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Analysis of the genomic diversity of human papillomavirus type 31 in cervical samples reveals the presence of novel sublineages in clade C

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Abstract

Human papillomavirus 31 (HPV31) is the fourth most frequent high-risk HPV (HR-HPV) genotype identified in cervical cancer (CC) worldwide and in Mexico. It has been recently classified into three lineages (A, B, and C) and eight sublineages (A1, A2, B1, B2, and C1 – C4). Here, we report the complete genomic sequences of 14 HPV31 isolates from cervical samples, and these were compared with viral genome sequences from the GenBank database for phylogenetic and genetic distance analysis. The formation of two novel clades within the C lineage (proposed as C5 and C6) was observed, with a well-defined variant-specific mutational pattern. The smallest average pairwise distance was 0.71% for lineages A and B, 0.94% for lineages A and C, and 1.01% for lineages B and C, and between sublineages, these values were 0.21% for clade A, 0.29% for clade B, and 0.24% for clade C. The isolates were grouped into the sublineages A1, B2, C1-C3, and C6. This is the first report on the whole-genome diversity of HPV31 in Mexico.

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Data availability

Genome sequences generated in the current study were deposited in the GenBank database under accession numbers MZ509095-MZ509108.

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Acknowledgments

The authors express their gratitude to Laboratorio Estatal de Salud Pública (LESP) de Jalisco for the residual clinical samples provided. Fabiola Garcés, Ernesto Ramírez, and Noé Escobar received support from Sistema Nacional de Investigadores (SNI), CONACyT.

Funding

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

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Authors and Affiliations

  1. Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) “Dr. Manuel Martínez Báez”, Secretaría de Salud, Mexico City, Mexico

    David Esaú Fragoso-Fonseca, Brenda Berenice Trujillo-Salgado, Rita Teresita Manuell-Barrios, Fabiola Garcés-Ayala, Juan Carlos del Mazo-López, Lucía Hernández-Rivas, José Ernesto Ramírez-González & Noé Escobar-Escamilla

  2. Laboratorio de Bioinformática Genómica, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Mexico City, Mexico

    David Esaú Fragoso-Fonseca & Alfonso Méndez-Tenorio

  3. Laboratorio de Investigación Clínica y Ambiental, ENCB, IPN, Mexico City, Mexico

    Ubaldo Emilio Ruiz-Hernández

  4. Facultad de Ciencia y Tecnología, Universidad Simón Bolívar, Mexico City, Mexico

    Brenda Berenice Trujillo-Salgado, José Ernesto Ramírez-González & Noé Escobar-Escamilla

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  1. David Esaú Fragoso-Fonseca
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Contributions

DF and UR wrote the first draft of the manuscript. DF and NE contributed to the study conception, design, organization and supervision. BT, RM, FG, and JdM performed methodology, data collection, and formal analysis. LH and ER contributed to resource management. AM reviewed the manuscript for appropriate academic content. All authors reviewed critically, commented on previous versions, and approved the final manuscript.

Corresponding author

Correspondence to Noé Escobar-Escamilla.

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Conflict of interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The findings and conclusions in this report are those of the authors and do not necessarily represent the official opinion of the Secretaría de Salud in Mexico.

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This article does not contain any studies with human participants performed by any of the authors.

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Handling Editor: Zhongjie Shi.

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Fragoso-Fonseca, D.E., Ruiz-Hernández, U.E., Trujillo-Salgado, B.B. et al. Analysis of the genomic diversity of human papillomavirus type 31 in cervical samples reveals the presence of novel sublineages in clade C. Arch Virol 167, 2795–2800 (2022). https://doi.org/10.1007/s00705-022-05589-2

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