Open Access Highly Accessed Research

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

Tracy L Meiring13, Anna T Salimo3, Beatrix Coetzee5, Hans J Maree5, Jennifer Moodley4, Inga I Hitzeroth3, Michael-John Freeborough5, Ed P Rybicki13 and Anna-Lise Williamson12*

Author Affiliations

1 Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, 7925, Cape Town, South Africa

2 National Health Laboratory Service, Groote Schuur Hospital, Cape Town, 7925, South Africa

3 Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7700, South Africa

4 School of Public Health and Family Medicine, University of Cape Town, Cape Town, Observatory, 7925, South Africa

5 Department of Genetics, University of Stellenbosch, Stellenbosch, 7600, South Africa

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Virology Journal 2012, 9:164  doi:10.1186/1743-422X-9-164

Published: 16 August 2012



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.

Human papillomavirus; Human immunodeficiency virus; Next generation sequencing; Rolling circle amplification