Pasquier C, Millot N, Njouom R, Sandres K, Cazabat M, Puel J, Izopet J
Laboratoire de Virologie, Hôpital Purpan, Place Baylac, Toulouse, France.
J Virol Methods. 2001 May;94(1-2):45-54. doi: 10.1016/s0166-0934(01)00272-5.
HIV-1 pol gene sequencing is now used routinely in France to identify mutations associated with resistance to reverse transcriptase (RT) or protease (PR) inhibitors. These sequences may also provide other information, such as the HIV-1 subtype. HIV-1 subtyping was compared using the RT and PR gene sequences to heteroduplex mobility assay (HMA) of the envelope gene. The RT and PR genes of 51 samples that had been subtyped earlier by HMA were sequenced. Sequences were aligned and subtypes were determined by phylogenetic analysis with reference HIV sequences. HMA gave the following subtypes: A (20), B (19), C (1), D (3), F (1), G (3) and CRF01-AE (4). Phylogenetic analysis of the RT gene gave: A (5), B (19), C (2), D (3), F (1), G (6), J (2), CRF01_AE (4), CFR02_AG (7) and undetermined (2). PR gene analysis did not infer subtypes with sufficient confidence. HMA and RT subtyping was not in agreement in nine cases. RT subtyping can identify CFR02_AG and CRF01_AE variants from A subtype RT. It was shown that phylogenetic analysis of the RT gene could provide a useful method for HIV-1 subtyping. The length of the amplicon and the relative performance of each primer pair used in this study favoured RT sequences as a subtyping tool. One potential advantage over env subtyping HMA is the ability to identify some circulating recombinant forms (CRFs).
目前，法国常规使用HIV-1 pol基因测序来鉴定与对逆转录酶（RT）或蛋白酶（PR）抑制剂耐药相关的突变。这些序列还可能提供其他信息，如HIV-1亚型。使用RT和PR基因序列对HIV-1进行亚型分析，并与包膜基因的异源双链迁移率分析（HMA）进行比较。对51个先前已通过HMA进行亚型分析的样本的RT和PR基因进行测序。将序列进行比对，并通过与参考HIV序列进行系统发育分析来确定亚型。HMA得出的亚型如下：A（20个）、B（19个）、C（1个）、D（3个）、F（1个）、G（3个）和CRF01-AE（4个）。RT基因的系统发育分析得出：A（5个）、B（19个）、C（2个）、D（3个）、F（1个）、G（6个）、J（2个）、CRF01_AE（4个）、CFR02_AG（7个）和未确定（2个）。PR基因分析无法足够自信地推断出亚型。在9个案例中，HMA和RT亚型分析结果不一致。RT亚型分析可以从A亚型RT中识别出CFR02_AG和CRF01_AE变体。结果表明，RT基因的系统发育分析可为HIV-1亚型分析提供一种有用的方法。本研究中使用的扩增子长度和每个引物对的相对性能使RT序列成为一种亚型分析工具。相对于包膜基因亚型分析HMA的一个潜在优势是能够识别一些循环重组形式（CRF）。
