Characterization of novel recombinant HIV-1 genomes using the branching index.
We have characterized six novel genomes of human immunodeficiency virus type 1 (HIV-1) sampled from individuals infected in Uganda and former Zaire. Four isolates (SE6954, SE8603, UG035, and UG266) had clear recombination patterns that included subtypes A1, D and C. The two remaining strains (SE8646 and SE9010) also appeared to be recombinant but had a more complex pattern. To facilitate the classification of these two genomes we developed a metric, the branching index, for characterization of "problematic" sequence fragments that associate to a subtype cluster with a high bootstrap value but are only distantly related to the reference sequences. The branching index is able to signal when parental representatives may be missing and a subtype classification thus is not meaningful. Several fragments of SE8646 and SE9010 had a branching index below the subtype defining cutoff value (0.55) and, therefore, these genomes could not be unequivocally classified. The branching index, with a cutoff value defined from analyses of HIV-1 reference sequences, may be a useful approach not only for more conservative classifications of HIV-1 subtypes but also for analyzing relationships among other types of sequences.
Wilbe
Karin
K
Department of Virology, Swedish Institute for Infectious Disease Control, SE-171 82, Solna, Sweden. karin.wilbe@smi.ki.se
Salminen
Mika
M
Laukkanen
Tiina
T
McCutchan
Francine
F
Ray
Stuart C
SC
Albert
Jan
J
Leitner
Thomas
T
D019143:Evolution, Molecular; D016679:Genome, Viral; D015658:HIV Infections / Q000821:virology; D015497:HIV-1 / Q000145:classification* / Q000235:genetics; D006801:Humans; D010802:Phylogeny; D011995:Recombination, Genetic; D012015:Reference Standards