The public health significance of HIV-1 subtypes

Introduction Since the first descriptions of HIV/AIDS, HIV-1 has emerged as the most significant pathogen worldwide, with approaching 60 million infections to the end of 2000. Over 18 million deaths from AIDS have occurred, and HIV/AIDS is now classed among the top five causes of global mortality [1]. As with other infectious pathogens that exhibit a high degree of genetic variation, such as influenza, the extensive genetic variability of HIV-1 poses significant challenges for disease control and epidemiological surveillance [2]. The genetic heterogeneity of HIV-1 isolates is one of the major characteristics of the virus and the epidemic. This diversity, generated by the processes of mutation and recombination [3], has led to the development of a subtype nomenclature for the classification of isolates [4]. The major (M) group of HIV-1, responsible for the majority of infections in the epidemic, contains several recognized non-recombinant subtypes and sub-subtypes, and at least 10 circulating recombinant forms (CRFs) [4]. These subtypes show uneven regional distribution, and past attempts have been made to use them to describe the global molecular epidemiology of HIV-1 [5,6]. In this context, undertaking systematic sampling and monitoring of populations is important to determine the value of these studies. We review here the public health and clinical significance of HIV-1 genetic variability, and the methods and rationale for public health surveillance of subtypes. Diversity of subtypes Epidemiological and genetic evidence suggest that the two main types of HIV (HIV-1 and HIV-2) are zoonoses (human infections originating from animals), acquired via several independent transmission events from the chimpanzee (Pan troglodytes) and sooty mangabey (Cercocebus atys), respectively [7,8]. While HIV-1 appears to have been present in humans since around the 1930s [9], modern sociodemographic changes together with chance introductions into vulnerable populations have created optimal conditions for its rapid spread [10]. HIV-1 genetic variability is generated by the lack of proof-reading ability of the reverse transcriptase (RT) [11], the rapid turnover of HIV-1 in vivo[12], host selective immune pressures [13], and recombination events during replication [3]. This variability has allowed HIV-1 to be classified into the M group of sequences as well as outlier (O), and non-M, non-O (N) groups [14-16]. Recently, guidelines for the definition of subtypes and CRFs have been proposed that take into account the genetic diversity and evolution of the epidemic [17]. A new subtype or CRF may be defined by the existence of at least three fully characterized genomes, obtained from epidemiologically unlinked individuals. Phylogenetic analyses should group these sequences approximately equidistantly from all other subtypes. At the time of writing, group M consists of nine 'full-length' subtypes, designated A-D, F-H, J and K [4,14]. Further analysis of complete genome sequences from viruses initially described as belonging to subtype E (now classified CRF_01AE) and subtype I has revealed these viruses to be recombinant strains, and not distinct subtypes as initially proposed [18,19]. More detailed phylogenetic analysis has also led to the re-classification of some subtype groupings. For example, subtype F was originally classified into three sub-subtypes (F1, F2 and F3) based on gag and env phylogenetic comparisons [20]. However, subsequent full-length genome analysis has led to the re-classification of sub-subtype F3 as subtype K [21]. Groups O and N currently represent only a small number of characterized strains, although env and gag sequence analysis of group O isolates has demonstrated that they belong to four distinct phylogenetic clusters of similar diversity to the group M subtypes [22]. Inter-subtype and intra-subtype recombination may occur within dual-infected individuals to generate novel recombinant strains, even between highly diverse viruses such as those belonging to different groups [23,24]. There are currently 10 CRFs responsible for sub-epidemics worldwide (http://hiv-web.lanl.gov/CRFs/CRFs.html). In 1995, it was estimated that recombinant viruses accounted for up to 15% of global infections [25], and we have shown that up to 20% of heterosexual infections in the United Kingdom may be attributable to recombinant viral strains [26]. Additional CRFs and mosaics continue to be characterized, such as the recent discovery of a C/D CRF (CRF10_CD) found among perinatally infected infants in Tanzania [27], and an A/J recombinant infecting pregnant women in Cameroon [28]. Given the continued global spread of HIV-1, it is likely that recombinants will play an increasing role in the generation of HIV-1 diversity [6,23]. Genetic sequencing is the definitive method for subtyping [29]. Despite advances in long-polymerase chain reaction (PCR) technology [30], practical limitations have historically led to a subtype being assigned based on single genomic regions, most commonly env, gag, or pol[31]. There are