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@#Abstract: Objective To understand the difference of DNA sequence and RNA sequence of paired pol region in HIV patients in constructing HIV genetic transmission network, and to provide scientific data for constructing molecular transmission networks using DNA sequences. Methods The whole blood and plasma samples of HIV patients living in 2014 and newly reported in 2015-2018 in Liuzhou, Guangxi, were collected, DNA and RNA sequences were extracted, amplified, sequenced, spliced and aligned, and then genetic transmission networks were constructed, and the connectivity consistency of genetic transmission networks constructed by DNA and RNA sequences was compared. Results In this study, a total 2 983 participants were investigated, which were 2014 baseline and 2015-2018 newly reported HIV patients, of which 2 590 participants were only DNA sequences in 2014 baseline, 196 HIV patients were both DNA and RNA sequences of paired pol region in 2014 baseline, and 197 newly reported HIV patients were both DNA and RNA sequences of paired pol region in 2015-2018. In 393 DNA and RNA sequences of paired pol region, the genotype of DNA sequence and RNA sequence were consistent, and there was no statistically significant difference in genetic distance between paired DNA sequences and RNA sequences (Z=-2.72, P=1.00). The connection consistency rate of genetic transmission networks constructed by DNA and RNA sequences of paired pol region of 2015-2018 newly reported with the baseline DNA sequences was 91.4% (108/197). And the connection consistency rate of genetic transmission networks constructed by DNA and RNA sequences of paired pol region of 2015-2018 newly reported with the baseline RNA sequences was 97.0% (191/197). There was no statistical difference in antiretroviral therapy to reduce the risk of HIV secondary transmission between genetic transmission networks constructed by DNA and RNA sequences of paired of pol gene newly reported from 2015 to 2018 with baseline DNA sequence. Conclusion DNA sequence and RNA sequence of paired pol region of HIV patients have good consistency in genotype, genetic distance, and genetic transmission network construction, and both DNA and RNA sequences can be used for genetic transmission network analysis.
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ObjectiveThis study aimed to investigate the HIV genotypic subtypes and molecular transmission clusters among men who have sex with men （MSM） with newly reported HIV infections in Dehong Dai and Jingpo Autonomous Prefecture （Dehong Prefecture）， Yunnan Province， China， between 2010 and 2019. The study aimed to identify potential high-risk transmitters and provide reference data for screening， management， and intervention of infection sources. MethodsPlasma samples from newly reported HIV-positive MSM individuals in Dehong Prefecture between 2010 and 2019 were collected. The viral pol gene fragments were amplified， sequenced， and genotyped. Genetic distances （GD） between pairwise sequences were analyzed and calculated. MEGA 7.0 and Gephi were used for phylogenetic and molecular transmission network analysis. ResultsA total of 159 newly reported HIV infections among MSM were included in the study， with successful genotyping of 100 cases. Nine HIV-1 subtypes were identified， with the most prevalent being CRF01_AE subtype （52%）， followed by CRF07_BC subtype （31%）， CRF55_01B subtype （10%）， and others （7%）. Cluster analysis revealed a total network access rate of 67%， forming three transmission clusters. CRF01_AE subtype formed two transmission clusters with 38 and 3 infected individuals， while CRF07_BC subtypes formed one transmission cluster with 26 infected individuals. The transmission network within the CRF01_AE clusters exhibited a more complex relationship. Significant differences in educational level were observed between the two main transmission clusters. ConclusionThe predominant HIV subtypes among newly reported MSM cases in Dehong Prefecture between 2010 and 2019 were CRF01_AE and CRF07_BC. Significant cultural differences are observed between the main transmission clusters. Continued monitoring of genotypic subtypes and targeted interventions within transmission clusters are warranted.
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Objective:To understand the molecular transmission characteristics of human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome(AIDS) patients in the mountainous area of southwest Zhejiang Province(Lishui city).Methods:A total of 147 blood samples were collected from newly-diagnosed HIV-1 infected who received no antiviral therapy, and pol gene was amplified, followed by sequencing. MEGA6.0 software was used to construct phylogenetic tree and determine gene subtypes. HIVDB online was used to analyze drug resistance mutation, then the pairwise genetic distance(GD) was calculated and the opitimal threshold of GD was selected, finally the molecular transmission network was constructed by Cytoscape3.7.0 software. Chi-square or Fisher′s exact probability method was used for statistical analysis. Results:A total of 134 sequences were obtained successfully, and nine subtypes were detected. The dominant subtypes were CRF08_BC (34.33%, 46/134), CRF01_AE (29.85%, 40/134) and CRF07_BC (23.88%, 32/134). It also found that age, registered residence, education level and transmission route had significant differences in distribution of subtypes ( P<0.05). Nineteen drug resistance individuals were found, and the total drug resistance rate was 14.18% (19/134). The HIV-1 molecular transmission network was plotted based on 1.2% GD threshold. A total of 15 transmission clusters (cluster size ranging from 2 to 29) were found. The network access rate was 49.25% (66/134), mainly including male (75.76%, 50/66), heterosexual (81.82%, 54/66) and patientsrinfected with CRF08_ BC (50.00%, 33/66). A transmission cluster including two cases of female sex workers and seven cases of drug resistance was identified, in which the average age of the patients was 57.21 years old and the average degree value was 22.7, and the cases were mainly infected through heterosexual contact (96.55%, 28/29). The highest homology of the sequences in the cluster was in Yunnan. Conclusions:The HIV-1 subtypes were diverse in the mountainous area of southwest Zhejiang Province(Lishui city). Drug resistant transmission had reached a moderate epidemic level. There were molecular transmission clusters with the aggregation characteristics of elderly clients in specific regions. It was urgent to formulate and implement precise intervention strategies to curb the spread of HIV.
