Genetic diversity of HIV in Africa

AIDS is caused by two lentiviruses: HIV-1 and HIV-2 [1,2]. AIDS was first recognized in the 1980s and is presently the leading cause of death in developing countries. Globally, it is believed that 40 million individuals have been infected with HIV, of which approximately 70% live in sub-Saharan Africa [3]. There is currently no cure or vaccine for AIDS. One of the major characteristics of lentiviruses is their extensive genetic variability, which is the result of the high error rate, the recombinogenic properties of the reverse transcriptase enzyme [4,5] and the fast turnover of virions in HIV-infected individuals [6]. Classification of HIV On the basis of phylogenetic analyses of numerous isolates obtained from diverse geographical origins, HIV is subdivided into types, groups, subtypes, sub-subtypes, circulating recombinant forms (CRF) and unique recombinants [7] (Fig. 1a–c).Fig. 1.: Phylogenetic tree of full-length genome sequences of HIV-1 isolates and mosaic structures of circulating and unique complex recombinant forms of HIV-1 in Africa. (a) Neighbour-joining phylogenetic tree of near full-length genome sequences of representative HIV-1 isolates from group M subtypes and sub-subtypes, group O and group N. Branch lengths are drawn to scale (the bar indicates 10% divergence). The numbers at the nodes indicate the percentage bootstrap values supporting the cluster to the right. (b) Mosaic structures of HIV-1 circulating recombinant forms (CRF) documented in Africa. Subtype E is the non-subtype A part of CRF01-AE. ▪ A; ▪ C; ▪ D; ▪ E; ▪ F; ▪ G; ▪ J; ▪ K; □ unclassified; ▪ not sequenced. LTR, Long terminal repeat. (c) Mosaic structures of HIV-1 of unique complex recombinants involving two CRF, and mosaic structure of an intergroup M/O recombinant HIV-1 strain. ▨ CRF02-AG; ▨ CFR06-cpx; ▪ HIV-1 group O; □ unclassified; ▪ not sequenced. LTR, Long terminal repeat.Classification of HIV-1 strains Three HIV-1 groups (M, N and O) exist. Group M (for major) represents the vast majority of HIV-1 strains found worldwide, and is responsible for the pandemic. Each of the three HIV-1 groups is thought to represent independent cross-species transmissions with a closely related virus. On the basis of inferences from phylogenetic tree topologies, HIV-1 thus originated from simian immunodeficiency virus (SIVcpz) from Pan troglodytes troglodytes chimpanzees in west-central Africa [8–10]. Within group M viruses most sequences fall into a limited number of discrete clades, allowing the classification of HIV-1 M strains into subtypes. The subtypes are approximately equidistant from each other and in order to be considered a subtype, isolates should resemble each other within the subtypes across the entire genome. Currently, nine subtypes of HIV-1 group M exist: A–D, F–H, J and K [7]. Within some subtypes, further distinct sequence clusters exist, leading to the classification of virus isolates into sub-subtypes. For example, subtype A has been subdivided into sub-subtype A1 and A2 and subtype F has been subdivided into F1 and F2 [11,12]. It is clear that subtypes B and D would be better considered as sub-subtypes of a single subtype; however, for historical reasons, it is difficult to change these designations (Fig. 1a). As our knowledge of HIV sequences improved over time, it became clear from phylogenetic tree analysis that some isolates clustered with different subtypes in different regions of their genomes [13]. Currently, some of the mosaic HIV-1 genomes play a major role in the global AIDS epidemic and are now designated as ‘circulating recombinant forms’ (CRF) [7]. By definition, CRF should resemble each other over the entire genome, with similar breakpoints reflecting common ancestry from the same recombination event(s). At present, 15 CRF of HIV-1 exist; each is designated by an identifying number, with letters indicating the subtypes involved, the letters are replaced by ‘cpx', denoting ‘complex’ if more than two subtypes are involved. In Africa, all groups, subtypes, and seven of the 15 known CRF have been documented (Fig. 1b). HIV-2 strains Compared with HIV-1, only a limited number of HIV-2 strains have been genetically characterized. The close phylogenetic relationship and the similarities in the organization of the viral genome indicate that HIV-2 is the result of a zoonotic transmission from SIVsm originating from sooty mangabeys to humans in west Africa [8]. The natural habitat of sooty mangabeys coincides with the geographical region where HIV-2 is prevalent in west Africa and sooty mangabeys are regularly hunted for food or kept as pets, thus allowing direct contact between mangabeys and humans [14]. Detailed phylogenetic analysis showed that cross-species transmissions from SIVsm to humans occurred on several occasions [8]. Most HIV-2 subtypes have only been found in countries where sooty mangabeys are widely present [15,16]. So far, seven subtypes (A–G) of HIV-2 have been described [17], with subtypes A and B being the predominant strains. Subtype A is most frequent in the western part of west Africa (Senegal and Guinea-Bissau) and subtype B predominates in Ivory Coast [18–21]. The other subtypes have been documented in only a few individuals. Except for subtype G, which was isolated from a blood donor in Ivory Coast [17], subtypes C, D, E and F were isolated in rural areas in Sierra Leone and Liberia. These viruses are more closely related to the SIVsm strains obtained from sooty mangabeys found in the same area than to any other HIV-2 strains [15,16]. This suggests that the different clades of HIV-2 must be the result of multiple independent cross-species transmissions of SIVsm into the human population [8]. Overall, on the basis of genetic distances, HIV-2 subtypes correspond to what is considered as groups for HIV-1. Distribution of HIV variants in Africa The classification of HIV strains has helped in tracking the course of the HIV pandemic. Extensive efforts have been made to collect and characterize HIV isolates from around the world and Africa, and a broad picture of the distribution of HIV strains has emerged. As mentioned above, HIV-2 is resticted to west Africa, and the prevalence remains low and appears to be decreasing in some areas [22]. HIV-1 group O seems to be endemic in Cameroon and neighboring countries in west-central Africa, and represents in this region only approximately 1–5% of HIV-1-positive samples [23]. Elsewhere in the world, group O viruses have been identified mainly from individuals with epidemiological links to central Africa, mainly Cameroon and some neighbouring countries. Interestingly, group N viruses have only been identified in a limited number of individuals from Cameroon [24,25]. HIV-1 group M strains are distributed in specific patterns in different regions of Africa. Studies performed on samples collected between 1995 and 2001 have revealed a detailed distribution of HIV subtypes in Africa. Although subtypes A, C and CRF02-AG are most frequent, the distribution of HIV-variants is very heterogeneous across Africa [26–28]. Most information on genetic subtypes has been based on the envelope, mainly the V3–V5 or C2–V3 regions by the heteroduplex mobility assay (HMA) or sequencing. However, some studies have analysed gp41 env, gag (p17 or p24) or pol (protease or reverse transcriptase genes) fragments and near fully genome sequences. The distribution of the different HIV-1 group M variants in Africa is summarized in Table 1 and Fig. 2 [29–69]. The data shown are the summary of different published studies that often used different molecular techniques, including the HMA, and partial or full-length genome sequencing. Because some of the techniques are not sensitive enough to discriminate between CRF and unique recombinants, the role played by CRF may be underestimated in some countries. The classification of HIV strains is evolving, and depends on the evolution and sensitivity of techniques used in molecular epidemiology. As molecular screening techniques improve, the resolution of pure subtypes, CRF, and unique recombinants will improve. For example, many studies used HMA, which needs less sophisitated equipment but is not sensitive enough to discrimate between pure subtypes and CRF.Fig. 2.: Geographical distribution of HIV-1 genetic forms circulating in different African countries. ▧ CRF02; ▪ A; ▪ B; ▪ C; ▪ D; ▪ F; ▪ G; ▨ CRF06; ▪ H; ▪ J; ▪ K; ▪ CRF01; ▪ U Adapted from data summarized in Table 1.Table 1: Proportion (%) of the different HIV-1 subtypes and circulating recombinant forms circulating in several African countries.Overall, subtype A (or CRF02-AG, see below) predominates in west and west-central Africa; however, there is a decrease in the proportion of subtype A from west to central Africa. Subtype G (or CRF06-cpx, see below) seems to be the second most prevalent subtype in west Africa. The highest genetic diversity is observed in central Africa, with the Democratic Republic of Congo harbouring the highest number of HIV-1 subtypes. All known subtypes have been identified in this country, and a relatively substantial number of strains cannot be classified into the current subtypes [54,70–72]. In east Africa, subtypes A and D predominate, but subtype C is also present and is the predominant and almost unique subtype in the eastern tip of Africa, Ethiopia. Subtype C also predominates