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You are here: Home / RESEARCH . . . . / Human Papillomavirus Research / Signature sequence validation of human papillomavirus type 16 (HPV-16) in clinical specimens.

Signature sequence validation of human papillomavirus type 16 (HPV-16) in clinical specimens.

February 6, 2011 By Norma

Lee SH, Vigliotti VS, Pappu S.

J Clin Pathol. 2010 Mar;63(3):235-9. Epub 2009 Oct 26.

Abstract

AIMS: Persistent infection indicated by detection of human papillomavirus 16 (HPV-16) on repeat testing over a period of time poses the greatest cervical cancer risk. However, variants of HPV-16, HPV-31 and HPV-33 may share several short sequence homologies in the hypervariable L1 gene commonly targeted for HPV genotyping. The purpose of this study was to introduce a robust laboratory procedure to validate HPV-16 detected in clinical specimens, using the GenBank sequence database as the standard reference for genotyping.

METHODS: A nested PCR with two pairs of consensus primers was used to amplify the HPV DNA released in crude proteinase K digest of the cervicovaginal cells in liquid-based Papanicolaou cytology specimens. The positive nested PCR products were used for direct automated DNA sequencing.

RESULTS: A 48-base sequence downstream of the GP5+ priming site, or a 34-base sequence upstream thereof, was needed for unequivocal validation of an HPV-16 isolate. Selection of a 45-base, or shorter, sequence immediately downstream of the GP5+ site for Basic Local Alignment Search Tool sequence analysis invariably led to ambiguous genotyping results.

CONCLUSIONS: DNA sequence analysis may be used for differential genotyping of HPV-16, HPV-31 and HPV-33 in clinical specimens. However, selection of the signature sequence for Basic Local Alignment Search Tool algorithms is crucial to distinguish certain HPV-16 variants from other closely related HPV genotypes.

Access entire paper here.

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Filed Under: Human Papillomavirus Research Tagged With: DNA sequence analysis, genotyping, HPV

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HPV Vaccine VAERS Reports

Description 12/14/2019  TOTAL
Disabled 3,092
Deaths 523
Did Not Recover 13,072
Abnormal Smear 695
Cervical Cancer 186
Infertility 52
Life-threatening 1,001
Emergency Room 15,419
Hospitalized 6,448
Extended Hosp. Stay 304
Serious 9,497
Total Adverse Events 64,270

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