by Pepin
It took more than twenty years for another ancient specimen containing HIV-1 to be located. Finding old tissue blocks collected between 1958 and 1960 and kept at the pathology department of the University of Kinshasa, scientists discovered HIV-1 sequences in a lymph node biopsy obtained in 1960 from an adult woman. It was given the name DRC60. Twenty-six other specimens (lymph nodes, livers and placentas) did not contain HIV. DRC60 and ZR59 differed by about 12%. It was calculated that DRC60 and ZR59 shared a common ancestor around 1921, as we will discuss later. Although the exact time of its introduction into human populations remains debated, there is no doubt that HIV-1 was present in Léopoldville by 1959–60.34
Viral diversity
Now we will examine how the genetic diversity of HIV-1 in different parts of the world helped scientists trace back the origins of the virus. But first, we need to review quickly what ‘sequencing’ is all about. Sequencing is the identification in their proper order of the series of ‘nucleotides’ that constitute a gene. There are four types of nucleotides: adenine (A), thymine (T), guanine (G) and cytosine (C). The genome of any living organism is a long list of these four letters. When scientists compare viruses, the similarity between sequences is called ‘homology’, and non-similarity ‘divergence’. If 90% of the nucleotide sequences between two isolates are the same, they have 90% homology or 10% divergence. This degree of divergence is used to decide whether two isolates constitute subtypes of one viral species, or two distinct species. For instance, sequences of HIV-1 and HIV-2 differ by more than 50%.
Based on such analyses, HIV-1 is now divided into four ‘groups’: group M (main), which is responsible for the current pandemic and causes more than 99% of all HIV-1 infections in the world, group O (outlier), group N (non-M non-O) and group P, which did not spread outside central Africa, for reasons still unclear.
HIV-1 group M is further subdivided into nine ‘subtypes’: A, B, C, D, F, G, H, J and K (the alphabet is not respected because subtypes E and I were found not to be real subtypes and have been renamed). HIV-1 often makes mistakes when replicating, a phenomenon compounded by the high level of viral production throughout the long natural history of the infection. Up to ten billion copies of the virus are produced every day, and the potential for errors in replication is commensurate. Over time, the accumulation of these errors leads to viral diversity. When around 20% of the nucleotide sequences of the initial virus have undergone replication errors, the result will be a new subtype, as defined arbitrarily by scientific consensus.35–36
High-risk individuals (especially in Africa) can get infected with a first subtype, and later with a second subtype, which can recombine into ‘circulating recombinant forms’ (CRF): part of their genome is derived from the first subtype, part from the second. Recombinants can be transmitted forward. Forty-eight recombinants have now been recognised. Their names correspond to the two subtypes involved in the recombination, for example CRF02_AG is a recombination of subtypes A and G. Some recombinants have generated their own epidemic in specific countries or regions.37
There is no clear-cut difference between subtypes with regard to their propensity to cause AIDS, with one exception: individuals infected with subtype D die faster than others. Do subtypes differ in their transmissibility? Shedding of HIV-1 in the genital tract of women infected with subtype C is higher than for other subtypes, which would imply more effective female-to-male sexual transmission. With subtype C, the high degree of ‘viraemia’ (the quantity of virus in the blood) that characterises acute infections may be worse than with other subtypes, increasing its infectiousness. Subtype C spread like wildfire in southern Africa, even if other subtypes had been introduced at the same time. These findings do suggest that subtype C is transmitted more efficiently than the others, which might explain its current worldwide preponderance.38–42
Some subtypes are associated in specific locations with particular modes of transmission. This represents a founder effect within specific risk groups: a subtype originally introduced in a group of intravenous drug users will continue to be transmitted preferentially to other addicts, another subtype originally introduced in sexual networks of homosexuals will be transmitted preferentially to other gay men, and so on. A good example of this is South Africa, where subtype B is found in 96% of white homosexuals (probably after it was imported from the US in the 1970s–80s), while subtype C accounts for 81% of infections of black heterosexuals. There is limited mixing between these two groups: few homosexual Afrikaners have sex with heterosexual Zulus! To date, there is no evidence that some subtypes are intrinsically better transmitted by one route than another. As the relative contribution of some modes of transmission varies over time, depending on the effectiveness of control efforts targeting a specific risk group, the distribution of subtypes within a given country can also change.43
HIV-1 evolves at a rate about one million times faster than that of animal desoxyribonucleic acid (DNA). This means that, in just over a decade, HIV-1 will change as much as all the genetic changes and the ensuing diversity that accrued among the common predecessors of Homo sapiens, chimpanzees and gorillas over ten million years. The longer HIV-1 has been present somewhere, the more opportunities it will have had to undergo a series of mutations which will eventually allow it to evolve into different subtypes, and the more likely it is that recombinants will be created. Conversely, if we were to examine all of the HIV-1 isolates in a city or country in which the very first case was introduced only a year earlier, for example in a population of drug addicts, we would find little genetic variation and the viruses of all the individuals infected after this first case would still belong to the same original subtype, the founder. There would not have been enough replication errors to result in new subtypes.
