Characterizing genetic transmission networks among newly diagnosed HIV-1 infected individuals in eastern China: 2012-2016.
We aimed to elucidate the characteristics of HIV molecular epidemiology and identify transmission hubs in eastern China using genetic transmission network and lineage analyses. HIV-TRACE was used to infer putative relationships. Across the range of epidemiologically-plausible genetic distance (GD) t...
| Main Authors: | , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2022-01-01
|
| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0269973 |
| _version_ | 1797867511442571264 |
|---|---|
| author | Xiaobei Ding Antoine Chaillon Xiaohong Pan Jiafeng Zhang Ping Zhong Lin He Wanjun Chen Qin Fan Jun Jiang Mingyu Luo Yan Xia Zhihong Guo Davey M Smith |
| author_facet | Xiaobei Ding Antoine Chaillon Xiaohong Pan Jiafeng Zhang Ping Zhong Lin He Wanjun Chen Qin Fan Jun Jiang Mingyu Luo Yan Xia Zhihong Guo Davey M Smith |
| author_sort | Xiaobei Ding |
| collection | DOAJ |
| description | We aimed to elucidate the characteristics of HIV molecular epidemiology and identify transmission hubs in eastern China using genetic transmission network and lineage analyses. HIV-TRACE was used to infer putative relationships. Across the range of epidemiologically-plausible genetic distance (GD) thresholds (0.1-2.0%), a sensitivity analysis was performed to determine the optimal threshold, generating the maximum number of transmission clusters and providing reliable resolution without merging different small clusters into a single large cluster. Characteristics of genetically linked individuals were analyzed using logistic regression. Assortativity (shared characteristics) analysis was performed to infer shared attributes between putative partners. 1,993 persons living with HIV-1 were enrolled. The determined GD thresholds within subtypes CRF07_BC, CRF01_AE, and B were 0.5%, 1.2%, and 1.7%, respectively, and 826 of 1,993 (41.4%) sequences were linked with at least one other sequence, forming 188 transmission clusters of 2-80 sequences. Clustering rates for the main subtypes CRF01_AE, CRF07_BC, and B were 50.9% (523/1027), 34.2% (256/749), and 32.1% (25/78), respectively. Median cluster sizes of these subtypes were 2 (2-52, n = 523), 2 (2-80, n = 256), and 3 (2-6, n = 25), respectively. Subtypes in individuals diagnosed and residing in Hangzhou city (OR = 1.423, 95% CI: 1.168-1.734) and men who have sex with men (MSM) were more likely to cluster. Assortativity analysis revealed individuals were more likely to be genetically linked to individuals from the same age group (AIage = 0.090, P<0.001) and the same area of residency in Zhejiang (AIcity = 0.078, P<0.001). Additionally, students living with HIV were more likely to be linked with students than show a random distribution (AI student = 0.740, P<0.01). These results highlight the importance of Hangzhou City in the regional epidemic and show that MSM comprise the population rapidly transmitting HIV in Zhejiang Province. We also provide a molecular epidemiology framework for improving our understanding of HIV transmission dynamics in eastern China. |
| first_indexed | 2024-04-09T23:41:20Z |
| format | Article |
| id | doaj.art-2a2b8aae70094e68b76e8f7f73bc0607 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-09T23:41:20Z |
| publishDate | 2022-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-2a2b8aae70094e68b76e8f7f73bc06072023-03-18T05:32:34ZengPublic Library of Science (PLoS)PLoS ONE1932-62032022-01-01176e026997310.1371/journal.pone.0269973Characterizing genetic transmission networks among newly diagnosed HIV-1 infected individuals in eastern China: 2012-2016.Xiaobei DingAntoine ChaillonXiaohong PanJiafeng ZhangPing ZhongLin HeWanjun ChenQin FanJun JiangMingyu LuoYan XiaZhihong GuoDavey M SmithWe aimed to elucidate the characteristics of HIV molecular epidemiology and identify transmission hubs in eastern China using genetic transmission network and lineage analyses. HIV-TRACE was used to infer putative relationships. Across the range of epidemiologically-plausible genetic distance (GD) thresholds (0.1-2.0%), a sensitivity analysis was performed to determine the optimal threshold, generating the maximum number of transmission clusters and providing reliable resolution without merging different small clusters into a single large cluster. Characteristics of genetically linked individuals were analyzed using logistic regression. Assortativity (shared characteristics) analysis was performed to infer shared attributes between putative partners. 