Near full-length genome analysis of low prevalent human immunodeficiency virus type 1 subclade F1 in São Paulo, Brazil

Sanabani, Sabri Saeed; Pastena, Évelyn Regina de Souza; Neto, Walter Kleine; Barreto, Cristine Chaves; Ferrari, Kelly T.; Kalmar, E.; Ferreira, Suzete Cleusa; Sabino, Éster Cerdeira

doi:10.1186/1743-422x-6-78

Cited by 11 publications

(13 citation statements)

References 51 publications

(45 reference statements)

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“…For example, the previous report identified six donors infected with Subclade F1, all of which turned out to be recombinants when their NFLGs were sequenced. These results are in accordance with the conclusions that most, if not all, HIV‐1 Subclade F1 strains circulating in Brazil may contain recombinant genomes that are unrecognized by partial sequencing. The lack of prototypic Subclade F1 reported here lends further support to the reduced rate of transmission of this subclade estimated in a previous study .…”

Section: Discussionsupporting

confidence: 91%

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

et al. 2014

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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.

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Section: Discussionsupporting

confidence: 91%

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

et al. 2014

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“…Use of WGS for molecular epidemiology has been limited to a handful of studies involving primarily viral pathogens, including linkage of hepatitis C virus strains in humans and wild boars ( 24 ); genotyping of HIV strains by using near full-length genomes ( 25 ); and molecular epidemiology of influenza A (H5N1) virus in waterfowl outbreaks ( 26 ). A more recent study used next gen sequencing to link hospital-associated isolates of methicillin-resistant Staphylococcus aureus in Thailand ( 3 ).…”

Section: Discussionmentioning

confidence: 99%

Next-Generation Sequencing ofCoccidioides immitisIsolated during Cluster Investigation

Engelthaler¹,

Chiller²,

Schupp³

et al. 2011

Emerg. Infect. Dis.

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Next-generation sequencing enables use of whole-genome sequence typing (WGST) as a viable and discriminatory tool for genotyping and molecular epidemiologic analysis. We used WGST to confirm the linkage of a cluster of Coccidioides immitis isolates from 3 patients who received organ transplants from a single donor who later had positive test results for coccidioidomycosis. Isolates from the 3 patients were nearly genetically identical (a total of 3 single-nucleotide polymorphisms identified among them), thereby demonstrating direct descent of the 3 isolates from an original isolate. We used WGST to demonstrate the genotypic relatedness of C. immitis isolates that were also epidemiologically linked. Thus, WGST offers unique benefits to public health for investigation of clusters considered to be linked to a single source.

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“…To make complementary DNAs, the extracted RNA samples were subjected to reverse transcription PCR using SuperScript III (Invitrogen, Carlsbad, CA). Both cDNAs and proviral DNAs were used as the PCR template, as this allowed amplification of the NFLGs from five overlapping fragments as previously described [24], [25], [26]. Amplification reactions were done in duplicate to eliminate PCR artifacts, ensuring that sequenced full-length genomes were not assembled from heterogeneous DNA targets.…”

Section: Methodsmentioning

confidence: 99%

Variability of HIV-1 Genomes among Children and Adolescents from São Paulo, Brazil

et al. 2013

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BackgroundGenetic variability is a major feature of the human immunodeficiency virus type 1 (HIV-1) and considered the key factor to frustrating efforts to halt the virus epidemic. In this study, we aimed to investigate the genetic variability of HIV-1 strains among children and adolescents born from 1992 to 2009 in the state of Sao Paulo, Brazil.MethodologyPlasma and peripheral blood mononuclear cells (PBMC) were collected from 51 HIV-1-positive children and adolescents on ART followed between September 1992 and July 2009. After extraction, the genetic materials were used in a polymerase chain reaction (PCR) to amplify the viral near full length genomes (NFLGs) from 5 overlapped fragments. NFLGs and partial amplicons were directly sequenced and data were phylogenetically inferred.ResultsOf the 51 samples studied, the NFLGs and partial fragments of HIV-1 from 42 PBMCs and 25 plasma were successfully subtyped. Results based on proviral DNA revealed that 22 (52.4%) patients were infected with subtype B, 16 (38.1%) were infected with BF1 mosaic variants and 4 (9.5%) were infected with sub-subtype F1. All the BF1 recombinants were unique and distinct from any previously identified unique or circulating recombinant forms in South America. Evidence of dual infections was detected in 3 patients coinfected with the same or distinct HIV-1 subtypes. Ten of the 31 (32.2%) and 12 of the 21 (57.1%) subjects with recovered proviral and plasma, respectively, protease sequences were infected with major mutants resistant to protease inhibitors. The V3 sequences of 14 patients with available sequences from PBMC/or plasma were predicted to be R5-tropic virus except for two patients who harbored an X4 strain.ConclusionsThe high proportion of HIV-1 BF1 recombinant, coinfection rate and vertical transmission in Brazil merits urgent attention and effective measures to reduce the transmission of HIV among spouses and sex partners.

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Near full-length genome analysis of low prevalent human immunodeficiency virus type 1 subclade F1 in São Paulo, Brazil

Abstract: All together, our findings showed a surprisingly low prevalence rate of subclade F1 in Brazil and suggest that these isolates originated in Central Africa and subsequently introduced to South America.

Cited by 11 publications

References 51 publications

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

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

Next-Generation Sequencing ofCoccidioides immitisIsolated during Cluster Investigation

Variability of HIV-1 Genomes among Children and Adolescents from São Paulo, Brazil

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