Reanalysis of full-length HIV type 1 group M subtype K and sub-subtype F2 with an MS-DOS bootscanning program

Five new complete HIV-1 group M genome sequences have been published (Triqu es et al,, AIDS Res Hum Retroviruses 2000;16:139-151), One of these cluster ed consistently with subtype F sequences, while two others were identified as representatives of a subcluster within the subtype F clade, called F2, a nd the two remaining sequences were described as a new subtype K. We reanal yzed these sequences by means of bootscanning and phylogeny, using a newly developed MS-DOS bootscanning program. Although our analysis does not contr adict the existence of the new subtype K, it also indicates that in some re gions the F2 sequences do not cluster with the F1 clade. This suggests that some fragments in the F2 sequences have an uncertain origin, and care shou ld be taken when F2 sequences are used in analyses.