Deep sequencing of HIV-1 near full-length proviral genomes identifies high rates of BF1 recombinants including two novel circulating recombinant forms (CRF) 70_BF1 and a disseminating 71_BF1 among blood donors in Pernambuco, Brazil.
BACKGROUND
The findings of frequent circulation of HIV-1 subclade F1 viruses and the scarcity of BF1 recombinant viruses based on pol subgenomic fragment sequencing among blood donors in Pernambuco (PE), Northeast of Brazil, were reported recently. Here, we aimed to determine whether the classification of these strains (n = 26) extends to the whole genome sequences.


METHODS
Five overlapping amplicons spanning the HIV near full-length genomes (NFLGs) were PCR amplified from peripheral blood mononuclear cells (PBMCs) of 26 blood donors. The amplicons were molecularly bar-coded, pooled, and sequenced by Illumina paired-end protocol. The prevalence of viral variants containing drug resistant mutations (DRMs) was compared between plasma and PBMCs.


RESULTS
Of the 26 samples studied, 20 NFLGs and 4 partial fragments were de novo assembled into contiguous sequences and successfully subtyped. Two distinct BF1 recombinant profiles designated CRF70_BF1 and CRF71_BF1, with 4 samples in profile I and 11 in profile II were detected and thus constitute two novel recombinant forms circulating in PE. Evidence of dual infections was detected in four patients co-infected with distinct HIV-1 subtypes. According to our estimate, the new CRF71_BF1 accounts for 10% of the HIV-1 circulating strains among blood donors in PE. Discordant data between the plasma and PBMCs-virus were found in 15 of 24 donors. Six of these strains displayed major DRMs only in PBMCs and four of which had detectable DRMs changes at prevalence between 1-20% of the sequenced population.


CONCLUSIONS
The high percentage of the new RF71_BF1 and other BF1 recombinants found among blood donors in Pernambuco, coupled with high rates of transmitted DRMs and dual infections confirm the need for effective surveillance to monitor the prevalence and distribution of HIV variants in a variety of settings in Brazil.
Virology Department, São Paulo Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil.
Rodrigo
R
Pessôa
Virology Department, São Paulo Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil.
Jaqueline Tomoko
JT
Watanabe
Virology Department, São Paulo Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil.
Paula
P
Calabria
Virology Department, São Paulo Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil.
Alvina Clara
AC
Felix
Pernambuco State Center of Hematology and Hemotherapy, Recife, Pernambuco, Brazil.
Paula
P
Loureiro
Department of Infectious Disease/Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil.
Ester C
EC
Sabino
Blood Systems Research Institute, San Francisco, California, United States of America.
Michael P
MP
Busch
Clinical Laboratory, Department of Pathology, Hospital das Clínicas, School of Medicine, University of São Paulo, São Paulo, Brazil.
Sabri S
SS
Sanabani
D001782:Blood Donors; D001938:Brazil / Q000453:epidemiology; D024882:Drug Resistance, Viral / Q000235:genetics; D016679:Genome, Viral; D005838:Genotype; D015658:HIV Infections / Q000453:epidemiology / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008969:Molecular Sequence Data; D009154:Mutation; D010802:Phylogeny; D011533:Proviruses; D016865:Reassortant Viruses / Q000235:genetics; D011995:Recombination, Genetic