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Objective:To analyze the variation characteristics of gag gene sequence of human immunodeficiency virus type 1 (HIV-1) epidemic strains in four major acquired immunodeficiency syndrome (AIDS) endemic areas in Yunnan Province. Methods:A total of 480 human immunodeficiency virus (HIV)/AIDS patients from designated antiviral treatment institutions in Kunming City, Dehong Dai and Jingpo Autonomous Prefecture, Hani-Yi Autonomous Prefecture of Honghe and Lincang City in Yunnan Province from January 2019 to December 2020 were randomly selected. The epidemiological information of the patients was collected. The plasma samples were collected and sent to the Yunnan Provincial Infectious Diseases Hospital for analysis. HIV-1 gag gene was amplified by nested polymerase chain reaction for genotyping.The phylogenetic tree was constructed by MEGA 6.06, and the characteristic amino acids were analyzed by VESPA online analysis tool. The gene distances of gag and matrix protein p17, capsid protein p24, nucleocapsid protein p7 and p6 protein of gag protein were calculated by Distance program. The ratio of synonymous mutation frequnency and non-synonymous mutation frequnency (Ks/Ka) was analyzed by SNAP program. Statistical comparison among multiple groups was performed using analysis of variance. Results:The gag gene sequences were successfully obtained from 404 patients.Most of these patients were men (250 cases, 61.9%), 59.7%(241/404) of patients were aged 40 to 59 years, and the main transmission route was heterosexual transmission (61.4%, 248/404). The main epidemic subtypes of HIV-1 were circulating recombinant form(CRF)08_BC (38.4%, 155/404), CRF01_AE (18.3%, 74/404), unique recombinant form (URF) (12.9%, 52/404), CRF07_BC(9.7%, 39/404), C subtype (8.4%, 34/404), other subtypes (6.9%, 28/404) and B subtype (5.4%, 22/404). Two main spreading clusters were formed by CRF08_BC in the phylogenetic tree, and there were significant differences in the distribution of characteristic amino acids of eight loci between the two spreading clusters, including No.79, 93, 121, 122, 151, 363, 395 and 396. The gag gene distances of CRF01_ AE, CRF07_ BC and CRF08_ BC were 0.090±0.004, 0.088±0.004 and 0.078±0.002, respectively, and the difference was statistically significant ( F=118.33, P<0.001). The Ks/Ka values of gag of the three subtypes were 4.003±1.309, 4.141±0.860 and 4.514±1.215, respectively, and the difference was statistically significant ( F=1.35, P<0.001). The Ks/Ka values of p17 were 2.590±0.186, 2.831±0.496 and 2.936±0.475, respectively, and the difference was statistically significant ( F=1.59, P<0.001). The Ks/Ka values of p24 were 12.579±1.116, 10.185±0.494 and 8.522±0.595, respectively, and the difference was statistically significant ( F=1.61, P<0.001). The Ks/Ka values of p7 were 10.850±0.711, 9.717±0.932 and 8.522±0.026, respectively, and the difference was statistically significant ( F=4.24, P<0.001). The Ks/Ka values of p6 were 3.122±0.134, 3.040±1.498 and 4.841±0.353, respectively, and the difference was statistically significant ( F=10.68, P<0.001). Conclusions:CRF08_ BC is the main subtype in these four areas in Yunnan Province.The different clusters of CRF08_BC result in a different pattern of amino acid composition.The variation degree of different subtype gag gene is different in each section. Surveillance of HIV variant strains should be strengthened to control the epidemics of HIV.
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Objective @#To analyze the influencing factors for the molecular network transmission clusters of HIV/AIDS, and to provide scientific evidence for the precise prevention and control of AIDS. @*Methods@#A case-control study was conducted. The HIV/AIDS cases reported from January 2017 to June 2019 in Huzhou with strong clustering of HIV molecular transmission were recruited as the case group, and the residents with same gender, similar age ( ±three years ) and HIV negative in the same community and period were matched ( 1∶4 ) as the control group. Demographic characteristics, AIDS related knowledge and sexual behaviors were collected by a questionnaire survey. The Cox regression model was used to analyze the influencing factors for HIV/AIDS molecular network transmission cluster.@*Results @#There was 100 people in the case group and 400 people in the control group, the differences between them in age, sex, marital status, place of residence and educational level were not statistically significant ( P>0.05 ) . The results of multivariate Cox regression analysis showed that awareness of AIDS related knowledge ( HR=0.145, 95%CI: 0.059-0.352 ) was a protective factor for molecular network transmission clusters of HIV/AIDS; men who have sex wth men ( MSM, HR=9.614, 95%CI: 4.645-19.901) , seeking homosexual partners through the internet (HR=16.321, 95%CI: 7.016-32.968) and having syphilis ( HR=3.314, 95%CI: 1.073-10.232 ) were risk factors for molecular network transmission clusters of HIV/AIDS.@*Conclusions@#The awareness of AIDS related knowledge, MSM, seeking homosexual partners through the internet and suffering from syphilis are the influencing factors for molecular network transmission clusters of HIV/AIDS.
