Presence of HPV APOBEC-related Minority Variants in HPV16 Genomes from Anal and Cervical Samples but not in HPV52 and HPV58

Presence of HPV APOBEC-related Minority Variants in HPV16 Genomes from Anal and Cervical Samples... Abstract Background The aim of this study was to investigate the presence of minority variants (MV) in high-risk Human Papillomavirus types (hrHPV16, HPV52, HPV58) from cervical and anal smears. Methods Whole HPV genome ultra-deep sequencing (UDS) was performed on cervical and anal smears collected during patients' follow-up. Bioinformatics analyses were performed using Bowtie2® (Geneious®). Results We assessed 55 HPV16+, 20 HPV52+ and 17 HPV58+ samples, with significant differences in patient characteristics for the two anatomic sites. HPV16 MV were detected in 20 samples (36%), with no difference between cervical and anal samples. We did not find association between the presence of MV and cyto-virological parameters. Seven HPV16 genomes (13%) were APOBEC-edited. Among the cervical HPV16 samples, most MV (55%) resulted from APOBEC-related mutations. MV were detected in 10 HPV52 (50%) and 12 HPV58 (71%) samples, with no difference between cervical and anal samples. No APOBEC-related mutations were found on HPV58 or HPV52 genomes. Conclusions Overall, hrHPV MV were found in about half of all cases both in anal and cervical samples. Interestingly, we reported for the first time a differential impact of APOBEC3 mutagenic activity depending on hrHPV type. HPV, minority viral variants, ultra-deep sequencing, anal smears, APOBEC3 © The Author(s) 2018. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com. This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/about_us/legal/notices) http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png The Journal of Infectious Diseases Oxford University Press

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Publisher
Oxford University Press
Copyright
© The Author(s) 2018. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.
ISSN
0022-1899
eISSN
1537-6613
D.O.I.
10.1093/infdis/jiy287
Publisher site
See Article on Publisher Site

Abstract

Abstract Background The aim of this study was to investigate the presence of minority variants (MV) in high-risk Human Papillomavirus types (hrHPV16, HPV52, HPV58) from cervical and anal smears. Methods Whole HPV genome ultra-deep sequencing (UDS) was performed on cervical and anal smears collected during patients' follow-up. Bioinformatics analyses were performed using Bowtie2® (Geneious®). Results We assessed 55 HPV16+, 20 HPV52+ and 17 HPV58+ samples, with significant differences in patient characteristics for the two anatomic sites. HPV16 MV were detected in 20 samples (36%), with no difference between cervical and anal samples. We did not find association between the presence of MV and cyto-virological parameters. Seven HPV16 genomes (13%) were APOBEC-edited. Among the cervical HPV16 samples, most MV (55%) resulted from APOBEC-related mutations. MV were detected in 10 HPV52 (50%) and 12 HPV58 (71%) samples, with no difference between cervical and anal samples. No APOBEC-related mutations were found on HPV58 or HPV52 genomes. Conclusions Overall, hrHPV MV were found in about half of all cases both in anal and cervical samples. Interestingly, we reported for the first time a differential impact of APOBEC3 mutagenic activity depending on hrHPV type. HPV, minority viral variants, ultra-deep sequencing, anal smears, APOBEC3 © The Author(s) 2018. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com. This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/about_us/legal/notices)

Journal

The Journal of Infectious DiseasesOxford University Press

Published: May 17, 2018

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