Computational protocol: Characteristics of HIV-infected U.S. Army soldiers linked in molecular transmission clusters, 2001-2012

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Protocol publication

[…] A 918 base pair partial pol sequence available for any Soldier diagnosed with HIV-1 infection from 2001 through 2012 was compiled and aligned using Geneious Pro 5.6.7.[] Sequence alignment was further refined manually. HIV-1 subtype designations and transmission clusters, defined as ≥2 linked sequences, were identified from phylogenetic analysis of sequences using the maximum likelihood (ML) method and Kimura-2-parameter (K2P) model in MEGA6 ().[, ] Forty references consisting of pure HIV-1 subtype and main circulating recombinant forms (CRFs) were used to identify and designate HIV-1 subtypes (). Recombinant subtype analysis was performed using a combination of HIV-1 Genotyping Tool[], Jumping Profile Hidden Markov model [], visual inspection, and construction of subregion ML trees with bootstrap analyses to confirm breakpoint assignments. Bootstrap values of 95 percent or higher and a genetic distance cutoff value of ≤1.5% (≤0.015 nucleotide substitutions per site) were used to identify sequences that were highly related to each other (i.e. a cluster). The cutoff value was established by identifying an optimal intra-cluster genetic distance using available sequences for all Soldiers (). The Tamura-Nei 93 distance model was used as well to confirm sequence relatedness and showed no significant differences from the K2P model (). Transmitted drug resistance mutations were identified using the World Health Organization’s 2009 standard surveillance list available from the Stanford HIV database; any resistance to non-/nucleoside reverse transcriptase or protease inhibitor resistance was considered. […]

Pipeline specifications

Software tools Geneious, MEGA, jpHMM, TN93
Applications Phylogenetics, Nucleotide sequence alignment
Diseases Sexually Transmitted Diseases, HIV Infections