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Objective To understand the transmission patterns and risk factors of HIV-1 strain CRF01_AE subtypes in China,and to provide guidance for the implementation of precise intervention.Methods A total of 2 094 CRF01_AE pol sequences were collected in 19 provinces in China between 1996 and 2014.Phylogenetic tree was constructed by PhyML 3.0 software to select the transmission clusters.Transmission network was constructed by Cytoscape 3.6.0,which was further used for exploring of the major risk factors.Results Of the 2 094 sequences,12.18％ (255/2 094) were in clusters.A total of 82 transmission clusters were identified.The numbers of clusters and contained sequences in intra-provincial transmission (61,173) were significantly more than those in inter-provincial transmission (21,82).The ratio of transmission clustering in MSM increased over time from 2.41％ (2/83) during 1996-2008 to 23.61％ (72/305) during 2013-2014,showing a significant upward trend (x2 =27.800,df=1,P =0.000).The proportion of MSM with inter-provincial transmission clusters were higher than those with intra-provincial transmission clusters,which increased from 0.67％ (2/297) during 1996-2008 to 6.36％(30/472) during 2013-2014,showing a significant upward trend (x2=20.276,df=1,P=0.000).The transmission rate in homosexuals of the inter-transmission clusters (86.59％,71/82) was higher than that of intra-provincial transmission clusters (56.65％,98/173),and the difference was statistically significant (x2=22.792,P=0.000).The proportion of inter-provincial transmission clusters with more than 2 transmission routes (33.33％,7/21) was higher than that of intra-provincial clusters (13.11％,8/61),and the difference was statistically significant (x2=4.273,P=0.039).Results from the transmission network analysis indicated that the proportion of high risk population (degree≥4) with inter-provincial transmission clusters (51.22％,42/82) was significantly higher than that with intra-provincial transmission clusters (26.59％,46/173),and the difference was statistically significant (x2=14.932,P=0.000).Inter-provincial clusters were mainly detected in and and MSM.Conclusions Complex transmission networks were found for HIV-1 CRF01_AE strains in the mainland of China.Inter-provincial transmission clusters increased rapidly,MSM played an important role in the wide spread of the strain.More researches in transmission networks are needed to guide the precision intervention.
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Objective To understand the transmission patterns and risk factors of HIV-1 strain CRF01_AE subtypes in China,and to provide guidance for the implementation of precise intervention.Methods A total of 2 094 CRF01_AE pol sequences were collected in 19 provinces in China between 1996 and 2014.Phylogenetic tree was constructed by PhyML 3.0 software to select the transmission clusters.Transmission network was constructed by Cytoscape 3.6.0,which was further used for exploring of the major risk factors.Results Of the 2 094 sequences,12.18％ (255/2 094) were in clusters.A total of 82 transmission clusters were identified.The numbers of clusters and contained sequences in intra-provincial transmission (61,173) were significantly more than those in inter-provincial transmission (21,82).The ratio of transmission clustering in MSM increased over time from 2.41％ (2/83) during 1996-2008 to 23.61％ (72/305) during 2013-2014,showing a significant upward trend (x2 =27.800,df=1,P =0.000).The proportion of MSM with inter-provincial transmission clusters were higher than those with intra-provincial transmission clusters,which increased from 0.67％ (2/297) during 1996-2008 to 6.36％(30/472) during 2013-2014,showing a significant upward trend (x2=20.276,df=1,P=0.000).The transmission rate in homosexuals of the inter-transmission clusters (86.59％,71/82) was higher than that of intra-provincial transmission clusters (56.65％,98/173),and the difference was statistically significant (x2=22.792,P=0.000).The proportion of inter-provincial transmission clusters with more than 2 transmission routes (33.33％,7/21) was higher than that of intra-provincial clusters (13.11％,8/61),and the difference was statistically significant (x2=4.273,P=0.039).Results from the transmission network analysis indicated that the proportion of high risk population (degree≥4) with inter-provincial transmission clusters (51.22％,42/82) was significantly higher than that with intra-provincial transmission clusters (26.59％,46/173),and the difference was statistically significant (x2=14.932,P=0.000).Inter-provincial clusters were mainly detected in and and MSM.Conclusions Complex transmission networks were found for HIV-1 CRF01_AE strains in the mainland of China.Inter-provincial transmission clusters increased rapidly,MSM played an important role in the wide spread of the strain.More researches in transmission networks are needed to guide the precision intervention.
