138AKT AND 148HKR => 10, + 138K AND 263K => 10, + 140ACS AND 148HKR => 10, + 147G AND 148HKR => 10, + 147G AND 155H => 10, + 148HKR AND 149A => 10, + 148HKR AND 151I => 5, + 148HKR AND 155H => 20, + 148HKR AND 163KR => 5, + 151I AND 155H => 5, + 155H AND 263K => 20, + 157Q AND 263K => 10, + 51Y AND 263K => 10, + 92Q AND 155H => 10, + 97A AND 118R => 10, + 97A AND 148HKR => 15 +)]]> + + + + + + + + + CAB + cabotegravir + + 15, + MAX(66A => 5, 66I => 10, 66K => 20), + MAX(74F => 5, 74M => 5, 74I => 10), + MAX(92Q => 15, 92G => 10, 92V => 10), + 118R => 60, + MAX(121C => 30, 121Y => 15), + MAX(138A => 15, 138K => 15, 138T => 15), + MAX(140A => 15, 140C => 15, 140R => 60, 140S => 15), + MAX(146I => 10, 146L => 10, 146P => 10, 146R => 10), + 147G => 15, + MAX(148H => 60, 148K => 60, 148R => 60, 148N => 10), + 149A => 5, + 151L => 15, + MAX(153F => 25, 153Y => 25), + MAX(155H => 25, 155S => 10, 155T => 10), + 230R => 15, + 263K => 60, + 49G AND 263K => 10, + 74F AND 75I => 10, + 74I AND 118R => 5, + MAX(74I AND 148HKR => 5, 74FM AND 148HKR => 15), + 74I AND 155H => 10, + 75A AND 148HKR => 5, + 138AKT AND 140ACS => 15, + 138K AND 263K => 10, + 147G AND 148HKR => 10, + 147G AND 155H => 15, + 148HKR AND 149A => 10, + 148HKR AND 151I => 5, + 148HKR AND 163KR => 15, + 151I AND 155H => 10, + 157Q AND 263K => 10, + 51Y AND 263K => 10, + 92Q AND 155H => 20, + 97A AND 148HKR => 20, + 75A => 10, + 122N => 10, + MAX(143A => 5, 143C => 5, 143G => 5, 143H => 5, 143K => 5, 143R => 5, 143S => 5), + 97A AND 143ACGHRS => 5 +)]]> + + + + + + + + + DTG + dolutegravir + + 10, + MAX(66A => 5, 66I => 5, 66K => 15), + MAX(74F => 5, 74M => 5), + 92Q => 10, + 118R => 60, + MAX(121C => 15, 121Y => 10), + MAX(138A => 10, 138K => 10, 138T => 10), + MAX(140A => 10, 140C => 10, 140R => 10, 140S => 10), + MAX(146I => 5, 146L => 5, 146P => 5, 146R => 5), + 147G => 10, + MAX(148H => 25, 148K => 30, 148R => 25), + 149A => 5, + 151L => 15, + MAX(153F => 15, 153Y => 15), + 155H => 10, + 230R => 10, + 263K => 30, + 49G AND 263K => 10, + 74F AND 75I => 10, + 74I AND 118R => 5, + MAX(74I AND 148HKR => 5, 74FM AND 148HKR => 15), + 74I AND 155H => 5, + 75A AND 148HKR => 5, + 122N AND 148HKR => 5, + 138AKT AND 140ACS => 10, + 138AKT AND 148HKR => 10, + 138K AND 263K => 10, + 140ACS AND 148HKR => 10, + 147G AND 148HKR => 10, + 147G AND 155H => 10, + 148HKR AND 149A => 10, + 148HKR AND 151I => 5, + 148HKR AND 155H => 20, + 148HKR AND 163KR => 5, + 151I AND 155H => 5, + 155H AND 263K => 20, + 157Q AND 263K => 10, + 51Y AND 263K => 10, + 92Q AND 155H => 10, + 97A AND 148HKR => 15 +)]]> + + + + + + + + + EVG + elvitegravir + + 15, + MAX(66A => 60, 66I => 60, 66K => 60), + MAX(74F => 5, 74M => 5), + MAX(92Q => 60, 92G => 30, 92V => 60), + 118R => 60, + MAX(121C => 60, 121Y => 60), + MAX(138A => 15, 138K => 15, 138T => 15), + MAX(140A => 30, 140C => 30, 140R => 30, 140S => 30), + MAX(146I => 60, 146L => 30, 146P => 60, 146R => 5), + 147G => 60, + MAX(148H => 60, 148K => 60, 148R => 60, 148N => 10), + 149A => 5, + MAX(151L => 60, 151A => 30, 151I => 5), + MAX(153F => 25, 153Y => 25), + MAX(155H => 60, 155S => 30, 155T => 30), + 230R => 20, + 263K => 30, + 49G AND 263K => 10, + 74F AND 75I => 10, + 74FM AND 148HKR => 15, + 138AKT AND 140ACS => 15, + 138K AND 263K => 10, + 51Y AND 263K => 15, + 92Q AND 155H => 10, + MAX(143A => 10, 143C => 10, 143G => 10, 143H => 10, 143K => 10, 143R => 10, 143S => 10), + 97A AND 143ACGHRS => 5, + 95K => 10, + 97A => 10, + 145S => 60, + 157Q => 10, + MAX(163K => 15, 163R => 15), + 232N => 10, + 143ACGHRS AND 163R => 10, + 143ACGHRS AND 230R => 10 +)]]> + + + + + + + + + RAL + raltegravir + + 15, + MAX(66A => 15, 66I => 15, 66K => 60), + MAX(74F => 5, 74M => 5), + MAX(92Q => 30, 92G => 15, 92V => 30), + 118R => 60, + MAX(121C => 60, 121Y => 60), + MAX(138A => 15, 138K => 15, 138T => 15), + MAX(140A => 30, 140C => 30, 140R => 30, 140S => 30), + MAX(146I => 15, 146R => 5), + 147G => 10, + MAX(148H => 60, 148K => 60, 148R => 60, 148N => 10), + 149A => 5, + MAX(151L => 30, 151A => 15, 151I => 5), + MAX(153F => 10, 153Y => 10), + MAX(155H => 60, 155S => 30, 155T => 30), + 230R => 20, + 263K => 15, + 49G AND 263K => 10, + 66I AND 118R => 5, + 74F AND 75I => 10, + 74FM AND 118R => 10, + 74FM AND 148HKR => 15, + 75A AND 118R => 10, + 118R AND 138AKT => 10, + 138AKT AND 140ACS => 15, + 138K AND 263K => 10, + 157Q AND 263K => 10, + 92Q AND 155H => 10, + 97A AND 118R => 10, + MAX(143A => 60, 143C => 60, 143G => 60, 143H => 60, 143K => 60, 143R => 60, 143S => 60), + 95K => 10, + 97A => 10, + 157Q => 10, + MAX(163K => 15, 163R => 15), + 232N => 10 +)]]> + + + + + + + + + LEN + lenacapavir + + 60, + 57S => 20, + 66I => 60, + MAX(67H => 30, 67K => 20, 67N => 20, 67Y => 30), + MAX(70R => 10, 70S => 20, 70N => 45, 70H => 60), + MAX(74D => 60, 74K => 15, 74S => 15, 74T => 10), + MAX(105E => 10, 105S => 10, 105T => 10), + MAX(107C => 10, 107N => 10), + 67H AND 70R => 30, + 67H AND 74S => 15, + 67H AND 107N => 30 +)]]> + + + + + + + + + + CA + + 56I + + + + + + 57S + + + + + + 66I + + + + + + 67HYNK + + + + + + 70NH + + + + + + 70RS + + + + + + 74D + + + + + + 74SK + + + + + + 74T + + + + + + 105TSE + + + + + + 107NSAC + + + + + + + IN + + 118ACDEFHIKLMNPQSTVWYid + + + + + + 118R + + + + + + 119R + + + + + + 121ADEGHIKLMNPQRSTVWid + + + + + + 121C + + + + + + 121Y + + + + + + 122N + + + + + + 128T + + + + + + 138CDFGHILMNPQRSVWYid + + + + + + 138KAT + + + + + + 140DEFHIKLMNPQTVWYid + + + + + + 140R + + + + + + 140SAC + + + + + + 143CRH + + + + + + 143DEFILMNPQTVWid + + + + + + 143KGSA + + + + + + 145ACDEFGHIKLMNQRTVWYid + + + + + + 145S + + + + + + 146ACDEFGHKMNSTVWYid + + + + + + 146PRLI + + + + + + 147ACDEFHIKLMNPQRTVWYid + + + + + + 147G + + + + + + 148ACDEFGILMPSTVWYid + + + + + + 148HKR + + + + + + 148N + + + + + + 149A + + + + + + 151A + + + + + + 151CDEFGHKMNPQRSTWYid + + + + + + 151I + + + + + + 151L + + + + + + 153CDEGHIKLMNPQRTVWid + + + + + + 153YFA + + + + + + 155ACDEFGIKLMPQRVWYid + + + + + + 155H + + + + + + 155ST + + 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67ACFIKLMPQRVWYi + + + + + + 67GESTH + + + + + + 67N + + + + + + 68G + + + + + + 68N + + + + + + 69CFHKLMPQRVWY + + + + + + 69D + + + + + + 69G + + + + + + 69i + + + + + + 69NSAIE + + + + + + 70ACDFHILMPVWYi + + + + + + 70EGQNST + + + + + + 70R + + + + + + 74ACDEFGHKMNPQRSTWYid + + + + + + 74VI + + + + + + 75CDEFGHKNPQRWYid + + + + + + 75I + + + + + + 75MTAS + + + + + + 77ACDEGHIKMNPQRSTVWYid + + + + + + 77L + + + + + + 90I + + + + + + 98G + + + + + + + + + + + DTG + 5 + + + + + + + + + + DTG + 4 + + + + + + + + + + DTG + 3 + + + + + + + + + + DRV/r + 5 + + + + + + + + + + DRV/r + 4 + + + + + + + + + + DRV/r + 3 + + + + + + + + diff --git a/sierralocal/data/mutation-type-pairs_hiv1.csv b/sierralocal/data/mutation-type-pairs_hiv1.csv index 5bf2cef..962c620 100644 --- a/sierralocal/data/mutation-type-pairs_hiv1.csv +++ b/sierralocal/data/mutation-type-pairs_hiv1.csv @@ -14,7 +14,7 @@ HIV1,RT,NRTI,67,GESTH,NRTI,FALSE HIV1,RT,NRTI,67,N,NRTI,FALSE HIV1,RT,NRTI,68,-,NRTI,FALSE HIV1,RT,NRTI,68,G,NRTI,FALSE -HIV1,RT,NRTI,68,DNR,NRTI,FALSE +HIV1,RT,NRTI,68,N,NRTI,FALSE HIV1,RT,NRTI,69,-,NRTI,FALSE HIV1,RT,NRTI,69,D,NRTI,FALSE HIV1,RT,NRTI,69,G,NRTI,FALSE @@ -32,6 +32,8 @@ HIV1,RT,NRTI,75,MTAS,NRTI,FALSE HIV1,RT,NRTI,75,CDEFGHKNPQRWY_-,Other,TRUE HIV1,RT,NRTI,77,L,NRTI,FALSE HIV1,RT,NRTI,77,ACDEGHIKMNPQRSTVWY_-,Other,TRUE +HIV1,RT,NRTI,114,S,NRTI,FALSE +HIV1,RT,NRTI,114,CDEFGHIKLMNPQRTVWY_-,Other,TRUE HIV1,RT,NRTI,115,F,NRTI,FALSE HIV1,RT,NRTI,115,ACDEGHIKLMNPQRSTVW_-,Other,TRUE HIV1,RT,NRTI,116,Y,NRTI,FALSE @@ -104,12 +106,12 @@ HIV1,RT,NNRTI,190,R,Other,FALSE HIV1,RT,NNRTI,221,Y,NNRTI,FALSE HIV1,RT,NNRTI,225,H,NNRTI,FALSE HIV1,RT,NNRTI,225,ACDEFGIKLMNQRSTVWY_-,Other,TRUE -HIV1,RT,NNRTI,227,C,NNRTI,FALSE -HIV1,RT,NNRTI,227,ILV,NNRTI,FALSE -HIV1,RT,NNRTI,227,ADEGHKMNPQRSTWY_-,Other,TRUE +HIV1,RT,NNRTI,227,CILVY,NNRTI,FALSE +HIV1,RT,NNRTI,227,ADEGHKMNPQRSTW_-,Other,TRUE HIV1,RT,NNRTI,230,I,NNRTI,FALSE HIV1,RT,NNRTI,230,L,NNRTI,FALSE HIV1,RT,NNRTI,230,ACDEFGHKNPQRSTVWY_-,Other,TRUE +HIV1,RT,NNRTI,232,H,NNRTI,FALSE HIV1,RT,NNRTI,234,I,NNRTI,FALSE HIV1,RT,NNRTI,234,ACDEFGHKMNPQRSTWY_-,Other,TRUE HIV1,RT,NNRTI,236,L,NNRTI,FALSE @@ -204,9 +206,8 @@ HIV1,IN,INSTI,51,ACDEFGIKLMNPQRSTVW_-,Other,TRUE HIV1,IN,INSTI,66,AI,Major,FALSE HIV1,IN,INSTI,66,CDEFGHLMNPQRSVWY_-,Other,TRUE HIV1,IN,INSTI,66,K,Major,FALSE -HIV1,IN,INSTI,74,MF,Accessory,FALSE -HIV1,IN,INSTI,74,I,Other,FALSE -HIV1,IN,INSTI,75,A,Accessory,FALSE +HIV1,IN,INSTI,74,IMF,Accessory,FALSE +HIV1,IN,INSTI,75,IA,Accessory,FALSE HIV1,IN,INSTI,92,ACDFHIKLMNPRSTWY_-,Other,TRUE HIV1,IN,INSTI,92,GV,Major,FALSE HIV1,IN,INSTI,92,Q,Major,FALSE @@ -232,8 +233,8 @@ HIV1,IN,INSTI,143,DEFILMNPQTVW_-,Other,TRUE