New method for automatic identification and typing of single and multiple superimposed human papillomavirus sequences

This study of specimens of human papillomaviruses (HPV) through HPV-specifi c polymerase chain reaction (PCR), followed by direct sequencing, resulted in 11% (38/354) superimposed HPV sequences, signifying coinfection with mor e than one HPV type. To address the diagnostic problem that these superimpo sed ("degenerated," overlapping) sequences pose, the authors created a papi llomavirus database in Microsoft Excel (Microsoft Corporation, Redmond, WA, U.S.A.) and Corel Quattro Pro 9 (Corel Corporation, Ottawa, Ontario, Canad a) formats, retrievable from http://www2.crosswinds.net/similar to crosswin dswatson/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 r eadily identified from a single input; (2) the search is restricted to the currently known 121 PV types, which speeds up the typing; (3) the most comm on HPV sequencing artifacts are included for quick detection; (4) there is no proprietary code and the database could be easily improved; (5) HPV sequ ence identification does not require internet connection; and (6) new HPV t ypes could be easily detected This method allowed resolution of all but 1 o f 354 HPV-positive specimens. From 38 superimposed HPV sequences, this meth od identified one known HPV type (3 specimens), two HPV types (30 specimens ) and three HPV types (4 specimens).