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Genetic Diversity and Evolution

Comparative Circulation Dynamics of the Five Main HIV Types in China

Bram Vrancken, Bin Zhao, Xingguang Li, Xiaoxu Han, Haizhou Liu, Jin Zhao, Ping Zhong, Yi Lin, Junjie Zai, Mingchen Liu, Davey M. Smith, Simon Dellicour, Antoine Chaillon
Guido Silvestri, Editor
Bram Vrancken
aDepartment of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Computational and Evolutionary Virology, KU Leuven, Leuven, Belgium
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  • ORCID record for Bram Vrancken
Bin Zhao
bNHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
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Xingguang Li
cDepartment of Hospital Office, The First People’s Hospital of Fangchenggang, Fangchenggang, China
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Xiaoxu Han
bNHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
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Haizhou Liu
dCentre for Emerging Infectious Diseases, The State Key Laboratory of Virology, Wuhan Institute of Virology, University of Chinese Academy of Sciences, Wuhan, China
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Jin Zhao
eShenzhen Center for Disease Control and Prevention, Shenzhen, China
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Ping Zhong
fDepartment of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
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Yi Lin
fDepartment of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
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Junjie Zai
gImmunology innovation Team, School of Medicine, Ningbo University, Ningbo, Zhejiang China
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Mingchen Liu
bNHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
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Davey M. Smith
hDivision of Infectious Diseases and Global Public Health, University of California San Diego, California, USA
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Simon Dellicour
aDepartment of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Computational and Evolutionary Virology, KU Leuven, Leuven, Belgium
iSpatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
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Antoine Chaillon
hDivision of Infectious Diseases and Global Public Health, University of California San Diego, California, USA
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Guido Silvestri
Emory University
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DOI: 10.1128/JVI.00683-20
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ABSTRACT

The HIV epidemic in China accounts for 3% of the global HIV incidence. We compared the patterns and determinants of interprovincial spread of the five most prevalent circulating types. HIV pol sequences sampled across China were used to identify relevant transmission networks of the five most relevant HIV-1 types (B and circulating recombinant forms [CRFs] CRF01_AE, CRF07_BC, CRF08_BC, and CRF55_01B) in China. From these, the dispersal history across provinces was inferred. A generalized linear model (GLM) was used to test the association between migration rates among provinces and several measures of human mobility. A total of 10,707 sequences were collected between 2004 and 2017 across 26 provinces, among which 1,962 are newly reported here. A mean of 18 (minimum and maximum, 1 and 54) independent transmission networks involving up to 17 provinces were identified. Discrete phylogeographic analysis largely recapitulates the documented spread of the HIV types, which in turn, mirrors within-China population migration flows to a large extent. In line with the different spatiotemporal spread dynamics, the identified drivers thereof were also heterogeneous but are consistent with a central role of human mobility. The comparative analysis of the dispersal dynamics of the five main HIV types circulating in China suggests a key role of large population centers and developed transportation infrastructures as hubs of HIV dispersal. This advocates for coordinated public health efforts in addition to local targeted interventions.

IMPORTANCE While traditional epidemiological studies are of great interest in describing the dynamics of epidemics, they struggle to fully capture the geospatial dynamics and factors driving the dispersal of pathogens like HIV as they have difficulties capturing linkages between infections. To overcome this, we used a discrete phylogeographic approach coupled to a generalized linear model extension to characterize the dynamics and drivers of the across-province spread of the five main HIV types circulating in China. Our results indicate that large urbanized areas with dense populations and developed transportation infrastructures are facilitators of HIV dispersal throughout China and highlight the need to consider harmonized country-wide public policies to control local HIV epidemics.

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Comparative Circulation Dynamics of the Five Main HIV Types in China
Bram Vrancken, Bin Zhao, Xingguang Li, Xiaoxu Han, Haizhou Liu, Jin Zhao, Ping Zhong, Yi Lin, Junjie Zai, Mingchen Liu, Davey M. Smith, Simon Dellicour, Antoine Chaillon
Journal of Virology Nov 2020, 94 (23) e00683-20; DOI: 10.1128/JVI.00683-20

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Comparative Circulation Dynamics of the Five Main HIV Types in China
Bram Vrancken, Bin Zhao, Xingguang Li, Xiaoxu Han, Haizhou Liu, Jin Zhao, Ping Zhong, Yi Lin, Junjie Zai, Mingchen Liu, Davey M. Smith, Simon Dellicour, Antoine Chaillon
Journal of Virology Nov 2020, 94 (23) e00683-20; DOI: 10.1128/JVI.00683-20
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KEYWORDS

HIV
phylodynamics
discrete phylogeography
generalized linear model
China

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