HIV is subdivided into two very broad types: HIV-1 and HIV-2. HIV-1 is by far the most common and broadly distributed HIV type, accounting for most HIV infections worldwide. HIV-2 is genetically closer to simian immunodeficiency virus (SIV) than HIV-1 and as a consequence, HIV-2 can be refractory towards certain HIV-1 reverse transcriptase and HIV protease inhibitor drugs. The pathogenicity of HIV-2 in vivo is far less than HIV-1 . This also is reflected in the limited global prevalence of HIV-2 (estimated between 1 to 2 million cases worldwide) with restriction primarily to areas within West Africa.
The differences between HIV-1 and HIV-2 reflect their distinct zoonotic origin . HIV-1 is most similar to SIV strains isolated from chimpanzees and HIV-2 to those from the sooty mangabey. HIV-2 results in a less virulent infection than HIV-1, with generally lower viral loads, lower rates of vertical transmission and slower disease progression [10-13].
HIV-1 is divided into three quite distinct lineages: groups M, N and O. Again, the worldwide distribution of these groups is not equal: group M (for Main) strains are substantially more common in the global epidemic than the group O (Outlier) strains, which are largely confined to Africa, with sporadic cases reported elsewhere. The group N (non-M, non-O) strains have only been isolated in Cameroon .
HIV-1 subtypes and circulating recombinant forms
There are currently nine subtypes of HIV-1 that are consistently identified as different subtypes regardless of the genomic region analysed (Figure 1.4). Additionally, several recombinant forms of the virus, the genomes of which are made up of different regions from distinct subtypes, have been separately classified as circulating recombinant forms (CRFs).
The subtypes and CRFs show strong patterns of distribution in the global pandemic. Western countries, including Australia, continue to have an epidemic that is almost exclusively subtype B in all risk groups. Thailand originally showed a sharp segregation of subtypes between risk groups, with heterosexual transmission largely due to CRF01-AE, and injecting drug use (IDU) transmission due to subtype B; since then CRF01-AE has come to predominate in all risk groups [15-17]. India and South Africa are experiencing explosive epidemics of subtype C [18, 19]. All HIV subtypes described to date have also been detected in sub-Saharan Africa.
HIV subtype A/E was first described in Thailand as a new subtype E. Subsequent analysis of the entire genome of this form showed it to be a recombinant between subtypes A (that is most prevalent in Africa) and subtype E (that is unique). Isolates of this strain were then termed subtype A/E. As this strain is so prevalent in Asia, it was among the first to be renamed under the new nomenclature of CRFs. It is now referred to as HIV CRF01-AE.
A further refinement in the subtype classification has been made recently to distinguish strains that form distinct groups within subtypes but are not sufficiently different to warrant classification as a novel subtype. A detailed description of the most recent HIV taxonomy has been published by the Los Alamos National Laboratory (USA) HIV Sequence Database and is continuously updated on the Laboratory’s database website.