ArticleVirology journal2012
Next-generation sequencing of cervical DNA detects human papillomavirus types not detected by commercial kits.
Article in Virology journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers, 1 of them a synthesis that pooled it.
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Who cites it
37 citing papers in PubMed, 1 synthesis or guideline pooled it, 74 citations in OpenAlex.
- Pooled it
- Ensemble Deep Learning Models on Raw DNA Sequences for Viral Genome Identification in Human Samples.Sensors (Basel, Switzerland) · 2026Article
- Article
- Human papillomavirus spectrum of HPV-infected women in Nigeria: an analysis by next-generation sequencing and type-specific PCR.Virology journal · 2023Article
- Prevalence and distribution of selected cervical human papillomavirus types in HIV infected and HIV uninfected women in South Africa, 1989-2021: A narrative review.Southern African journal of infectious diseases · 2022Review
- Explainable deep neural networks for novel viral genome prediction.Applied intelligence (Dordrecht, Netherlands) · 2022Article
- The genetic diversity of "papillomavirome" in bovine teat papilloma lesions.Animal microbiome · 2021Article
- Nested PCR followed by NGS: Validation and application for HPV genotyping of Tunisian cervical samples.PloS one · 2021Article
- Article
- Detection of Alpha, Beta, Gamma, and Unclassified Human Papillomaviruses in Cervical Cancer Samples From Mexican Women.Frontiers in cellular and infection microbiology · 2020Article
- A rigorous exploration of anal HPV genotypes using a next-generation sequencing (NGS) approach in HIV-infected men who have sex with men at risk for developing anal cancer.Cancer medicine · 2020Article
- Identification by high-throughput sequencing of HPV variants and quasispecies that are untypeable by linear reverse blotting assay in cervical specimens.Papillomavirus research (Amsterdam, Netherlands) · 2019Article
- ViraMiner: Deep learning on raw DNA sequences for identifying viral genomes in human samples.PloS one · 2019Article
- Machine Learning for detection of viral sequences in human metagenomic datasets.BMC bioinformatics · 2018Article
- Utility of high-throughput DNA sequencing in the study of the human papillomaviruses.Virus genes · 2018Review
- Article
- Characterisation of complete high- and low-risk human papillomavirus genomes isolated from cervical specimens in southern Brazil.Memorias do Instituto Oswaldo Cruz · 2017Article
- Genotyping of high-risk anal human papillomavirus (HPV): ion torrent-next generation sequencing vs. linear array.Virology journal · 2017Article
- Deep sequencing of HPV E6/E7 genes reveals loss of genotypic diversity and gain of clonal dominance in high-grade intraepithelial lesions of the cervix.BMC genomics · 2017Article
- Universal Human Papillomavirus Typing Assay: Whole-Genome Sequencing following Target Enrichment.Journal of clinical microbiology · 2017Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHuman papillomavirus (HPV) is the aetiological agent for cervical cancer and genital warts. Concurrent HPV and HIV infection in the South African population is high. HIV positive (+) women are often infected with multiple, rare and undetermined HPV types. Data on HPV incidence and genotype distribution are based on commercial HPV detection kits, but these kits may not detect all HPV types in HIV + women. The objectives of this study were to (i) identify the HPV types not detected by commercial genotyping kits present in a cervical specimen from an HIV positive South African woman using next generation sequencing, and (ii) determine if these types were prevalent in a cohort of HIV-infected South African women.
methodsTotal DNA was isolated from 109 cervical specimens from South African HIV + women. A specimen within this cohort representing a complex multiple HPV infection, with 12 HPV genotypes detected by the Roche Linear Array HPV genotyping (LA) kit, was selected for next generation sequencing analysis. All HPV types present in this cervical specimen were identified by Illumina sequencing of the extracted DNA following rolling circle amplification. The prevalence of the HPV types identified by sequencing, but not included in the Roche LA, was then determined in the 109 HIV positive South African women by type-specific PCR.
resultsIllumina sequencing identified a total of 16 HPV genotypes in the selected specimen, with four genotypes (HPV-30, 74, 86 and 90) not included in the commercial kit. The prevalence's of HPV-30, 74, 86 and 90 in 109 HIV positive South African women were found to be 14.6%, 12.8%, 4.6% and 8.3% respectively.
conclusionsOur results indicate that there are HPV types, with substantial prevalence, in HIV positive women not being detected in molecular epidemiology studies using commercial kits. The significance of these types in relation to cervical disease remains to be investigated.
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