Genetic transmission networks reveal the transmission patterns of HIV-1 CRF01_AE in China

Li, Xiaoshan; Gao, Rong; Zhu, Kexin; Fan, Wei; Fang, Kun; Li, Wei; Song, Yao; Ge, You; Ji, Yu; Zhong, Ping; Wei, Ping

doi:10.1136/sextrans-2016-053085

Cited by 21 publications

(20 citation statements)

References 27 publications

(20 reference statements)

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“…The flow chart of transmission network analysis included four steps: construction of phylogenetic tree, extraction of transmission cluster, identification of minimum patristic genetic distance and visualization of the network 3 . We used Cluster Picker 14 to extract transmission clusters from the phylogenetic tree, with the intra-cluster maximum pairwise distance <3.0% nucleotide substitutions per site and bootstrap support value ≥95%.…”

Section: Methodsmentioning

confidence: 99%

“…The patristic genetic distances of all sequences within the available clusters were calculated in Patristic software ( http://www.bioinformatics.org/patristic/manual.html ) (Supplementary Material 2 ). Among all distances, one that minimizes the sum of edge weights (patristic genetic distances) was selected to define the linkages within a cluster 3 . Lastly, the network data were visualized and analyzed using the network software Cytoscape 3.5 15 .…”

Section: Methodsmentioning

confidence: 99%

“…Among the 134,512 newly diagnosed HIV-1 infections in 2017, 69.4% was attributed to heterosexual and 25.3% to homosexual transmission 1 . One of the current challenges was that China faced the rapid increase of HIV-1 prevalence among floating population and lacking effective intervention strategies for this group 2 , 3 . With the rapid urbanization of China, outgoing migrant-workers had become the main component of the floating population in China, who worked outside the place where the household registrations were located 4 .…”

Section: Introductionmentioning

confidence: 99%

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Impact of worker emigration on HIV epidemics in labour export areas: a molecular epidemiology investigation in Guangyuan, China

Liang

Hou³

et al. 2018

Sci Rep

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We aimed to investigate the molecular epidemic characteristics and viral transmission patterns of HIV-1 in a typical labor export area, Guangyuan city, China. Based on conducting phylogenetic trees and molecular transmission networks, a phylogenetic analysis was performed on HIV-1 pol sequences obtained from 211 migrant-history workers, 83 non-migrant-history individuals, and 21 migrant-history unknown individuals between January, 2012 and February, 2017 in Guangyuan city. Phylogenetic analysis revealed that CRF07_BC (48.3%, n = 152) and CRF01_AE (33.3%, n = 105) were the dominant strains in Guangyuan city, and circulated by multiple lineages with various epidemic characteristics. Geographic network analysis showed that Guangyuan city-related sequences with 20.3% CRF07_BC and 28.3% CRF01_AE were linked to that of other provinces, compared to that with 1.7% CRF07_BC and 5.0% CRF01_AE in cities of Sichuan. Molecular transmission network analysis further illustrated that migrant-history workers linked more sequences from other provinces than non-migrant-history individuals in both CRF07_BC (29.3% versus 0.0%, P = 0.013) and CRF01_AE (40.5% versus 10.0%, P = 0.001) networks. Our results highlighted that migrant-history workers in recent year played a vital role in fueling HIV-1 epidemic in Guangyuan city. Molecular transmission network analysis could be a useful approach for disclosing the transmission mechanism of HIV, which should be used in prevention and intervention efforts.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Impact of worker emigration on HIV epidemics in labour export areas: a molecular epidemiology investigation in Guangyuan, China

Liang

Hou³

et al. 2018

Sci Rep

Self Cite

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“…The rapid increase of HIV-1 prevalence among migrant populations and the lack of effective intervention strategies is one of the current challenges for China (74,75). In this study, the…”

Section: Downloaded Frommentioning

confidence: 93%

Comparative Circulation Dynamics of the Five Main HIV Types in China

Vrancken

Zhao

et al. 2020

J Virol

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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, 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 between 2004-2017 across 26 provinces were collected, among which 1,962 newly reported here. A mean of 18 (Min-Max:1-54) independent transmission networks involving up to 17 provinces were identified. Discrete phylogeographic analysis largely recapitulate the documented spread of the HIV types which, in turn, to large extent mirror within-China population migration flows. In line with the different spatio-temporal 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 populations 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 cannot fully capture the geospatial dynamics and factors driving the dispersal of pathogens such as HIV as they struggle to capture 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 population 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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“…Putative transmission ties of the network were identi ed by dichotomized data, which is determined by whether the pairwise genetic distance is less than 0.015 substitutions per site within all sequences [22,23] . In our study, the Tamura-Nei 93 pairwise genetic distances were calculated by Mega V.7.0 [24].…”

Section: Sequence Analysismentioning

confidence: 99%

Identifying the key nodes of HIV molecular transmission network among men who have sex with men in Guangzhou, China: A cross-sectional study

Yang

Han

et al. 2020

Preprint

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Background Identifying the most influential spreaders in HIV transmission networks is crucial to develop effective prevention strategies. The purpose of this study is to identify the key nodes of the molecular transmission network among MSM, which has significant insight into developing effective HIV prevention strategies. Methods We analyzed HIV-1 pol sequences provided through the Center for Disease Control and Prevention, Guangzhou, China. Sequences were obtained from newly-HIV diagnosed MSM during 2015–2017. We calculated pairwise genetic distance, identified linked pairs of sequences (those with distance ≤ 1.5%), and examined key nodes of these potential transmission partners. Results Of 184 HIV recently diagnosed men who have sex with men (MSM), 40.76% were linked to other MSM. Social network analysis demonstrated that there were 9 key nodes were detected. From the results of multivariate logistic regression model, young MSM born in the 1990s and 1980s was 0.06 and 0.12 times as likely to be a key node as was the older MSM born in the 1970s and before. Conclusions There were a lot of subgroups connected by sharing comembers in HIV molecular transmission network among MSM in Guangzhou. Some HIV-infected MSM called as key nodes mediated the transmission of HIV among different subpopulations. Young MSM were less likely to promote HIV transmission than older MSM.

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Genetic transmission networks reveal the transmission patterns of HIV-1 CRF01_AE in China

Abstract: The outcome of this study could help improve our ability to understand HIV transmission among various regions and risk groups in China, and highlighted the importance of targeting MSM and migrants by prevention and intervention efforts.

Cited by 21 publications

References 27 publications

Impact of worker emigration on HIV epidemics in labour export areas: a molecular epidemiology investigation in Guangyuan, China

Impact of worker emigration on HIV epidemics in labour export areas: a molecular epidemiology investigation in Guangyuan, China

Comparative Circulation Dynamics of the Five Main HIV Types in China

Identifying the key nodes of HIV molecular transmission network among men who have sex with men in Guangzhou, China: A cross-sectional study

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