Genomic diversity and phylogenetic relationships of human papillomavirus 16 (HPV16) in Nepal

• Published in: Infection, genetics and evolution genetics and evolution, 2016-12, Vol.46, p.7-11
• Main Authors: Makowsky, Robert, Lhaki, Pema, Wiener, Howard W., Bhatta, Madhav P., Cullen, Michael, Johnson, Derek C., Perry, Rodney T., Lama, Mingma, Boland, Joseph F., Yeager, Meredith, Ghimire, Sarita, Broker, Thomas R., Shrestha, Sadeep
• Format: Article
• Language: English
• Subjects: Cervix Uteri - virology; Cohort Studies; Female; Genome, Viral - genetics; HPV16 lineage; HPV16 sequence; HSIL; Human papillomavirus 16 - classification; Human papillomavirus 16 - genetics; Humans; Molecular Epidemiology; Nepal; Nepal - epidemiology; Papillomavirus Infections - epidemiology; Papillomavirus Infections - virology; Phylogenetic tree; Phylogeny; Uterine Diseases - epidemiology; Uterine Diseases - virology
• ISSN: 1567-1348; 1567-7257
• DOI: 10.1016/j.meegid.2016.10.004

Sequence variants in HPV16 confer differences in oncogenic potential; however, to date there have not been any HPV sequence studies performed in Nepal. The objective of this study was to characterize HPV16 viral genome sequences from Nepal compared to a reference sequence in order to determine their lineages. Additionally, we sought to determine if five High-grade Squamous Intraepithelial Lesion (HSIL) subjects were genetically distinct from the non-HSIL subjects. DNA was isolated from exfoliated cervical cells from 17 individuals in Nepal who were previously identified to be HPV16-positive. A custom HPV16 Ion Ampliseq panel of multiplexed degenerate primers was designed that generated 47 overlapping amplicons and covered 99% of the viral genome for all known HPV16 variant lineages. All sequence data were processed through a custom quality control and analysis pipeline of sequence comparisons and phylogenetic analysis. There were high similarities across the genomes, with two major indels observed in the non-coding region between E5 and L2. Compared to the PAVE reference HPV16 genome, there were up to 9, 4, 38, 27, 8, 7, 52, and 32 nucleotide variants in the E6, E7, E1, E2, E4, E5, L2, and L1 genes in the Nepalese samples, respectively. Based on sequence variation, HPV16 from Nepal falls across the A, C, and D lineages in this study. We found no evidence of genetic distinctness between HSIL and non-HSIL subjects. The evolutionary and pathological characteristics of the representative HPV16 genomes from Nepal seem similar to results from other parts of the world and provide the basis for further studies. •First report of HPV16 deep-sequencing from Nepal•HSIL subjects did not contain HPV lineages that clustered together phylogenetically•Phylogeny based on two marginalized populations from two distinct regions in Nepal•HPV16 sequences from samples were closely related to HPV lineages “A”, “C” and “D”.