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Objective To understand the characteristics of distribution on HIV-1 subtypes and the transmission clusters in Yiwu in Zhejiang province.Methods A cross-sectional study of molecular epidemiology was carried out on newly reported H1V/AIDS cases in Yiwu.RNA was extracted from 168 plasma samples,followed by RT-PCR and nest-PCR for pol gene amplification,sequencing,phylogenetic tree construction used for analyzing the subtypes and transmission clusters.Mutations on drug resistance was analyzed by CPR 6.0 online tool.Results Subjects were mainly males (86.3％,145/168),with average age as (39.1 ± 13.4) years old and most of them were migrants (66.7％,112/168).The major routes of transmission included homosexual (51.2％,86/168) and heterosexual (48.8％,82/168) contacts.The rate of success for sequence acquisition was 89.9％ (151/168).The dominant subtypes showed as CRF01_AE (74,49.0％) and CRF07_BC (64,42.4％),followed by CRF08_BC (5,3.3％),CRF55_01B (3,2.0％),each case of subtype B,CRF45_cpx,CRF59_01B,CRF85_BC and URF (B/C).CRF45_cpx and CRF85_BC were discovered the first time in Zhejiang province.Twenty-six transmission clusters involving 65 cases were found,with the total clustered rate as 43.0％ (65/151),in which the CRF01_AE clustered rate appeared as 54.1％ (40/74),higher than that of CRF07_BC (21/64,32.8％).The average size of cluster was 2.5 cases/cluster,with average size of cluster in CRF01_AE patients infected through heterosexual transmission as the largest (3.5 cases/cluster).The prevalence of transmitted drug resistance was 4.6％ (7/151).Seven cases with surveillance drug resistant mutations (SDRM) were found,including 5 cases of M46L (3.3％),and one case of F77L or Y181C.Conclusion HIV genetic diversity and a variety of transmission clusters had been noticed in this study area (Yiwu).Programs on monitoring the subtypes and transmission clusters should be continued and strengthened.
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Objective To understand the distribution of HIV-1 subtype diversity and its transmission characteristics in Zhejiang province. Methods A total of 302 newly diagnosed HIV-1 positive patients were selected through stratified random sampling in Zhejiang in 2015. HIV-1 pol genes were sequenced successfully with reverse transcription PCR/nested PCR and phylogenetic analysis was conducted for 276 patients. Then a molecular epidemiologic study was performed combined with field epidemiological investigation. Results Of 276 sequence samples analyzed, 122 CRF07_BC strains (44.2%), 103 CRF01_AE strains (37.3%), 17 CRF08_BC strains (6.1%), 9 B strains (3.2%), 6 CRF55_01B strains (2.2%), 5 C strains (1.8%), 1 CRF59_01B strain (0.4%), 1 CRF67_01B strain (0.4%), 1 A1 strain (0.4%), and 11 URFs strains (4.0%) were identified. Phylogenetic analysis revealed 16 clusters with only 15.1% (34/225) sequences involved among CRF07_BC and CRF01_AE strains. The clustered cases in MSM were higher than that in populations with other transmission routes. And clusters existed between the populations with different transmission routes. Conclusion The major strains of HIV-1 in Zhejiang are CRF07_BC and CRF01_AE. The HIV subtypes showed more complexity in Zhejiang. It is necessary to strengthen the surveillance for HIV subtypes, carry out classified management and conduct effective prevention and control in the population at high risk.
