Rhee Soo-Yon, Kantor Rami, Katzenstein David A, Camacho Ricardo, Morris Lynn, Sirivichayakul Sunee, Jorgensen Louise, Brigido Luis F, Schapiro Jonathan M, Shafer Robert W
Division of Infectious Disease, Stanford University, Stanford, California, USA.
AIDS. 2006 Mar 21;20(5):643-51. doi: 10.1097/01.aids.0000216363.36786.2b.
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.
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.
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.
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.
HIVseq于2000年开发，旨在使有关HIV-1 M组蛋白酶和逆转录酶（RT）突变频率的已发表数据能够实时提供给对这些基因进行测序的实验室和研究人员。由于大多数已发表的蛋白酶和RT序列属于B亚型，因此HIVseq的初始版本基于该亚型。随着来自具有明确抗逆转录病毒治疗治疗治疗录治疗史的患者的更多非B亚型序列可用，该程序已扩展到A、C、D、F、G、CRF01和CRF02亚型。
根据亚型和药物类别暴露情况，使用斯坦福HIV RT和蛋白酶序列数据库中的已发表序列计算每种蛋白酶和RT突变的最新频率。每个突变都超链接到包含该突变的病毒的已发表报告。
截至2005年9月，每个非B亚型的蛋白酶序列平均数在未接受蛋白酶抑制剂治疗的人群中为534个，在接受蛋白酶抑制剂治疗的人群中为133个，分别占B亚型可用数据的13.2%和2.3%。每个非B亚型的RT序列平均数在未接受RT抑制剂治疗的人群中为373个，在接受RT抑制剂治疗的人群中为288个，分别占B亚型可用数据的17.9%和3.8%。
HIVseq允许用户在这些基因先前发表的序列背景下检查蛋白酶和RT突变。然而，需要公布来自具有明确治疗史的患者的更多非B蛋白酶和RT序列，以便能够进行与数量多得多的B亚型序列相同类型的分析。
