Molecular surveillance of HIV-1 newly diagnosed infections in Shenzhen, China from 2011 to 2018.

OBJECTIVES: Shenzhen is suffering severe HIV epidemic. No systematic surveillance on high risk populations, HIV genetic diversity, transmitted drug resistance (TDR) and molecular transmission clusters (MTCs) have been reported yet. In this study, we described them based on newly diagnosed HIV positive cases from 2011 to 2018 in Shenzhen city, China. METHODS: Plasma samples of newly reported HIV positive cases in Shenzhen, China were collected from 2011 to 2018. The HIV pol gene was amplified and sequenced for subtyping, genetic characterization, TDR and phylogenetic analysis. Demographic and risk characteristics associated with transmitted drug resistance-associated mutations (TDRAMs) and MTCs were explored by using logistic regression analyses. RESULTS: 10,378 HIV pol sequences were successfully obtained from newly diagnosed patients with available background information. The most prevalent HIV-1 subtype was CRF07_BC (40.92%). CRF07_BC, CRF55_01B and URFs increased across years. Total TDR was 6.02% during 2011 to 2018. CRF01_AE, CRF08_BC, CRF55_01B and subtype B were more likely to be associated with TDRAMs than CRF07_BC. 4460 (42.98%) patients were infected with strains included in MTCs. Patients younger than 30 and over 50 years were more likely to cluster. CONCLUSIONS: The prevalence of HIV-1 drug resistance and molecular transmission clusters in Shenzhen should raise a high alert. Interventions targeting on patients with strains locating in MTCs should be considered to improve prevention effect in Shenzhen.

SARS-CoV-2 Molecular Transmission Clusters and Containment Measures in Ten European Regions during the First Pandemic Wave.

BACKGROUND: The spatiotemporal profiling of molecular transmission clusters (MTCs) using viral genomic data can effectively identify transmission networks in order to inform public health actions targeting SARS-CoV-2 spread. METHODS: We used whole genome SARS-CoV-2 sequences derived from ten European regions belonging to eight countries to perform phylogenetic and phylodynamic analysis. We developed dedicated bioinformatics pipelines to identify regional MTCs and to assess demographic factors potentially associated with their formation. RESULTS: The total number and the scale of MTCs varied from small household clusters identified in all regions, to a super-spreading event found in Uusimaa-FI. Specific age groups were more likely to belong to MTCs in different regions. The clustered sequences referring to the age groups 50-100 years old (y.o.) were increased in all regions two weeks after the establishment of the lockdown, while those referring to the age group 0-19 y.o. decreased only in those regions where schools' closure was combined with a lockdown. CONCLUSIONS: The spatiotemporal profiling of the SARS-CoV-2 MTCs can be a useful tool to monitor the effectiveness of the interventions and to reveal cryptic transmissions that have not been identified through contact tracing.

[Characteristics of subtypes and transmission of HIV-1 infected persons among student MSM in Zhejiang province, 2013-2015].

Objective: To investigate the characteristics of subtype diversity and transmission on HIV-1 among 12 to 30 years old student MSM in Zhejiang province. Methods: A total of 290 newly diagnosed HIV infected student MSM were selected as the research objects for molecular studies on HIV, in Zhejiang province during 2013 to 2015. Data on epidemiology and plasma samples of these people were collected. HIV-1 nucleotide sequences of pol gene regions were amplified using the RT-PCR/nested PCR method and sequenced. Phylogenetic analysis was performed to determine the HIV-1 genotypes. Characteristics of transmission mode among these cases were also analyzed. Results: A total of 290 cases, 50.3% were diagnosed in Hangzhou and 81.0% had college or above degrees. 178 sequences including 10 subtypes, were obtained, with the main subtypes as CRF01_AE (49.4%, 88/178) and CRF07_BC (39.3%, 70/178). A total of 18 molecular transmission clusters were formed (42 cases, cluster size from 2 to 4), with the proportions of clusters as 23.6% (42/178). 61.9% (26/42) of student MSM with their schools located in the same district within the transmission clusters. Their sexual partners would include both student MSM and non-student MSM. The proportion of clusters among middle school students was 38.2% (13/34), higher than that of college students (20.1%, 29/144) ( χ(2)=4.996, P<0.05). Conclusions: The HIV-1 subtypes of student MSM in Zhejiang province appeared diversity, which indicated with the diversity of sources of infection. The geographical distribution of cluster cases is relatively centralized. In order to effectively control the spread of AIDS, more attention should be paid to the sexual partners involved and to specific programs on intervention.