in the epidemic in all countries in southern Africa, where the AIDS epidemic is explosive. CRF02-AG strains form a subcluster within subtype A in the envelope, which cannot be discriminated by HMA in env; therefore, in the overall data it is not always possible to discriminate between subtype A and CRF02-AG [37]. Sequence and phylogenetic analysis from env subtype A strains in several west, west-central and east African countries indicate that the majority of the env subtype A strains in west and west-central Africa are CRF02-AG strains, whereas in east Africa the majority of the strains cluster with the non-recombinant, pure subtype A prototype strains [47,73]. Similarly, as for the overall subtype A strains, the proportion of CRF02-AG strains within subtype A decreases from west to central Africa, with almost a complete absence of CRF02-AG in the Democratic Republic of Congo. Detailed analyses of env subtype G strains in west Africa have revealed that they are in fact CRF06-cpx strains, which is a complex variant involving at least four subtypes: A, G, J and K [74]. More detailed sequence analyses thus revealed that CRF02-AG and CRF06-cpx predominate in west Africa [33,39,74]. In west-central Africa, a variable proportion of env subtype A strains (2–5% in Cameroon and 18% in Chad) are representatives of CRF11-cpx, a complex mosaic virus involving subtypes A, G, J and CRF01-AE [43,75,76]. In the Democratic Republic of Congo, CRF05-FD has been described, but its relative frequency is unknown [77]. In Tanzania, where subtypes A, C and D exist, a C/D recombinant (CRF10_CD) has been described [78]. Finally, in Cameroon another complex recombinant virus, CRF13_cpx, involving subtypes A, G, J, and CRF01-AE has been reported. However, compared with CRF11-cpx, different breakpoints have been described, and the prevalence of this virus in the epidemic is unknown [76]. Because the highest genetic diversity is observed in central Africa, it is thought that all HIV-1 subtypes originated there. The epidemic in the different countries from west, east and southern Africa is probably the result of different founder effects. The initial diversification of group M may have occured within or near the Democratic Republic of Congo, where the highest diversity of group M strains has been observed and the earliest case of HIV-1 infection, dating from 1959, has been documented [54,79,80]. Attempts to estimate the time of origin of HIV-1 using different methods of molecular clock analysis showed that the origin of HIV-1 group M radiation was in the 1930s [81,82]. Recombinant HIV strains In addition to CRF, which play a major role in the global epidemic, many unique recombinant viruses have also been documented. Because only a few systematic studies have been conducted, the exact prevalence of recombinant strains is unknown. On the basis of preliminary data, the proportion of discordant subtypes between the gag and env genes vary from less than 10% to more than 40%, according to the countries or regions studied [29,30,33,37,39,41,42,47,51,54,64, 83–85]. Fig. 3 illustrates the estimated prevalences of unique recombinant HIV-1 viruses on the basis of discordant subtype/CRF designations in different regions of the genome. The subtypes involved in these discordant samples depend on the subtypes that co-circulate in the region. For example, in Nigeria only subtypes A and G co-circulate, and these are the only subtypes involved in the 37% discordant samples [41,42]. Also, in Kenya, where subtypes A and D predominate, large numbers of diverse A/D recombinants are documented [83]. In the Democratic Republic of Congo, where many subtypes circulate concurrently, a wide variety of recombinants has been reported with all subtypes involved in the recombination events [54].Fig. 3.: Estimates of unique recombinant HIV-1 viruses based on discordant subtype or circulating recombinant form designations in different regions of the genome. ░ < 10%; ░ ░ □ no data of recombinants on HIV-1 of recombination As more HIV-1 variants in different of the world, the of recombinant viruses will the distribution of different forms of HIV-1 in the world will to be a Mosaic genomes will more recombination involving viruses that are recombinant will involving have been observed in African countries and some of the CRF, and sequences that are from CRF01-AE. between two CRF has also been described in a in three full-length genome sequences revealed the of complex and diverse recombinants (Fig. related viruses have been shown to For example, recombinants between group O and M HIV-1 strains have been documented in Cameroon (Fig. between strains from may to HIV-1 strains, and have At present, group