The penetration of HIV-1 from the equatorial region into West Africa differed markedly from its expansion to the east and south. Except in Côte d'lvoire, it was more gradual and less complete, reaching in the early 2000s prevalences only one-fifth or one-sixth of the highest elsewhere. The reasons for this are unclear but probably include obstacles to overland mobility from east to west, the wider economic opportunities open to West African women in towns, widespread male circumcision, relatively low HSV-2 prevalences, and the barriers to infection presented by Islamic moral and marital patterns. Another difference, of less certain relevance, was that when the HIV-1 virus entered West Africa, it found HIV-2 already established.

As a human disease, HIV-2 was probably older than HIV-1. It was closely related to the simian immunodeficiency virus found in sooty mangabey monkeys (SIVsm) living only in the West African forest region between the Casamance River in Senegal and the Sassandra River in Côte d'lvoire, which was also the endemic location of the human virus. HIV-2 shared some 70 per cent of its genome with SIVsm but only about 42 per cent with HIV-1. Indeed, some of the eight groups of HIV-2 known in 2004 were more like SIVsm than they were like one another. This was because SIVsm was very widespread and diverse (although completely harmless) in sooty mangabey monkeys and because each HIV-2 group was probably the result of a separate transmission from a monkey. Of the eight groups, six had failed to establish themselves in human beings, having infected only seven known cases between them. Of the two more successful, group A was the more common throughout the coastal region west of Côte d'lvoire, while group B was found chiefly in Côte d'lvoire and Ghana, although scattered cases of both existed elsewhere. A study using molecular clock techniques estimated that the most recent common ancestor of group A existed in 1940±16 and of group B in 1945±14. Yet, given the high prevalence of SIV among sooty mangabeys, their close interaction with human beings, and the frequency of twentieth-century transmissions, similar transmissions had probably taken place in earlier centuries.