The HIV-1 pol sequences were comprised of 1,020 nucleotides, HXB2 [K03455] positions 2267–3287. HIV-1 RNA was purified from patient blood plasma using the RNeasy Lipid Tissue Mini Kit (QIAGEN) as previously described (Esbjörnsson et al., 2010 (link)). Reverse transcription and amplification of partial pol gene were performed using the One-Step Superscript III RT/Platinum Taq High Fidelity Enzyme Mix (Thermo Fisher Scientific™) with the pol-specific primer pair JA269 and JA272 (Hedskog et al., 2010 (link)). First-round PCR products were amplified in a nested PCR with DreamTaq Green DNA Polymerase (Thermo Fisher Scientific™) using pol-specific primers JA271 and JA270 (Hedskog et al., 2010 (link)). PCR products were sequenced in both directions with the nested PCR primers using the BigDye terminator kit v1.1 (Applied Biosystems), and the sequences were determined on an ABI PRISM 3130xl Genetic Analyzer (Applied Biosystems).
Additional Kenyan HIV-1 pol sequences (referred to as published sequences, 2006–2019) were retrieved (October 11th 2021) from the Los Alamos HIV-1 sequence database (Los Alamos National Laboratory, 2019 ). The combined new and published sequences (referred to as the Kenyan dataset) were annotated with information on sampling dates and geographical area of residence during sampling (i.e., province; Coast, Nairobi, and Nyanza).
Additional Kenyan HIV-1 pol sequences (referred to as published sequences, 2006–2019) were retrieved (October 11th 2021) from the Los Alamos HIV-1 sequence database (Los Alamos National Laboratory, 2019 ). The combined new and published sequences (referred to as the Kenyan dataset) were annotated with information on sampling dates and geographical area of residence during sampling (i.e., province; Coast, Nairobi, and Nyanza).
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