HIV type 1 CRF13_cpx revisited: identification of a new sequence from Cameroon and signal for subsubtype J2.

A nearly full-length genome sequence of an HIV-1 isolate originating from Cameroon, 02CM.3226MN, was found to cluster together with previously reported CRF13 sequences 96CM-4164 and 96CM-1849. Similarity plotting, bootscanning, breakpoint analysis, and phylogenetic trees confirmed similar genomic structures with almost identical breakpoint positions among these three isolates. Thus, CRF13 now fulfills the HIV-1 nomenclature requirements. A X2 analysis across all three genomes simultaneously was applied to more accurately determine breakpoints and address the uncertainty in such estimates. Some fragments were found to be difficult to classify, as indicated by a low branching index (BI), due to limited knowledge about parental and reference subtype sequences. One fragment with low BI association to reference subtype J sequences (BI = 0.27, cut-off for subtype classification >0.55) was found to be closer to J fragments of CRF11 similar to the way that A1-A2 and F1-F2 subsubtypes associate. This suggests that subtype J may need to be reclassified into subsubtypes J1 and J2. The CRF13 genome consists of fragments from subtypes A1, G, and both J1 and J2 as well as CRF01 and one region that was left unclassified.