The acquired immune deficiency syndrome (AIDS) is caused by the human immunodeficiency virus (HIV). HIV-1 was initially identified by Luc Montagnier at the Institute Pasteur, Paris, in 19831 and was then more fully characterised in 1984 by Robert Gallo in Washington 2 and Jay Levy in San Francisco. 3, 4 A second virus, HIV-2, was isolated from West African patients in 1986. 5 Viruses similar to HIV-1 and HIV-2 have been isolated from chimpanzees and wild African monkeys. 6 It is most likely that HIV-1 and HIV-2 crossed species from primates to humans in Africa several times over the last hundred years with the earliest known samples of HIV-1 isolated from preserved tissues samples from 1959 and 1960. 6-8 The genetic diversity of these two HIV-1 isolates at that time estimates the most recent common ancestor for HIV-1 to be around 1908. 6-8
HIV structure and organisation
HIV is classified in the family Retroviridae, subfamily Lentivirinae, and genus Lentivirus. 9, 10 The structure of HIV follows the typical pattern of a complex retrovirus family, comprising a single- stranded, positive-sense ribonucleic acid (RNA) genome of about 9.7 kilobases that encodes from structural, enzymatic and accessory proteins. An HIV virion is largely spherical in shape, with a diameter of 100 to 120 nm, and encloses its genome within a fullerene (cone-shaped) capsid core. The virus is enveloped with a lipid bilayer derived from the host cell, thus incorporating proteins found in the host membrane, such as the major histocompatibility (MHC) molecules, 11, 12 CD44 and lymphocyte function-associated antigen 1 (LFA-1). 13 Embedded within this membrane are the viral glycoproteins; the gp120 surface glycoprotein and the gp41 transmembrane glycoprotein. Each envelope subunit displays on the virion surface as a trimer of the outer envelope gp120, non-covalently liked to a trimer of gp41, the transmembrane protein that anchors this glycoprotein complex to the surface of the virion. The envelope protein is the most variable component of HIV, although gp120 itself is structurally divided into highly variable (V) and more constant (C) regions. The constant regions of the gp120 envelope are often associated with the ‘non-neutralising face’, as they are buried within the trimer. 14, 15 While the variable domains are associated with the ‘neutralising face’ of the envelope glycoprotein that is exposed to the humoral immune system and thus variability in this context is derived from immune escape. The variable domains also give the capacity of the virus to change receptor usage. In particular the V3 loop of HIV gp120 can change the virus’s ability to use the HIV coreceptors CXCR4 and CCR5 (receptors for HIV will be covered later in this chapter). Of note, the envelope glycoprotein gp120 has over half its molecular weight attributed to carbohydrate structures, in the form of complex and high mannose N-linked glycans. These glycans decorate the majority of the exposed outer gp120 surface and are known as the ‘silent face’, given their ability to protect this face of the envelope from the humoral immune response.14, 15
The viral structural proteins are derived from the Gag polyprotein, which is present in approximately 2400 copies in an immature virion, according to current estimates. 16 Viral maturation leads to the cleavage of the Gag polyprotein, giving rise to matrix (MA; p17) and capsid (CA; p24) proteins, as well as the smaller peptides nucleocapsid (NC; p7), p6, p2 and p1.17 Matrix associates with the inner membrane of the mature virion, while capsid forms the viral core, enclosing two single strands of viral RNA. The core structure is a cone shape comprised of approximately 1500 capsid proteins assembled into hexameric and pentameric rings. 18, 19 Viral proteins found within the capsid core include the NC, which is found associated with the viral RNA, as well as protease (PR), integrase (IN) and reverse transcriptase (RT) proteins. 20
The genomic organisation of HIV is extremely efficient. Use of all three reading frames (the triplet codes) of the genetic sequence permits overlapping of gene-coding regions. There are nine genes of HIV (Figure HIV genomic structure). These encode proteins that may be broadly classified into structural, catalytic, regulatory, and accessory classes (Table 1).
