The changing HIV-1 genetic characteristics and transmitted drug resistance among recently infected population in Yunnan, China

Multiple human immunodeficiency virus (HIV)-1 genotypes in China were first discovered in Yunnan Province before disseminating throughout the country. As the HIV-1 epidemic continues to expand in Yunnan, genetic characteristics and transmitted drug resistance (TDR) should be further investigated among the recently infected population. Among 2828 HIV-positive samples newly reported in the first quarter of 2014, 347 were identified as recent infections with BED-captured enzyme immunoassay (CEIA). Of them, 291 were successfully genotyped and identified as circulating recombinant form (CRF)08-BC (47.4%), unique recombinant forms (URFs) (18.2%), CRF01-AE (15.8%), CRF07-BC (14.4%), subtype C (2.7%), CRF55-01B (0.7%), subtype B (0.3%) and CRF64-BC (0.3%). CRF08-BC and CRF01-AE were the predominant genotypes among heterosexual and homosexual infections, respectively. CRF08-BC, URFs, CRF01-AE and CRF07-BC expanded with higher prevalence in central and eastern Yunnan. The recent common ancestor of CRF01-AE, CRF07-BC and CRF08-BC dated back to 1983.1, 1992.1 and 1989.5, respectively. The effective population sizes (EPS) for CRF01-AE and CRF07-BC increased exponentially during 1991-1999 and 1994-1999, respectively. The EPS for CRF08-BC underwent two exponential growth phases in 1994-1998 and 2001-2002. Lastly, TDR-associated mutations were identified in 1.8% of individuals. These findings not only enhance our understanding of HIV-1 evolution in Yunnan but also have implications for vaccine design and patient management strategies.