Members of HIV-1 group M are responsible for the vast majority of AIDS case
s worldwide and have been classified on the basis of their phylogenetic rel
ationships into nine roughly equidistant clades, termed subtypes, Although
there are no known phenotypic correlates for these genotypes, the dispropor
tionate spread of certain of these lineages has been taken to indicate that
subtype-specific biological differences may exist, The subtype nomenclatur
e thus remains an important molecular epidemiological tool with which to tr
ack the course of the group M pandemic, In this study, we have characterize
d HIV-1 strains described previously as unusual subtype A variants on the b
asis of partial sequence analysis, Six such strains from Cyprus (CY), South
Korea (KR), and the Democratic Republic of Congo (CD) were PCR amplified f
rom infected cell culture or patient PBMC DNA, cloned, and sequences in the
ir entirety (94CY017, 97KR004, 97CDKTB48, and 97CDKP58) or as half genomes
(97CDKS10 and 97CDKFE4), Distance and phylogenetic analyses showed that fou
r of these viruses (94CY017, 97CDKTB48, 97CDKFE4, and 97CDKS10) were closel
y related to each other, but quite divergent from all other HIV-1 strains,
except for subtype A viruses, which represented their closest relatives. In
phylogenetic trees from gag, pol, env, and nef regions, the four newly cha
racterized HIV-1 strains formed a distinct sister clade to subtype A, which
was as closely related to subtype A as subsubtypes F1 and F2 are to each o
ther. According to current nomenclature rules, this defines a subsubtype, w
hich we have tentatively termed A2, The two other viruses, 97KR004 and 97CD
KP58, as well as a full-length HIV-1 sequence from the sequence database (Z
AM184), were found to represent complex A2/D, A2/G, and A2/C recombinants,
respectively, These results indicate that HIV-1 subtype A is composed of tw
o subsubtypes (A1 and A2), both of which appear to have a widespread geogra
phic distribution. The A2 viruses described here represent the first refere
nce reagents for this new group M lineage.