several available techniques for subtype assignation, and deciding which is appropriate will often depend on the objectives of the surveillance strategy (Table 1).Table 1: HIV-1 subtype classification techniques.Serological assays have proved useful for screening populations of limited subtype diversity, especially where one subtype predominates [32,33]. However, such assays are not applicable where multiple subtypes co-circulate as they can lead to subtype misclassification [34-36]. In such circumstances, PCR-based subtyping approaches, most commonly the heteroduplex mobility assay, have been widely applied [37-41]. In addition, by obtaining partial sequences from different gene regions, most commonly gag and env, recombinant prevalences can be estimated and potentially interesting genomes identified [26,39-41]. Epidemiology and global distribution of subtypes There have been numerous descriptions of the HIV-1 genetic diversity within populations [5,6,42]. However, most studies have derived estimates using unsystematic, opportunistic sampling frames with relatively small numbers of specimens [43-46]. As such, current understanding of the distribution of HIV-1 subtypes may inadequately represent the worldwide diversity of the virus [6]. In particular, reporting bias can distort the global description through an over-representation of unusual subtypes and limited surveillance of populations with a more homogeneous subtype profile. Equally, the complex distribution of HIV across different transmission modes and sexual groups, coupled with the fact that transmission rates may differ within groups even within a single country or locality, complicates the surveillance of HIV infection. The greatest genetic diversity is observed among HIV-1 strains from Africa [47] where transmission occurs primarily via heterosexual, iatrogenic (blood transfusion) and mother-to-child routes [48]. Distinct geographic subtype patterns are seen within Africa, with subtypes A and D most prevalent in Eastern Africa [49,50], subtype A in Western Africa [51,52], and subtype C in South Africa [53], although the epidemic in the latter region appears to be increasing in diversity, with subtypes A, B, D and recombinant forms now prevalent [39,54](Fig. 1). Phylogenetic analysis of the gag gene from isolates obtained from Senegal, Cameroon, Gabon, and Djibouti has suggested that between 60 and 84% of subtype A viruses circulating in Africa may in fact be similar to CRF_02AG [55], and not 'pure' subtype A viruses as previously described.Fig. 1: Geographical distribution of HIV-1 major (M) group subtypes. For clarity, only the most prevalent subtypes are shown. CRF, circulating recombinant form.In Asia, an epidemic spread of HIV-1 is occurring with fewer co-circulating subtypes than in Africa. The epidemics in India and China are dominated by subtype C, the most prevalent subtype worldwide, which is thought to account for approximately 50% of infections [56,57]. Subtypes A, B, and recombinant strains have also been identified [56]. In contrast, two strains, subtypes B and CRF_01AE, co-circulate within the injecting drug user (IDU) population in Thailand [58]. These two subtypes have also been shown to co-circulate among Thai fishermen [59]. The original spread of HIV-1 in North America, Western Europe, and Australia was of subtype B strains among the MSM and IDU populations [14,60]. Heterosexual spread is increasing in these regions with non-B subtypes and recombinant strains observed, mostly among individuals with epidemiological links to areas where multiple subtypes co-circulate [26,43,44,61-65]. Most South American viruses appear to be subtype B, although there also the epidemic is increasing in diversity with subtypes A, C, and F, and recombinant viruses being reported [66,67]. The continued global expansion of subtypes has created the potential for recombinant virus generation and transmission, and the number of reports of recombinant infections is increasing. In part, this is due to improvements in surveillance methodology, and recombinant strains have been detected in many countries [26,31,55,67-71]. Intersubtype recombinant forms now appear to be circulating among IDU in China (B/C) [56], North Vietnam and Southeast Asia (CRF_01AE) [72], Argentina (B/F) [73], and Russia (A/B) [70]. Public health implications of genetic diversity The genetic variability of infectious pathogens, and any consequent phenotypic variation, poses a significant challenge to disease control and surveillance [74,75]. Differences between subtypes in their viral properties can be argued from several lines of evidence. HIV-1 and HIV-2 show approximately ∼50% similarity at the nucleotide level [14] and differ in their pathogenicity and transmissibility [76,77]. While both are zoonoses [7,8], neither virus appears harmful to their natural primate hosts [78], and yet they are pathogenic when transferred to foreign primate host species [79]. In addition, the extraordinarily rapid rate of HIV-1 evolution in humans, estimated at around 0.0024 substitutions per base pair per year [9], coupled with