[Molecular transmission clusters on HCV genotypes among newly reported HIV/HCV co-infection in Dehong Dai and Jingpo autonomous prefecture of Yunnan province, 2016].

Objective: To understand the characteristics on major strain subtypes of hepatitis C virus among HIV/HCV co-infected patients, so as to explore the molecular transmission clusters and related risk factors of HCV strains. Methods: A total of 336 newly reported HIV-infected patients were diagnosed as HIV/HCV co-infection in Dehong Dai and Jingpo autonomous prefecture (Dehong) in 2016. We used Nested PCR to amplify CE1 and NS5B genes among 318 samples with plasma levels above 200 µl, before using the combining phylogenetic tree and constructing molecular propagation network method to analyze the related data. Results: A total of 267 HIV/HCV co-infection patients who had met the HCV genotyping requirements were screened the gene subtypes were diversified. Among these genotypes, proportions of 3b, 6n, 6u, 1a, 3a and other subtypes appeared as 32.6% (87/267), 18.4% (49/267), 15.7%(42/267), 13.1%(35/267), 11.2%(30/267) and 9.0%(24/267) respectively. Molecular transmission network of five major HCV genotypes was constructed with a clustering rate of 39.1% (95/243). The clustering rate of subtype 1a was the highest, as 71.4% (25/35). Results from the multivariate logistic regression showed that ethnic minorities other than the Yi and Jingpo (vs. the Han, OR=0.17, 95%CI: 0.04-0.71), the married spouses (vs. the unmarried, OR=0.42, 95%CI: 0.18-0.94), the 6n and 3a subtype (vs. the 3b subtype, OR=0.34, 95%CI: 0.12-0.95; OR=0.22, 95%CI: 0.05-0.93) were more difficult to form transmission clusters. However, the 6u and 1a subtype (vs. the 3b subtype, OR=3.10, 95%CI: 1.21-7.94; OR=4.00, 95%CI: 1.32-12.11) seemed more likely to form the transmission clusters. Conclusion: Ethnicity, marital status and genetic subtypes were factors significantly associated with the formation of transmission clusters related to the major HCV gene subtypes among newly reported HIV/HCV co-infection in Dehong.

[Epidemiological characteristics of molecular transmission cluster among reported HIV/AIDS cases in Jiaxing city, Zhejiang province, 2017].

Objective: To understand the epidemiological characteristics of one large HIV molecular transmission cluster in Jiaxing city, Zhejiang province, 2017 in order to select those people under high-risk and providing basis for programs on prevention. Methods: During 2017, newly diagnosed HIV/AIDS cases in this city were recruited. Plasma samples were collected from subjects, followed by RNA extraction, RT-PCR and nest-PCR for pol gene amplification, before being sequenced and aligned. Mega 6.0 software was used to construct phylogenetic tree, and Cytoscape 3.6.0 software was used to identify HIV molecular transmission clusters. Cases within the large transmission clusters were investigated, using a field-epidemiology-questionnaire. Data related to socio-demographics and previous sexual behaviors were collected and EpiData 3.0 and SPSS 20.0 software were used. Results: In the large transmission cluster with subtype identified as CRF07_BC, in Jiaxing, 2017, 26 cases of the total 30 cases were investigated. A total of 80.8% (21/26) could be identified as newly infected within the last two years and 30.8%(8/26) could be identified as newly infected within the last one year, including 22 cases infected locally. Among several infected cases who were at age 45 years or older, they admitted that they had experienced unprotected sexual contacts in local city for long time and having had more than 10 disclosed sexual contacts within the last two years at the local venues. Conclusions: This molecular cluster had been formed and scaled up quickly in recent two years, it has played an important role in promoting and scaling up the HIV transmission. Three cases identificed as high risk played an importantrde role in scaling up this cluster.

