Identification of New HIV-1 Circulating Recombinant Forms CRF81_cpx and CRF99_BF1 in Central Western Brazil and of Unique BF1 Recombinant Forms

Frontiers in Microbiology
Monica Nogueira Guarda ReisMariane Martins Araújo Stefani

Abstract

Intersubtype recombinants classified as circulating recombinant forms (CRFs) or unique recombinant forms (URFs) have been shown to play an important role in the complex and dynamic Brazilian HIV/AIDS epidemic. Previous pol region studies (2003-2013) in 828 patients from six states from Central Western, Northern and Northeastern Brazil reported variable rates of BF1, F1CB, BC, and CF1 mosaics. In this study HIV-1 subtype diversity BF1, F1CB, BC, and CF1 recombinants in pol were analyzed. Full/near-full/partial genome sequences were generated from F1CB and BF1 recombinants. Genomic DNA extracted from whole blood was used in nested-PCR to amplify four overlapping fragments encompassing the full HIV-1 genome. Phylogenetic trees were generated using the neighbor-joining/NJ method (MEGA 6.0). The time of the most recent common ancestor (TMRCA) of F1CB and BF1 clades was estimated using a Bayesian Markov Chain Monte Carlo approach (BEAST v1.8; BEAGLE). Bootscanning was used for recombination analyses (Simplot v3.5.1); separate NJ phylogenetic analysis of fragments confirmed subtypes. The phylogenetic analyses of protease/reverse-transcriptase sequences in 828 patients revealed 76% subtype B (n = 629), 6.4% subtype C (n = 53), 4.2% sub...Continue Reading

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Citations

Apr 20, 2019·Frontiers in Microbiology·Elena DelgadoUNKNOWN Spanish Group for the Study of New HIV Diagnoses
Dec 8, 2020·Colloids and Surfaces. B, Biointerfaces·Sarjana YadavJ P Singh
Jul 17, 2021·The Brazilian Journal of Infectious Diseases : an Official Publication of the Brazilian Society of Infectious Diseases·Myuki Alfaia Esashika CrispimMariane Martins de Araujo Stefani
Dec 7, 2021·Frontiers in Microbiology·Joan BacquéMichael M Thomson
Nov 7, 2020·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Matías CastellsRodney Colina

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Datasets Mentioned

BETA
MH986018
KX888281
KX888291

Methods Mentioned

BETA
PCR

Software Mentioned

BLAST
BioEdit
DAMBE
FigTree
Tracer
BEAST
BEAGLE
Clustal X
Basic Local Alignment Search Tool ( BLAST )
TreeAnnotator

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