HIV-1 pol mutation frequency by subtype and treatment experience: extension of the HIVseq program to seven non-B subtypes.
OBJECTIVE
HIVseq was developed in 2000 to make published data on the frequency of HIV-1 group M protease and reverse transcriptase (RT) mutations available in real time to laboratories and researchers sequencing these genes. Because most published protease and RT sequences belonged to subtype B, the initial version of HIVseq was based on this subtype. As additional non-B sequences from persons with well-characterized antiretroviral treatment histories have become available, the program has been extended to subtypes A, C, D, F, G, CRF01, and CRF02.


METHODS
The latest frequency of each protease and RT mutation according to subtype and drug-class exposure was calculated using published sequences in the Stanford HIV RT and Protease Sequence Database. Each mutation was hyperlinked to published reports of viruses containing the mutation.


RESULTS
As of September 2005, the mean number of protease sequences per non-B subtype was 534 from protease inhibitor-naive persons and 133 from protease inhibitor-treated persons, representing 13.2% and 2.3%, respectively, of the data available for subtype B. The mean number of RT sequences per non-B subtype was 373 from RT inhibitor-naive persons and 288 from RT inhibitor-treated persons, representing 17.9% and 3.8%, respectively, of the data available for subtype B.


CONCLUSIONS
HIVseq allows users to examine protease and RT mutations within the context of previously published sequences of these genes. The publication of additional non-B protease and RT sequences from persons with well-characterized treatment histories, however, will be required to perform the same types of analysis possible with the much larger number of subtype B sequences.
Rhee
Soo-Yon
SY
Division of Infectious Disease, Stanford University, Stanford, California, USA. syrhee@stanford.edu
Kantor
Rami
R
Katzenstein
David A
DA
Camacho
Ricardo
R
Morris
Lynn
L
Sirivichayakul
Sunee
S
Jorgensen
Louise
L
Brigido
Luis F
LF
Schapiro
Jonathan M
JM
Shafer
Robert W
RW
D001483:Base Sequence; D030541:Databases, Genetic; D024921:Drug Resistance, Multiple, Viral; D005787:Gene Frequency; D015751:Genes, pol; D015658:HIV Infections / Q000188:drug therapy / Q000821:virology; D016333:HIV Protease / Q000235:genetics; D017320:HIV Protease Inhibitors / Q000627:therapeutic use; D054303:HIV Reverse Transcriptase / Q000235:genetics; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D009154:Mutation; D012189:Retrospective Studies; D017422:Sequence Analysis, DNA; D014584:User-Computer Interface
D017320:HIV Protease Inhibitors; D054303:HIV Reverse Transcriptase; D016333:HIV Protease