Fig. 1

Phylogenetic and recombination analysis of HLJ17137. (A) The near full-length genome (NFLG) of HLJ17137 virus was aligned with representative references of HIV-1 subtypes A, G and CRFs containing A and G genes using MAFFT 7 (https://mafft.cbrc.jp/alignment/server/index.html). A phylogenetic tree was then constructed using neighbor-joining method based on Kimura 2-parameter model with 1000 bootstrap replicates in Mega 7.0.26 software. The HLJ17137 sequence is marked with a black dot. (B) The similarity plot analysis was carried out by Simplot 3.5.1 software. Sub-subtypes A1, A7 and subtype G were colored according to the legend, while the others (A2-A4, A6, A8, B-D, F1, F2, H, J, K, L and N) were not colored for the convenience of reading. (C) Bootscan analysis was performed using a window size of 400 bp and a step size of 20 bp, together with reference sequences of sub-subtypes A1, A7 and subtype G, and an out-group control of subtype J. (D) Genomic map of HLJ17137 was visualized with the Recombinant HIV-1 Drawing Tool (https://www.hiv.lanl.gov/content/sequence/DRAW_CRF/recom_mapper.html).