HIV1,IN,INSTI,143,KGSA,Major,FALSE HIV1,IN,INSTI,145,S,Major,FALSE HIV1,IN,INSTI,145,ACDEFGHIKLMNQRTVWY_-,Other,TRUE -HIV1,IN,INSTI,146,PRL,Major,FALSE -HIV1,IN,INSTI,146,ACDEFGHIKMNSTVWY_-,Other,TRUE +HIV1,IN,INSTI,146,PRLI,Accessory,FALSE +HIV1,IN,INSTI,146,ACDEFGHKMNSTVWY_-,Other,TRUE HIV1,IN,INSTI,147,ACDEFHIKLMNPQRTVWY_-,Other,TRUE HIV1,IN,INSTI,147,G,Major,FALSE HIV1,IN,INSTI,148,ACDEFGILMPSTVWY_-,Other,TRUE @@ -241,9 +242,8 @@ HIV1,IN,INSTI,148,HKR,Major,FALSE HIV1,IN,INSTI,148,N,Major,FALSE HIV1,IN,INSTI,149,A,Accessory,FALSE HIV1,IN,INSTI,151,L,Major,FALSE -HIV1,IN,INSTI,151,A,Accessory,FALSE +HIV1,IN,INSTI,151,AI,Accessory,FALSE HIV1,IN,INSTI,151,CDEFGHKMNPQRSTWY_-,Other,TRUE -HIV1,IN,INSTI,151,I,Other,FALSE HIV1,IN,INSTI,153,YFA,Accessory,FALSE HIV1,IN,INSTI,153,CDEGHIKLMNPQRTVW_-,Other,TRUE HIV1,IN,INSTI,155,ACDEFGIKLMPQRVWY_-,Other,TRUE @@ -259,18 +259,10 @@ HIV1,IN,INSTI,263,ACDEFGHILMNPQSTVWY_-,Other,TRUE HIV1,CA,CAI,56,I,Major,FALSE HIV1,CA,CAI,57,S,Accessory,FALSE HIV1,CA,CAI,66,I,Major,FALSE -HIV1,CA,CAI,67,H,Major,FALSE -HIV1,CA,CAI,67,Y,Accessory,FALSE -HIV1,CA,CAI,67,N,Accessory,FALSE -HIV1,CA,CAI,67,K,Accessory,FALSE -HIV1,CA,CAI,70,R,Accessory,FALSE -HIV1,CA,CAI,70,S,Major,FALSE -HIV1,CA,CAI,70,N,Major,FALSE -HIV1,CA,CAI,70,H,Major,FALSE -HIV1,CA,CAI,74,D,Major,FALSE -HIV1,CA,CAI,74,S,Major,FALSE -HIV1,CA,CAI,105,T,Accessory,FALSE -HIV1,CA,CAI,105,E,Accessory,FALSE -HIV1,CA,CAI,105,S,Accessory,FALSE -HIV1,CA,CAI,107,N,Accessory,FALSE -HIV1,CA,CAI,107,A,Accessory,FALSE \ No newline at end of file +HIV1,CA,CAI,67,HYNK,Major,FALSE +HIV1,CA,CAI,70,NH,Major,FALSE +HIV1,CA,CAI,70,RS,Accessory,FALSE +HIV1,CA,CAI,74,DSK,Major,FALSE +HIV1,CA,CAI,74,T,Accessory,FALSE +HIV1,CA,CAI,105,TSE,Accessory,FALSE +HIV1,CA,CAI,107,NSAC,Accessory,FALSE diff --git a/sierralocal/data/rx-all_subtype-all.csv b/sierralocal/data/rx-all_subtype-all.csv index 4746270..b94da4e 100644 --- a/sierralocal/data/rx-all_subtype-all.csv +++ b/sierralocal/data/rx-all_subtype-all.csv @@ -1,21782 +1,24959 @@ gene,position,aa,percent,count,total,reason,isUnusual -PR,1,A,2.3993761621978286e-05,4,166710,PCNT,True -PR,1,C,0.0,0,166710,PCNT,True -PR,1,D,0.0,0,166710,PCNT,True -PR,1,E,5.9984404054945715e-06,1,166710,PCNT,True -PR,1,F,5.9984404054945715e-06,1,166710,PCNT,True -PR,1,G,0.0,0,166710,PCNT,True -PR,1,H,2.9992202027472856e-05,5,166710,PCNT,True -PR,1,I,0.0,0,166710,PCNT,True -PR,1,K,0.0,0,166710,PCNT,True -PR,1,L,0.00042588926879011456,71,166710,PCNT,False -PR,1,M,0.0,0,166710,PCNT,True -PR,1,N,0.0,0,166710,PCNT,True -PR,1,P,0.999370163757423,166605,166710,PCNT,False -PR,1,Q,1.1996880810989143e-05,2,166710,PCNT,True -PR,1,R,1.1996880810989143e-05,2,166710,PCNT,True -PR,1,S,7.198128486593485e-05,12,166710,PCNT,True -PR,1,T,4.1989082838462e-05,7,166710,PCNT,True -PR,1,V,0.0,0,166710,PCNT,True -PR,1,W,0.0,0,166710,PCNT,True -PR,1,Y,0.0,0,166710,PCNT,True -PR,1,_,0.0,0,166710,PCNT,True -PR,1,-,0.0,0,166710,PCNT,True -PR,1,*,0.0,0,166710,PCNT,True -PR,2,A,0.0,0,168323,PCNT,True -PR,2,C,0.0,0,168323,PCNT,True -PR,2,D,0.0,0,168323,PCNT,True -PR,2,E,0.00016040588630193142,27,168323,PCNT,False -PR,2,F,0.0,0,168323,PCNT,True -PR,2,G,0.0,0,168323,PCNT,True -PR,2,H,0.00039210327762694344,66,168323,PCNT,False -PR,2,I,5.940958751923386e-06,1,168323,PCNT,True -PR,2,K,0.0002554612263327056,43,168323,PCNT,False -PR,2,L,6.535054627115725e-05,11,168323,PCNT,True -PR,2,M,0.0,0,168323,PCNT,True -PR,2,N,0.0,0,168323,PCNT,True -PR,2,P,0.00024952026758078217,42,168323,PCNT,False -PR,2,Q,0.9984197049719884,168057,168323,PCNT,False -PR,2,R,5.940958751923385e-05,10,168323,PCNT,True -PR,2,S,0.0003564575251154031,60,168323,PCNT,False -PR,2,T,1.1881917503846771e-05,2,168323,PCNT,True -PR,2,V,5.940958751923386e-06,1,168323,PCNT,True -PR,2,W,5.940958751923386e-06,1,168323,PCNT,True -PR,2,Y,1.1881917503846771e-05,2,168323,PCNT,True -PR,2,_,0.0,0,168323,PCNT,True -PR,2,-,0.0,0,168323,PCNT,True -PR,2,*,0.0,0,168323,PCNT,True -PR,3,A,5.9118076534261884e-06,1,169153,PCNT,True -PR,3,C,0.0,0,169153,PCNT,True -PR,3,D,5.9118076534261884e-06,1,169153,PCNT,True -PR,3,E,0.0,0,169153,PCNT,True -PR,3,F,0.0001477951913356547,25,169153,PCNT,False -PR,3,G,5.9118076534261884e-06,1,169153,PCNT,True -PR,3,H,0.0,0,169153,PCNT,True -PR,3,I,0.9946202550353822,168243,169153,PCNT,False -PR,3,K,1.1823615306852377e-05,2,169153,PCNT,True -PR,3,L,0.00041973834339325937,71,169153,PCNT,False -PR,3,M,1.7735422960278565e-05,3,169153,PCNT,True -PR,3,N,0.00026011953675075225,44,169153,PCNT,False -PR,3,P,0.0,0,169153,PCNT,True -PR,3,Q,5.9118076534261884e-06,1,169153,PCNT,True -PR,3,R,0.0,0,169153,PCNT,True -PR,3,S,2.9559038267130942e-05,5,169153,PCNT,True -PR,3,T,0.00011232434541509757,19,169153,PCNT,False -PR,3,V,0.004351090432921674,736,169153,PCNT,False -PR,3,W,0.0,0,169153,PCNT,True -PR,3,Y,5.9118076534261884e-06,1,169153,PCNT,True -PR,3,_,0.0,0,169153,PCNT,True -PR,3,-,0.0,0,169153,PCNT,True -PR,3,*,0.0,0,169153,PCNT,True -PR,4,A,0.0003578337058606938,69,192827,PCNT,False -PR,4,C,5.185995737111504e-06,1,192827,PCNT,True -PR,4,D,4.667396163400354e-05,9,192827,PCNT,True -PR,4,E,0.0,0,192827,PCNT,True -PR,4,F,1.0371991474223009e-05,2,192827,PCNT,True -PR,4,G,0.0,0,192827,PCNT,True -PR,4,H,7.260394031956106e-05,14,192827,PCNT,True -PR,4,I,0.00022818381243290618,44,192827,PCNT,False -PR,4,K,5.185995737111504e-06,1,192827,PCNT,True -PR,4,L,3.111597442266903e-05,6,192827,PCNT,True -PR,4,M,0.0,0,192827,PCNT,True -PR,4,N,0.00017632385506179113,34,192827,PCNT,False -PR,4,P,0.0009490372198914052,183,192827,PCNT,False -PR,4,Q,5.185995737111504e-06,1,192827,PCNT,True -PR,4,R,0.0,0,192827,PCNT,True -PR,4,S,0.0021003282735301593,405,192827,PCNT,False -PR,4,T,0.9960119692781613,192058,192827,PCNT,False -PR,4,V,0.0,0,192827,PCNT,True -PR,4,W,0.0,0,192827,PCNT,True -PR,4,Y,0.0,0,192827,PCNT,True -PR,4,_,0.0,0,192827,PCNT,True -PR,4,-,0.0,0,192827,PCNT,True -PR,4,*,0.0,0,192827,PCNT,True -PR,5,A,5.14289534722258e-06,1,194443,PCNT,True -PR,5,C,0.0,0,194443,PCNT,True -PR,5,D,0.0,0,194443,PCNT,True -PR,5,E,0.0,0,194443,PCNT,True -PR,5,F,0.0007868629881250547,153,194443,PCNT,False 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+IN,285,K,3.5695163305372124e-05,1,28015,PCNT,True +IN,285,L,0.0,0,28015,PCNT,True +IN,285,M,0.0,0,28015,PCNT,True +IN,285,N,0.0,0,28015,PCNT,True +IN,285,P,0.001463501695520257,41,28015,PCNT,False +IN,285,Q,0.9970373014456542,27932,28015,PCNT,False +IN,285,R,0.0010351597358557916,29,28015,PCNT,False +IN,285,S,0.0,0,28015,PCNT,True +IN,285,T,0.0,0,28015,PCNT,True +IN,285,V,0.0,0,28015,PCNT,True +IN,285,W,0.0,0,28015,PCNT,True +IN,285,Y,0.0,0,28015,PCNT,True +IN,285,_,0.0,0,28015,PCNT,True +IN,285,-,0.0,0,28015,PCNT,True +IN,285,*,0.0,0,28015,PCNT,True +IN,286,A,0.0011235547823565655,31,27591,PCNT,False +IN,286,C,0.0,0,27591,PCNT,True +IN,286,D,0.951868362871951,26263,27591,PCNT,False +IN,286,E,0.0028270088072197457,78,27591,PCNT,False +IN,286,F,0.0,0,27591,PCNT,True +IN,286,G,0.0005074118371932877,14,27591,PCNT,False +IN,286,H,3.62437026566634e-05,1,27591,PCNT,True +IN,286,I,0.0,0,27591,PCNT,True +IN,286,K,3.62437026566634e-05,1,27591,PCNT,True +IN,286,L,0.0,0,27591,PCNT,True +IN,286,M,0.0,0,27591,PCNT,True +IN,286,N,0.04327498097205611,1194,27591,PCNT,False +IN,286,P,0.0,0,27591,PCNT,True +IN,286,Q,0.0,0,27591,PCNT,True +IN,286,R,0.0,0,27591,PCNT,True +IN,286,S,7.24874053133268e-05,2,27591,PCNT,True +IN,286,T,7.24874053133268e-05,2,27591,PCNT,True +IN,286,V,0.00018121851328331703,5,27591,PCNT,False +IN,286,W,0.0,0,27591,PCNT,True +IN,286,Y,0.0,0,27591,PCNT,True +IN,286,_,0.0,0,27591,PCNT,True +IN,286,-,0.0,0,27591,PCNT,True +IN,286,*,0.0,0,27591,PCNT,True +IN,287,A,0.0010618820944708898,29,27310,PCNT,False +IN,287,C,0.0,0,27310,PCNT,True +IN,287,D,0.00043939948736726475,12,27310,PCNT,False +IN,287,E,0.9972903698279019,27236,27310,PCNT,False +IN,287,F,0.0,0,27310,PCNT,True +IN,287,G,0.0001830831197363603,5,27310,PCNT,False +IN,287,H,0.0,0,27310,PCNT,True +IN,287,I,0.0,0,27310,PCNT,True +IN,287,K,0.000585865983156353,16,27310,PCNT,False +IN,287,L,0.0,0,27310,PCNT,True +IN,287,M,0.0,0,27310,PCNT,True +IN,287,N,0.0,0,27310,PCNT,True +IN,287,P,0.0,0,27310,PCNT,True +IN,287,Q,0.0002929329915781765,8,27310,PCNT,False +IN,287,R,3.661662394727206e-05,1,27310,PCNT,True +IN,287,S,3.661662394727206e-05,1,27310,PCNT,True +IN,287,T,3.661662394727206e-05,1,27310,PCNT,True +IN,287,V,3.661662394727206e-05,1,27310,PCNT,True +IN,287,W,0.0,0,27310,PCNT,True +IN,287,Y,0.0,0,27310,PCNT,True +IN,287,_,0.0,0,27310,PCNT,True +IN,287,-,0.0,0,27310,PCNT,True +IN,287,*,0.0,0,27310,PCNT,True +IN,288,A,3.685548962517967e-05,1,27133,PCNT,True +IN,288,C,0.0,0,27133,PCNT,True +IN,288,D,0.9589061290679247,26018,27133,PCNT,False +IN,288,E,0.0007002543028784137,19,27133,PCNT,False +IN,288,F,0.0,0,27133,PCNT,True +IN,288,G,0.0012530866472561088,34,27133,PCNT,False +IN,288,H,0.0,0,27133,PCNT,True +IN,288,I,0.000110566468875539,3,27133,PCNT,False +IN,288,K,0.0,0,27133,PCNT,True +IN,288,L,0.0,0,27133,PCNT,True +IN,288,M,0.0,0,27133,PCNT,True +IN,288,N,0.038808830575314195,1053,27133,PCNT,False +IN,288,P,0.0,0,27133,PCNT,True +IN,288,Q,0.0,0,27133,PCNT,True +IN,288,R,0.0,0,27133,PCNT,True +IN,288,S,0.00018427744812589837,5,27133,PCNT,False +IN,288,T,0.0,0,27133,PCNT,True +IN,288,V,0.0,0,27133,PCNT,True +IN,288,W,0.0,0,27133,PCNT,True +IN,288,Y,0.0,0,27133,PCNT,True +IN,288,_,0.0,0,27133,PCNT,True +IN,288,-,0.0,0,27133,PCNT,True +IN,288,*,0.0,0,27133,PCNT,True diff --git a/sierralocal/jsonwriter.py b/sierralocal/jsonwriter.py index 6e17af7..b4ece6f 100644 --- a/sierralocal/jsonwriter.py +++ b/sierralocal/jsonwriter.py @@ -10,6 +10,12 @@ class JSONWriter(): + """ + Define a class for handling the formatting for the final JSON output of + mutations and validation results. The main write function is in + write_to_json. Generally, @param algorithm will be an instance of the + HIVdb class. + """ def __init__(self, algorithm, apobec_csv, unusual_csv, sdrms_csv, mutation_csv): # possible alternative drug abbrvs self.names = {'3TC': 'LMV'} diff --git a/sierralocal/nucaminohook.py b/sierralocal/nucaminohook.py index 365f55d..dc4f3df 100644 --- a/sierralocal/nucaminohook.py +++ b/sierralocal/nucaminohook.py @@ -23,7 +23,7 @@ def __init__(self, algorithm, binary=None, program='post'): if program == 'post': print('Aligning using post-align') - pass # TODO include post align as a submodule: I'm here now! + pass # TODO include post align as a sub module: I'm here now! else: # get necessary binaries for nucAmino if binary is None: target = 'nucamino-{}-{}'.format( @@ -153,6 +153,13 @@ def get_aligned_seq(self, nuc, sites): return aligned def makeReferenceFASTA(self, fragmentName, refSeq): + """ + Makes a temporary FASTA file for the reference sequence of a given fragment. + @param fragmentName: str, name of fragment + @param refSeq: str, reference sequence for a given fragment + @return: str, path to temporary FASTA file + """ + tempFasta = tempfile.NamedTemporaryFile('w', prefix='postalign-ref-', suffix='.fas', delete=False) tempFasta.write(">Ref_{}\n".format(fragmentName)) tempFasta.write("{}\n".format(refSeq)) @@ -160,6 +167,17 @@ def makeReferenceFASTA(self, fragmentName, refSeq): return os.path.abspath(tempFasta.name) def getConfigField(self, config, field): + """ + Retrieves entry information from each fragmentConfig entry in the alignment + config JSON file, and depending on whether the field is refSequence or not, + stores the corresponding FASTA file path or the field value in a dictionary + that is mapping fragmentName to field value. + @param config: dict, JSON configuration for post-align + @param field: str, field to retrieve from config + @return: dict, dictionary of fragmentName to a path to a corresponding + temporary FASTA filed and/or field value. + """ + resultmap = {} for entry in config['fragmentConfig']: if field == 'refSequence': @@ -695,6 +713,11 @@ def is_unsequenced(self, triplet): return (triplet.replace("-", "N").count("N") > 1) # TODO: incorporate !isInsertion && def is_stop_codon(self, triplet): + """Determines whether a nucleotide triplet encodes a stop codon. ("*" is + present in the translated triplet) + @param triplet: str, nucleotide triplet as a string + @return: bool, True when it is a stop codon + """ return ("*" in self.translate_na_triplet(triplet)) def is_apobec_drm(self, gene, consensus, position, AA): @@ -739,7 +762,13 @@ def get_highest_mut_prevalance(self, mutation, gene, subtype): def get_mut_prevalence(self, position, cons, aa, gene, subtype): """ - ??? + Determines prevalence of a specific mutation in the subtype alignment, by looking up the position, consensus amino acid, mutant amino acid, gene and subtype in the prevalence dictionaries. + @param position: int, position of mutation relative to POL + @param cons: str, consensus amino acid at this position + @param aa: str, mutant amino acid at this position + @param gene: str, PR, RT, or INT + @param subtype: str, predicted from Subtyper.get_closest_subtype() + @return: float, prevalence of the mutation in the subtype alignment """ key2 = str(position) + str(cons) + str(aa) + subtype diff --git a/sierralocal/updater.py b/sierralocal/updater.py index 909dcb4..d32ca54 100644 --- a/sierralocal/updater.py +++ b/sierralocal/updater.py @@ -163,6 +163,9 @@ def update_genotype_properties(target_dir=None): print("Couldn't update subtyper genotype property file, please get manually at: https://hivdb.stanford.edu/page/hiv-subtyper/") def main(updater_outdir=None): # pragma: no cover + """ + Main function called when running updater.py directly. + """ update_hivdb(updater_outdir) update_apobec(updater_outdir) update_is_unusual(updater_outdir) From 5af78e1e8ea370cdc0c95aa446ac47fb7a7e2a1d Mon Sep 17 00:00:00 2001 From: immasushiroll Date: Sun, 21 Jun 2026 16:39:16 -0400 Subject: [PATCH 2/5] cleanup extra tab space --- sierralocal/nucaminohook.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sierralocal/nucaminohook.py b/sierralocal/nucaminohook.py index dc4f3df..63391c7 100644 --- a/sierralocal/nucaminohook.py +++ b/sierralocal/nucaminohook.py @@ -23,7 +23,7 @@ def __init__(self, algorithm, binary=None, program='post'): if program == 'post': print('Aligning using post-align') - pass # TODO include post align as a sub module: I'm here now! + pass # TODO include post align as a submodule: I'm here now! else: # get necessary binaries for nucAmino if binary is None: target = 'nucamino-{}-{}'.format( From 1f873146b5d9f5d7c3fc6964996b8f2f86040792 Mon Sep 17 00:00:00 2001 From: immasushiroll Date: Mon, 29 Jun 2026 21:19:56 -0400 Subject: [PATCH 3/5] revert changes in sierralocal/data/ folder --- sierralocal/data/alignment-config_hiv1.json | 4 +- sierralocal/data/mutation-type-pairs_hiv1.csv | 44 +- sierralocal/data/rx-all_subtype-all.csv | 46739 +++++++--------- 3 files changed, 21809 insertions(+), 24978 deletions(-) diff --git a/sierralocal/data/alignment-config_hiv1.json b/sierralocal/data/alignment-config_hiv1.json index 35ba2bf..11ca8ae 100644 --- a/sierralocal/data/alignment-config_hiv1.json +++ b/sierralocal/data/alignment-config_hiv1.json @@ -13,7 +13,7 @@ "--min-gap-distance=15", "--gap-placement-score=2756/3ins:20,2756/6ins:30,2756/9ins:40,2756/12ins:50", "--gap-placement-score=4994/6ins:20", - "2088", + "2085", "5096", "codon-alignment", "--min-gap-distance=15", @@ -82,7 +82,7 @@ "geneName": "HIV1pol", "refRanges": [ [ - 2088, + 2085, 5093 ] ], diff --git a/sierralocal/data/mutation-type-pairs_hiv1.csv b/sierralocal/data/mutation-type-pairs_hiv1.csv index 962c620..5bf2cef 100644 --- a/sierralocal/data/mutation-type-pairs_hiv1.csv +++ b/sierralocal/data/mutation-type-pairs_hiv1.csv @@ -14,7 +14,7 @@ HIV1,RT,NRTI,67,GESTH,NRTI,FALSE HIV1,RT,NRTI,67,N,NRTI,FALSE HIV1,RT,NRTI,68,-,NRTI,FALSE HIV1,RT,NRTI,68,G,NRTI,FALSE -HIV1,RT,NRTI,68,N,NRTI,FALSE +HIV1,RT,NRTI,68,DNR,NRTI,FALSE HIV1,RT,NRTI,69,-,NRTI,FALSE HIV1,RT,NRTI,69,D,NRTI,FALSE HIV1,RT,NRTI,69,G,NRTI,FALSE @@ -32,8 +32,6 @@ HIV1,RT,NRTI,75,MTAS,NRTI,FALSE HIV1,RT,NRTI,75,CDEFGHKNPQRWY_-,Other,TRUE HIV1,RT,NRTI,77,L,NRTI,FALSE HIV1,RT,NRTI,77,ACDEGHIKMNPQRSTVWY_-,Other,TRUE -HIV1,RT,NRTI,114,S,NRTI,FALSE -HIV1,RT,NRTI,114,CDEFGHIKLMNPQRTVWY_-,Other,TRUE HIV1,RT,NRTI,115,F,NRTI,FALSE HIV1,RT,NRTI,115,ACDEGHIKLMNPQRSTVW_-,Other,TRUE HIV1,RT,NRTI,116,Y,NRTI,FALSE @@ -106,12 +104,12 @@ HIV1,RT,NNRTI,190,R,Other,FALSE HIV1,RT,NNRTI,221,Y,NNRTI,FALSE HIV1,RT,NNRTI,225,H,NNRTI,FALSE HIV1,RT,NNRTI,225,ACDEFGIKLMNQRSTVWY_-,Other,TRUE -HIV1,RT,NNRTI,227,CILVY,NNRTI,FALSE -HIV1,RT,NNRTI,227,ADEGHKMNPQRSTW_-,Other,TRUE +HIV1,RT,NNRTI,227,C,NNRTI,FALSE +HIV1,RT,NNRTI,227,ILV,NNRTI,FALSE +HIV1,RT,NNRTI,227,ADEGHKMNPQRSTWY_-,Other,TRUE HIV1,RT,NNRTI,230,I,NNRTI,FALSE HIV1,RT,NNRTI,230,L,NNRTI,FALSE HIV1,RT,NNRTI,230,ACDEFGHKNPQRSTVWY_-,Other,TRUE -HIV1,RT,NNRTI,232,H,NNRTI,FALSE HIV1,RT,NNRTI,234,I,NNRTI,FALSE HIV1,RT,NNRTI,234,ACDEFGHKMNPQRSTWY_-,Other,TRUE HIV1,RT,NNRTI,236,L,NNRTI,FALSE @@ -206,8 +204,9 @@ HIV1,IN,INSTI,51,ACDEFGIKLMNPQRSTVW_-,Other,TRUE HIV1,IN,INSTI,66,AI,Major,FALSE HIV1,IN,INSTI,66,CDEFGHLMNPQRSVWY_-,Other,TRUE HIV1,IN,INSTI,66,K,Major,FALSE -HIV1,IN,INSTI,74,IMF,Accessory,FALSE -HIV1,IN,INSTI,75,IA,Accessory,FALSE +HIV1,IN,INSTI,74,MF,Accessory,FALSE +HIV1,IN,INSTI,74,I,Other,FALSE +HIV1,IN,INSTI,75,A,Accessory,FALSE HIV1,IN,INSTI,92,ACDFHIKLMNPRSTWY_-,Other,TRUE HIV1,IN,INSTI,92,GV,Major,FALSE HIV1,IN,INSTI,92,Q,Major,FALSE @@ -233,8 +232,8 @@ HIV1,IN,INSTI,143,DEFILMNPQTVW_-,Other,TRUE HIV1,IN,INSTI,143,KGSA,Major,FALSE HIV1,IN,INSTI,145,S,Major,FALSE HIV1,IN,INSTI,145,ACDEFGHIKLMNQRTVWY_-,Other,TRUE -HIV1,IN,INSTI,146,PRLI,Accessory,FALSE -HIV1,IN,INSTI,146,ACDEFGHKMNSTVWY_-,Other,TRUE +HIV1,IN,INSTI,146,PRL,Major,FALSE +HIV1,IN,INSTI,146,ACDEFGHIKMNSTVWY_-,Other,TRUE HIV1,IN,INSTI,147,ACDEFHIKLMNPQRTVWY_-,Other,TRUE HIV1,IN,INSTI,147,G,Major,FALSE HIV1,IN,INSTI,148,ACDEFGILMPSTVWY_-,Other,TRUE @@ -242,8 +241,9 @@ HIV1,IN,INSTI,148,HKR,Major,FALSE HIV1,IN,INSTI,148,N,Major,FALSE HIV1,IN,INSTI,149,A,Accessory,FALSE HIV1,IN,INSTI,151,L,Major,FALSE -HIV1,IN,INSTI,151,AI,Accessory,FALSE +HIV1,IN,INSTI,151,A,Accessory,FALSE HIV1,IN,INSTI,151,CDEFGHKMNPQRSTWY_-,Other,TRUE +HIV1,IN,INSTI,151,I,Other,FALSE HIV1,IN,INSTI,153,YFA,Accessory,FALSE HIV1,IN,INSTI,153,CDEGHIKLMNPQRTVW_-,Other,TRUE HIV1,IN,INSTI,155,ACDEFGIKLMPQRVWY_-,Other,TRUE @@ -259,10 +259,18 @@ HIV1,IN,INSTI,263,ACDEFGHILMNPQSTVWY_-,Other,TRUE HIV1,CA,CAI,56,I,Major,FALSE HIV1,CA,CAI,57,S,Accessory,FALSE HIV1,CA,CAI,66,I,Major,FALSE -HIV1,CA,CAI,67,HYNK,Major,FALSE -HIV1,CA,CAI,70,NH,Major,FALSE -HIV1,CA,CAI,70,RS,Accessory,FALSE -HIV1,CA,CAI,74,DSK,Major,FALSE -HIV1,CA,CAI,74,T,Accessory,FALSE -HIV1,CA,CAI,105,TSE,Accessory,FALSE -HIV1,CA,CAI,107,NSAC,Accessory,FALSE +HIV1,CA,CAI,67,H,Major,FALSE +HIV1,CA,CAI,67,Y,Accessory,FALSE +HIV1,CA,CAI,67,N,Accessory,FALSE +HIV1,CA,CAI,67,K,Accessory,FALSE +HIV1,CA,CAI,70,R,Accessory,FALSE +HIV1,CA,CAI,70,S,Major,FALSE +HIV1,CA,CAI,70,N,Major,FALSE +HIV1,CA,CAI,70,H,Major,FALSE +HIV1,CA,CAI,74,D,Major,FALSE +HIV1,CA,CAI,74,S,Major,FALSE +HIV1,CA,CAI,105,T,Accessory,FALSE +HIV1,CA,CAI,105,E,Accessory,FALSE +HIV1,CA,CAI,105,S,Accessory,FALSE +HIV1,CA,CAI,107,N,Accessory,FALSE +HIV1,CA,CAI,107,A,Accessory,FALSE \ No newline at end of file diff --git a/sierralocal/data/rx-all_subtype-all.csv b/sierralocal/data/rx-all_subtype-all.csv index b94da4e..4746270 100644 --- a/sierralocal/data/rx-all_subtype-all.csv +++ b/sierralocal/data/rx-all_subtype-all.csv @@ -1,24959 +1,21782 @@ gene,position,aa,percent,count,total,reason,isUnusual -CA,1,P,0.998521327014218,26336,26375,PCNT,False -CA,1,S,0.00026540284360189573,7,26375,PCNT,True -CA,1,A,0.00015165876777251184,4,26375,PCNT,True -CA,1,H,7.582938388625592e-05,2,26375,PCNT,True -CA,1,G,7.582938388625592e-05,2,26375,PCNT,True -CA,1,Q,0.00015165876777251184,4,26375,PCNT,True -CA,1,M,0.00011374407582938388,3,26375,PCNT,True -CA,1,E,7.582938388625592e-05,2,26375,PCNT,True -CA,1,F,7.582938388625592e-05,2,26375,PCNT,True -CA,1,L,0.00011374407582938388,3,26375,PCNT,True -CA,1,T,3.791469194312796e-05,1,26375,PCNT,True -CA,1,R,0.00015165876777251184,4,26375,PCNT,True -CA,1,K,7.582938388625592e-05,2,26375,PCNT,True -CA,1,N,3.791469194312796e-05,1,26375,PCNT,True -CA,1,D,3.791469194312796e-05,1,26375,PCNT,True -CA,1,Y,3.791469194312796e-05,1,26375,PCNT,True -CA,2,I,0.9836805950889976,25919,26349,PCNT,False -CA,2,V,0.013283236555467001,350,26349,PCNT,False -CA,2,L,0.0016698925955444229,44,26349,PCNT,False -CA,2,*,0.00015180841777676573,4,26349,PCNT,True -CA,2,K,0.00026566473110934,7,26349,PCNT,True -CA,2,M,0.00015180841777676573,4,26349,PCNT,True -CA,2,T,7.590420888838287e-05,2,26349,PCNT,True -CA,2,R,7.590420888838287e-05,2,26349,PCNT,True -CA,2,S,0.00011385631333257428,3,26349,PCNT,True -CA,2,Q,7.590420888838287e-05,2,26349,PCNT,True -CA,2,P,0.00018976052222095715,5,26349,PCNT,True -CA,2,E,3.795210444419143e-05,1,26349,PCNT,True -CA,2,H,3.795210444419143e-05,1,26349,PCNT,True -CA,2,G,3.795210444419143e-05,1,26349,PCNT,True -CA,2,A,3.795210444419143e-05,1,26349,PCNT,True -CA,2,N,7.590420888838287e-05,2,26349,PCNT,True -CA,2,D,3.795210444419143e-05,1,26349,PCNT,True -CA,3,V,0.9889175649005617,26056,26348,PCNT,False -CA,3,E,0.00037953544861090024,10,26348,PCNT,True -CA,3,I,0.004933960831941703,130,26348,PCNT,False -CA,3,M,0.0025049339608319418,66,26348,PCNT,False -CA,3,A,0.0003415819037498102,9,26348,PCNT,True -CA,3,L,0.001594048884165781,42,26348,PCNT,False -CA,3,G,0.0006452102626385304,17,26348,PCNT,True -CA,3,C,7.590708972218005e-05,2,26348,PCNT,True -CA,3,S,0.00011386063458327007,3,26348,PCNT,True -CA,3,K,0.0001518141794443601,4,26348,PCNT,True -CA,3,P,3.7953544861090024e-05,1,26348,PCNT,True -CA,3,W,7.590708972218005e-05,2,26348,PCNT,True -CA,3,Q,7.590708972218005e-05,2,26348,PCNT,True -CA,3,_,7.590708972218005e-05,2,26348,PCNT,True -CA,3,F,3.7953544861090024e-05,1,26348,PCNT,True -CA,3,T,3.7953544861090024e-05,1,26348,PCNT,True -CA,4,Q,0.9895303846445641,26086,26362,PCNT,False -CA,4,L,0.00018966694484485243,5,26362,PCNT,True -CA,4,A,0.0009104013352552917,24,26362,PCNT,True -CA,4,S,0.0006448676124724983,17,26362,PCNT,True -CA,4,P,0.002048403004324406,54,26362,PCNT,False -CA,4,T,0.0008724679462863213,23,26362,PCNT,True -CA,4,R,0.0042864729534936655,113,26362,PCNT,False -CA,4,H,0.0006448676124724983,17,26362,PCNT,True -CA,4,*,7.586677793794098e-05,2,26362,PCNT,True -CA,4,N,0.00011380016690691146,3,26362,PCNT,True -CA,4,K,0.00018966694484485243,5,26362,PCNT,True -CA,4,G,7.586677793794098e-05,2,26362,PCNT,True -CA,4,E,0.0002276003338138229,6,26362,PCNT,True -CA,4,Y,3.793338896897049e-05,1,26362,PCNT,True -CA,4,M,3.793338896897049e-05,1,26362,PCNT,True -CA,4,-,3.793338896897049e-05,1,26362,PCNT,True -CA,4,F,3.793338896897049e-05,1,26362,PCNT,True -CA,4,C,3.793338896897049e-05,1,26362,PCNT,True -CA,5,N,0.9961701804944638,26271,26372,PCNT,False -CA,5,S,0.0009100561201274078,24,26372,PCNT,True -CA,5,I,0.00015167602002123465,4,26372,PCNT,True -CA,5,K,0.0006825420900955559,18,26372,PCNT,True -CA,5,D,0.0004550280600637039,12,26372,PCNT,True -CA,5,T,0.0004929470650690126,13,26372,PCNT,True -CA,5,G,0.0005687850750796299,15,26372,PCNT,True -CA,5,Q,7.583801001061732e-05,2,26372,PCNT,True -CA,5,H,7.583801001061732e-05,2,26372,PCNT,True -CA,5,Y,3.791900500530866e-05,1,26372,PCNT,True -CA,5,M,3.791900500530866e-05,1,26372,PCNT,True -CA,5,R,0.00011375701501592598,3,26372,PCNT,True -CA,5,L,3.791900500530866e-05,1,26372,PCNT,True -CA,5,E,7.583801001061732e-05,2,26372,PCNT,True -CA,5,F,3.791900500530866e-05,1,26372,PCNT,True -CA,5,*,3.791900500530866e-05,1,26372,PCNT,True -CA,5,W,3.791900500530866e-05,1,26372,PCNT,True -CA,6,I,0.05138370054128231,1348,26234,PCNT,False -CA,6,L,0.5457421666539605,14317,26234,PCNT,False -CA,6,A,0.27651139742319125,7254,26234,PCNT,False -CA,6,M,0.09064572691926508,2378,26234,PCNT,False -CA,6,P,0.003621254860105207,95,26234,PCNT,False 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-CA,7,*,0.00011376564277588168,3,26370,PCNT,True -CA,7,S,3.792188092529389e-05,1,26370,PCNT,True -CA,7,L,0.00041714069017823285,11,26370,PCNT,True -CA,7,G,0.00022753128555176336,6,26370,PCNT,True -CA,7,F,3.792188092529389e-05,1,26370,PCNT,True -CA,7,T,3.792188092529389e-05,1,26370,PCNT,True -CA,7,N,3.792188092529389e-05,1,26370,PCNT,True -CA,7,A,7.584376185058778e-05,2,26370,PCNT,True -CA,7,V,3.792188092529389e-05,1,26370,PCNT,True -CA,8,G,0.9985972095844707,26339,26376,PCNT,False -CA,8,E,0.00011373976342129209,3,26376,PCNT,True -CA,8,R,0.0006824385805277526,18,26376,PCNT,True -CA,8,Q,7.582650894752806e-05,2,26376,PCNT,True -CA,8,N,0.00011373976342129209,3,26376,PCNT,True -CA,8,V,7.582650894752806e-05,2,26376,PCNT,True -CA,8,A,0.00011373976342129209,3,26376,PCNT,True -CA,8,K,7.582650894752806e-05,2,26376,PCNT,True -CA,8,C,3.791325447376403e-05,1,26376,PCNT,True -CA,8,W,3.791325447376403e-05,1,26376,PCNT,True -CA,8,L,3.791325447376403e-05,1,26376,PCNT,True -CA,8,S,3.791325447376403e-05,1,26376,PCNT,True -CA,9,Q,0.9930605589473285,26188,26371,PCNT,False -CA,9,E,0.0002654431003754124,7,26371,PCNT,True -CA,9,H,0.003488680747791134,92,26371,PCNT,False -CA,9,R,0.0005308862007508248,14,26371,PCNT,True -CA,9,P,0.00022752265746463918,6,26371,PCNT,True -CA,9,A,0.00094801107276933,25,26371,PCNT,True -CA,9,N,7.58408858215464e-05,2,26371,PCNT,True -CA,9,L,0.0003412839861969588,9,26371,PCNT,True -CA,9,K,0.0003033635432861856,8,26371,PCNT,True -CA,9,I,0.0001516817716430928,4,26371,PCNT,True -CA,9,T,7.58408858215464e-05,2,26371,PCNT,True -CA,9,F,3.79204429107732e-05,1,26371,PCNT,True -CA,9,G,0.00011376132873231959,3,26371,PCNT,True -CA,9,V,0.0003033635432861856,8,26371,PCNT,True -CA,9,*,3.79204429107732e-05,1,26371,PCNT,True -CA,9,Y,3.79204429107732e-05,1,26371,PCNT,True -CA,10,M,0.9815904346175744,25860,26345,PCNT,False -CA,10,W,0.0039855760106282025,105,26345,PCNT,False -CA,10,A,0.0013664832036439551,36,26345,PCNT,False 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+IN,287,H,0.0,0,25911,PCNT,True +IN,287,I,0.0,0,25911,PCNT,True +IN,287,K,0.0006174983597699819,16,25911,PCNT,False +IN,287,L,0.0,0,25911,PCNT,True +IN,287,M,0.0,0,25911,PCNT,True +IN,287,N,0.0,0,25911,PCNT,True +IN,287,P,0.0,0,25911,PCNT,True +IN,287,Q,0.00030874917988499094,8,25911,PCNT,False +IN,287,R,3.859364748562387e-05,1,25911,PCNT,True +IN,287,S,3.859364748562387e-05,1,25911,PCNT,True +IN,287,T,3.859364748562387e-05,1,25911,PCNT,True +IN,287,V,3.859364748562387e-05,1,25911,PCNT,True +IN,287,W,0.0,0,25911,PCNT,True +IN,287,Y,0.0,0,25911,PCNT,True +IN,287,_,0.0,0,25911,PCNT,True +IN,287,-,0.0,0,25911,PCNT,True +IN,287,*,0.0,0,25911,PCNT,True +IN,288,A,3.884852958315528e-05,1,25741,PCNT,True +IN,288,C,0.0,0,25741,PCNT,True +IN,288,D,0.9590536498193544,24687,25741,PCNT,False +IN,288,E,0.0007381220620799502,19,25741,PCNT,False +IN,288,F,0.0,0,25741,PCNT,True +IN,288,G,0.0011654558874946584,30,25741,PCNT,False +IN,288,H,0.0,0,25741,PCNT,True +IN,288,I,0.00011654558874946584,3,25741,PCNT,False +IN,288,K,0.0,0,25741,PCNT,True +IN,288,L,0.0,0,25741,PCNT,True +IN,288,M,0.0,0,25741,PCNT,True +IN,288,N,0.038693135464822656,996,25741,PCNT,False +IN,288,P,0.0,0,25741,PCNT,True +IN,288,Q,0.0,0,25741,PCNT,True +IN,288,R,0.0,0,25741,PCNT,True +IN,288,S,0.00019424264791577638,5,25741,PCNT,False +IN,288,T,0.0,0,25741,PCNT,True +IN,288,V,0.0,0,25741,PCNT,True +IN,288,W,0.0,0,25741,PCNT,True +IN,288,Y,0.0,0,25741,PCNT,True +IN,288,_,0.0,0,25741,PCNT,True +IN,288,-,0.0,0,25741,PCNT,True +IN,288,*,0.0,0,25741,PCNT,True From 4c710b55d97b1d814a1ad0f58be98d9a7c5cedb1 Mon Sep 17 00:00:00 2001 From: immasushiroll Date: Mon, 29 Jun 2026 22:00:30 -0400 Subject: [PATCH 4/5] revert changes again by pulling from master instead of dev this time --- sierralocal/data/alignment-config_hiv1.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/sierralocal/data/alignment-config_hiv1.json b/sierralocal/data/alignment-config_hiv1.json index 11ca8ae..35ba2bf 100644 --- a/sierralocal/data/alignment-config_hiv1.json +++ b/sierralocal/data/alignment-config_hiv1.json @@ -13,7 +13,7 @@ "--min-gap-distance=15", "--gap-placement-score=2756/3ins:20,2756/6ins:30,2756/9ins:40,2756/12ins:50", "--gap-placement-score=4994/6ins:20", - "2085", + "2088", "5096", "codon-alignment", "--min-gap-distance=15", @@ -82,7 +82,7 @@ "geneName": "HIV1pol", "refRanges": [ [ - 2085, + 2088, 5093 ] ], From 6cbe1d5737bc04261c9b9431709ef78863c330cd Mon Sep 17 00:00:00 2001 From: immasushiroll Date: Mon, 29 Jun 2026 22:33:54 -0400 Subject: [PATCH 5/5] removing extra file --- sierralocal/data/HIVDB_10.2.xml | 4408 ------------------------------- 1 file changed, 4408 deletions(-) delete mode 100644 sierralocal/data/HIVDB_10.2.xml diff --git a/sierralocal/data/HIVDB_10.2.xml b/sierralocal/data/HIVDB_10.2.xml deleted file mode 100644 index 4a98f13..0000000 --- a/sierralocal/data/HIVDB_10.2.xml +++ /dev/null @@ -1,4408 +0,0 @@ - - - - HIVDB - 10.2 - 2026-04-26 - - - CA - CAI - - - PR - PI - - - RT - NRTI,NNRTI - - - IN - INSTI - - - 1 - Susceptible - S - - - 2 - Potential Low-Level Resistance - S - - - 3 - Low-Level Resistance - I - - - 4 - Intermediate Resistance - I - - - 5 - High-Level Resistance - R - - - NRTI - ABC,AZT,D4T,DDI,FTC,3TC,TDF,ISL - - - NNRTI - DOR,EFV,ETR,NVP,RPV,DPV - - - PI - ATV/r,DRV/r,FPV/r,IDV/r,LPV/r,NFV,SQV/r,TPV/r - - - INSTI - BIC,CAB,DTG,EVG,RAL - - - CAI - LEN - - 1, 10 TO 14 => 2, 15 TO 29 => 3, 30 TO 59 => 4, 60 TO INF => 5)]]> - 1 - - - - - - 1 - - - - - - 1 - - - - - 1000-fold reduced LEN susceptibility. It has an RC of 1%-6%. It occurred in 6 patients in the CAPELLA study usually in combination with other mutations.]]> - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - 1000 reduced LEN susceptibility.]]> - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - 10-fold reduced susceptibility to RAL but has minimal if any effect on susceptibility to CAB, DTG, and BIC. F121C is an extremely rare mutation. Preliminary data suggests it may confers high level phenotypic resistance to RAL, EVG, and possibly CAB. $listMutsIn{121(NOT CY)} is an unusual mutation at this position.]]> - 1 - - - - - - 1 - - - - - 10-fold reduced susceptibility to RAL but has minimal if any effect on susceptibility to CAB, DTG, and BIC.]]> - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - 10-fold while reducing DTG, BIC, and CAB by about 1.5-fold. N155S/T are extremely rare nonpolymorphic mutations that reduce RAL and EVG susceptibility about 5-fold and greater than 30-fold respectively but have little effect on CAB, DTG, and BIC. $listMutsIn{155(NOT HST)} is an unusual mutation at this position.]]> - 1 - - - - - 10-fold while reducing DTG, BIC, and CAB by about 1.5-fold.]]> - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - =10-fold but do not appear to reduce susceptibility to other INSTIs. $listMutsIn{92(NOT GQV)} is an unusual mutation at this position.]]> - 1 - - - - - =10-fold but do not appear to reduce susceptibility to other INSTIs.]]> - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - - ABC - abacavir - - 5, - 62V => 5, - MAX(65E => 10, 65N => 30, 65R => 45), - MAX(67E => 5, 67G => 5, 67H => 5, 67N => 5, 67S => 5, 67T => 5, 67d => 15), - 68d => 15, - MAX(69G => 10, 69i => 60, 69d => 15), - MAX(70E => 15, 70G => 15, 70N => 15, 70Q => 15, 70R => 5, 70S => 15, 70T => 15, 70d => 15), - MAX(74I => 15, 74V => 30), - 75I => 5, - 77L => 5, - 115F => 30, - 116Y => 5, - MAX(151L => 30, 151M => 60), - MAX(184I => 15, 184V => 15), - 210W => 5, - MAX(215F => 10, 215Y => 10), - 65RN AND 151M => 10, - 77L AND 116Y AND 151ML => 15, - 74V AND 184IV => 15, - 115F AND 184IV => 15, - 41L AND 215FY => 10, - 210W AND 215FY => 10, - 41L AND 210W => 5, - 41L AND 210W AND 215FY => 15, - 41L AND 44AD AND 210W AND 215FY => 5, - 40F AND 41L AND 210W AND 215FY => 5, - 41L AND 67EGNHST AND 215FY => 5, - 67EGNHST AND 215FY AND 219ENQRW => 5, - 67EGNHST AND 70R AND 219ENQRW => 10, - 41L AND 184VI AND 215FY => 10, - 67EGNHST AND 70R AND 184VI AND 219ENQRW => 10 -)]]> - - - - - - - - - AZT - zidovudine - - 15, - 62V => 5, - 65R => -10, - MAX(67E => 15, 67G => 15, 67H => 15, 67N => 15, 67S => 15, 67T => 15, 67d => 30), - MAX(69G => 5, 69i => 60), - 70R => 30, - MAX(75I => 5, 75A => 10, 75M => 10, 75S => 10, 75T => 10), - 77L => 5, - 116Y => 10, - MAX(151L => 30, 151M => 60), - MAX(184I => -10, 184V => -10), - 210W => 15, - MAX(215F => 60, 215Y => 60, 215A => 10, 215C => 10, 215D => 10, 215E => 10, 215I => 20, 215L => 10, 215N => 10, 215S => 10, 215V => 20), - 65RN AND 151M => 10, - 77L AND 116Y AND 151ML => 15, - MAX(41L AND 215FY => 10, 41L AND 215ACDEILNSV => 10), - MAX(210W AND 215FY => 10, 210W AND 215ACDEILNSV => 10), - 41L AND 210W => 10, - 41L AND 44AD AND 210W AND 215FY => 5, - 40F AND 41L AND 210W AND 215FY => 5, - 41L AND 67EGNHST AND 215FY => 5, - 67EGNHST AND 215FY AND 219ENQRW => 5, - 67EGNHST AND 70R AND 219ENQRW => 15, - MAX(219E => 10, 219N => 10, 219Q => 10, 219R => 10, 219W => 10), - 151M AND 184IV => 10 -)]]> - - - - - - - - - D4T - stavudine - - 15, - 62V => 5, - MAX(65E => 10, 65N => 30, 65R => 60), - MAX(67E => 10, 67G => 10, 67H => 10, 67N => 15, 67S => 10, 67T => 10, 67d => 30), - 68d => 30, - MAX(69G => 10, 69i => 60, 69d => 30, 69D => 10), - MAX(70E => 15, 70G => 15, 70N => 15, 70Q => 15, 70R => 15, 70S => 15, 70T => 15, 70d => 30), - MAX(75I => 5, 75A => 30, 75M => 30, 75S => 30, 75T => 60), - 77L => 10, - 116Y => 10, - MAX(151L => 30, 151M => 60), - MAX(184I => -10, 184V => -10), - 210W => 15, - MAX(215F => 40, 215Y => 40, 215A => 20, 215C => 20, 215D => 20, 215E => 20, 215I => 20, 215L => 20, 215N => 20, 215S => 20, 215V => 20), - MAX(41L AND 215FY => 10, 41L AND 215ACDEILNSV => 5), - MAX(210W AND 215FY => 10, 210W AND 215ACDEILNSV => 5), - 41L AND 210W => 10, - 41L AND 44AD AND 210W AND 215FY => 5, - 40F AND 41L AND 210W AND 215FY => 5, - MAX(219E => 10, 219N => 10, 219Q => 10, 219R => 10, 219W => 10), - 151M AND 184IV => 10, - 41L AND 67EGN AND 215FY => 5, - 67EGN AND 215FY AND 219ENQR => 5, - 67EGN AND 70R AND 219ENQR => 10, - 70R AND 215FY => 5, - 77L AND 116Y AND 151M => 10, - 70EGNQST AND 184IV => 10 -)]]> - - - - - - - - - DDI - didanosine - - 10, - 62V => 5, - MAX(65E => 10, 65N => 30, 65R => 60), - MAX(67E => 5, 67G => 5, 67H => 5, 67N => 5, 67S => 5, 67T => 5, 67d => 30), - 68d => 30, - MAX(69G => 10, 69i => 60, 69d => 30, 69D => 30), - MAX(70E => 15, 70G => 15, 70N => 15, 70Q => 15, 70R => 10, 70S => 15, 70T => 15, 70d => 30), - MAX(74I => 60, 74V => 60), - MAX(75I => 5, 75A => 15, 75M => 15, 75S => 15, 75T => 30), - 77L => 10, - 116Y => 10, - MAX(151L => 30, 151M => 60), - MAX(184I => 10, 184V => 10), - 210W => 10, - MAX(215F => 15, 215Y => 15, 215A => 10, 215C => 10, 215D => 10, 215E => 10, 215I => 10, 215L => 10, 215N => 10, 215S => 10, 215V => 10), - MAX(41L AND 215FY => 10, 41L AND 215ACDEILNSV => 5), - MAX(210W AND 215FY => 10, 210W AND 215ACDEILNSV => 5), - 41L AND 210W => 10, - 41L AND 44AD AND 