the recombination events that may introduce large-scale genetic changes, creates the conditions for increased viral evolution. Interventions such as antiviral drug therapies may further accelerate genetic change through the preferential selection of resistant strains [80]. As we will describe, such variability may impact on vaccine modelling and diagnostic testing, the generation of antiviral resistance, and aid the surveillance of transmission patterns within the epidemic. Selection of candidate vaccines The development of a protective vaccine remains the greatest challenge in the global battle against HIV-1. It has been hindered by the lack of a suitable animal model, the limited understanding of the markers of protective immunity, and the intracellular mode of transmission and persistent nature of HIV infection in the immune system [81]. Several approaches have been applied to the development of vaccines with varying degrees of success, including epitope vaccines [82,83], live vector constructs containing various combinations of env, gag, pol, and nef[84,85], DNA vaccine constructs [86,87], live attenuated nef-deletion vaccines [88], and whole-killed viral constructs [89]. The genetic variability of HIV-1 complicates vaccine development [90]. 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For example, the of new to the original was shown to its ability to subtypes A and E assays that in the such as the assay, have also been shown to of the highly group N viruses In areas where subtype variability is an that a highly such as pol, may the most estimates of viral a such as the may also There is a for viral genome sequences of different subtypes to the of various A control containing HIV-1 isolates initially classified as subtypes on the of phylogenetic analysis of their gag env is available for this However, further analysis of the gag, pol, and env regions from this has shown it to four recombinants and two group O the for complete genome of strains The increasing genetic diversity of HIV-1 that the and of based diagnostic viral and assays to be an to for all HIV-1 Genetic markers of antiviral The and transmission of HIV-1 to in areas where those therapies are commonly poses a challenge to the phenotypic of by of virus is and genetic markers with are by A review of the genetic of antiviral is the of this and is available [80]. It is to in antiviral that diverse viral forms such as HIV-1 group O have been shown to to reverse transcriptase The high level of genetic diversity of HIV-1, coupled with the turnover of has been shown to lead to the rapid generation of strains The of assays as an aid to the clinical of as well as studies of antiviral in populations of has allowed a more complete of mutation patterns to occurring drug have been demonstrated among individuals infected with subtypes F and and with to have been shown in individuals to be more prevalent among non-B subtypes than among subtype B strains individuals infected with subtypes and may occurring at that to in subtype B viruses However, evidence is by several studies that have demonstrated in the mutation among individuals infected with a of subtypes and recombinant virus further is to determine role the subtype may play in the development of antiviral may among the drug The mutation is present in subtype C viruses from both in the United Kingdom and to both and and and have also been found to be more among non-B subtypes with subtype B viruses A of drug in HIV-1 infections in the United Kingdom has shown among infected with a subtype B the of being infected with a virus has increased with time the transmission of may the of infected individuals is not to be markers of transmission patterns The of circulating viral strains can an important role in the of the epidemic. For example, the genetic variability of HIV-1 can be to transmission both to transmission events and to the more spread of the epidemic. transmission events can be detected with although it is often to determine the of infection. In one recent from genetic led to the of a infected when of Epidemiological studies subtype has allowed of the of distinct HIV-1 subtypes into the and several countries In some subtype may be with a of transmission, such as in Thailand where subtypes B MSM and and a similar time although these subtype patterns are now distinct Phylogenetic evidence has also the of the subtype virus into the heterosexual Thai population to around transmissibility The that HIV subtype may viral transmissibility and pathogenicity has been suggested other HIV-1 transmission including with other and protective diverse as HIV and and the of the These attempts to determine the of subtype on viral For example, the of the two epidemics in Thailand and some properties of subtype in led to the of a transmissibility of subtype However, the not be and the epidemiological evidence for the of in different populations There is now between these two subtypes and of transmission in populations where HIV-1 subtype B predominates have suggested transmission rates than those where non-B subtypes are most prevalent