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Objective@#Using field epidemiological investigation and molecular analysis to construct the molecular transmission network of human immunodeficiency virus/acquired immunodeficiency syndrome cases (HIV/AIDS) newly diagnosed in Huzhou in 2017, Zhejiang Province.@*Methods@#A total of 160 participants were obtained through a web-based system from Chinese Center for Disease Control and Prevention (CCDC) with the features of diagnosed in Huzhou in 2017 who also had been collected samples for the first follow-up. The basic information of demographic characteristics and risk factors was extracted from the website. RNA was extracted from plasma samples of untreated cases, followed by RT-PCR and nest-PCR for pol gene amplification, sequencing. Phylogenetic tree was constructed by MEGA software for HIV gene subtyping. TN93 model was used for calculating the distance between two sequences. Cytoscape software was used for drawing molecular transmission network. And then an epidemiological survey was conducted to cases in the primary cluster.@*Results@#A total of 138 sequenced individuals (86.3%) were acquired from 160 individuals. Among which, 123 (89.1%) were male. The highest proportion of subtype was CRF07_BC (60, 43.5%), followed by CRF01_AE (46, 33.3%), and with four cases of Unique Recombinant Form (URF, CRF01_AE and CRF07_BC) and one case of URF (subtype B and C). A total of 18 molecular clusters included 56 individuals (40.6%) were found in the transmission network under the optimal genetic distance threshold (1.0%). The clustering proportion of CRF07_BC (66.1%, 37 cases) was higher than that of CRF01_AE. There were 9 clusters formed among CRF07_BC, including 37 cases (accounting for 61.7%, 37/60). The primary transmission cluster contained 11 cases, among which 9 cases were transmitted by homosexual sex. The first time of the cases to have homosexual behavior is range from 2010 to 2016, whose media number (P25, P75) of partners was 6 (3.5, 8.5). Most of the cases come from Anhui Province and engaged in garment industry (5 cases), between which there were 8 cases used Blued software to seek for casual partners, 1 case seeking for casual partners in garden.@*Conclusion@#With CRF07_BC and CRF01_AE predominantly circulating, HIV genetic diversity had been noticed in this area. The primary cluster was consisted of high proportion of locally new infections, and a specific population aggregation in limited place existed.
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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 explore HIV-1 drug resistance and influencing factors among people living with HIV/AIDS before antiretroviral therapy in Liangshan Yi Autonomous Prefecture (Liangshan).@*Methods@#Between January 1 and June 30, in both 2017 and 2018, a cross-sectional survey was conducted in Liangshan HIV-1 pol sequences were gathered and analyzed according to WHO Guidelines on HIV drug resistance surveillance of 2014. Both HyPhy 2.2.4 and Cytoscape 3.6.1 software were used to analyze the drug resistant strains of HIV-1 transmission network.@*Results@#A total of 464 people living with HIV/AIDS was recruited. The proportion of HIV-1 CRF07_BC subtype was 88.6% (411/464), with HIV-1 drug resistance rate was 9.9% (46/464). The HIV-1 drug resistance rates of non-nucleoside reverse transcriptase inhibitors (NNRTI), nucleoside reverse transcriptase inhibitors(NRTI) and protease inhibitors (PI) were 6.7% (31/464), 1.9% (9/464) and 0.4% (2/464) respectively. New recombinant strains of HIV-1 URF_01BC subtype was independently clustered according to the drug resistant mutation sites. Results from the multivariate logistic analysis showed that injected drug users group had higher risk on HIV-1 drug resistance (aOR=3.03, 95%CI:1.40-6.54) than heterosexual group among people living with HIV/AIDS.@*Conclusions@#HIV-1 drug resistance rate had already been in a high level before antiretroviral therapy was in place. The newly identified recombinant strains of HIV-1 URF_01BC subtype were independently clustered according to the drug resistant mutation sites. It was necessary to strengthen the prevention of the HIV-1 drug resistant strains transmission.
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HIV molecular network is a recently reported method for studying the transmission characteristics of HIV-infected people. Countries have used this method to conduct a large number of researches on transmission relations, transmission hotspots and epidemic surveillance for the purpose of providing evidence for precise AIDS intervention and control. At present, there are three major methods for constructing molecular networks in the world, i.e. genetic distance method based on pairwise alignment, phylogenetic node support method, and joint parameter method based on the two methods. This paper reviews the progress of the three methods for constructing HIV molecular network to study the transmission characteristics of HIV-infected patients, in order to provide data support for the prevention and control of HIV. Since the emergence of the molecular network method, Beijing, Shanghai, Zhejiang, Sichuan and other provinces in China have reported relevant research results using molecular network analysis, which provided scientific data for further precise AIDS prevention and control. Recent international studies have also predicted that molecular network based transmission cluster detection is expected to become a new method to stop AIDS epidemic.
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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.