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

Meiring, Tracy L., Salimo, Anna T., Coetzee, Beatrix, Maree, Hans J., Moodley, Jennifer, Hitzeroth, Inga I., Freeborough, Michael-John J., Rybicki, Edward P., & Williamson, Anna-Lise (2012) Next-generation sequencing of cervical DNA detects human papillomavirus types not detected by commercial kits. Virology Journal, 9(164).

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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.


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.


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.


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.

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ID Code: 54918
Item Type: Journal Article
Refereed: Yes
Additional Information: Export Date: 12 November 2012 Source: Scopus Article in Press
Keywords: Human papillomavirus; Human immunodeficiency virus; Next generation sequencing; Rolling circle amplification
DOI: 10.1186/1743-422x-9-164
ISSN: 1743-422X
Divisions: Current > QUT Faculties and Divisions > Faculty of Health
Copyright Owner: Copyright 2012 Meiring et al.; licensee BioMed Central Ltd.
Copyright Statement: This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Deposited On: 20 Nov 2012 02:46
Last Modified: 27 Nov 2013 01:12

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