Identification of a novel HIV-1 second-generation circulating recombinant form (CRF136_0107) among men who have sex with men in China.

Abstract

To investigate the molecular epidemiology of HIV-1 in Heilongjiang, China, and try to spot signs of new circulating recombinant form (CRF) in this region. A molecular epidemiological study was conducted in Heilongjiang, China during 2011-2020. Plasma samples were collected from three HIV-1 positive patients. The near full-length genome sequences (NFLGs) of a novel circulating recombinant form (CRF) were then obtained and subjected to phylogenetic analysis using Mega 7.0.26. Recombination analysis was performed by the jumping profile Hidden Markov Model (jpHMM). Finally, the origin time of this novel CRF was inferred using the Bayesian phylogenetic analysis in Beast v1.10.4. The three NFLGs formed a distinct monophyletic cluster in the neighbor-joining (NJ) tree. Recombination analysis revealed that the recombinant genome was composed of five segments derived from CRF01_AE, subtypes B, and C, but further confirmed to be a second-generation recombinant form of CRF01_AE/CRF07_BC by a comparison of genome maps and subregion phylogenetic analysis and therefore designated as CRF136_0107. With Bayesian phylogenetic analysis, CRF136_0107 was estimated to originate around 2010-2011. A novel HIV-1 CRF01_AE/CRF07_BC second-generation CRF called CRF136_0107 was identified among men who have sex with men (MSM) in Heilongjiang, a northeast province of China.