Because HIV evolves in only one direction, from a single model of virus to an increasingly complex differentiation into numerous subtypes and recombinants, we can reconstruct the sequence of its progress in a particular region or country by examining the local distribution of subtypes. Starting in the early 1990s, as new tools made it easier to examine nucleotide sequences from a large number of HIV-1 isolates obtained in various locations, an additional and most convincing argument emerged which supported a central African origin: the extreme genetic diversity of HIV-1 isolates from this part of the world.
Worldwide, subtype C accounts for about 50% of all HIV-1 infections, followed by subtypes B and A (10–12% each), G (6%), CRF02_AG (5%), CRF01_AE (5%) and D (2.5%), while subtypes F, H, J and K have undergone limited transmission (each fewer than 1% of cases). However, the contribution of each subtype varies dramatically from region to region.44–45
In North America and Western Europe, respectively 98% and 88% of HIV-1 infections correspond to subtype B, which is clearly the subtype that was originally introduced into these two continents, the founder strain. Subtypes other than B are usually found in migrants, who acquired HIV-1 in their countries of origin. In contrast, in Eastern Europe and central Asia, subtype A accounts for 79% of HIV-1 infections: clearly, this epidemic had a different origin than that of Western Europe, and it spread initially through needles rather than gay sex.36,44–46
In Latin America and the Caribbean, subtype B accounts for respectively 75–80% and 95% of strains. Cuba stands out as the country with not only the lowest HIV prevalence in the Americas but also the highest diversity: about half of Cuban isolates are either non-B subtypes or recombinants. This reflects the acquisition of multiple subtypes of HIV-1 (or recombinants) by some of the internationalistas, the soldiers that Castro sent to fight alongside the leftist Movimento Popular de Libertação de Angola during the civil war in Angola, and very limited opportunities for transmission upon their return to the island. The whole Cuban population was screened for HIV in 1986–9; seropositives were quarantined for years in AIDS sanatoria and brainwashed with preventive messages (Cuba was indeed the only country that tried to control HIV like an infectious disease, rather than making it a human rights issue).
At the peak of their intervention in 1986, 35,000 Cuban troops were stationed in Angola, which became one of the most corrupt and capitalist regimes in Africa, while smaller numbers of Cuban soldiers were stationed in sixteen other African countries. Recent studies documented a high diversity in HIV-1 isolates in Angola, where all non-B subtypes found in Cuba are present. This illustrates how political and military events, even ideologies, had a measurable impact on the transmission of HIV.47–52
In southern Africa, subtype C corresponds to 92–8% of HIV-1 infections. This implies that the virus was introduced relatively recently into this region now so afflicted by AIDS, a finding corroborated by epidemiological investigations. Subtype C accounts for 99% of infections in Ethiopia and also predominates in Zambia, while subtype A accounts for 70% of infections in Kenya. In Tanzania, subtypes A, C and D are the major players. In Uganda, which borders not only Tanzania and Kenya but also the DRC, there is more diversity, with a high prevalence of A, D and recombinants, and lower frequencies of C, B and G. In West Africa, all the way from Nigeria to Senegal, CRF02_AG predominates, implying that this part of the continent was infected only after subtypes A and G had had the opportunity to recombine.36,45,46
Countries of central Africa (the two Congos, Cameroon, Gabon, the Central African Republic and Equatorial Guinea) display by far the widest diversity in HIV-1 subtypes. All subtypes of HIV-1 group M and many recombinants have been found in this region, where there is also more genetic diversity within each subtype. Map 2, reproduced from a 2003 review paper, illustrates the extreme genetic variation of HIV-1 in central Africa compared to other parts of the continent. Additional studies published since might indicate small changes in the distribution of this or that subtype, without modifying the general pattern. The conclusion is crystal clear: HIV-1 must have originated in central Africa, where it has had more time to diversify genetically.45
Map 2 Genetic diversity of HIV-1 in sub-Saharan Africa. The circles show the distribution of HIV-1 subtypes in various countries (U stands for unknown).
