Computational protocol: Risk Factors for HIV-1 seroconversion among Taiwanese men visiting gay saunas who have sex with men

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Protocol publication

[…] Participants provided 5~10 ml of peripheral blood for HIV-1 antibody testing and subtyping. Recombinant HIV-1/HIV-2 EIA (Murex Diagnostics Limited, Dartford, UK) was used for HIV screening. Positive samples were reconfirmed by HIV Western blot 2.2 (Genelabs, Singapore). A nested polymerase chain reaction (PCR) was used to determine the gag and env subtypes []. Sequence alignments with different subtype reference sequences from the Los Alamos HIV database (available at: http://www.hiv.lanl.gov) were conducted using the BioEdit program (vers. 7.0.9) []. Phylogenetic trees were constructed using the Neighbor-joining (NJ) and maximum-likelihood (ML) methods using the MEGA program (vers. 5.0) []. The General Time Reversible (GTR)+G+I substitution model was the best fitting model as tested using MEGA5 Bayesian information criterion (BIC) scores, the corrected Akaike information criterion (AIC) value, and the maximum-likelihood value (lnL). The gamma distribution shape parameter (G) was 1.0342. The robustness of the phylogenetic trees was statistically evaluated by a bootstrap analysis with 1000 bootstrap samples. […]

Pipeline specifications

Software tools BioEdit, MEGA
Application Phylogenetics
Organisms Human immunodeficiency virus 1, Homo sapiens, Human immunodeficiency virus 2
Diseases HIV Infections