New method for automatic identification identification and typing of single and multiple superimposed human papillomavirus sequences.
This study of specimens of human papillomaviruses (HPV) through HPV-specific polymerase chain reaction (PCR), followed by direct sequencing, resulted in 11% (38/354) superimposed HPV sequences, signifying coinfection with more than one HPV type. To address the diagnostic problem that these superimposed ("degenerated," overlapping) sequences pose, the authors created a papillomavirus database in Microsoft Excel (Microsoft Corporation, Redmond, WA, U.S.A.) and Corel Quattro Pro 9 (Corel Corporation, Ottawa, Ontario, Canada) formats, retrievable from http://www2.crosswinds.net/ -crosswindswatson/index.html. This sequence database is simultaneously a search and comparison tool for quick (several seconds) typing of HPV from regular and "degenerated" sequencing results. Some of the advantages of the method are as follows: (1) superimposed HPV sequences that differ in length could be readily identified from a single input; (2) the search is restricted to the currently known 127 PV types, which speeds up the typing; (3) the most common HPV sequencing artifacts are included for quick detection; (4) there is no proprietary code and the database could be easily improved; (5) HPV sequence identification does not require internet connection; and (6) new HPV types could be easily detected. This method allowed resolution of all but 1 of 354 HPV-positive specimens. From 38 superimposed HPV sequences, this method identified one known HPV type (3 specimens), two HPV types (30 specimens) and three HPV types (4 specimens).
Feoli-Fonseca
J C
JC
Département de pathologie, Faculté des études supérieures, Université de Montréal, Quebec, Canada.
Oligny
L L
LL
Yotov
W V
WV
D017931:DNA Primers / Q000737:chemistry; D015344:DNA Probes, HPV / Q000235:genetics; D004279:DNA, Viral / Q000032:analysis; D016208:Databases, Factual; D005260:Female; D006801:Humans; D027383:Papillomaviridae / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D030361:Papillomavirus Infections / Q000175:diagnosis* / Q000821:virology; D016133:Polymerase Chain Reaction / Q000379:methods; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D014412:Tumor Virus Infections / Q000175:diagnosis* / Q000821:virology
D017931:DNA Primers; D015344:DNA Probes, HPV; D004279:DNA, Viral