Adapted from Peeters.45
Within central Africa, however, there are differences between countries, which help us to track past events. In Cameroon, the CRF02_AG recombinant is by far the predominant subtype, as in Nigeria to the north and Gabon and Equatorial Guinea to the south. This means that most of the HIV-1 transmission occurred relatively recently in these countries, without excluding the possibility that the initial case occurred there.53–56
In the Central African Republic, there is a strong preponderance of subtype A. In Chad, a country not inhabited by the Pan troglodytes troglodytes chimpanzee, there is diversity but the distribution differs: subtype A represents only 20% of isolates, while 40% are recombinants. This suggests that the virus disseminated there later than in the DRC.57,58
HIV-1 isolates obtained in 1997 from Kinshasa, Bwamanda and Mbuji-Mayi (all in DRC) were characterised. In Kinshasa, by descending order these were subtypes A (44%), D (13%), G (11%), H (10%), F (6%), K (3%), J (4%) and C (2%), while 8% could not be properly subtyped. Of note, only one subtype B strain was found, from a patient in Bwamanda in the Equateur region. This broad distribution of subtypes proved similar to what was measured retrospectively in samples collected in Kinshasa in the mid-1980s by Projet Sida: HIV-1 diversity in Kinshasa twenty-five years ago was far more complex than among strains currently found in any other parts of the world!59,60
Only recently has HIV-1 diversity in Congo-Brazzaville been evaluated on a large number of isolates, obtained mainly in Brazzaville. A pattern similar to that of Kinshasa was found: a predominance of A and G but few CRF02_AG recombinants and no subtype B. So in the final analysis, the two Congos are the countries with by far the greatest diversity of HIV-1 subtypes. This implies that the oldest epidemic did in fact start in the DRC and Congo-Brazzaville.61
The genetic diversity of HIV-1 in a given location is influenced not only by how long it has been there, but also by how efficiently it propagated. An HIV-1 strain producing only one case of secondary infection every five years would present fewer variations after fifty years compared to the same strain which, introduced into another environment, would have generated a secondary case every three months, with each secondary case in turn producing a tertiary case every three months, and so on. The more people are infected, the more copies of the virus are produced each day, which increases the number of mutations and differentiation into subtypes. In practice, what the great genetic diversity of HIV-1 in Kinshasa and Brazzaville means is that for the first time the virus found in this large urban area conditions conducive to its dissemination on a scale that enabled it to flourish and differentiate, after an initial phase of stagnation or very slow multiplication, which could have occurred elsewhere in any of the countries inhabited by its simian source.
It is still a mystery why subtype B remained rare in central Africa, where it represents only 0.2% of all HIV-1 infections, but spread so successfully into the Americas and Western Europe. Presumably, chance (the founder effect) played a major role, depending on whether a given subtype was introduced into some mechanism of amplification, sexual or otherwise, which gave it the initial boost after which it could disseminate slowly but effectively.
2 The source
So, HIV-1 originated from central Africa. But then, one may ask, why central Africa? The answer, as we will see, is because this region corresponds to the habitat of the simian source of the virus.
