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Updated: Jan 26, 2026

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
Published on: January 16, 2019
HPV16 variant analysis in primary and recurrent CIN2/3 lesions demonstrates presence of the same consensus variant
Pascal van der Weele1, Audrey J King2, Chris J L M Meijer3
1National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Antonie van Leeuwenhoeklaan 9, Bilthoven, the Netherlands; Amsterdam UMC, Vrije Universiteit, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, the Netherlands.
Introduction:
Recurrent cervical intraepithelial lesions (rCIN2/3) after treatment of CIN2/3 occur in 5-15% of cases. rCIN2/3 can result from incomplete resection of CIN2/3, where the same HPV type and variant remains present. rCIN2/3 could also occur following a new infection with a different HPV variant of the same HPV type as the initial lesion. This study investigates HPV16 consensus variants in paired HPV16 positive scrapes from baseline CIN2/3 and rCIN2/3 lesions.
Methods:
Paired HPV16 positive cervical scrapes of women with CIN2/3 at baseline and rCIN2/3 6 or 12 months after treatment were selected for whole-genome amplification and Illumina sequencing. Sequences were compared and nucleotide changes over time were characterized.
Results:
From 14 paired samples, 10 had identical consensus variants in baseline CIN2/3 and rCIN2/3. Four paired samples showed one to three nucleotide variations at recurrent disease compared to baseline.
Conclusion:
Identical or nearly identical HPV16 consensus variants were found in scrapes of paired HPV16 positive baseline CIN2/3 and rCIN2/3 lesions after treatment, suggesting no need for HPV variant analysis when the same HPV type is found in both lesions. These results argue for either incomplete excision of baseline CIN2/3 or inability of clearance of the original HPV infection.
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