Notes: (a) HIV virion structure highlighting envelope (gp120, gp41) and structural (gag p17, gag p24) proteins. RT = reverse transcriptase; ssRNA = single-stranded RNA. (b) The single-stranded RNA genome of HIV efficiently encodes nine major structural and catalytic proteins by using overlapping parts of the genome. Additionally, the nucleic acid secondary and tertiary structure performs functions independent of translation. LTR = long-terminal repeat
In addition to the functions performed by these proteins in the viral lifecycle, the nucleic acid sequence of the virus possesses intrinsic functions. For example, the Rev responsive element, within the coding region for gp41, interacts with the Rev protein to assist export of spliced RNA transcripts from the nucleus of the cell. 21 The long-terminal repeat (LTR) region has a transcription-promoter function in the integrated deoxyribonucleic acid (DNA) provirus, 22 and contains regions essential for reverse transcription, integration into the host-cell genome and genomic RNA dimerisation. 23
HIV life cycle
The life cycle of a retrovirus is that of an obligatory intracellular parasite, and thus HIV cannot replicate outside human cells (Figure HIV life cycle).
|Viral gene||Viral protein||Designation and size (kDa)||Function||References|
|Matrix||MA, p17||Targets virion assembly through binding to PI(4,5)P2 domains at the plasma membrane; binds gp41 to incorporate Env in nascent virions||24-27|
|Capsid||CA, p24||Forms the capsid-rich core via hexameric and pentameric CA structures; mediates Gag oligomerisation and assembly||18, 19, 28|
|Nucleocapsid||NC, p7||Binds viral RNA and packages the genome in the core; mediates Gag oligomerisation and assembly||29-31|
|p6||p6||Promotes membrane fission of nascent virions via PTAP-Tsg101 recruitment of the ESCRT complex; binds Vpr protein and packages it in the core||32-34|
|Env||Surface envelope glycoprotein||SU, gp120||Envelope surface protein; binds to CD4 receptor and chemokine receptors on target cell||35-38|
|Transmembrane envelope glycoprotein||TM, gp41||Envelope transmembrane protein; mediates fusion via fusion peptide||39, 40|
|Pol||Reverse Transcriptase||RT, p66, p51||RNA-dependent-DNA-polymerase; converts viral ssRNA to linear DNA||41, 42|
|Integrase||IN, p32||Facilitates integration of HIV DNA into host genome; involved in dynein-mediated transport of the RTC.||43-46|
|Protease||PR, p10||Cleavage of polyprotein components of Gag-Pol||47, 48|
|Viral gene||Viral protein||Designation and size (kDa)||Function||References|
|Tat||Trans-activator of Transcription||Tat, p14||Activator of transcription of HIV RNA; essential for virus replication||49-52|
|Rev||Regulator of virion protein expression||Rev, p19||Post-transcriptional regulation of viral genes, including export of viral RNA from the nucleus
|Nef||Negative regulatory factor||Nef, p27||Infectivity enhancement; CD4 and MHC class I down-regulation; cellular activation and signalling||54-60|
|Vpr||Viral protein R||Vpr, p15||Helps in nuclear transport of HIV post entry; induces G2 cell cycle arrest in infected cells||61-66|
|Vpu||Viral protein U
||Vpu, p16||Enhances the release of virus particles by counter-acting the interferon induced restriction factor tetherin; promotes CD4 degradation||67-69|
|Vif||Virion infectivity factor||Vif, p23||Counteracts the anti-viral activity of APOBEC3 protein group. The latter protein group are HIV restriction factors that hypermutate HIV genomes and render them non-functional.||70-72|
Source: Furtado MR, Callaway DS, Phair JP, Kunstman KJ, Stanton JL, Macken CA, et al. Persistence of HIV-1 transcription in peripheral-blood mononuclear cells in patients receiving potent antiretroviral therapy. N Engl J Med 1999;340:1614-22. Used with permission
HIV binding and entry
Infection of the host cell commences when HIV binds to specific receptors on the cell membrane. In general, the interaction requires the recognition of two host-cell surface-receptor proteins by the viral gp120 envelope protein. The presence or absence of these cellular proteins restricts the range of host-cell types that are susceptible to infection by a strain of HIV.
