Subtypes of HIV

One of the obstacles to treatment of the human immunodeficiency virus is its high genetic variability. HIV can be divided into two major types, HIV type 1 (HIV-1) and HIV type 2 (HIV-2). HIV-1 is related to viruses found in chimpanzees and gorillas living in western Africa, while HIV-2 viruses are related to viruses found in sooty mangabeys. HIV-1 viruses may be further divided into groups. The HIV-1 group M viruses predominate and are responsible for the AIDS pandemic. Group M can be further subdivided into subtypes based on genetic sequence data. Some of the subtypes are known to be more virulent or are resistant to different medications. Likewise, HIV-2 viruses are thought to be less virulent and transmissible than HIV-1 M group viruses, although HIV-2 is known to cause AIDS.

HIV-1
HIV-1 is the most common and pathogenic strain of the virus. Scientists divide HIV-1 into a Group M (major) and two or more minor groups.

With 'M' for "major", this is by far the most common type of HIV, with more than 90% of HIV/AIDS cases deriving from infection with HIV-1 group M. The M group is subdivided further into clades, called subtypes, that are also given a letter. There are also "circulating recombinant forms" or CRFs derived from recombination between viruses of different subtypes which are each given a number. CRF12_BF, for example, is a recombination between subtypes B and F.
 * Group M
 * Subtype A is common in West Africa.
 * Subtype B is the dominant form in Europe, the Americas, Japan, Thailand, and Australia.
 * Subtype C is the dominant form in Southern Africa, India, and Nepal.
 * Subtype D is generally only seen in Eastern and central Africa.
 * (Subtype E) has never been identified as a nonrecombinant, only recombined with subtype A as CRF01_AE.
 * Subtype F has been found in central Africa, South America and Eastern Europe.
 * Subtype G (and the CRF02_AG) have been found in Africa and central Europe.
 * Subtype H is limited to central Africa.
 * (Subtype I) was originally used to describe a strain that is now accounted for as CRF04_cpx, with the cpx for a "complex" recombination of several subtypes.
 * Subtype J is primarily found in North, Central and West Africa, and the Caribbean
 * Subtype K is limited to the Democratic Republic of Congo and Cameroon.

These subtypes are sometimes further split into sub-subtypes such as A1 and A2 or F1 and F2. This is not thought to be a complete or final list, and further types are likely to be found.

The 'N' stands for "non-M, non-O". This group was discovered in 1998 and has only been seen in Cameroon. As of 2006, only 10 Group N infections had been identified.
 * Group N

The O ("Outlier") group is not usually seen outside of West-central Africa. It is reportedly most common in Cameroon, where a 1997 survey found that about 2% of HIV-positive samples were from Group O. The group caused some concern because it could not be detected by early versions of the HIV-1 test kits. More advanced HIV tests have now been developed to detect both Group O and Group N.
 * Group O

In 2009, a newly-analyzed HIV sequence was reported to have greater similarity to a simian immunodeficiency virus recently discovered in wild gorillas (SIVgor) than to SIVs from chimpanzees (SIVcpz). The virus had been isolated from a Cameroonian woman residing in France who was diagnosed with HIV-1 infection in 2004. The scientists reporting this sequence placed it in a proposed Group P "pending the identification of further human cases".
 * Group P

HIV-2
HIV-2 has not been widely seen outside of Africa. The first case in the United States was in 1987. Many test kits for HIV-1 will also detect HIV-2.

As of 2010, there are 8 known HIV-2 groups (A to H). Of these, only groups A and B are epidemic. Group A spread mainly in West Africa, but also to Angola, Mozambique, Brazil, India, and very limitedly to Europe or the US. Group B is mainly confined to West Africa.

HIV-2 is mostly related to simian immunodeficiency virus endemic in sooty mangabeys (Cercocebus atys atys) (SIVsmm), a monkey species inhabiting the forests of litoral West Africa. Phylogenetic analyses show that the viruses most closely related to the two strains of HIV-2 which spread considerably in humans (HIV-2 groups A and B) are the SIVsmm found in the sooty mangabeys of the Tai forest, in western Ivory Coast.

There are six additional known HIV-2 groups, each having been found in just one person. They all seem to derive from independent transmissions from sooty mangabeys to humans. Groups C and D have been found in two people from Liberia, groups E and F have been discovered in two people from Sierra Leone, and groups G and H have been detected in two people from the Ivory Coast. These HIV-2 strains are probably dead end infections, and each of them is most closely related to SIVsmm strains from sooty mangabeys living in the same country where the human infection was found.

Drug resistance mutations
Isolates of HIV-1 and HIV-2 with resistance to antiretroviral drugs arise through genetic mutations, which have been tracked and analyzed. The Stanford HIV Drug Resistance Database and the International AIDS Society publish lists of the most important of these; first year listing 80 common mutations, and the latest year 93 common mutations, and made available through the Stanford HIV RT and Protease Sequence Database.