A Newly Emerging HIV-1 Recombinant Lineage (CRF58_01B) Disseminating among People Who Inject Drugs in Malaysia
Figure 1
The near full length mosaic structure of HIV-1 CRF58_01B determined using bootscanning and informative site analysis.
CRF58_01B composed of three subtype B′ fragments recombined with CRF01_AE in the gag-RT, pol and env regions of HIV-1. Analysis revealed the sharing of similar unique mosaic structures and recombination breakpoints between the six strains (09MYPR37, 10MYKJ036, 10MYPR87, 11MY1ZK731, 11MY1RJ704 and 11MY1EP794), thus constituting a novel CRF58_01B genotype. HIV-1 reference strains CRF01_CM240 (CRF01_AE) and B′_RL42 (Thai subtype B′) were selected as the putative parental genotypes by similarity plotting, and C_95IN21068 (subtype C) as outgroup, with a window size of 400 nucleotides moving along the alignment in increments of 50 nucleotides to define the recombination structures. Sub-region neighbour-joining trees were constructed in MEGA 5.05 using Kimura 2-parameter method for nucleotide substitutions to estimate pair-wise evolutionary distance. The reliability of the branch nodes were assessed by bootstrap analysis of 1000 replicates. Bootstrap values of greater than 70% were indicated on the branch nodes. The scale bar of the individual sub-region trees were indicated in substitutions per site.