Back to Search
Start Over
Molecular characteristic of HIV-1 CRF01_AE in Nanjing from 2015 to 2017.
- Source :
-
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases [Infect Genet Evol] 2019 Nov; Vol. 75, pp. 104038. Date of Electronic Publication: 2019 Sep 11. - Publication Year :
- 2019
-
Abstract
- Objective: To investigate the evolutionary dynamics and characteristic of the molecular transmission networks of HIV-1 CRF01&#95;AE in Nanjing.<br />Methods: Viral samples were collected from 580 newly diagnosed HIV-1-infected patients. HIV-1 pol sequences were obtained and used for for molecular evolutionary analyses. The ML trees were constructed by MEGA 6.0 using under GTR+ G + I model with 1000 bootstrap replicates. The emergence and estimation of tMRCA and the evolutionary rate of the different CRF01&#95;AE clusters were inferred using Bayesian phylogenetic analysis approaches implemented in the BEAST package. Pairwise genetic distances were calculated under the Tamura-Nei 93 model, a genetic distance threshold of ≤1.2% was used to identify potential transmission clusters. Network diagrams were plotted using Cytoscape 3.3.0.<br />Results: Of these HIV-1-infected patients, 551 (91.5%) were males. The largest number of infections were attributed to homosexual (462, 79.7%). A total of 518 full-length pol genes were successfully amplified, based on the phylogenetic analysis CRF01&#95;AE was the most predominantly circulating strain (45.0%, 233/518). As shown in the ML tree, three distinct clusters were observed. The 'Nanjing lineage' 1, 2, 3 has an estimated tMRCA around1996.61, 1993.61, 1984.61 respectively. Of 233 Nanjing sequences, 123 (55.2%) distributed in 30 molecular clusters, average Links/node was 7.8 with range (1-33), most of Nanjing strains shared links with local strains.<br />Conclusion: HIV-1 CRF01&#95;AE was the most predominantly circulating strain, the epidemic of CRF01&#95;AE in Nanjing was driven by multiple clusters of HIV-1 strains, and most CRF01&#95;AE stains in our study were estimated to have originated in China in the 1990s.<br /> (Copyright © 2019 Elsevier B.V. All rights reserved.)
- Subjects :
- Bayes Theorem
China epidemiology
Evolution, Molecular
Female
Genotype
HIV Infections history
History, 21st Century
Humans
Male
Markov Chains
Molecular Epidemiology
Phylogeny
Public Health Surveillance
HIV Infections epidemiology
HIV Infections virology
HIV-1 classification
HIV-1 genetics
Reassortant Viruses genetics
Subjects
Details
- Language :
- English
- ISSN :
- 1567-7257
- Volume :
- 75
- Database :
- MEDLINE
- Journal :
- Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases
- Publication Type :
- Academic Journal
- Accession number :
- 31520786
- Full Text :
- https://doi.org/10.1016/j.meegid.2019.104038