Emergence of a New HIV Type 1 CRF01_AE Variant in Guangxi, Southern China

Abstract

The distribution of HIV-1 subtypes and genetic characterization of CRF01_AE in Guangxi, southern China were identified. The distribution of HIV-1 genotypes based on gag, pol, and partial env sequences (n=349) was as follows: CRF01_AE (66.5%), CRF08_BC (19.2%), CRF07_BC (7.2%), URF (4.6%), subtype B (1.7%), and subtype B' (0.9%). CRF01_AE predominated in all geographic regions and risk populations and there were multiple introductions of CRF01_AE strains in Guangxi. We found a peculiar CRF01_AE monophyletic lineage distinct from other CRF01_AE viruses, and we designated it "CRF01_AE-v" for convenience. CRF01_AE-v circulating in both heterosexuals and injecting drug users (IDUs) had accounted for 39.7% of CRF01_AE. It showed a selective advantage in the Guangxi population and formed its own characteristic compared with all the CRF01_AE references. Our results suggested that CRF01_AE-v was a new variant of CRF01_AE and it might lead to a new epidemic in Guangxi.

Identification of 3 Distinct HIV-1 Founding Strains Responsible for Expanding Epidemic Among Men Who Have Sex With Men in 9 Chinese Cities

“…However, many CRF01_AE sequences from the Liaoning heterosexual population7 have close phylogenetic links to MSM cluster 2. Additionally, a few CRF01_AE sequences from Yunnan30 or Guangxi28 infected cases with unknown transmission route and the heterosexual population in Liaoning7 and Beijing23 and Jiangsu IDUs31 were closely related to MSM cluster 1 (Fig. 1A).…”

Near Full-Length Genome Characterization of a New CRF01_AE/CRF08_BC Recombinant Transmitted Between a Heterosexual Couple in Guangxi, China

“…[1][2][3] At the same time, multiple cocirculating subtypes have been identified in this region, including CRF07_BC, CRF08_BC, and subtype B. 1,2 In particular, CRF_08BC is prevalent in the central cities and is also mainly transmitted through sexual routes.…”

Sequencing of Gag/Env association with HIV genotyping resolution and HIV-related epidemiologic studies of HIV in China

“…For example, one patient was reported to be infected with subtype C based on sequencing of the Pol gene and the p17 fragment of Gag gene; however, the same individual was classified as CRF07_BC with the p24 fragment of the Gag gene, as well as subtype B with the Vpu gene (Robertson et al, 2000;Chen et al, 2013). To avoid such discrepancies, simultaneous analysis of different gene fragments, such as Gag/Env Chen et al, 2013), Gag/Pol (Yao et al, 2012), Pol/Env (Chen et al, 2012;Pang et al, 2012), and Gag/Pol/ Env (Lan et al, 2008;Ye et al, 2012;Zeng et al, 2012;Li et al, 2014a;Dai et al, 2015), will facilitate the clear identification of potential new inter-subtype recombinants. However, the field still lacks a set of standard markers for identifying HIV strains, which precludes inter-study comparisons and hampers the comprehensive understanding of the panorama of HIV infection.…”

“…Rather, many groups have opted to sequence single genes or combinations of two or three genes to reduce costs. In this regard, the eight markers Env, Gag, Pol, Vpr, Gag/Env, Gag/Pol, Pol/Env, and Gag/Pol/Env have often been used to subtype HIV in China (Lan et al, 2008;Chen et al, 2012;Pang et al, 2012;Yao et al, 2012;Ye et al, 2012;Zeng et al, 2012;Li et al, 2014a;Dai et al, 2015). However, the high mutation and recombination rates associated with the HIV genome (Robertson et al, 1995;Robertson et al, 2000), have led to ambiguous and sometimes contradictory genotyping results, even in the same individual (Robertson et al, 2000;Qiu et al, 2005;Chen et al, 2013).…”