The HIV Nomenclature
The HIV nomenclature has been important to our understanding of the AIDS pandemic. In particular it has implications for research including epidemiological tracking, vaccine design, and as a foundation for understanding whether there is a relationship between biology and genetic diversity. Due to the continued discovery of divergent viral strains plus the high prevalence of recombination, which obscures our ability to understand the "true" evolutionary relationships between lineages, the HIV nomenclature has the potential of becoming increasingly confusing. Thus, a meeting took place at the Santa Fe Institute, New Mexico (September 1999) to discuss HIV nomenclature. Questions that arose included: What criteria should be used to define a novel subtype? How should recombinants with the same form be named? Should subtypes "E" and "I" that appear to exist as complex genotypes with no full parental strains be called subtypes or recombinant subtypes? As a result of the discussion at the meeting, and subsequent communications, a unified proposal was created (HIV-1 Nomenclature Proposal: a Reference Guide to HIV-1 Classification by Robertson DL, Anderson J, Bradac JA, Carr JK, Foley B, Funkhouser RK, Gao F, Hahn BH, Kuiken C, Learn GH, Leitner T, McCutchan F, Osmanov S, Peeters M, Pieniazek D, M.L. Kalish, Salminen M, Sharp PM, Wolinsky S, and Korber B, available at http://hiv-web.lanl.gov). While it was agreed there are shortcomings in the current nomenclature system it was felt that remaining consistent with the present system was of vital importance. In particular, four categories should be used to describe the major HIV-1 lineages: groups, subtypes, sub-subtypes and Circulating Recombinant Forms (CRFs). The HIV-1 group O lineage also exhibits comparable diversity to group M, and an important question is whether group M-like subtypes can be identified within it. New strains of this lineage have furthered our understanding of its evolution (Characterization and Phylogenetic Analysis of 48 Newly Derived HIV-1 Group O Strains from Patients Living in France and Cameroon by Roques P, Robertson DL, Souquiere S, Damond F, Ayouba A, Farfara I, Depienne C, Nerrienet E, Dormont D, Brun-Vézinet F, Simon F, Mauclère P [submitted]). While group O can be sub-divided into major "subtype"-like clades to provide reference points, the group O branching pattern is clearly different to that of group M. This difference between the group O and M tree structures appears to be epidemiological in origin, i.e., the result of sampling from a Cameroonian-centered group O endemic as opposed to sampling from the pan-African/global group M epidemic.
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