O viruses represent a of the strains responsible for the HIV-1 pandemic. However, if recombinant viruses have a better than the group O their prevalence may with for and molecular and between to have been observed in The fact that large numbers of recombinant viruses that with HIV-1 strains is more frequent than with different subtypes has been reported in regions where multiple strains In order to an it is to the course of HIV infection, and to what and are strains. two studies documented of with a virus from another subtype with HIV-1 and HIV-2 have been reported in regions where viruses however, no recombinants between these two viruses have been HIV-1 and HIV-2 are of zoonotic and the HIV-1 group M for the and the that result from a single of zoonotic showed that humans in frequent contact with in many of sub-Saharan Africa thus the of zoonotic Fig. illustrates the diversity of currently described to which humans are the and of in Africa. The fact that HIV the as to related and HIV in individuals are and to by cross-species this related more into the human Phylogenetic analysis of group N viruses that they are the result of a recombination between an and an virus Phylogenetic tree analysis from the known sequences. Phylogenetic tree analysis was performed using the on a in Branch lengths are drawn to scale (the bar indicates 10% divergence). The numbers at the nodes indicate the percentage bootstrap values supporting the cluster values are recombination also has for vaccine based on these with strains, the two may be of and vaccine in Africa documented between HIV-1 and HIV-1, HIV-2 is less less and is to reverse transcriptase However, it is not clear similar the forms of HIV-1 subtypes, and in of and to Because these viruses are very closely related and also of and that may data from studies may a time to will the current of knowledge on the of HIV genetic diversity on and and the of and and vaccine efforts in Africa. of HIV on a HIV diversity has an on studies have shown that some individuals infected with diverse strains of HIV, as group to be by some Although and are sensitive and specific for individuals with with HIV-1 group M subtypes, some in individuals with used for the were based on HIV-1 subtype B strains. and have a to individuals infected with subtypes In Africa, is being on from as the of to transmission of HIV, to in the of in HIV-infected and and These that be and are in a There is thus of in different countries. the of to be used in Africa obtained from subtypes are Also, the of from HIV-1 subtypes in the has to be considered for the of these in of and in individuals for HIV-1 of the viral has in for on and for and transmission in Africa. Although has been made to the sensitivity of to viral some viral In a individuals infected with CRF02-AG strains the sensitivity and viral values were for the assay the than for the HIV-1 and the HIV-1 The of these is thus subtype distribution is a The HIV assay is the only assay that group O strains for HIV-2 of HIV and subtypes and of a of data on in Africa, there was as to individuals infected with HIV-1 subtypes would to in a similar to infected with HIV-1 subtype B strains. HIV-1 group O and HIV-2 strains are to reverse transcriptase studies have that some subtypes may be less to of For example, subtype G strains are less in to of the from strains revealed that are often present as natural variants in HIV-1 strains (or may not result in a decrease in but may be with an in viral or an in the with major thus of The in the of subtypes A and C are enough to the of the However, the of the of only to the of has to be in The of in west Africa where CRF02-AG and CRF06-cpx predominate and in with a majority of subtype A and D as as studies on African in showed that the of in the at not the of the of to in viral and in African is to reported infected with subtype B in western countries studies have also not found to for subtypes A, C, and D However, more data and a are to will the of of viruses and to what they for the of As are to be widely used in Africa, studies are to the of in infected with different subtypes. The of may be by of viral and distribution and genetic Subtype G viruses have the at a where major However, or major related to have not been documented as natural variants in group M strains. A major of studies in Africa is the of an for for subtypes. However, of the few published studies on in Africa, a has been documented between and and observed correspond to in subtype B similar but other studies that with the few studies reported in Africa have shown that the of of depends on the of the than on the HIV-1 subtypes. For example, more than has been reported in and and