210W AND 215FY => 5, - 40F AND 41L AND 210W AND 215FY => 5, - MAX(219E => 5, 219N => 5, 219Q => 5, 219R => 5, 219W => 5), - 41L AND 67EGN AND 215FY => 5, - 67EGN AND 215FY AND 219ENQR => 5, - 67EGN AND 70R AND 219ENQR => 10, - 70R AND 215FY => 5, - 77L AND 116Y AND 151M => 10 -)]]> - - - - - - - - - FTC - emtricitabine - - 15, 65R => 15), - 67d => 15, - 68d => 15, - MAX(69i => 30, 69d => 15), - MAX(70E => 10, 70G => 10, 70N => 10, 70Q => 10, 70S => 10, 70T => 10, 70d => 10), - 75I => 5, - 77L => 5, - 116Y => 5, - MAX(151L => 10, 151M => 15), - MAX(184I => 60, 184V => 60), - 65RN AND 151M => 10, - 77L AND 116Y AND 151ML => 15, - 41L AND 210W AND 215FY => 15, - 67EGNHST AND 70R AND 219ENQRW => 10 -)]]> - - - - - - - - - 3TC - lamivudine - - 15, 65R => 15), - 67d => 15, - 68d => 15, - MAX(69i => 30, 69d => 15), - MAX(70E => 10, 70G => 10, 70N => 10, 70Q => 10, 70S => 10, 70T => 10, 70d => 10), - 75I => 5, - 77L => 5, - 116Y => 5, - MAX(151L => 10, 151M => 15), - MAX(184I => 60, 184V => 60), - 65RN AND 151M => 10, - 77L AND 116Y AND 151ML => 15, - 41L AND 210W AND 215FY => 15, - 67EGNHST AND 70R AND 219ENQRW => 10 -)]]> - - - - - - - - - TDF - tenofovir - - 5, - 62V => 5, - MAX(65E => 10, 65N => 30, 65R => 45), - MAX(67E => 5, 67G => 5, 67H => 5, 67N => 5, 67S => 5, 67T => 5, 67d => 15), - 68d => 15, - MAX(69G => 5, 69i => 60, 69d => 15), - MAX(70E => 15, 70G => 15, 70N => 15, 70Q => 15, 70R => 5, 70S => 15, 70T => 15, 70d => 15), - 74I => 5, - 75I => 5, - 77L => 5, - 115F => 15, - 116Y => 5, - MAX(151L => 10, 151M => 15), - MAX(184I => -10, 184V => -10), - 210W => 5, - MAX(215F => 10, 215Y => 10), - 65RN AND 151M => 10, - 77L AND 116Y AND 151ML => 15, - 41L AND 215FY => 10, - 210W AND 215FY => 10, - 41L AND 210W => 5, - 41L AND 210W AND 215FY => 15, - 41L AND 44AD AND 210W AND 215FY => 5, - 40F AND 41L AND 210W AND 215FY => 5, - 41L AND 67EGNHST AND 215FY => 5, - 67EGNHST AND 215FY AND 219ENQRW => 5, - 67EGNHST AND 70R AND 219ENQRW => 10, - 70EGNQST AND 184IV => 10, - 65R AND 151M AND 184IV => 10, - 65R AND 68GN => 5, - 62V AND 65R => 5, - 69i AND 184VI => 10 -)]]> - - - - - - - - - ISL - islatravir - - 5, - 65R => -10, - 69i => 60, - 70R => 5, - MAX(74I => -5, 74V => -5), - 75I => -5, - 151M => -10, - MAX(184I => 30, 184V => 30), - 210W => 5, - MAX(215F => 10, 215Y => 10), - 41L AND 215FY => 5, - 210W AND 215FY => 5, - 41L AND 210W => 5, - 41L AND 210W AND 215FY => 5, - 41L AND 67EGNHST AND 215FY => 5, - 67EGNHST AND 215FY AND 219ENQRW => 5, - 67EGNHST AND 70R AND 219ENQRW => 5, - 41L AND 184VI AND 215FY => 10, - 114S => 15, - 114S AND 184IV => 15 -)]]> - - - - - - - - - DOR - doravirine - - 10, - MAX(100I => 10, 100V => 5), - MAX(101E => 5, 101P => 5), - MAX(106A => 60, 106I => 5, 106L => 30, 106M => 30), - 108I => 5, - 179F => 5, - MAX(181C => 5, 181I => 10, 181V => 10), - MAX(188F => 30, 188L => 60), - MAX(190C => 10, 190E => 60, 190Q => 30, 190S => 10, 190T => 10, 190V => 10), - 221Y => 5, - 225H => 10, - MAX(227C => 60, 227I => 45, 227L => 60, 227V => 45, 227Y => 15), - 230L => 60, - 234I => 45, - 236L => 5, - 318F => 60, - 98G AND 234I => 15, - 100I AND 103N => 20, - 103N AND 181C => 5, - 103N AND 225H => 20, - 106I AND 181C => 10, - 106I AND 190S => 10, - MAX(106I AND 227CLIVY => 15, 106A AND 227CL => 15), - 108I AND 181C => 10, - 108I AND 234I => 15, - 181CIV AND 190ACSTV => 10, - 181CIV AND 221Y => 10, - 98G AND 106I => 5, - 98G AND 190ASC => 5, - 98G AND 181CIV => 10, - 101E AND 181C => 5, - MAX(101E AND 190A => 5, 101E AND 190S => 5), - 106I AND 234I => 15, - 106I AND 221Y => 5, - 98G AND 227CL => 15 -)]]> - - - - - - - - - EFV - efavirenz - - 10, - MAX(100I => 45, 100V => 15), - MAX(101E => 15, 101P => 60, 101H => 10), - MAX(106A => 45, 106I => 5, 106L => 10, 106M => 60), - 108I => 10, - MAX(138K => 10, 138G => 10, 138Q => 10, 138R => 10), - MAX(179F => 10, 179D => 10, 179E => 10, 179L => 10), - MAX(181C => 30, 181I => 30, 181V => 30, 181F => 15, 181G => 15, 181S => 15), - MAX(188F => 60, 188L => 60, 188C => 30, 188H => 30), - MAX(190C => 60, 190E => 60, 190Q => 60, 190S => 60, 190T => 60, 190V => 60, 190A => 45), - 221Y => 10, - 225H => 45, - MAX(227C => 45, 227I => 10, 227L => 15, 227V => 10), - MAX(230I => 10, 230L => 45), - 318F => 10, - 98G AND 234I => 5, - MAX(106I AND 227CLIVY => 10, 106A AND 227CL => 15), - 98G AND 181CIV => 5, - 101E AND 181C => 5, - 98G AND 227CL => 15, - MAX(103H => 60, 103N => 60, 103S => 45, 103T => 15), - MAX(238N => 10, 238T => 30), - 103R AND 179D => 20 -)]]> - - - - - - - - - ETR - etravirine - - 10, - MAX(100I => 30, 100V => 10), - MAX(101E => 10, 101P => 45, 101H => 10), - 106I => 5, - MAX(138K => 10, 138G => 10, 138Q => 10, 138R => 10, 138A => 10), - MAX(179F => 15, 179D => 10, 179E => 10, 179L => 10), - MAX(181C => 30, 181I => 60, 181V => 60, 181F => 15, 181G => 15, 181S => 15), - 188L => 15, - MAX(190C => 10, 190E => 45, 190Q => 45, 190S => 10, 190T => 10, 190V => 10, 190A => 10), - 221Y => 10, - 227C => 30, - 230L => 30, - 98G AND 234I => 5, - 106I AND 227CLIVY => 10, - 181CIV AND 190ACSTV => 10, - 98G AND 181CIV => 5, - 101E AND 181C => 5, - MAX(101E AND 190A => 5, 101E AND 190S => 5), - 98G AND 227CL => 15, - 101E AND 188L => 5, - MAX(179F AND 181C => 15, 179T AND 181C => 10) -)]]> - - - - - - - - - NVP - nevirapine - - 30, - MAX(100I => 60, 100V => 30), - MAX(101E => 30, 101P => 60, 101H => 15), - MAX(106A => 60, 106I => 5, 106L => 30, 106M => 60), - 108I => 15, - MAX(138K => 10, 138G => 10, 138Q => 10, 138R => 10), - MAX(179F => 15, 179D => 10, 179E => 10, 179L => 10), - MAX(181C => 60, 181I => 60, 181V => 60, 181F => 60, 181G => 60, 181S => 60), - MAX(188F => 60, 188L => 60, 188C => 60, 188H => 60), - MAX(190C => 60, 190E => 60, 190Q => 60, 190S => 60, 190T => 60, 190V => 60, 190A => 60), - 221Y => 15, - 225H => 45, - MAX(227C => 45, 227I => 30, 227L => 30, 227V => 30, 227Y => 10), - MAX(230I => 30, 230L => 60), - 318F => 30, - 98G AND 234I => 5, - 106I AND 227CLIVY => 10, - 98G AND 227CL => 15, - MAX(103H => 60, 103N => 60, 103S => 60, 103T => 60), - MAX(238N => 10, 238T => 30), - 103R AND 179D => 20, - 348I => 15 -)]]> - - - - - - - - - RPV - rilpivirine - - 15, - MAX(100I => 45, 100V => 15), - MAX(101E => 45, 101P => 60, 101H => 10), - MAX(106A => 5, 106I => 5), - 108I => 5, - MAX(138K => 45, 138G => 20, 138Q => 20, 138R => 20, 138A => 10), - MAX(179F => 15, 179D => 10, 179E => 10, 179L => 10), - MAX(181C => 45, 181I => 60, 181V => 60, 181F => 30, 181G => 30, 181S => 30), - MAX(188F => 30, 188L => 60), - MAX(190C => 10, 190E => 60, 190Q => 45, 190S => 15, 190T => 10, 190V => 10, 190A => 15), - 221Y => 10, - MAX(227C => 45, 227L => 5, 227Y => 15), - MAX(230I => 30, 230L => 60), - 98G AND 234I => 5, - 100I AND 103N => 15, - 106I AND 181C => 10, - MAX(106I AND 227CLIVY => 15, 106A AND 227CL => 10), - 181CIV AND 190ACSTV => 10, - 181CIV AND 221Y => 10, - 98G AND 106I => 5, - 98G AND 190ASC => 5, - 98G AND 181CIV => 5, - 98G AND 227CL => 15, - 103R AND 179D => 15, - MAX(179F AND 181C => 15, 179T AND 181C => 10), - 101E AND 184I => 15, - 138K AND 184I => 15, - 90I => 5 -)]]> - - - - - - - - - DPV - dapirivine - - 30, - MAX(100I => 60, 100V => 15), - MAX(101E => 45, 101P => 60, 101H => 10), - MAX(106A => 5, 106I => 5, 106M => 10), - 108I => 5, - MAX(138K => 45, 138G => 20, 138Q => 20, 138R => 20, 138A => 15), - MAX(179F => 15, 179D => 10, 179E => 10, 179L => 15), - MAX(181C => 60, 181I => 60, 181V => 60, 181F => 30, 181G => 30, 181S => 30), - MAX(188F => 30, 188L => 60, 188C => 5, 188H => 5), - MAX(190C => 10, 190E => 60, 190Q => 45, 190S => 15, 190T => 10, 190V => 10, 190A => 15), - 221Y => 15, - 225H => 10, - MAX(227C => 60, 227L => 10, 227Y => 10), - MAX(230I => 30, 230L => 60), - 90I => 5 -)]]> - - - - - - - - - ATV/r - atazanavir/r - - 5, - 20T => 5, - MAX(24F => 5, 24I => 10, 24M => 5), - 32I => 15, - 33F => 5, - MAX(46I => 10, 46L => 10, 46V => 5), - 47V => 10, - MAX(48A => 10, 48L => 10, 48M => 30, 48Q => 10, 48S => 10, 48T => 10, 48V => 30), - 50L => 60, - MAX(53L => 10, 53Y => 5), - MAX(54A => 15, 54L => 15, 54M => 15, 54S => 15, 54T => 15, 54V => 15), - MAX(73A => 10, 73C => 10, 73D => 5, 73S => 10, 73T => 10, 73V => 5), - 74P => 10, - MAX(82A => 15, 82C => 15, 82F => 15, 82L => 10, 82M => 10, 82S => 30, 82T => 30), - 83D => 10, - MAX(84A => 60, 84C => 45, 84V => 60), - MAX(88D => 10, 88G => 15, 88S => 60, 88T => 15), - 89T => 5, - 90M => 20, - 32I AND 47AV => 5, - 32I AND 54LM => 5, - 46IL AND 84V AND 90M => 5, - 46ILV AND 82ACFLMST => 10, - 46ILV AND 90M => 10, - 47AV AND 54LM => 5, - 53L AND 90M => 10, - 54ALMSTV AND 82ACFLMST => 10, - 54ALMSTV AND 90M => 10, - 73ACSTV AND 90M => 10, - 82ACFLMST AND 90M => 10 -)]]> - - - - - - - - - DRV/r - darunavir/r - - 5, - 32I => 15, - 33F => 5, - MAX(47A => 10, 47V => 10), - MAX(50L => -10, 50V => 20), - MAX(54L => 20, 54M => 20), - 74P => 5, - 76V => 20, - 82F => 15, - MAX(84A => 30, 84C => 15, 84V => 15), - 88S => -5, - 89V => 5, - 32I AND 47AV => 5, - 32I AND 54LM => 5, - 47AV AND 54LM => 5, - 11IL AND 32I => 5, - 11IL AND 54LM => 5, - 32I AND 76V => 5, - 32I AND 84V => 5, - 32I AND 89V => 5, - 47AV AND 84V => 5, - 54LM AND 84V => 5, - 54LM AND 89V => 5 -)]]> - - - - - - - - - FPV/r - fosamprenavir/r - - 15, - 20T => 5, - MAX(24F => 5, 24I => 10, 24M => 5), - 32I => 30, - 33F => 10, - MAX(46I => 10, 46L => 10, 46V => 10), - MAX(47A => 60, 47V => 35), - MAX(50L => -5, 50V => 60), - MAX(54A => 10, 54L => 60, 54M => 60, 54S => 10, 54T => 10, 54V => 10), - MAX(73A => 10, 73C => 10, 73D => 5, 73S => 10, 73T => 10, 73V => 5), - 74P => 10, - 76V => 60, - MAX(82A => 15, 82C => 15, 82F => 30, 82L => 15, 82M => 15, 82S => 15, 82T => 15), - MAX(84A => 60, 84C => 60, 84V => 60), - 88S => -10, - 89V => 10, - 90M => 20, - 32I AND 47AV => 5, - 32I AND 54LM => 5, - 46IL AND 84V AND 90M => 5, - 46ILV AND 82ACFLMST => 10, - 46ILV AND 90M => 10, - 47AV AND 54LM => 5, - 53L AND 90M => 10, - 54ALMSTV AND 82ACFLMST => 10, - 54ALMSTV AND 90M => 10, - 73ACSTV AND 90M => 10, - 82ACFLMST AND 90M => 10, - 11IL AND 32I => 5, - 11IL AND 54LM => 5, - 32I AND 76V => 5, - 32I AND 84V => 5, - 32I AND 89V => 5, - 47AV AND 84V => 5, - 54LM AND 84V => 5, - 54LM AND 89V => 5, - 46ILV AND 76V => 10 -)]]> - - - - - - - - - IDV/r - indinavir/r - - 10, - 20T => 5, - MAX(24F => 5, 24I => 15, 24M => 5), - 32I => 15, - 33F => 5, - MAX(46I => 10, 46L => 10, 46V => 10), - MAX(47A => 15, 47V => 15), - MAX(48A => 10, 48L => 10, 48M => 10, 48Q => 10, 48S => 10, 48T => 10, 48V => 10), - 50L => -5, - MAX(54A => 15, 54L => 10, 54M => 15, 54S => 15, 54T => 15, 54V => 15), - MAX(73A => 15, 73C => 15, 73D => 5, 73S => 15, 73T => 15, 73V => 5), - 74P => 10, - 76V => 30, - MAX(82A => 30, 82C => 15, 82F => 30, 82L => 10, 82M => 30, 82S => 30, 82T => 30), - 83D => 10, - MAX(84A => 60, 84C => 60, 84V => 60), - 88S => 15, - 89V => 5, - 90M => 30, - 32I AND 47AV => 5, - 32I AND 54LM => 5, - 46IL AND 84V AND 90M => 5, - 46ILV AND 82ACFLMST => 10, - 46ILV AND 90M => 10, - 47AV AND 54LM => 5, - 53L AND 90M => 10, - 54ALMSTV AND 82ACFLMST => 10, - 54ALMSTV AND 90M => 10, - 73ACSTV AND 90M => 10, - 82ACFLMST AND 90M => 10, - 11IL AND 32I => 5, - 11IL AND 54LM => 5, - 32I AND 76V => 5, - 32I AND 84V => 5, - 32I AND 89V => 5, - 47AV AND 84V => 5, - 54LM AND 84V => 5, - 54LM AND 89V => 5, - 46ILV AND 76V => 10 -)]]> - - - - - - - - - LPV/r - lopinavir/r - - 5, - MAX(24F => 5, 24I => 10, 24M => 5), - 32I => 15, - 33F => 5, - MAX(46I => 10, 46L => 10, 46V => 5), - MAX(47A => 60, 47V => 15), - MAX(48A => 10, 48L => 10, 48M => 10, 48Q => 10, 48S => 10, 48T => 10, 48V => 10), - MAX(50L => -10, 50V => 30), - MAX(54A => 15, 54L => 20, 54M => 20, 54S => 15, 54T => 15, 54V => 15), - MAX(73A => 5, 73C => 5, 73D => 5, 73S => 5, 73T => 5, 73V => 5), - 74P => 5, - 76V => 30, - MAX(82A => 30, 82C => 15, 82F => 30, 82L => 10, 82M => 25, 82S => 30, 82T => 30), - MAX(84A => 60, 84C => 10, 84V => 30), - 90M => 10, - 32I AND 47AV => 5, - 32I AND 54LM => 5, - 46IL AND 84V AND 90M => 5, - 46ILV AND 82ACFLMST => 10, - 46ILV AND 90M => 5, - 47AV AND 54LM => 5, - 54ALMSTV AND 82ACFLMST => 10, - 54ALMSTV AND 90M => 5, - 82ACFLMST AND 90M => 5, - 11IL AND 32I => 5, - 11IL AND 54LM => 5, - 32I AND 76V => 5, - 32I AND 84V => 5, - 32I AND 89V => 5, - 47AV AND 84V => 5, - 54LM AND 84V => 5, - 54LM AND 89V => 5, - 46ILV AND 76V => 10 -)]]> - - - - - - - - - NFV - nelfinavir - - 15, - 20T => 15, - 23I => 15, - MAX(24F => 10, 24I => 10, 24M => 10), - 30N => 60, - 32I => 15, - 33F => 10, - 43T => 10, - MAX(46I => 30, 46L => 20, 46V => 20), - MAX(47A => 30, 47V => 20), - MAX(48A => 30, 48L => 30, 48M => 30, 48Q => 30, 48S => 30, 48T => 30, 48V => 30), - 50V => 15, - 53L => 10, - MAX(54A => 20, 54L => 20, 54M => 20, 54S => 20, 54T => 20, 54V => 20), - 58E => 10, - MAX(73A => 15, 73C => 15, 73D => 10, 73S => 15, 73T => 15, 73V => 10), - 74P => 20, - 76V => 10, - MAX(82A => 30, 82C => 30, 82F => 30, 82L => 10, 82M => 30, 82S => 30, 82T => 30), - 83D => 15, - MAX(84A => 60, 84C => 60, 84V => 60), - MAX(88D => 60, 88G => 30, 88S => 60, 88T => 30), - 89V => 10, - 90M => 60, - 32I AND 47AV => 5, - 32I AND 54LM => 5, - 46IL AND 84V AND 90M => 5, - 46ILV AND 82ACFLMST => 10, - 46ILV AND 90M => 10, - 47AV AND 54LM => 5, - 53L AND 90M => 10, - 54ALMSTV AND 82ACFLMST => 10, - 54ALMSTV AND 90M => 10, - 73ACSTV AND 90M => 10, - 82ACFLMST AND 90M => 10, - 11IL AND 32I => 5, - 11IL AND 54LM => 5, - 32I AND 76V => 5, - 32I AND 84V => 5, - 32I AND 89V => 5, - 47AV AND 84V => 5, - 54LM AND 84V => 5, - 54LM AND 89V => 5, - 46ILV AND 76V => 10 -)]]> - - - - - - - - - SQV/r - saquinavir/r - - 5, - MAX(24F => 5, 24I => 10, 24M => 5), - 33F => 5, - MAX(46I => 10, 46L => 10, 46V => 5), - MAX(48A => 60, 48L => 60, 48M => 60, 48Q => 60, 48S => 60, 48T => 60, 48V => 60), - MAX(50L => -5, 50V => 15), - 53L => 15, - MAX(54A => 15, 54L => 15, 54M => 15, 54S => 15, 54T => 15, 54V => 15), - MAX(73A => 15, 73C => 15, 73D => 10, 73S => 15, 73T => 15, 73V => 10), - 74P => 10, - MAX(82A => 15, 82C => 15, 82F => 10, 82L => 10, 82M => 15, 82S => 15, 82T => 15), - 83D => 10, - MAX(84A => 60, 84C => 60, 84V => 60), - MAX(88D => 10, 88S => 15), - 90M => 45, - 46IL AND 84V AND 90M => 5, - 46ILV AND 82ACFLMST => 10, - 46ILV AND 90M => 5, - 53L AND 90M => 10, - 54ALMSTV AND 82ACFLMST => 10, - 54ALMSTV AND 90M => 10, - 73ACSTV AND 90M => 10, - 82ACFLMST AND 90M => 10 -)]]> - - - - - - - - - TPV/r - tipranavir/r - - -5, - 32I => 5, - 33F => 10, - 43T => 10, - MAX(46I => 5, 46L => 10, 46V => 5), - MAX(47A => 30, 47V => 30), - MAX(50L => -5, 50V => -5), - MAX(54A => 20, 54L => -10, 54M => 20, 54S => 20, 54T => 20, 54V => 20), - 58E => 15, - 74P => 25, - 76V => -5, - MAX(82C => 10, 82L => 45, 82M => 10, 82S => 30, 82T => 45), - 83D => 25, - MAX(84A => 60, 84C => 30, 84V => 30), - 46IL AND 84V AND 90M => 5 -)]]> - - - - - - - - - BIC - bictegravir - - 10, - MAX(66A => 5, 66I => 5, 66K => 15), - MAX(74F => 5, 74M => 5), - 92Q => 10, - 118R => 45, - MAX(121C => 15, 121Y => 10), - MAX(138A => 10, 138K => 10, 138T => 10), - MAX(140A => 10, 140C => 10, 140R => 10, 140S => 10), - MAX(146I => 5, 146L => 5, 146P => 5, 146R => 5), - 147G => 10, - MAX(148H => 25, 148K => 30, 148R => 25), - 149A => 5, - 151L => 15, - MAX(153F => 15, 153Y => 15), - 155H => 10, - 230R => 10, - 263K => 30, - 49G AND 263K => 10, - 66I AND 118R => 5, - 74F AND 75I => 10, - MAX(74I AND 118R => 5, 74FM AND 118R => 10), - MAX(74I AND 148HKR => 5, 74FM AND 148HKR => 15), - 74I AND 155H => 5, - 75A AND 118R => 10, - 75A AND 148HKR => 5, - 118R AND 138AKT => 10, - 122N AND 148HKR => 5, - 138AKT AND 140ACS => 10, - 138AKT AND 148HKR => 10, - 138K AND 263K => 10, - 140ACS AND 148HKR => 10, - 147G AND 148HKR => 10, - 147G AND 155H => 10, - 148HKR AND 149A => 10, - 148HKR AND 151I => 5, - 148HKR AND 155H => 20, - 148HKR AND 163KR => 5, - 151I AND 155H => 5, - 155H AND 263K => 20, - 157Q AND 263K => 10, - 51Y AND 263K => 10, - 92Q AND 155H => 10, - 97A AND 118R => 10, - 97A AND 148HKR => 15 -)]]> - - - - - - - - - CAB - cabotegravir - - 15, - MAX(66A => 5, 66I => 10, 66K => 20), - MAX(74F => 5, 74M => 5, 74I => 10), - MAX(92Q => 15, 92G => 10, 92V => 10), - 118R => 60, - MAX(121C => 30, 121Y => 15), - MAX(138A => 15, 138K => 15, 138T => 15), - MAX(140A => 15, 140C => 15, 140R => 60, 140S => 15), - MAX(146I => 10, 146L => 10, 146P => 10, 146R => 10), - 147G => 15, - MAX(148H => 60, 148K => 60, 148R => 60, 148N => 10), - 149A => 5, - 151L => 15, - MAX(153F => 25, 153Y => 25), - MAX(155H => 25, 155S => 10, 155T => 10), - 230R => 15, - 263K => 60, - 49G AND 263K => 10, - 74F AND 75I => 10, - 74I AND 118R => 5, - MAX(74I AND 148HKR => 5, 74FM AND 148HKR => 15), - 74I AND 155H => 10, - 75A AND 148HKR => 5, - 138AKT AND 140ACS => 15, - 138K AND 263K => 10, - 147G AND 148HKR => 10, - 147G AND 155H => 15, - 148HKR AND 149A => 10, - 148HKR AND 151I => 5, - 148HKR AND 163KR => 15, - 151I AND 155H => 10, - 157Q AND 263K => 10, - 51Y AND 263K => 10, - 92Q AND 155H => 20, - 97A AND 148HKR => 20, - 75A => 10, - 122N => 10, - MAX(143A => 5, 143C => 5, 143G => 5, 143H => 5, 143K => 5, 143R => 5, 143S => 5), - 97A AND 143ACGHRS => 5 -)]]> - - - - - - - - - DTG - dolutegravir - - 10, - MAX(66A => 5, 66I => 5, 66K => 15), - MAX(74F => 5, 74M => 5), - 92Q => 10, - 118R => 60, - MAX(121C => 15, 121Y => 10), - MAX(138A => 10, 138K => 10, 138T => 10), - MAX(140A => 10, 140C => 10, 140R => 10, 140S => 10), - MAX(146I => 5, 146L => 5, 146P => 5, 146R => 5), - 147G => 10, - MAX(148H => 25, 148K => 30, 148R => 25), - 