Phylogenetic and temporal dynamics of human immunodeficiency virus type 1 CRF01_AE and CRF07_BC among recently infected antiretroviral therapy-naïve men who have sex with men in Jiangsu province, China, 2012 to 2015

Abstract

The prevalence and incidence of human immunodeficiency virus type 1 (HIV-1) among men who have sex with men (MSM) are on the rise throughout China. With a large population of MSM, Jiangsu Province is facing an escalating HIV-1 epidemic.The aim of this study was to explore the phylogenetic and temporal dynamics of HIV-1 CRF01_AE and CRF07_BC among antiretroviral therapy (ART)-naïve MSM recently infected with HIV-1 in Jiangsu Province.We recruited MSM in Jiangsu Province (Suzhou, Wuxi, Nantong, Taizhou and Yancheng) 2012 to 2015. We collected information on demographics and sexual behaviors and a blood sample for HIV genome RNA extraction, RT-PCR amplification, and DNA sequencing. Multiple alignments were made using Gene Cutter, with the selected reference sequences of various subtypes/recombinants from the Los Alamos HIV-1 database. Phylogenetic and Bayesian evolutionary analysis was performed by MEGA version 6.0, Fasttree v2.1.7. and BEAST v1.6.2. Categorical variables were analyzed using χ2 test (or Fisher exact test where necessary). χ2 test with trend was used to assess the evolution of HIV-1 subtype distribution over time. All data were analyzed using SPSS20.0 software package (IBM Company, New York, NY).HIV-1 phylogenetic analysis revealed a broad viral diversity including CRF01_AE (60.06%), CRF07_BC (22.29%), subtype B (5.88%), CRF67_01B (5.26%), CRF68_01B (2.79%), CRF55_01B (1.55%), CRF59_01B (0.93%), and CRF08_BC (0.62%). Two unique recombination forms (URFs) (0.62%) were also detected. Four epidemic clusters and 1 major cluster in CRF01_AE and CRF07_BC were identified. The introduction of CRF01_AE strain (2001) was earlier than CRF07_BC strain (2004) into MSM resided in Jiangsu based on the time of the most recent common ancestor.Our study demonstrated HIV-1 subtype diversity among ART-naïve MSM recently infected with HIV-1 in Jiangsu. We first depicted the spatiotemporal dynamics, traced the dates of origin for the HIV-1 CRF01_AE/07_BC strains and made inference for the effective population size among newly infected ART-naïve MSM in Jiangsu from 2012 to 2015. A real-time surveillance of HIV-1 viral diversity and phylodynamics of epidemic cluster would be of great value to the monitoring of the epidemic and control of transmission, improvement of antiretroviral therapy strategies, and design of vaccines.

The evolutionary and transmission characteristic of HIV‐1 CRF07_BC in Nanjing, Jiangsu

“…Our analyses dated the first introduction of HIV‐1 CRF07_BC into Nanjing in 1998 from IDU and to MSMs and HEs. The second epidemic wave was introduced into Nanjing in 2001 from MSM, which was consistent with previous studies 32,33 . Our results indicated that CRF07_BC in Nanjing likely originated from similar strains previously found among IDUs in Yunnan province.…”

Diversity of HIV-1 genotypes and high prevalence of pretreatment drug resistance in newly diagnosed HIV-infected patients in Shanghai, China

“…Our study found a total of 11 HIV-1 genotypes and 10 HIV-1 strains of URFs in 317 newly diagnosed HIV/AIDS patients in 2017, indicating that the distribution of HIV-1 genotypes in Shanghai is diverse and complex. The results were similar to that of the study conducted in Jiangsu province (a close neighbor of Shanghai), showing that the prevalence of genotype CRF01_AE, CRF07_BC, and B were 60.06, 22.29, and 5.88%, respectively [13]. Similarly, the surveys carried out in Hebei, Fujian, and regions across China also reported that CRF01_AE, CRF07_BC, and B were the predominant subtypes [9, 14, 15].…”

The prevalence, temporal trends, and geographical distribution of HIV-1 subtypes among men who have sex with men in China: A systematic review and meta-analysis

“…From 2006 to 2012 in Shenzhen, the prevalence of HIV-1 subtype B decreased from 37.5% to 5.7% and that of CRF01_AE decreased from 50.0% to 32.3%; however, the prevalence of CRF07_BC increased from 12.5% to 43.2% and that of CRF55_01B increased from 0% to 16.0% [25]. Between 2012 and 2015 in Jiangsu province, the prevalence of HIV-1 subtype CRF01_AE decreased from 56.5% to 49.3%, and that of CRF07_BC increased from 13.0% to 39.4% [26]. In the span of a few years, the prevalence of multiple HIV-1 subtypes have changed considerably.…”