ABSTRACT
Phylogenetic analyses were crucial to elucidate the origin and spread of the pandemic human immunodeficiency virus type 1 (HIV-1) group M virus, both during the pre-epidemic period of cryptic dissemination in human populations as well as during the epidemic phase of spread. The use of phylogenetics and phylodynamics approaches has provided important insights to track the founder events that resulted in the spread of HIV-1 strains across vast geographic areas, specific countries and within geographically restricted communities. In the recent years, the use of phylogenetic analysis combined with the huge availability of HIV sequences has become an increasingly important approach to reconstruct HIV transmission networks and understand transmission dynamics in concentrated and generalised epidemics. Significant efforts to obtain viral sequences from newly HIV-infected individuals could certainly contribute to detect rapidly expanding HIV-1 lineages, identify key populations at high-risk and understand what public health interventions should be prioritised in different scenarios.
Subject(s)
Humans , Animals , HIV Infections/transmission , HIV-1/genetics , Phylogeography , Phylogeny , Cluster Analysis , HIV Infections/virology , Gorilla gorillaABSTRACT
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.
ABSTRACT
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.
ABSTRACT
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.
ABSTRACT
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.
ABSTRACT
As part of an ongoing study on the features of AIDS spread towards small cities and rural areas, we present a molecular survey of human immunodeficiency virus type 1 (HIV-1) polymerase sequences recovered between 2004 and 2006 from 71 patients receiving care in the city of Saquarema, inner state of Rio de Janeiro. Phylogenetic reconstructions found the two prevalent lineages in the state (subtypes B [59 strains, 83.1 percent], F1 [6 strains; 8.4 percent], and BF1 recombinants [four strains; 5.6 percent]), as well as two (2.8 percent) CRF02_AG strains, which seems to be an emerging lineage in the capital. These CRF02_AG sequences were recovered from a married heterosexual couple who never traveled abroad, thus providing the first molecular evidence of autochthonous horizontal transmission of this lineage of major global importance. Also, three phylogenetic clusters of strains recovered from a total of 18.3 percent of the cohort were uncovered. Their close genetic relatedness suggests they were recovered from patients who probably took part in the same chain of viral spread. In conjunction with our previous surveys from inner Rio de Janeiro, these results suggest that although small cities harbor unique molecular features of HIV-1 infection, they also clearly reflect and may rapidly absorb the diversity recorded in large urban centers.