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

Abstract

BackgroundThe 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.MethodsFive 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.ResultsOf 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.ConclusionsThe 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.

Frequency of coreceptor tropism in PBMC samples from HIV-1 recently infected blood donors by massively parallel sequencing: the REDS II study

“…The near full-length genomes and/or larger fragments of the 45 V3 MPS data used in this study have recently been described for their genetic variability [ 23 ]. This analysis indicated that 28 (62.2 %) were subtype B sequences, 11 (24.4 %) BF1 recombinants, 2 (4.4 %) BC recombinants, 1 (2.2 %) were BC and BCF1 each, 1 (2.2 %) CRF45_cpx, and 1 (2.2 %) were the newly described CRF70_BF1 [ 30 ]. The tropism predictions, FPR values, and V3 net charges are shown in Table 1 .…”

Quasispecies Analyses of the HIV-1 Near-full-length Genome With Illumina MiSeq

“…As a comparative method, we applied the simple quality-filtering correction method reported by others (Dudley et al, 2012 ; Gall et al, 2012 ; Pessoa et al, 2014 ) to the same pNL4-3 wt sequence reads. The quality-filtering method simply discards any nucleotides with a QS below 20 or 30 as a cut-off value (Supplementary Figure S3 ).…”

Human Immunodeficiency Virus (HIV)

“…The former subtype I is likewise a recombinant virus (CRF04_cpx) and therefore no longer contained in the A-K grouping. Up to now, more than 70 different epidemiologically stable CRF have been described [8,14,15,16], and the development of additional CRF is to be expected.…”

“…In addition to HIV-1 M:B (and especially the Brazilian subtype Bb), HIV-1 M:A, A/E (CRF01_AE), C and F are prevalent [96]. Further recombinants are found in Brazil and in neighbouring countries [16]. Two other recombinant strains of the subtypes B and F (CRF12_BF and CRF17_BF) are circulating in Argentina [110].…”