1,993 persons living with HIV-1 were enrolled. The determined GD thresholds within subtypes CRF07_BC, CRF01_AE, and B were 0.5%, 1.2%, and 1.7%, respectively, and 826 of 1,993 (41.4%) sequences were linked with at least one other sequence, forming 188 transmission clusters of 2-80 sequences. Clustering rates for the main subtypes CRF01_AE, CRF07_BC, and B were 50.9% (523/1027), 34.2% (256/749), and 32.1% (25/78), respectively. Median cluster sizes of these subtypes were 2 (2-52, n = 523), 2 (2-80, n = 256), and 3 (2-6, n = 25), respectively. Subtypes in individuals diagnosed and residing in Hangzhou city (OR = 1.423, 95% CI: 1.168-1.734) and men who have sex with men (MSM) were more likely to cluster. Assortativity analysis revealed individuals were more likely to be genetically linked to individuals from the same age group (AIage = 0.090, P<0.001) and the same area of residency in Zhejiang (AIcity = 0.078, P<0.001). Additionally, students living with HIV were more likely to be linked with students than show a random distribution (AI student = 0.740, P<0.01). These results highlight the importance of Hangzhou City in the regional epidemic and show that MSM comprise the population rapidly transmitting HIV in Zhejiang Province. We also provide a molecular epidemiology framework for improving our understanding of HIV transmission dynamics in eastern China.https://doi.org/10.1371/journal.pone.0269973 |
| spellingShingle | Xiaobei Ding Antoine Chaillon Xiaohong Pan Jiafeng Zhang Ping Zhong Lin He Wanjun Chen Qin Fan Jun Jiang Mingyu Luo Yan Xia Zhihong Guo Davey M Smith Characterizing genetic transmission networks among newly diagnosed HIV-1 infected individuals in eastern China: 2012-2016. PLoS ONE |
| title | Characterizing genetic transmission networks among newly diagnosed HIV-1 infected individuals in eastern China: 2012-2016. |
| title_full | Characterizing genetic transmission networks among newly diagnosed HIV-1 infected individuals in eastern China: 2012-2016. |
| title_fullStr | Characterizing genetic transmission networks among newly diagnosed HIV-1 infected individuals in eastern China: 2012-2016. |
| title_full_unstemmed | Characterizing genetic transmission networks among newly diagnosed HIV-1 infected individuals in eastern China: 2012-2016. |
| title_short | Characterizing genetic transmission networks among newly diagnosed HIV-1 infected individuals in eastern China: 2012-2016. |
| title_sort | characterizing genetic transmission networks among newly diagnosed hiv 1 infected individuals in eastern china 2012 2016 |
| url | https://doi.org/10.1371/journal.pone.0269973 |
| work_keys_str_mv | AT xiaobeiding characterizinggenetictransmissionnetworksamongnewlydiagnosedhiv1infectedindividualsineasternchina20122016 AT antoinechaillon characterizinggenetictransmissionnetworksamongnewlydiagnosedhiv1infectedindividualsineasternchina20122016 AT xiaohongpan characterizinggenetictransmissionnetworksamongnewlydiagnosedhiv1infectedindividualsineasternchina20122016 AT jiafengzhang characterizinggenetictransmissionnetworksamongnewlydiagnosedhiv1infectedindividualsineasternchina20122016 AT pingzhong characterizinggenetictransmissionnetworksamongnewlydiagnosedhiv1infectedindividualsineasternchina20122016 AT linhe characterizinggenetictransmissionnetworksamongnewlydiagnosedhiv1infectedindividualsineasternchina20122016 AT wanjunchen characterizinggenetictransmissionnetworksamongnewlydiagnosedhiv1infectedindividualsineasternchina20122016 AT qinfan characterizinggenetictransmissionnetworksamongnewlydiagnosedhiv1infectedindividualsineasternchina20122016 AT junjiang characterizinggenetictransmissionnetworksamongnewlydiagnosedhiv1infectedindividualsineasternchina20122016 AT mingyuluo characterizinggenetictransmissionnetworksamongnewlydiagnosedhiv1infectedindividualsineasternchina20122016 AT yanxia characterizinggenetictransmissionnetworksamongnewlydiagnosedhiv1infectedindividualsineasternchina20122016 AT zhihongguo characterizinggenetictransmissionnetworksamongnewlydiagnosedhiv1infectedindividualsineasternchina20122016 AT daveymsmith characterizinggenetictransmissionnetworksamongnewlydiagnosedhiv1infectedindividualsineasternchina20122016 |