Multilocus Variation in Phylogenetic Support for HIV-1 Subtype B Assignment in an Institutional Cohort from Central Mexico

Background/Objectives: This study evaluated variation in nodal support for provisional HIV-1 subtype B compatibility across pol, gag, vif, tat and vpr in an institutional cohort from central Mexico. Methods: We performed a secondary descriptive bioinformatics reanalysis of 60 treatment-naïve adults. Paired FASTQ files were available for 58 samples, and 42 were retained across all five regions. Robust support required SH-aLRT ≥ 80 and UFBoot ≥ 95. Additional analyses varied reference-composition thresholds, reselected assignment nodes, harmonized the reference panel and subsampled alignment columns. Results: At the originally recorded nodes, 18/210 sample–region records (8.6%) were robust; 25/42 samples had no robust region, 16 had one and one had two. Node reselection at the 60% composition threshold retained all 18 records and added S42/pol and S29/tat, yielding 20/210 (9.5%). Neither analysis identified robust support in three or more regions. With a common reference panel, the ordering of contextual internal-branch support between pol and vif changed. Conclusions: Support depended on the evaluated node and analytical dataset. Fixed-node threshold stability did not establish stability under node reselection. Differences among regional analyses could not be attributed independently to genomic region. Single-fragment assignments remain provisional and do not establish whole-genome subtype classifications. V3 and ViReMa analyses were exploratory.