Longitudinal follow‐up of HPV16 sequence after cervical infection: Low intrahost variation and no correlation with clinical evolution

Abstract

Human papillomavirus (HPV) 16 exhibits different variants that may differ in their carcinogenic risk. To identify some high-risk variants, we sequenced and compared HPV16 whole genomes obtained from a longitudinal cohort of 34 HPV16-infected women who had either spontaneously cleared their infection (clearance group or "C"), or developed cervical high-grade lesions following a viral persistence (group persistence or "P"). Phylogenetic analysis of paired samples obtained at the beginning (C0 or P0) and at the end (C2 or P2) of the follow-up (median intervals between C0-C2 and between P0-P2 were 16 and 36.5 months, respectively) revealed a low genetic variability within the host compared to the genetic interhost diversity. By comparing our HPV16 sequences to a reference sequence, we observed 301 different substitutions, more often transitions (60.9%) than transversions (39.1%), that occurred throughout the viral genome, but with a low frequency in E6 and E7 oncogenes (10 and 9 substitutions), suggesting a high conservation of these genes. Deletions and insertions were mostly observed in intergenic regions of the virus. The only significant substitution found between the subgroups C2 and P2 was observed in the L2 gene (L330F), with an unclear biological relevance.

Changes in intrahost genetic diversity according to lesion severity in longitudinal HPV16 samples

“…The TaME‐seq2 protocol can however reliably detect specific SNVs with an extremely low error rate 42 . In this study, SNV mutations were found to be conserved over time for most individuals (87.5% of individuals had all SNVs conserved over time) as also reported by other studies 20,23,39 . Genome conservation through time is a good indication of a persistent infection 20 .…”

“…42 In this study, SNV mutations were found to be conserved over time for most individuals (87.5% of individuals had all SNVs conserved over time) as also reported by other studies. 20,23,39 Genome conservation through time is a good indication of a persistent infection. 20 While we observed five individuals (12.5%) losing or acquiring mutations between time points, most other SNVs in those samples remained stable over time indicating the same ongoing HPV infection.…”

“…To our knowledge, this is the first study to examine how iSNVs and APOBEC3‐induced iSNVs change over time according to lesion severity in longitudinal samples. Previous longitudinal studies have either solely focused on SNVs 20,39 or not tested for association between lesion severity and iSNVs/APOBEC3‐induced iSNVs 23 …”

“…21,22,24,25,35,38 To our knowledge, this is the first study to examine how iSNVs and APOBEC3-induced iSNVs change over time according to lesion severity in longitudinal samples. Previous longitudinal studies have either solely focused on SNVs 20,39 or not tested for association between lesion severity and iSNVs/APOBEC3-induced iSNVs. 23 Unlike cross-sectional studies, which provide a snapshot in time, analyses of longitudinal samples can provide a better understanding of the viral variability over time within an individual.…”