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Identification of high-risk human papillomavirus isolates circulating in Nigeria and phylogenetic analysis based on the virus essential protein

  • Original Article
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Indian Journal of Gynecologic Oncology Aims and scope Submit manuscript

Abstract

Purpose

Human papillomavirus detection is crucial in determining preventive approach in cervical cancer. Different HPV genotypes have been reported worldwide and have shown variations with respect to geographic location and oncogenic capabilities. We aimed to conduct molecular characterization and phylogenetic analysis of human papillomavirus (HPV) in Northern Nigeria, to guide public health intervention.

Methods

Cervical smear samples were collected from 148 consenting subjects attending different Hospitals in Northern Nigeria. It was stained with Papanicolaou method and processed for molecular detection of HPV. Isolates of HPV were sequenced targeting HPVL1 gene. The sequences were analysed for single-nucleotide polymorphism. HPV variant lineages and relatedness was determined by phylogenetic analysis.

Results

The result of the present study showed that 26.4% (34) of the subjects had HPV infection. The result of the cytodiagnosis showed that 29.4% (10/34) had normal cytology, 23.5% (8/34) had ASCUS, and 20.6% (7/34) had LSIL, while those having HSIL and SCC accounts for 20.6% (7/34) and 5.9% (2/34), respectively. The result for sequence analysis shows about fifteen different circulating genotypes in Northern Nigeria. Out of these, HPV 16 has the highest frequency (20.6%), while HPV 11, 70, 18, 31, 33, 35, 52, 56 and 7 has the least frequency (2.9%) each. Total of 21 single-nucleotide polymorphisms were detected, out of which 15 are synonymous, while 6 are non-synonymous mutations. Phylogenetic analysis of HPV genotypes using maximum likelihood method showed that majority of HPV genotypes from Nigeria clustered with two undetermined lineages. Pairwise distance estimation of some sequences from this study and some reference sequence revealed a distance ranging from 0.0082 to 2.0994, indicating that the sequences are majorly closely related.

Conclusion

The present study provided important data about molecular epidemiology, characteristics, phylogeny and polymorphism which will aid in further studies that will advance in-depth understanding of the viral molecular epidemiology and possibly policy on public health intervention.

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Data Availability

All data and information regarding this manuscript will be made available on request.

Abbreviations

HPV:

Human papillomavirus

HR-HPV:

High-risk human papillomavirus

LR-HPV:

Low-risk human papillomavirus

SNP:

Single-nucleotide polymorphism

ASCUS:

Atypical squamous cells of undetermined significance

LSIL:

Low-grade squamous intraepithelial lesion

HSIL:

High-grade squamous intraepithelial lesion

PCR:

Polymerase chain reaction

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Acknowledgements

The authors gratefully acknowledge MLS. Sani Aliyu Mohammed, Dr. Yusuf M. Abdullahi, Dr. Aliyu Ibrahim Lawan and Dr. Aliyu Bala Umar for their useful contributions towards this research.

Funding

This research did not receive any specific grant from funding agencies in the public, commercial or not-for-profit sectors.

Author information

Authors and Affiliations

  1. Medical Virology/Immunology Unit, Department of Medical Laboratory Science, Faculty of Allied Health Sciences, Bayero University Kano, P.M.B. 3011, Kano, Nigeria

    Kabir Imam Malik, Bala Jamilu Abubakar, Yusuf Lukman, Kumurya Abdulhadi Sale, Bulama Hafsat Alkali, Abdulkadir Saidu, Doro Aliyu Bala, Audu Umoru & Aliyu Isah Abubakar

  2. Department of Microbiology, Faculty of Basic Medical Sciences, Bayero University Kano, P.M.B. 3011, Kano, Nigeria

    Dutsinma Usman Aliyu

  3. Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Usmanu Danfodiyo University Sokoto, P.M.B. 2346, Sokoto, Nigeria

    Nafi’u Lawal

Authors
  1. Kabir Imam Malik
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  11. Aliyu Isah Abubakar
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Contributions

KI, DU and AIA presented the methods, carryout the experiment, analysed the data and wrote the manuscript, KI, KA, BJ and AIA, conceptualized the work, supervised and approved the manuscript, and KI, YL, BH, AS, DA, NL and AU, performed laboratory work. All authors approved the manuscript as submitted.

Corresponding author

Correspondence to Aliyu Isah Abubakar.

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Conflict of interest

The authors declared that they have no conflict of interest.

Ethics Approval

Ethical approval was obtained from the research and ethics committee of the hospitals from which the study subjects were recruited.

Informed Consent

Samples were collected from consenting individuals.

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Consent to publish findings was obtained from the study subjects.

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Malik, K.I., Aliyu, D.U., Abubakar, B.J. et al. Identification of high-risk human papillomavirus isolates circulating in Nigeria and phylogenetic analysis based on the virus essential protein. Indian J Gynecol Oncolog 19, 87 (2021). https://doi.org/10.1007/s40944-021-00587-9

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  • DOI: https://doi.org/10.1007/s40944-021-00587-9

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