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Signature sequence validation of human papillomavirus type 16 (HPV-16) in clinical specimens
| Content Provider | Semantic Scholar |
|---|---|
| Author | Lee, Sin Hang Vigliotti, Veronica S. Pappu, Suri |
| Copyright Year | 2010 |
| 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. |
| Starting Page | 235 |
| Ending Page | 239 |
| Page Count | 5 |
| File Format | PDF HTM / HTML |
| DOI | 10.1136/jcp.2009.069401 |
| PubMed reference number | 19858529 |
| Journal | Medline |
| Volume Number | 63 |
| Alternate Webpage(s) | http://jcp.bmj.com/content/jclinpath/63/3/235.full.pdf |
| Alternate Webpage(s) | https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/fe/3a/jcp069401.PMC2921263.pdf |
| Alternate Webpage(s) | http://ftp.ncbi.nlm.nih.gov/pub/pmc/fe/3a/jcp069401.PMC2921263.pdf |
| Alternate Webpage(s) | http://europepmc.org/articles/pmc2921263?pdf=render |
| Journal | Journal of clinical pathology |
| Language | English |
| Access Restriction | Open |
| Content Type | Text |
| Resource Type | Article |
