(CRF) Reference Sequences, 2005

Recently there has been intensive activity in the area of discovering new HIV-1 CRFs, although many of the new CRFs have not yet been published (Table 1). In addition, there have been suggestions of new sub-subtypes and potentially a new subtype (10, 11). The classification of new HIV-1 sequences follows the proposed HIV nomenclature guidelines (13, 14). When classifying new sequences, the HIV-1 subtyping reference set is often used. The set of reference sequences has not been modified since 2001, and thus it is time for an update. The criteria for updating the reference set were: 1. Four sequences of each HIV-1 group, subtype and sub-subtype, are included, if available. 2. The four sequences should roughly describe the diversity of each class as an effective popula-tion. 3. Further selection criteria for reference sequences were: a) full length genomes that cover all genes, b) no clear sign of recombinant history, c) published with a peer reviewed citation, d) recent rather than older samples, e) covered major geographic distribution, f) no sign of hypermutation, g) not synthetic, i.e., real sequences from a patient h) no extreme indels, i) viable and intact as far as known. 4. The CRFs included are now described by one sequence, the prototype of each recombination pattern. Thus the breakpoint pattern is based on the prototype, and will agree with the updated CRF page. The alignments were based on the 2004 web and compendium alignments, which were constructed using HMMER (with a model calculated on the 2003 alignment) (2). The alignment was further im-proved using SynchAlign