In in a were in only of with and which is with what has been described for infected with subtype B viruses in western countries. However, showed related to subtypes: a by the HIV for in showed that to occurred more at in infected with subtype D than in infected with subtype A viruses Overall, in order to the of viruses on a large scale in developing it will be to have the to to in in these countries. will to be in the of and the of viruses will have to be to and HIV-1 subtypes and and Compared with HIV-1, HIV-2 is by a viral a in and a However, it is difficult to the of HIV-1 viral subtypes several may and studies on subtypes and have discordant A in that subtypes A, C and recombinants are more to be than subtype On the other a in reported similar of transmission for subtypes A and D, but a in showed that infected with subtype D were more to virus to their than infected with subtype In of the known as or is subtype individuals infected with subtype B strains, the of viruses is with a more to but it is not known the frequency of the subtype C viruses is with or different HIV-1 in to be For example, no in was found between infected with subtypes B and C in or infected with subtypes A, C and D in In a of in Kenya, viral and were in subtype C than in infected with subtypes A or D In a of from and Cameroon of individuals with unknown of analyses showed no in or for infected with CRF02-AG strains and infected with other strains However, two studies based on have found HIV-1 For in a based on more than for at showed that subtype D was with to death and with a compared with subtype A in reported that infected with subtypes were more to AIDS than were infected with subtype A HIV subtypes and vaccine and in Africa HIV vaccine is the to the epidemic in Africa, and should to all genetically diverse strains of HIV-1. a vaccine the of the of HIV-1 subtypes circulating in Africa is as of HIV-1 are and data on the between genetic subtypes and studies have not shown a between HIV-1 subtypes and However, reported for subtypes B and CRF01-AE in and another also clustered within subtype C Because of that are of in HIV-infected current efforts on HIV are the of gag and pol which to be more in Studies have between different HIV-1 subtypes to of in the gag This may that HIV vaccine to the prevalent HIV-1 strains be less for at the of to (for gag and However, are and more than and have also been identified a vaccine should and Because of the distribution of HIV-1 subtypes in Africa, current vaccine efforts have been For example, in a is between the for and and the of to a virus vaccine based on the CRF02-AG that predominates in the HIV epidemic in the are also between from Nigeria and the of to an HIV vaccine based on the genes of three different HIV-1 strains G, and that are frequent in the In the vaccine the is or which have the of being to and as and which may and In Kenya, a between the AIDS the of and is on a subtype A vaccine that is at by a of and This same vaccine is being considered for in where subtypes A and D co-circulate in almost In Africa, where subtype C the African AIDS is on a subtype C which is to be of the first HIV to be in Africa. The of African HIV-1 isolates for into the has been based on pol and env sequences based on the relationship to a African subtype C sequence obtained from the vaccine above, it is thought that HIV-1 may be more than for vaccine The of or sequences for a specific subtype has thus been in order to the genetic between vaccine strains and This and the of a vaccine relative to any single strain. In regions where several subtypes co-circulate, the of each prevalent subtype in the vaccine may studies are also to to what for subtype B in are similar to strains in the African A in reported with to HIV-1 subtypes AIDS is currently the most and its prevalence to In Africa, all HIV and subtypes co-circulate, but their geographical distribution in the is very heterogeneous and from to The geographical distribution of subtypes is and the of HIV-1 variants is The number of recombinant viruses that are documented that subtype distribution is a and viruses that are mosaic are involved in further recombination The genetic diversity of HIV will to be a in and vaccine in Africa. A vaccine should in of the of subtypes, and a vaccine with a based on any subtype may be more than a vaccine with multiple vaccine including will to the of different different subtypes, and in with different genetic The of HIV variants is in order to and vaccine The would to the of for data on The would also to and the from the from the in and in for data on subtypes in and of the was by the of and for HIV, and for and The was also by from the for AIDS in