Enhanced detection of viral diversity using partial and near full‐length genomes of human immunodeficiency virus Type 1 provirus deep sequencing data from recently infected donors at four blood centers in Brazil

Abstract

Background Here, we report application of high-throughput near-full-length genome (NFLG) and partial HIV-1 proviral genome deep sequencing to characterize HIV in recently infected blood donors at four major blood centers in Brazil. Study Design and Methods From 2007-2011, 341 HIV+ blood donors from 4 blood centers were recruited to participate in a case control study to identify HIV risk factors and motivations to donate. Forty-seven (17 from São Paulo [SP], 8 from Minas Gerais [MG], 11 from Pernambuco [PE] and 11 from Rio de Janeiro [RJ]) were classified as recently infected based on testing by less-sensitive enzyme immunoassays. Five overlapping amplicons spanning the HIV genome were PCR amplified from peripheral blood mononuclear cells (PBMCs). The amplicons were molecularly bar-coded, pooled, and sequenced by an Illumina paired-end protocol. Results Of the 47 recently infected donor samples studied, 39 (82.9%) NFLGs and 6 (12.7%) partial fragments were de novo assembled into contiguous sequences and successfully subtyped. Subtype B was the only non-recombinant virus identified in this study and accounted for 62.2% (28/45) of samples. The remaining 37.8% (17/45) of samples showed various patterns of subtype discordance in different regions of HIV-1 genomes, indicating 2- 4 circulating recombinant subtypes derived from clades B, F and C. Fourteen samples (31.1%) from this study harbored drug resistance mutations, indicating higher rate of drug resistance among Brazilian blood donors. Conclusion Our findings revealed a high proportion of HIV-1 recombinants among recently infected blood donors in Brazil which has implications for future blood screening, diagnosis, therapy and vaccine development.

Ultra-Deep Sequencing of HIV-1 near Full-Length and Partial Proviral Genomes Reveals High Genetic Diversity among Brazilian Blood Donors

“…However, this study found an additional eight cocirculating subtypes, three CRFs, and 20.6% novel unrelated URFs. A high intersubtype diversity (28.9%) observed in this study is consistent with the diversity reported in our previous study [ 17 ] and is even higher than what has been reported in previous studies, although results were difficult to compare, because our study was based on NFLGs and larger fragments whereas previous studies in Brazil used short partial sequences [ 18 , 29 , 30 ]. The high prevalence of HIV-1 inter-subtype recombinant viruses in this group of blood donors is likely to reflect the presence of highly exposed individuals and social networks of HIV-1 transmissions in Brazil.…”

“…The overall results indicate that the rate of HIV-1 mixed infections within this Brazilian group of non-recently infected donors is higher than 2%. This estimate is lower than the rate of 12% that was recently observed by our group in 45 recently infected first-time blood donors at the same four blood centers in Brazil [ 17 ]. The low prevalence of mixed infection in our long-standing HIV-infected blood donors could indicate a protective mechanism at work, such as immune responses that evolve over time or the ability of the original virus to ward off acquisition of another.…”

“…In addition, understanding monitoring the genetic variability of HIV-1 among donors has implications for understanding transmissibility, scrutinizing the prevalence of drug and vaccine escape mutants, and for detecting and monitoring rare variants that may be newly introduced or increasing in the Brazilian donor population. We have recently reported the application of high-throughput near full-length genome (NFLG) and partial human immunodeficiency virus Type 1 (HIV-1) proviral genome massively parallel sequencing [MPS] to characterize HIV in recently infected blood donors at four major blood centers in Brazil [ 17 ]. In continuation of our previous study, here, we assessed the genetic variability of HIV-1 on a genome-wide scale in MPS data generated from 257 seropositive blood donors collected between 2007 and 2011 from four Brazilian blood centers of the REDS-II (Retrovirus Epidemiological Donor Study) international program.…”

High prevalence of HIV-1 transmitted drug-resistance mutations from proviral DNA massively parallel sequencing data of therapy-naïve chronically infected Brazilian blood donors

“…Recent findings from multiple studies reporting on the application of MPS have considerably enhanced our understanding of not only HIV biology but also viral immune escape; mother-to-child HIV transmission; and HIV epidemiology, frequency of drug-resistance variants, and viral diversity [ 18 , 19 , 22 – 27 ].…”

“…Evidence for the dissemination of drug-resistance variants in Brazil stems from reports of primary resistance in recently infected individuals (0–12.7%) as well as those with longstanding infections (5%) [ 28 – 31 ]. Recently, we reported the overall prevalence of 31.1% of transmitted resistance in massively parallel sequencing (MPS) data of the proviral pol region from treatment-naïve recently HIV-infected blood donors [ 22 ]. Here, we extended our previous study to include the analysis of the primary TDRM across the entire proviral genome using the MPS data of ARV-naïve non-recently (longstanding) infected blood donors.…”