Evolutionary characteristics and genetic transmission patterns of predominant HIV-1 subtypes among men who have sex with men in China

Huangbo Yuan; Zhenqiu Liu; Xuefu Wu; Mingshan Wu; Qiwen Fang; Damien C. Tully; Tiejun Zhang

International Journal of Infectious Diseases (Jan 2020)

Evolutionary characteristics and genetic transmission patterns of predominant HIV-1 subtypes among men who have sex with men in China

Huangbo Yuan,
Zhenqiu Liu,
Xuefu Wu,
Mingshan Wu,
Qiwen Fang,
Damien C. Tully,
Tiejun Zhang

Affiliations

Huangbo Yuan: Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Shanghai, China
Zhenqiu Liu: Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Shanghai, China; State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
Xuefu Wu: Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Shanghai, China
Mingshan Wu: Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Shanghai, China
Qiwen Fang: Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Shanghai, China
Damien C. Tully: Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
Tiejun Zhang: Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Shanghai, China; Corresponding author at: Department of Epidemiology, School of Public Health, Fudan University, Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Room 513 Building FuXing, 131 Dong’an Road, Shanghai, 200032, China.

Journal volume & issue: Vol. 90
pp. 125 – 131

Abstract

Read online

Objectives: Men who have sex with men (MSM) represent one of the major risk groups for HIV-1 infection in China, and the predominant subtypes among this population has changed over the last two decades. The objective of this study was to determine the evolutionary characteristics and transmission patterns of the dominant HIV-1 strains in the Chinese MSM population. Methods: A total of 4980 published HIV-1 pol gene sequences from MSM in China were retrieved and comprehensive evolutionary and transmission analyses were then conducted. Bayesian coalescent-based methods and selection pressure analyses were used to reconstruct the time-scale and demographic history and to estimate other evolutionary parameters. Transmission patterns were characterized using network analyses. Results: There were 2546 (51.12%) CRF01_AE, 1263 (25.36%) CRF07_BC, and 623 (12.51%) subtype B, accounting for 88.99% of the total sequences. From 2000 to 2016, the prevalence of CRF01_AE was stable, comprising nearly half of all sequences over time (58.33–45.38%, p = 0.071). CRF07_BC increased slightly from 13.3% to 22.49% (p < 0.001), while subtype B decreased dramatically from 41.67% to 9.04% (p < 0.001). Demographic reconstruction showed that the greatest expansion of the HIV epidemic occurred between 1999 and 2005. CRF01_AE had a higher estimated evolutionary rate (2.97 × 10−3 substitutions/site/year) and exhibited more sites under positive selection (25/351 codons) compared to the other subtypes. Network analyses showed that CRF07_BC (68.29%, 84/123) had a higher proportion of cross-region networks than CRF01_AE (49.1%, 174/354) and subtype B (36.46%, 35/96) (p < 0.001). Conclusions: The predominant subtypes of HIV-1 in Chinese MSM have different evolutionary characteristics and transmission patterns, which poses a significant challenge to HIV treatment and disease prevention. Keywords: HIV, MSM, Virus evolution, Transmission

Published in International Journal of Infectious Diseases

ISSN: 1201-9712 (Print); 1878-3511 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Medicine: Internal medicine: Infectious and parasitic diseases
Website: http://www.journals.elsevier.com/international-journal-of-infectious-diseases/

About the journal