Next-generation sequencing of cervical DNA detects human papillomavirus types not detected by commercial kits

dc.contributor.authorMeiring, Tracyen_ZA
dc.contributor.authorSalimo, Annaen_ZA
dc.contributor.authorCoetzee, Beatrixen_ZA
dc.contributor.authorMaree, Hansen_ZA
dc.contributor.authorMoodley, Jenniferen_ZA
dc.contributor.authorHitzeroth, Ingaen_ZA
dc.contributor.authorFreeborough, Michael-Johnen_ZA
dc.contributor.authorRybicki, Eden_ZA
dc.contributor.authorWilliamson, Anna-Liseen_ZA
dc.date.accessioned2015-11-18T03:58:44Z
dc.date.available2015-11-18T03:58:44Z
dc.date.issued2012en_ZA
dc.description.abstractBACKGROUND: Human 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. METHODS: Total 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. RESULTS: Illumina 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. CONCLUSIONS: Our 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.en_ZA
dc.identifier.apacitationMeiring, T., Salimo, A., Coetzee, B., Maree, H., Moodley, J., Hitzeroth, I., ... Williamson, A. (2012). Next-generation sequencing of cervical DNA detects human papillomavirus types not detected by commercial kits. <i>Virology Journal</i>, http://hdl.handle.net/11427/15080en_ZA
dc.identifier.chicagocitationMeiring, Tracy, Anna Salimo, Beatrix Coetzee, Hans Maree, Jennifer Moodley, Inga Hitzeroth, Michael-John Freeborough, Ed Rybicki, and Anna-Lise Williamson "Next-generation sequencing of cervical DNA detects human papillomavirus types not detected by commercial kits." <i>Virology Journal</i> (2012) http://hdl.handle.net/11427/15080en_ZA
dc.identifier.citationMeiring, T. L., Salimo, A. T., Coetzee, B., Maree, H. J., Moodley, J., Hitzeroth, I. I., ... & Williamson, A. L. (2012). Next-generation sequencing of cervical DNA detects human papillomavirus types not detected by commercial kits. Virol J, 9(164), 422X-9.en_ZA
dc.identifier.ris TY - Journal Article AU - Meiring, Tracy AU - Salimo, Anna AU - Coetzee, Beatrix AU - Maree, Hans AU - Moodley, Jennifer AU - Hitzeroth, Inga AU - Freeborough, Michael-John AU - Rybicki, Ed AU - Williamson, Anna-Lise AB - BACKGROUND: Human 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. METHODS: Total 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. RESULTS: Illumina 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. CONCLUSIONS: Our 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. DA - 2012 DB - OpenUCT DO - 10.1186/1743-422X-9-164 DP - University of Cape Town J1 - Virology Journal LK - https://open.uct.ac.za PB - University of Cape Town PY - 2012 T1 - Next-generation sequencing of cervical DNA detects human papillomavirus types not detected by commercial kits TI - Next-generation sequencing of cervical DNA detects human papillomavirus types not detected by commercial kits UR - http://hdl.handle.net/11427/15080 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/15080
dc.identifier.urihttp://dx.doi.org/10.1186/1743-422X-9-164
dc.identifier.vancouvercitationMeiring T, Salimo A, Coetzee B, Maree H, Moodley J, Hitzeroth I, et al. Next-generation sequencing of cervical DNA detects human papillomavirus types not detected by commercial kits. Virology Journal. 2012; http://hdl.handle.net/11427/15080.en_ZA
dc.language.isoengen_ZA
dc.publisherBioMed Central Ltden_ZA
dc.publisher.departmentInstitute of Infectious Disease and Molecular Medicineen_ZA
dc.publisher.facultyFaculty of Health Sciencesen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution Licenseen_ZA
dc.rights.holder2012 Meiring et al.; licensee BioMed Central Ltd.en_ZA
dc.rights.urihttp://creativecommons.org/licenses/by/2.0en_ZA
dc.sourceVirology Journalen_ZA
dc.source.urihttp://virologyj.biomedcentral.com/en_ZA
dc.subject.otherHuman papillomavirusen_ZA
dc.subject.otherHuman immunodeficiency virusen_ZA
dc.subject.otherNext generation sequencingen_ZA
dc.subject.otherRolling circle amplificationen_ZA
dc.titleNext-generation sequencing of cervical DNA detects human papillomavirus types not detected by commercial kitsen_ZA
dc.typeJournal Articleen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
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