Genomic characterization and molecular evolution analysis of subtype B and BF recombinant HIV-1 strains among Argentinean men who have sex with men reveal a complex scenario

Autor: María A. Pando, Leandro Roberto Jones, Jean K. Carr, María M. Avila, Cintia Cevallos, Jorge Quarleri
Jazyk: angličtina
Rok vydání: 2017
Předmět:
RNA viruses
Male
0301 basic medicine
Heredity
Ciencias de la Salud
lcsh:Medicine
HIV Infections
Pathology and Laboratory Medicine
Biochemistry
Genome
Coalescent theory
Database and Informatics Methods
Sexual and Gender Minorities
Immunodeficiency Viruses
Medicine and Health Sciences
Clade
lcsh:Science
Phylogeny
Data Management
Genetics
Multidisciplinary
Phylogenetic tree
Phylogenetic Analysis
Nucleic acids
Phylogenetics
Genetic Mapping
Medical Microbiology
Mutant Genotypes
Viral Pathogens
Viruses
purl.org/becyt/ford/3 [https]
Pathogens
Sequence Analysis
SUBTYPE
Research Article
Adult
Computer and Information Sciences
CIENCIAS MÉDICAS Y DE LA SALUD
MEN WHO HAVE SEX WITH MEN
DNA recombination
Bioinformatics
Argentina
Men WHO Have Sex with Men
Genome
Viral
Biology
Research and Analysis Methods
Microbiology
Evolution
Molecular
purl.org/becyt/ford/3.3 [https]
03 medical and health sciences
Molecular evolution
Retroviruses
Genetic variation
Humans
Evolutionary Systematics
Microbial Pathogens
DNA sequence analysis
Taxonomy
Evolutionary Biology
Genetic diversity
Salud Ocupacional
Biology and life sciences
Lentivirus
lcsh:R
Organisms
Genetic Variation
HIV
DNA
030112 virology
MOLECULAR EVOLUTION
030104 developmental biology
pol Gene Products
Human Immunodeficiency Virus
People and Places
HIV-1
Population Groupings
lcsh:Q
Sexuality Groupings
Zdroj: PLoS ONE, Vol 12, Iss 12, p e0189705 (2017)
PLoS ONE
CONICET Digital (CONICET)
Consejo Nacional de Investigaciones Científicas y Técnicas
instacron:CONICET
ISSN: 1932-6203
Popis: Currently, data on HIV-1 circulating strains among men who have sex with men (MSM) in Argentina is scarce. In South America, the distribution and the prevalence of BF recombinants are dissimilar and exhibit an underappreciated heterogeneity of recombinant structures. Here, we studied for the first time the genetic diversity of HIV-1 BF recombinants and their evolution over time through in-depth phylogenetic analysis and multiple recombination detection methods involving 337 HIV-1 nucleotide sequences (25 near full-length (NFL) and 312 partial pol gene) obtained from Argentinean MSM. The recombination profiles were studied using multiple in silico tools to characterize the genetic mosaicism, and phylogenetic approaches to infer their relationships. The evolutionary history of BF recombinants and subtype B sequences was reconstructed by a Bayesian coalescent-based method. By phylogenetic inference, 81/312 pol sequences clustered within BF clade. Of them, 46 sequences showed a genetic mosaic with CRF12_BF-like patterns, including plausible second-generation recombinants. Other CRFs_BF like (CRF17, 28, 29, 39, 42, 44, 47) and probable URFs_BF were less frequently found. Phylogenetic and recombination analyses on NFL sequences allowed a meticulous definition of new BF mosaics of genomic patterns. The Bayesian analyses pointed out quite consistent onset dates for the CRFs_BF clade based on B and F gene datasets (~1986 and ~1991 respectively). These results indicate that the CRFs_BF variants have been circulating among Argentinean MSM for about 30 years. This study reveals, through growing evidence showing the importance of MSM in the dynamics of the HIV-1 epidemic in Argentina, the coexistence of CRF12_BF-like and high diversity of strains exhibiting several BF mosaic patterns, including non-reported URFs that may reflect active clusters as potential intervention targets to hinder HIV-1 transmission. Fil: Cevallos, Cintia Gisela. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas en Retrovirus y Sida. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas en Retrovirus y Sida; Argentina Fil: Jones, Leandro Roberto. Universidad Nacional de la Patagonia "San Juan Bosco". Facultad de Ciencias Naturales - Sede Trelew; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Pando, María de los Ángeles. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas en Retrovirus y Sida. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas en Retrovirus y Sida; Argentina Fil: Carr, Jean K.. Lake Erie College of Osteopathic Medicine; Estados Unidos Fil: Ávila, María Mercedes. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas en Retrovirus y Sida. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas en Retrovirus y Sida; Argentina Fil: Quarleri, Jorge Fabian. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas en Retrovirus y Sida. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas en Retrovirus y Sida; Argentina
Databáze: OpenAIRE
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