Abstract
Here, we report the genetic diversity of HIV-1 and emergence of novel HIV-1 unique recombinant forms (URF) in both HIV-infected intravenous drug users (IDU) and men who have sex with men (MSM) in Guangzhou, China. We further characterized a novel URF strain isolated from an HIV-infected MSM, GD698. Near full-length genome (NFLG) phylogenic analysis showed that this novel URF was composed of CRF07_BC and CRF55_01B, with two recombinant breakpoints (nt 6,003 and 8,251 relative to the HXB2 genome) in the vpu/env and env genes, respectively. Twenty six percent of the genome is classified as CRF55_01B, spanning part of vpu and most of the env gene. The remaining 74% of the genome is classified as CRF07_BC. Both the backbone CRF07_BC sequence and CRF55_01B fragment were clustered with the HIV-1 isolates found in MSM. The emergence of the novel HIV-1 recombinant indicates the ongoing recombinants derived from the CRF07_BC and CRF55_01B isolates, and provides critical insights into our understanding of the dynamics and complexity of the HIV-1 epidemic in China.
Highlights
One of the characteristics of human immunodeficiency virus type 1 (HIV-1) is its extremely high level of genetic variation, which results in the existence of four groups: M, O, N, and P
The genetic diversity of HIV-1 strains was analyzed in 183 plasma samples from HIV-1 infected intravenous drug users (IDU) and men who have sex with men (MSM)
About 6.0% of the samples were assigned as unique recombinant forms (URF) due to the discordant results of the 2 or 3 individual gene sequencing data
Summary
One of the characteristics of human immunodeficiency virus type 1 (HIV-1) is its extremely high level of genetic variation, which results in the existence of four groups: M, O, N, and P. Within HIV-1 group M, there are nine subtypes (A, B, C, D, F, G, H, J, and K) and six derivatives (A1-A4 and F1, F2). To date, co-infection and recombination of different HIV1 genotypes have resulted in emergence of as many as 88 circulating recombinant forms (CRFs) (https://www.hiv.lanl.gov/content/sequence/HIV/CRFs/CRFs.html) and numerous unique recombinant forms (URFs). Third generation HIV-1 recombinant forms have been identified as the result of recombination between various HIV-1 CRFs, such as the CRF30_0206 variant.
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