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Prevalence of Non-B HIV-1 Subtypes in North Italy and Analysis of Transmission Clusters Based on Sequence Data Analysis
- Source :
- Microorganisms, Vol 8, Iss 1, p 36 (2019), Microorganisms, Volume 8, Issue 1
- Publication Year :
- 2019
- Publisher :
- MDPI AG, 2019.
-
Abstract
- HIV-1 diversity is increasing in European countries due to immigration flows, as well as travels and human mobility, leading to the circulation of both new viral subtypes and new recombinant forms, with important implications for public health. We analyzed 710 HIV-1 sequences comprising protease and reverse-transcriptase (PR/RT) coding regions, sampled from 2011 to 2017, from naive patients in Spedali Civili Hospital, Brescia, Italy. Subtyping was performed by using a combination of different tools<br />the phylogenetic analysis with a structured coalescence model and Makarov Chain Monte Carlo was used on the datasets, to determine clusters and evolution. We detected 304 (43%) patients infected with HIV-1 non-B variants, of which only 293 sequences were available, with four pure subtypes and five recombinant forms<br />subtype F1 (17%) and CRF02_AG (51.1%) were most common. Twenty-five transmission clusters were identified, three of which included &gt<br />10 patients, belonging to subtype CRF02_AG and subtype F. Most cases of alleged transmission were between heterosexual couples. Probably due to strong migratory flows, we have identified different subtypes with particular patterns of recombination or, as in the case of the subtype G (18/293, 6.1%), to a complete lack of relationship between the sequenced strains, revealing that they are all singletons. Continued HIV molecular surveillance is most important to analyze the dynamics of the boost of transmission clusters in order to implement public health interventions aimed at controlling the HIV epidemic.
- Subjects :
- 0301 basic medicine
Microbiology (medical)
Hiv epidemic
Human immunodeficiency virus (HIV)
hiv
Biology
medicine.disease_cause
phylogeny
Clusters
Epidemic
HIV
Phylogeny
Subtypes
Microbiology
Article
epidemic
Therapy naive
03 medical and health sciences
0302 clinical medicine
Data sequences
Phylogenetics
Virology
medicine
Coding region
030212 general & internal medicine
clusters
lcsh:QH301-705.5
Genetics
Phylogenetic tree
subtypes
Subtyping
030104 developmental biology
lcsh:Biology (General)
Subjects
Details
- Language :
- English
- ISSN :
- 20762607
- Volume :
- 8
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- Microorganisms
- Accession number :
- edsair.doi.dedup.....69e785a0ab795534fdf3051f00f02516