HIV-1 subtyping using phylogenetic analysis of pol gene sequences

Area of Science:

• Virology
• Molecular Biology
• Infectious Diseases

Background:

• HIV-1 pol gene sequencing is standard for detecting drug resistance mutations.
• These sequences can also reveal HIV-1 subtypes, crucial for epidemiological tracking.
• Current subtyping methods like heteroduplex mobility assay (HMA) using the envelope gene have limitations.

Purpose of the Study:

• To compare the accuracy of HIV-1 subtyping using reverse transcriptase (RT) and protease (PR) gene sequences against the established envelope gene HMA method.
• To evaluate the utility of phylogenetic analysis of pol gene sequences for HIV-1 subtyping.

Main Methods:

• Sequencing of RT and PR genes from 51 HIV-1 samples previously subtyped by HMA.
• Phylogenetic analysis of aligned sequences using reference HIV sequences for subtype determination.
• Comparison of subtyping results obtained from RT, PR, and HMA methods.

Main Results:

• Phylogenetic analysis of the RT gene successfully identified various subtypes including A, B, C, D, F, G, J, CRF01_AE, and CRF02_AG.
• PR gene sequencing lacked sufficient confidence for reliable subtyping.
• Discrepancies between HMA and RT subtyping were observed in nine cases, with RT subtyping identifying specific recombinant forms (CRFs) missed by HMA.

Conclusions:

• Phylogenetic analysis of the HIV-1 RT gene is a valuable and reliable method for HIV-1 subtyping.
• RT gene sequencing offers advantages over env gene HMA, particularly in identifying circulating recombinant forms (CRFs).
• The RT gene's amplicon length and primer performance favor its use as a subtyping tool.