Identification of HPV16 Lineages in South African and Mozambican Women with Normal and Abnormal Cervical Cytology

Author:

Maueia Cremildo123ORCID,Carulei Olivia1,Murahwa Alltalents T.1ORCID,Taku Ongeziwe1,Manjate Alice2ORCID,Mussá Tufária2ORCID,Williamson Anna-Lise145ORCID

Affiliation:

1. Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa

2. Departamento de Microbiologia, Faculdade de Medicina, Universidade Eduardo Mondlane, Maputo P.O.Box 257, Mozambique

3. Instituto Nacional de Saúde, Maputo 3943, Mozambique

4. Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa

5. SAMRC Gynaecological Cancer Research Centre, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa

Abstract

Background: Human papillomavirus 16 (HPV16) is an oncogenic virus responsible for the majority of invasive cervical cancer cases worldwide. Due to genetic modifications, some variants are more oncogenic than others. We analysed the HPV16 phylogeny in HPV16-positive cervical Desoxyribonucleic Acid (DNA) samples collected from South African and Mozambican women to detect the circulating lineages. Methods: Polymerase chain reaction (PCR) amplification of the long control region (LCR) and 300 nucleotides of the E6 region was performed using HPV16-specific primers on HPV16-positive cervical samples collected in women from South Africa and Mozambique. HPV16 sequences were obtained through Next Generation Sequencing (NGS) methods. Geneious prime and MEGA 11 software were used to align the sequences to 16 HPV16 reference sequences, gathering the A, B, C, and D lineages and generating the phylogenetic tree. Single nucleotide polymorphisms (SNPs) in the LCR and E6 regions were analysed and the phylogenetic tree was generated using Geneious Prime software. Results: Fifty-eight sequences were analysed. Of these sequences, 79% (46/58) were from women who had abnormal cervical cytology. Fifteen SNPs in the LCR and eight in the E6 region were found to be the most common in all sequences. The phylogenetic analysis determined that 45% of the isolates belonged to the A1 sublineage (European variant), 34% belonged to the C1 sublineage (African 1 variant), 16% belonged to the B1 and B2 sublineage (African 2 variant), two isolates belonged to the D1–3 sublineages (Asian-American variant), and one to the North American variant. Conclusions: The African and European HPV16 variants were the most common circulating lineages in South African and Mozambican women. A high-grade squamous intraepithelial lesion (HSIL) was the most common cervical abnormality observed and linked to European and African lineages. These findings may contribute to understanding molecular HPV16 epidemiology in South Africa and Mozambique.

Funder

Swedish International Development Cooperation Agency

Wellcome Trust post-doctoral research fellowship

South African Research Chairs Initiative of the Department of Science and Technology and National Research Foundation

Publisher

MDPI AG

Reference53 articles.

1. Bruni, L., Albero, G., Serrano, B., Mena, M., Gómez, D., Muñoz, J., Bosch, F.X., de Sanjosé, S., and ICO/IARC Information Centre on HPV and Cancer (HPV Information Centre) (2019). Human Papillomavirus and Related Diseases in the World, ICO/IARC HPV Information Centre. Summary Report 17 June 2019.

2. WHO (2021). WHO Guideline for Screening and Treatment of Cervical Pre-Cancer Lesions for Cervical Cancer Prevention, WHO. [2nd ed.].

3. Bruni, L., Albero, G., Serrano, B., Mena, M., Gómez, D., Muñoz, J., Bosch, F.X., de Sanjosé, S., and ICO/IARC Information Centre on HPV and Cancer (HPV Information Centre) (2023). Human Papillomavirus and Related Diseases in Mozambique, ICO/IARC HPV Information Centre. Summary Report 10 March 2023.

4. Classification and evolution of human papillomavirus genome variants: Alpha-5 (HPV26, 51, 69, 82), Alpha-6 (HPV30, 53, 56, 66), Alpha-11 (HPV34, 73), Alpha-13 (HPV54) and Alpha-3 (HPV61);Chen;Virology,2018

5. Bruni, L., Albero, G., Serrano, B., Mena, M., Gómez, D., Muñoz, J., Bosch, F.X., de Sanjosé, S., and ICO/IARC Information Centre on HPV and Cancer (HPV Information Centre) (2019). Human Papillomavirus and Related Diseases in Africa, ICO/IARC HPV Information Centre. Summary Report 17 June 2019.

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