149A => 5, - 151L => 15, - MAX(153F => 15, 153Y => 15), - 155H => 10, - 230R => 10, - 263K => 30, - 49G AND 263K => 10, - 74F AND 75I => 10, - 74I AND 118R => 5, - MAX(74I AND 148HKR => 5, 74FM AND 148HKR => 15), - 74I AND 155H => 5, - 75A AND 148HKR => 5, - 122N AND 148HKR => 5, - 138AKT AND 140ACS => 10, - 138AKT AND 148HKR => 10, - 138K AND 263K => 10, - 140ACS AND 148HKR => 10, - 147G AND 148HKR => 10, - 147G AND 155H => 10, - 148HKR AND 149A => 10, - 148HKR AND 151I => 5, - 148HKR AND 155H => 20, - 148HKR AND 163KR => 5, - 151I AND 155H => 5, - 155H AND 263K => 20, - 157Q AND 263K => 10, - 51Y AND 263K => 10, - 92Q AND 155H => 10, - 97A AND 148HKR => 15 -)]]> - - - - - - - - - EVG - elvitegravir - - 15, - MAX(66A => 60, 66I => 60, 66K => 60), - MAX(74F => 5, 74M => 5), - MAX(92Q => 60, 92G => 30, 92V => 60), - 118R => 60, - MAX(121C => 60, 121Y => 60), - MAX(138A => 15, 138K => 15, 138T => 15), - MAX(140A => 30, 140C => 30, 140R => 30, 140S => 30), - MAX(146I => 60, 146L => 30, 146P => 60, 146R => 5), - 147G => 60, - MAX(148H => 60, 148K => 60, 148R => 60, 148N => 10), - 149A => 5, - MAX(151L => 60, 151A => 30, 151I => 5), - MAX(153F => 25, 153Y => 25), - MAX(155H => 60, 155S => 30, 155T => 30), - 230R => 20, - 263K => 30, - 49G AND 263K => 10, - 74F AND 75I => 10, - 74FM AND 148HKR => 15, - 138AKT AND 140ACS => 15, - 138K AND 263K => 10, - 51Y AND 263K => 15, - 92Q AND 155H => 10, - MAX(143A => 10, 143C => 10, 143G => 10, 143H => 10, 143K => 10, 143R => 10, 143S => 10), - 97A AND 143ACGHRS => 5, - 95K => 10, - 97A => 10, - 145S => 60, - 157Q => 10, - MAX(163K => 15, 163R => 15), - 232N => 10, - 143ACGHRS AND 163R => 10, - 143ACGHRS AND 230R => 10 -)]]> - - - - - - - - - RAL - raltegravir - - 15, - MAX(66A => 15, 66I => 15, 66K => 60), - MAX(74F => 5, 74M => 5), - MAX(92Q => 30, 92G => 15, 92V => 30), - 118R => 60, - MAX(121C => 60, 121Y => 60), - MAX(138A => 15, 138K => 15, 138T => 15), - MAX(140A => 30, 140C => 30, 140R => 30, 140S => 30), - MAX(146I => 15, 146R => 5), - 147G => 10, - MAX(148H => 60, 148K => 60, 148R => 60, 148N => 10), - 149A => 5, - MAX(151L => 30, 151A => 15, 151I => 5), - MAX(153F => 10, 153Y => 10), - MAX(155H => 60, 155S => 30, 155T => 30), - 230R => 20, - 263K => 15, - 49G AND 263K => 10, - 66I AND 118R => 5, - 74F AND 75I => 10, - 74FM AND 118R => 10, - 74FM AND 148HKR => 15, - 75A AND 118R => 10, - 118R AND 138AKT => 10, - 138AKT AND 140ACS => 15, - 138K AND 263K => 10, - 157Q AND 263K => 10, - 92Q AND 155H => 10, - 97A AND 118R => 10, - MAX(143A => 60, 143C => 60, 143G => 60, 143H => 60, 143K => 60, 143R => 60, 143S => 60), - 95K => 10, - 97A => 10, - 157Q => 10, - MAX(163K => 15, 163R => 15), - 232N => 10 -)]]> - - - - - - - - - LEN - lenacapavir - - 60, - 57S => 20, - 66I => 60, - MAX(67H => 30, 67K => 20, 67N => 20, 67Y => 30), - MAX(70R => 10, 70S => 20, 70N => 45, 70H => 60), - MAX(74D => 60, 74K => 15, 74S => 15, 74T => 10), - MAX(105E => 10, 105S => 10, 105T => 10), - MAX(107C => 10, 107N => 10), - 67H AND 70R => 30, - 67H AND 74S => 15, - 67H AND 107N => 30 -)]]> - - - - - - - - - - CA - - 56I - - - - - - 57S - - - - - - 66I - - - - - - 67HYNK - - - - - - 70NH - - - - - - 70RS - - - - - - 74D - - - - - - 74SK - - - - - - 74T - - - - - - 105TSE - - - - - - 107NSAC - - - - - - - IN - - 118ACDEFHIKLMNPQSTVWYid - - - - - - 118R - - - - - - 119R - - - - - - 121ADEGHIKLMNPQRSTVWid - - - - - - 121C - - - - - - 121Y - - - - - - 122N - - - - - - 128T - - - - - - 138CDFGHILMNPQRSVWYid - - - - - - 138KAT - - - - - - 140DEFHIKLMNPQTVWYid - - - - - - 140R - - - - - - 140SAC - - - - - - 143CRH - - - - - - 143DEFILMNPQTVWid - - - - - - 143KGSA - - - - - - 145ACDEFGHIKLMNQRTVWYid - - - - - - 145S - - - - - - 146ACDEFGHKMNSTVWYid - - - - - - 146PRLI - - - - - - 147ACDEFHIKLMNPQRTVWYid - - - - - - 147G - - - - - - 148ACDEFGILMPSTVWYid - - - - - - 148HKR - - - - - - 148N - - - - - - 149A - - - - - - 151A - - - - - - 151CDEFGHKMNPQRSTWYid - - - - - - 151I - - - - - - 151L - - - - - - 153CDEGHIKLMNPQRTVWid - - - - - - 153YFA - - - - - - 155ACDEFGIKLMPQRVWYid - - - - - - 155H - - - - - - 155ST - - - - - - 157Q - - - - - - 163RK - - - - - - 230N - - - - - - 230R - - - - - - 232N - - - - - - 263ACDEFGHILMNPQSTVWYid - - - - - - 263K - - - - - - 49G - - - - - - 50I - - - - - - 51ACDEFGIKLMNPQRSTVWid - - - - - - 51Y - - - - - - 66AI - - - - - - 66CDEFGHLMNPQRSVWYid - - - - - - 66K - - - - - - 74F - - - - - - 74I - - - - - - 74M - - - - - - 75IA - - - - - - 92ACDFHIKLMNPRSTWYid - - - - - - 92GV - - - - - - 92Q - - - - - - 95K - - - - - - 97A - - - - - - - PR - - 10ACDEGHKMNPQSTWid - - - - - - 10F - - - - - - 10IV - - - - - - 10RY - - - - - - 11IL - - - - - - 20I - - - - - - 20MV - - - - - - 20R - - - - - - 20T - - - - - - 23I - - - - - - 24ACDEGHKNPQRSTVWYid - - - - - - 24FM - - - - - - 24I - - - - - - 30ACEFGHIKLMPQRSTVWYid - - - - - - 30N - - - - - - 32ACDEFGHKLMNPQRSTWYid - - - - - - 32I - - - - - - 33i OR 34i OR 35i OR 36i OR 37i OR 38i OR 39i OR 40i OR 41i - - - - - - 33F - - - - - - 33IV - - - - - - 43T - - - - - - 46ACDEFGHKNPQRSTWYid - - - - - - 46IL - - - - - - 46V - - - - - - 47A - - - - - - 47CDEFGHKLMNPQRSTWYid - - - - - - 47V - - - - - - 48ASTQL - - - - - - 48CDEFHIKNPRWYid - - - - - - 48M - - - - - - 48V - - - - - - 50ACDEFGHKMNPQRSTWYid - - - - - - 50L - - - - - - 50V - - - - - - 53LY - - - - - - 54ATS - - - - - - 54CDEFGHKNPQRWYid - - - - - - 54LM - - - - - - 54V - - - - - - 58E - - - - - - 71IL - - - - - - 71TV - - - - - - 73EFHIKLMNPQRWYid - - - - - - 73STCA - - - - - - 74P - - - - - - 74S - - - - - - 76ACDEFGHIKMNPQRSTWYid - - - - - - 76V - - - - - - 82A - - - - - - 82C - - - - - - 82DEGHKNPQRWYid - - - - - - 82F - - - - - - 82I - - - - - - 82L - - - - - - 82M - - - - - - 82TS - - - - - - 83D - - - - - - 84AC - - - - - - 84DEFGHKLMNPQRSTWYid - - - - - - 84V - - - - - - 85V - - - - - - 88ACEFHIKLMPQRVWYid - - - - - - 88D - - - - - - 88S - - - - - - 88TG - - - - - - 89VT - - - - - - 90ACDEFGHIKNPQRSTVWYid - - - - - - 90M - - - - - - - RT - - 100ACDEFGHKMNPQRSTWYid - - - - - - 100I - - - - - - 100V - - - - - - 101CDFGILMSVWYid - - - - - - 101E - - - - - - 101H - - - - - - 101NAT - - - - - - 101P - - - - - - 101Q - - - - - - 103ACDFGILMPVWYid - - - - - - 103EQ - - - - - - 103H - - - - - - 103N - - - - - - 103R - - - - - - 103S - - - - - - 103T - - - - - - 106A - - - - - - 106CDEFGHKNPQRSTWYid - - - - - - 106I - - - - - - 106M - - - - - - 106L - - - - - - 108ACDEFGHKLMNPQRSTWYid - - - - - - 108I - - - - - - 114S - - - - - - 115ACDEGHIKLMNPQRSTVWid - - - - - - 115F - - - - - - 116ACDEGHIKLMNPQRSTVWid - - - - - - 116Y - - - - - - 118I - - - - - - 132ML - - - - - - 138A - - - - - - 138CDFHILMNPSTVWYid - - - - - - 138K - - - - - - 138QG - - - - - - 138R - - - - - - 151ACDEFGHIKNPRSTVWYid - - - - - - 151L - - - - - - 151M - - - - - - 179ACGHKMNPQRSWYid - - - - - - 179DE - - - - - - 179F - - - - - - 179I - - - - - - 179L - - - - - - 179T - - - - - - 181ADEHKLMNPQRTWid - - - - - - 181C - - - - - - 181FSG - - - - - - 181IV - - - - - - 184ACDEFGHKLNPQRSTWYid - - - - - - 184VI - - - - - - 188ADEGIKMNPQRSTVWid - - - - - - 188C - - - - - - 188F - - - - - - 188H - - - - - - 188L - - - - - - 190A - - - - - - 190CTV - - - - - - 190DFHIKLMNPWYid - - - - - - 190EQ - - - - - - 190S - - - - - - 210W - - - - - - 215GHKMPQRWid - - - - - - 215SCDEIVALN - - - - - - 215YF - - - - - - 219ACDFGHILMPSTVYid - - - - - - 219EQNR - - - - - - 219W - - - - - - 221Y - - - - - - 225ACDEFGIKLMNQRSTVWYid - - - - - - 225H - - - - - - 227ADEGHKMNPQRSTWid - - - - - - 227C - - - - - - 227ILV - - - - - - 227Y - - - - - - 230ACDEFGHKNPQRSTVWYid - - - - - - 230I - - - - - - 230L - - - - - - 232H - - - - - - 234ACDEFGHKMNPQRSTWYid - - - - - - 234I - - - - - - 236ACDEFGHIKMNQRSTVWYid - - - - - - 236L - - - - - - 238ACDEFGHILMPQSVWYid - - - - - - 238TN - - - - - - 318ACDEGHIKLMNPQRSTVWid - - - - - - 318F - - - - - - 348ACDEFGHKLMPQRSTVWYid - - - - - - 348I - - - - - - 40F - - - - - - 41L - - - - - - 44AD - - - - - - 62V - - - - - - 65ACDFGHILMPQSTVWYid - - - - - - 65E - - - - - - 65N - - - - - - 65R - - - - - - 67d OR 68d OR 69d OR 70d - - - - - - 67ACFIKLMPQRVWYi - - - - - - 67GESTH - - - - - - 67N - - - - - - 68G - - - - - - 68N - - - - - - 69CFHKLMPQRVWY - - - - - - 69D - - - - - - 69G - - - - - - 69i - - - - - - 69NSAIE - - - - - - 70ACDFHILMPVWYi - - - - - - 70EGQNST - - - - - - 70R - - - - - - 74ACDEFGHKMNPQRSTWYid - - - - - - 74VI - - - - - - 75CDEFGHKNPQRWYid - - - - - - 75I - - - - - - 75MTAS - - - - - - 77ACDEGHIKMNPQRSTVWYid - - - - - - 77L - - - - - - 90I - - - - - - 98G - - - - - - - - - - - DTG - 5 - - - - - - - - - - DTG - 4 - - - - - - - - - - DTG - 3 - - - - - - - - - - DRV/r - 5 - - - - - - - - - - DRV/r - 4 - - - - - - - - - - DRV/r - 3 - - - - - - - -