Recently, a in Tanzania suggested subtype may play a role in transmission, with subtypes A, C, and recombinant viruses being more likely to be perinatally than subtype due to the use of the A in transmissibility has yet to be with similar rates of both sexual and transmission, of been observed the of many HIV-1 subtypes than one or a suggest that subtype is to be the main in viral In this that any are more likely to be due to other than viral such as prevalences of other infections where non-B subtypes The lack of evidence for an between subtype and transmission not the existence of such an that it will studies and methods in those areas where multiple subtypes pathogenicity The rate of disease among individuals widely As well as is by host including and the of transmission and at time of infection the of disease and conditions and viral characteristics The of subtype on viral pathogenicity has been in several studies. It has been suggested that the may differ between subtypes for example, the or being among subtype C isolates While the has been with disease among individuals infected with subtype B, there is evidence that subtype C viruses are pathogenic than other subtypes. A has been suggested between the of an among subtype C viruses and viral and replication However, sequence analysis of subtype C isolates from South Africa, and China has revealed that this is present in only a small number of subtype C viruses This the to numbers of sequences in of the between HIV-1 subtype and disease have infected with subtype B strains and in infected with non-B subtype found in the rate of or disease a two further studies of disease one subtype and subtype in and infected with subtype B or in Thailand have found in rates of However, a of in that individuals infected with subtypes to disease than those infected with subtype A Several studies have a more rapid rate of disease among infected in Africa with those infected in Western and the United However, a lack of between host as a for viral and disease has been shown in several studies It is to such may be by such as the of to and the of as to viral host Epidemiological surveillance The impact of the genetic diversity of HIV-1 on public health in surveillance that and strains from populations at varying of infection. However, to most available subtype has been derived from studies that unsystematic, opportunistic sampling frames (Table of systematic surveillance of HIV-1 of specimens for HIV-1 subtype surveillance strategy for monitoring HIV-1 diversity will depend on the objectives of the (Table studies have been applied in several these are and often not of at of infection a number of countries have to for subtyping of or a individuals This strategy may not be applicable in where the majority of new infections are as it may in The of surveillance of population groups at varying of infection has been shown to estimates of subtype (Table these for example, it is in the United Kingdom that approximately of individuals are infected with a non-B subtype In addition, up to 20% of the infections in in the United Kingdom are with a recombinant non-B subtype virus [26]. While such studies have proved useful in and in the of new subtypes and they can be and to that are of populations is often to and a has been to sampling frames as to important changes time The genetic variability of HIV-1 the in which the epidemic is and is also a significant in the of HIV-1 diversity is likely to play a role in the generation of resistance, although to there is evidence of significant in transmissibility or pathogenicity of the subtypes. epidemiological studies have a of the global subtype distribution and these show increasing evidence of the of HIV-1 of the subtype distribution is of in the development of vaccines and is to that to and clinical and monitoring of HIV infections fully and sequencing has proved useful in epidemiological between infected and subtype surveillance as a to transmission patterns at a of the worldwide can be obtained by and Epidemiological surveillance to molecular techniques that are appropriate to the subtype in the population of and which also the ability to the of novel subtypes. The of the majority of current on subtyping a single genomic region their ability to unusual and new recombinant strains that may be multiple may also be epidemiologically for transmission The development of that several regions of the and where will play an important role in surveillance of the epidemic. a of the diversity of HIV within a attempts should be made to a of groups at varying of as well as with diverse modes of It is important that sampling and recent infections as to a of current transmission However, recent are not to in those groups not recognized to be at high of HIV where may not occur in the course of infection. The use of for HIV the may the of recent infections The of epidemiological and at for is also to the understanding of transmission patterns based on the subtypes of HIV-1. The and for their of this is by the of and is by a of of and also the many to the HIV and and especially the HIV and