Human papillomavirus 16 sub-lineage dispersal and cervical cancer risk worldwide: Whole viral genome sequences from 7116 HPV16-positive women

Papillomavirus Res. 2019 Jun;7:67-74. doi: 10.1016/j.pvr.2019.02.001. Epub 2019 Feb 6.


Background: Human papillomavirus (HPV)16 can be separated into genetic sub-lineages (A1-4, B1-4, C1-4, D1-4) which may have differential cervical cancer risk.

Methods: A next-generation sequencing assay was used to whole-genome sequence 7116 HPV16-positive cervical samples from well-characterised international epidemiological studies, including 2076 controls, 1878 squamous cell carcinoma (SCC) and 186 adenocarcinoma/adenosquamous cell carcinoma (ADC), and to assign HPV16 sub-lineage. Logistic regression was used to estimate region-stratified country-adjusted odds ratios (OR) and 95%CI.

Results: A1 was the most globally widespread sub-lineage, with others showing stronger regional specificity (A3 and A4 for East Asia, B1-4 and C1-4 for Africa, D2 for the Americas, B4, C4 and D4 for North Africa). Increased cancer risks versus A1 were seen for A3, A4 and D (sub)lineages in regions where they were common: A3 in East Asia (OR=2.2, 95%CI:1.0-4.7); A4 in East Asia (6.6, 3.1-14.1) and North America (3.8, 1.7-8.3); and D in North (6.2, 4.1-9.3) and South/Central America (2.2, 0.8-5.7), where D lineages were also more frequent in ADC than SCC (3.2, 1.5-6.5; 12.1, 5.7-25.6, respectively).

Conclusions: HPV16 genetic variation can strongly influence cervical cancer risk. However, burden of cervical cancer attributable to different sub-lineages worldwide is largely driven by historical HPV16 sub-lineage dispersal.

Keywords: Cervical cancer; HPV carcinogenesis; HPV epidemiology; HPV genomics; HPV16; Whole virus genome sequencing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenocarcinoma / epidemiology*
  • Adenocarcinoma / virology
  • Carcinoma, Squamous Cell / epidemiology*
  • Carcinoma, Squamous Cell / virology
  • Female
  • Genetic Variation
  • Genome, Viral
  • Genotype*
  • Global Health
  • High-Throughput Nucleotide Sequencing
  • Human papillomavirus 16 / classification*
  • Human papillomavirus 16 / genetics
  • Human papillomavirus 16 / isolation & purification*
  • Humans
  • Papillomavirus Infections / complications
  • Papillomavirus Infections / epidemiology*
  • Papillomavirus Infections / virology
  • Phylogeny
  • Risk Assessment
  • Uterine Cervical Neoplasms / epidemiology*
  • Uterine Cervical Neoplasms / virology
  • Whole Genome Sequencing