Phylogenetic reconstruction of 136 partial <i>gag-pol</i> gene sequences of 1.6kb amplified among the blood donors in Kuala Lumpur, Malaysia between 2013 and 2014.
<p>HIV-1 incidence was estimated using a limiting antigen avidity enzyme immunoassay (LAg-Avidity EIA) to identify recent (incident) and long-standing (prevalent) infections as indicated where available. Neighbour-joining tree was constructed in MEGA 5.05 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0161853#pone.0161853.ref022" target="_blank">22</a>] using Kimura 2-parameter method of nucleotide substitutions and the reliability of the branching nodes were assessed by bootstrap analysis of 1000 replicates. Eleven partial <i>gag</i>-PR (834bp) and two RT gene sequences (966bp) were genotyped separately using similar methods and their prevalence was reported in this study (figures not shown for clarity). Relevant HIV-1 reference genotypes in Southeast Asia include subtype B, CRF01_AE, CRF33_01B, CRF34_01B, CRF48_01B, CRF52_01B, CRF53_01B, CRF54_01B, CRF58_01B and CRF74_01B. Reference sequences of other genotypes prevalent in China (CRF07_BC, CRF08_BC and other recently-described B'/C CRFs) and Africa (subtype G, CRF02_AG and CRF45_cpx) were also included in the analysis. The reference sequences were labelled in the following order: genotype, country of origin, isolate name and GenBank accession number. A well-supported cluster of Malaysian subtype G strains was also highlighted as G<sub>MY</sub> within the subtype G clade of African reference strains. All 12 unique recombinant forms were denoted by closed diamonds and labelled according to incident or prevalent infection status. Clusters of novel B'/C recombinants (strains 13MYNBB108, 14MYNBB084, 14MYNBB090 and 14MYNBB164) and B'/G recombinants (13MYNBB064 and 13MYNBB065) were highlighted in the tree. Simian immunodeficiency virus (SIVcpz) reference strains were included as outgroup. Bootstrap values of greater than 70% were indicated on the branch nodes. The scale bar represents 1% genetic distance (0.01 substitutions per site).</p