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Objective To understand the characteristics of distribution on HIV-1 subtypes and the transmission clusters in Yiwu in Zhejiang province.Methods A cross-sectional study of molecular epidemiology was carried out on newly reported H1V/AIDS cases in Yiwu.RNA was extracted from 168 plasma samples,followed by RT-PCR and nest-PCR for pol gene amplification,sequencing,phylogenetic tree construction used for analyzing the subtypes and transmission clusters.Mutations on drug resistance was analyzed by CPR 6.0 online tool.Results Subjects were mainly males (86.3％,145/168),with average age as (39.1 ± 13.4) years old and most of them were migrants (66.7％,112/168).The major routes of transmission included homosexual (51.2％,86/168) and heterosexual (48.8％,82/168) contacts.The rate of success for sequence acquisition was 89.9％ (151/168).The dominant subtypes showed as CRF01_AE (74,49.0％) and CRF07_BC (64,42.4％),followed by CRF08_BC (5,3.3％),CRF55_01B (3,2.0％),each case of subtype B,CRF45_cpx,CRF59_01B,CRF85_BC and URF (B/C).CRF45_cpx and CRF85_BC were discovered the first time in Zhejiang province.Twenty-six transmission clusters involving 65 cases were found,with the total clustered rate as 43.0％ (65/151),in which the CRF01_AE clustered rate appeared as 54.1％ (40/74),higher than that of CRF07_BC (21/64,32.8％).The average size of cluster was 2.5 cases/cluster,with average size of cluster in CRF01_AE patients infected through heterosexual transmission as the largest (3.5 cases/cluster).The prevalence of transmitted drug resistance was 4.6％ (7/151).Seven cases with surveillance drug resistant mutations (SDRM) were found,including 5 cases of M46L (3.3％),and one case of F77L or Y181C.Conclusion HIV genetic diversity and a variety of transmission clusters had been noticed in this study area (Yiwu).Programs on monitoring the subtypes and transmission clusters should be continued and strengthened.
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Objective To understand the distribution of HIV-1 subtype diversity and its transmission characteristics in Zhejiang province. Methods A total of 302 newly diagnosed HIV-1 positive patients were selected through stratified random sampling in Zhejiang in 2015. HIV-1 pol genes were sequenced successfully with reverse transcription PCR/nested PCR and phylogenetic analysis was conducted for 276 patients. Then a molecular epidemiologic study was performed combined with field epidemiological investigation. Results Of 276 sequence samples analyzed, 122 CRF07_BC strains (44.2%), 103 CRF01_AE strains (37.3%), 17 CRF08_BC strains (6.1%), 9 B strains (3.2%), 6 CRF55_01B strains (2.2%), 5 C strains (1.8%), 1 CRF59_01B strain (0.4%), 1 CRF67_01B strain (0.4%), 1 A1 strain (0.4%), and 11 URFs strains (4.0%) were identified. Phylogenetic analysis revealed 16 clusters with only 15.1% (34/225) sequences involved among CRF07_BC and CRF01_AE strains. The clustered cases in MSM were higher than that in populations with other transmission routes. And clusters existed between the populations with different transmission routes. Conclusion The major strains of HIV-1 in Zhejiang are CRF07_BC and CRF01_AE. The HIV subtypes showed more complexity in Zhejiang. It is necessary to strengthen the surveillance for HIV subtypes, carry out classified management and conduct effective prevention and control in the population at high risk.
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Objective To construct the molecular transmission networks of HIV-1 CRF01 AE strains circulating in China and to analyze their characteristics. Methods Sequences of the pol genes of Chinese CRF01 AE strains were downloaded from Los Alamos database and the related demographic informa-tion was checked. Transmission networks were created by four steps,including phylogenetic tree construc-tion,transmission cluster extraction,minimum genetic distance identification and network visualization. Chi-square test was performed to analyze the differences in the distribution of different populations in the networks and the differences in the distribution of subjects with different degrees among different sub-populations. De-scriptive analysis was used to investigate the transmission links between sub-populations and various regions. Results The 2 419 sequences constituted 250 separate networks including 847 nodes and 610 edges. The number of subjects covered by different networks ranged from 2 to 25. Subjects with degree ≥2 represented only 26. 4%(224 / 847)of network-individuals,but were connected with 66. 5%(563 / 847)of all network-individuals. There were 37. 6%(669 / 1 781)of men who have sex with men(MSM),28. 4%(102 / 359) of heterosexual men,16. 1%(10 / 62)of intravenous drug users(IDUs)and 30. 4%(66 / 217)of hetero-sexual women involved in the networks(χ2 =23. 774,P﹤0. 001). The percentage of subjects with degree ≥2 was high in MSM(10. 8% ,193 / 1 781)compared to that in heterosexual men(5. 6% ,20 / 359)(P =0. 002)and heterosexual women(4. 6% ,10 / 217)(P=0. 004). Of the 669 MSM in the networks,95. 5%(639 / 669)linked to other MSM and only 2. 4% (16 / 669)linked to heterosexual women. However, 15. 1%(10 / 66)of the heterosexual women in the networks linked to MSM. Of the heterosexual men in the networks,35. 3%(36 / 102)linked to heterosexual women,9. 8%(10 / 102)linked to MSM. Of the sub-jects in the networks,20. 9%(177 / 847)linked to other regions' individuals. Conclusion The super-spreaders played an important role in the molecular transmission networks of HIV-1 CRF01 AE strains even though they were in a minority. The transmission of HIV-1 CRF01 AE strains between sub-populations and various regions was complicated and active.