Phylogenetic analysis of HIV1 isolates in the early 1980 and 90s showed that HIV1 could be divided into at least six distinct env types which were equidistant from each other and formed a “star phylogeny”. These were called clades and named alphabetically from A to F. Subsequently, new HIV-1 isolates were discovered which were approximately equidistant to each other and their mutual divergence was comparable to that found between the older clades of HIV-1. These recent strains had an amino acid sequence identity of only about 50% in the env gene and formed a distinct phylogenetic group were named group O for ‘outlier’. While, the older and larger group of HIV-1 strains was called the group M for ‘major’. Another virus which was distinct from group M and group O was described in 1998 and named N group or ‘non M, non-O ‘group. Recently, a P group of virus was described in two patients from Cameroon.
Currently, the M group has successfully spread globally and causes majority (>95%) of the infections worldwide and has been studied extensively. It is further differentiated into 9 subtypes, namely A, B, C, D, F, G, H, J and K. Sub-subtypes have been described in sub types A (A1 to A6) and in subtype F (F1 and F2). An amino acid sequence similarity between 80 and 85% within a subtype is seen, whereas between subtypes it ranges between 65 and 75%.
Recombinant forms: Whole genome sequencing/near complete genome sequencing has led to the discovery of recombinant forms. A recombinant virus is formed when a cell is infected by two or more HIV lineages and there is an exchange of genetic material amongst each other. When there is an evidence that a recombinant virus is transmitted to three or more unrelated persons it is termed a circulating recombinant form (CRF), and in the absence of such an evidence it is called unique recombinant form (URF). To date 79 CRFs and multiple URFs have been described in HIV-1 group M. HIV-1 group M isolates which are not related to any of the currently defined subtypes or recombinant forms are called unique or unlabeled.
O group: The second largest group of HIV type 1 is the O group, which causes 1% of all HIV infections in Cameroon. The HIV type1 group O strains exhibit immense intragroup diversity which is higher than that in the M group. Two studies have analyzed the phylogeny of group O HIV viruses. Roques et al identified three clusters, namely A, B, and C among the isolates studied and concluded that there was no M group like subtype structure. Whereas Yamaguchi et al reported five clusters of isolates along with some non-clustering isolates and concluded that the five clusters had characters similar to that of the group M subtypes. However, these clades and clusters overlap and final classification agreeable to all is yet to be finalized.
N & P groups: Less than 20 infections due to group N and two cases of P group infections have been reported which mainly occur in or originate from Cameroon.
Molecular epidemiological studies to find the origin of HIV type 1 have shown that each of these four groups (M, N, O and P) were established in humans after independent cross species transmission of Simian immunodeficiency virus from chimpanzees (Pan troglodytes troglodytes in M, N and O groups) and Cameroonian gorillas (Gorilla gorilla gorilla in P groups).