Our closest relatives
Chimpanzees are the closest relatives of humans, sharing between 98 and 99% of their genome with us, and are considered the most intelligent non-human animal. Chimpanzees and humans shared a common ancestor and are thought to have diverged between four and six million years ago. In fact, chimpanzees are so close to humans that it was recently proposed to move them into the genus Homo. Long-term studies in the Gombe reserve of Tanzania revealed that, like humans, chimpanzees have their own personalities. Some are gentle, others are more aggressive. Some have a good relationship with their parents or other members of the troop while others are loners. Some have a strong maternal instinct, others do not. This marked individualisation and their ability to laugh are what make chimpanzees most like humans. Rather than reacting predictably and instinctively to a given situation, chimpanzees show intelligence and spirit and experience all kinds of emotions.1–3
According to current taxonomy, there are two species: Pan troglodytes, the common chimpanzee, and Pan paniscus, the bonobo. Based on analyses of mitochondrial DNA (DNA that comes solely from the mother), there are now four subspecies of Pan troglodytes: Pan troglodytes verus (western chimpanzee), Pan troglodytes ellioti (Nigerian chimpanzee, until recently P.t. vellerosus), Pan troglodytes schweinfurthii (eastern chimpanzee) and Pan troglodytes troglodytes (central chimpanzee) (Map 3).4
Map 3 Distribution of the four subspecies of Pan troglodytes and the Pan paniscus bonobo.
Chimpanzees are poor swimmers, so that large rivers like the Cross, Sanaga, Ubangui and Congo became natural boundaries between the habitat of various species and subspecies. Pan troglodytes verus (total population in 2004: between 21,300 and 55,600, according to the International Union for Conservation of Nature) inhabits West Africa, from southern Senegal to the west bank of the Cross River in Nigeria; most of its population is now found in Guinea and Ivory Coast. Pan troglodytes ellioti (total population: 5,000–8,000) is found from east of the Cross to the Sanaga River in Cameroon, its southern boundary. Pan troglodytes schweinfurthii (total population: 76,400–119,600) inhabits mostly the DRC, east of the Ubangui and north of the Congo rivers, but its range extends into the Central African Republic, southern Sudan and eastwards to Uganda, Rwanda and Tanzania.5
Pan troglodytes troglodytes (total population: 70,000–116,500) inhabits an area south of the Sanaga River in Cameroon and extending eastward to the Ubangui and Congo rivers, spread over seven countries: southern Cameroon, Gabon, the continental part of Equatorial Guinea, Congo-Brazzaville, a small area i
n the south-west of the Central African Republic, the Cabinda enclave of Angola and the adjacent Mayombe area of the DRC. The largest populations are found in Gabon (27,000–64,000), where unfortunately they are rapidly declining, Cameroon (31,000–39,000) and Congo-Brazzaville (about 10,000). Other countries have fewer than 2,000 each, with probably less than 200 in the DRC. It is estimated that P.t. troglodytes and P.t. schweinfurthii diverged approximately 440,000 years ago.5,6
Chimpanzee populations in the first half of the twentieth century were certainly higher than now, because there had been relatively little opportunity for human activities to disrupt the natural equilibrium of the species. Human populations were much smaller than today, with fewer hunters and fewer clients willing to purchase bush meat. As an educated guess, some experts suggested that, combining all subspecies, there was around one million chimps in 1960. The subsequent decline was particularly severe for P.t. verus, and is generally attributed to the destruction of its habitat by increasing human populations who farmed or logged and hunted for bush meat, to diseases like Ebola fever, and captures for medical experiments.6–10
The rest of this section will focus on the central P.t. troglodytes chimpanzee, but the morphologic, demographic and behavioural differences between the four subspecies of Pan troglodytes are minor, at least for the non-expert. P.t.troglodytes chimps have a life expectancy of 40–60 years. An adult male weighs 40–70 kg, a female 30–50 kg. They live in rather loose communities (‘troops’) of 15 to 160 individuals, with a dominant male leader. When they reach sexual maturity, males generally remain in the community into which they were born, while females often join other troops. This intuitive exogamy maintains the genetic diversity of the subspecies and avoids the potentially devastating effects of inbreeding.