Molecular transmission clusters on HCV genotypes among newly reported HIV/HCV co-infection in Dehong Dai and Jingpo autonomous prefecture of Yunnan province, 2016 / 中华流行病学杂志

Objective: To understand the characteristics on major strain subtypes of hepatitis C virus among HIV/HCV co-infected patients, so as to explore the molecular transmission clusters and related risk factors of HCV strains. Methods: A total of 336 newly reported HIV-infected patients were diagnosed as HIV/HCV co-infection in Dehong Dai and Jingpo autonomous prefecture (Dehong) in 2016. We used Nested PCR to amplify CE1 and NS5B genes among 318 samples with plasma levels above 200 μl, before using the combining phylogenetic tree and constructing molecular propagation network method to analyze the related data. Results: A total of 267 HIV/HCV co-infection patients who had met the HCV genotyping requirements were screened the gene subtypes were diversified. Among these genotypes, proportions of 3b, 6n, 6u, 1a, 3a and other subtypes appeared as 32.6% (87/267), 18.4% (49/267), 15.7%(42/267), 13.1%(35/267), 11.2%(30/267) and 9.0%(24/267) respectively. Molecular transmission network of five major HCV genotypes was constructed with a clustering rate of 39.1% (95/243). The clustering rate of subtype 1a was the highest, as 71.4% (25/35). Results from the multivariate logistic regression showed that ethnic minorities other than the Yi and Jingpo (vs. the Han, OR=0.17, 95%CI: 0.04-0.71), the married spouses (vs. the unmarried, OR=0.42, 95%CI: 0.18-0.94), the 6n and 3a subtype (vs. the 3b subtype, OR=0.34, 95%CI: 0.12-0.95; OR=0.22, 95%CI: 0.05-0.93) were more difficult to form transmission clusters. However, the 6u and 1a subtype (vs. the 3b subtype, OR=3.10, 95%CI: 1.21-7.94; OR=4.00, 95%CI: 1.32-12.11) seemed more likely to form the transmission clusters. Conclusion: Ethnicity, marital status and genetic subtypes were factors significantly associated with the formation of transmission clusters related to the major HCV gene subtypes among newly reported HIV/HCV co-infection in Dehong.

Epidemiological characteristics of molecular transmission cluster among reported HIV/AIDS cases in Jiaxing city, Zhejiang province, 2017 / 中华流行病学杂志

Objective: To understand the epidemiological characteristics of one large HIV molecular transmission cluster in Jiaxing city, Zhejiang province, 2017 in order to select those people under high-risk and providing basis for programs on prevention. Methods: During 2017, newly diagnosed HIV/AIDS cases in this city were recruited. Plasma samples were collected from subjects, followed by RNA extraction, RT-PCR and nest-PCR for pol gene amplification, before being sequenced and aligned. Mega 6.0 software was used to construct phylogenetic tree, and Cytoscape 3.6.0 software was used to identify HIV molecular transmission clusters. Cases within the large transmission clusters were investigated, using a field-epidemiology-questionnaire. Data related to socio-demographics and previous sexual behaviors were collected and EpiData 3.0 and SPSS 20.0 software were used. Results: In the large transmission cluster with subtype identified as CRF07_BC, in Jiaxing, 2017, 26 cases of the total 30 cases were investigated. A total of 80.8% (21/26) could be identified as newly infected within the last two years and 30.8%(8/26) could be identified as newly infected within the last one year, including 22 cases infected locally. Among several infected cases who were at age 45 years or older, they admitted that they had experienced unprotected sexual contacts in local city for long time and having had more than 10 disclosed sexual contacts within the last two years at the local venues. Conclusions: This molecular cluster had been formed and scaled up quickly in recent two years, it has played an important role in promoting and scaling up the HIV transmission. Three cases identificed as high risk played an importantrde role in scaling up this cluster.

Molecular transmission dusters on HCV genotypes among newly reported HIV/HCV co-infection in Dehong Dai and Jingpo autonomous prefecture of Yunnan province, 2016 / 中华流行病学杂志

Objective To understand the characteristics on major strain subtypes of hepatitis C virus among HIV/HCV co-infected patients,so as to explore the molecular transmission clusters and related risk factors of HCV strains.Methods A total of 336 newly reported HIV-infected patients were diagnosed as HIV/HCV co-infection in Dehong Dai and Jingpo autonomous prefecture (Dehong)in 2016.We used Nested PCR to amplify CE 1 and NS5B genes among 318 samples with plasma levels above 200 μl,before using the combining phylogenetic tree and constructing molecular propagation network method to analyze the related data.Results A total of 267 HIV/HCV co-infection patients who had met the HCV genotyping requirements were screened the gene subtypes were diversified.Among these genotypes,proportions of 3b,6n,6u,1a,3a and other subtypes appeared as 32.6％ (87/267),18.4％ (49/267),15.7％(42/267),13.1％(35/267),11.2％(30/267) and 9.0％(24/267) respectively.Molecular transmission network of five major HCV genotypes was constructed with a clustering rate of 39.1％ (95/243).The clustering rate of subtype la was the highest,as 71.4％ (25/35).Results from the multivariate logistic regression showed that ethnic minorities other than the Yi and Jingpo (vs.the Han,OR=0.17,95％ CI:0.04-0.71),the married spouses (vs.the unmarried,OR=0.42,95％ CI:0.18-0.94),the 6n and 3a subtype (vs.the 3b subtype,OR=0.34,95％CI:0.12-0.95;OR=0.22,95％CI:0.05-0.93) were more difficult to form transmission clusters.However,the 6u and 1a subtype (vs.the 3b subtype,OR=3.10,95％CI:1.21-7.94;OR=4.00,95％CI:1.32-12.11) seemed more likely to form the transmission clusters.Conclusion Ethnicity,marital status and genetic subtypes were factors significantly associated with the formation of transmission clusters related to the major HCV gene subtypes among newly reported HIV/HCV co-infection in Dehong.

Epidemiological characteristics of molecular transmission cluster among reported HIV/AIDS cases in Jiaxing city, Zhejiang province, 2017 / 中华流行病学杂志

Objective To understand the epidemiological characteristics of one large HIV molecular transmission cluster in Jiaxing city,Zhejiang province,2017 in order to select those people under high-risk and providing basis for programs on prevention.Methods During 2017,newly diagnosed HIV/AIDS cases in this city were recruited.Plasma samples were collected from subjects,followed by RNA extraction,RT-PCR and nest-PCR for pol gene amplification,before being sequenced and aligned.Mega 6.0 software was used to construct phylogenetic tree,and Cytoscape 3.6.0 software was used to identify HIV molecular transmission clusters.Cases within the large transmission clusters were investigated,using a field-epidemiology-questionnaire.Data related to socio-demographics and previous sexual behaviors were collected and EpiData 3.0 and SPSS 20.0 software were used.Results In the large transmission cluster with subtype identified as CRF07_BC,in Jiaxing,2017,26 cases of the total 30 cases were investigated.A total of 80.8％ (21/26) could be identified as newly infected within the last two years and 30.8％(8/26) could be identified as newly infected within the last one year,including 22 cases infected locally.Among several infected cases who were at age 45 years or older,they admitted that they had experienced unprotected sexual contacts in local city for long time and having had more than 10 disclosed sexual contacts within the last two years at the local venues.Conclusions This molecular cluster had been formed and scaled up quickly in recent two years,it has played an important role in promoting and scaling up the HIV transmission.Three cases identificed as high risk played an importantrde role in scaling up this cluster.