The first HIV receptor described was the CD4 protein 35 which is present predominantly on cells of the T lymphocyte and myeloid lineages. The distribution of CD4 receptors has been thought to restrict HIV susceptibility to cells of the lymphocyte, monocyte/macrophage and other CD4-expressing lineages, although there is precedent for HIV-1, HIV-2 and the related virus simian immunodeficiency virus (SIV) to be able to fuse with cells not expressing CD4 23. 73, 74
Subsequently, the requirement of a second coreceptor for viral entry was recognised. 75-80 This function may be performed by a range of proteins within the class of seven-transmembrane receptors, although the most important are CCR5 (CC chemokine receptor type 5) and CXCR4 (CXC chemokine receptor type 4). The seven- transmembrane class of receptors is very large, containing over 100 related proteins. Several of these proteins have been shown to facilitate the binding of HIV in vitro.81 The in vivo significance of entry via these minor coreceptors, however, remains unclear.
After HIV gp120 binds to CD4 receptor and the coreceptor, a conformational change in gp41 causes insertion of the N-terminal hydrophobic fusion-peptide region into the target-cell membrane.82 This insertion results in membrane fusion and the entry of the viral particle contents into the cytoplasm, a process critically dependent upon interactions between the N- and C-terminal regions of the gp41 ectodomain. This intra-protein interaction led to the discovery of a novel class of antivirals called fusion inhibitors, e.g. T-20 (enfuvirtide) which is a short peptide that mimics the structure of the conserved C-terminal region of gp41. 83
Although all HIV strains will recognise and bind to CD4, affinity for either CCR5 or CXCR4 varies. These differences account for the observed distinct tropisms between HIV strains. Binding ability and tropism of the virus are dependent on the protein structure of gp120. Particular patterns of sequence of the V3 and V4 variable regions, and other regions of gp120, relate to CD4 binding and differential coreceptor affinity. 81, 84, 85
In general, viral strains that bind to CCR5 (R5 strains) infect macrophages, activated CD4 T lymphocyte cells and subsets of resting CD4 T cells where CCR5 is expressed. The majority of strains present in vivo are R5 strains and variants of R5 strains known as founder viral strains (see below) are selected during the process of sexual HIV transmission. Other HIV strains that recognise CXCR4 (X4 strains) can exist, but by contrast, infect only T cells and T cell lines and are only present in approximately 40 to 50% of clinical cases during the latter stages of HIV disease. 81 The reason for the lack of CXCR4 variants in early stages of HIV disease, is presently hypothesised to be related to their susceptibility to the adaptive immune response in addition to other factors that limit their growth. 86 The adaptive immune hypothesis does fit well with the time that these isolates emerge, as it is typically at the latter stages of HIV disease when the immune system is being steadily degraded. In theory CXCR4 isolates can emerge via two mechanisms. Firstly, by CXCR4 viruses being transmitted alongside CCR5 using strains or secondly by progressive genetic evolution of a CCR5-using strain to a CXCR4-using strain. To date the majority of scientific observations support the latter hypothesis. 87 Indeed, some investigators argue that all HIV-positive patients would generate a X4-usingHIV strain, if given enough time (i.e. patients can succumb to the effects of R5 HIV before the emergence of X4 strains). The emergence of X4 strains is often clinically associated with subsequent accelerated loss in CD4 T cells and as a consequence accelerated disease progression due to fundamental lack of total CD4 T cells. This latter phenomena is a consequence of increased HIV target cells that can be accessed by X4 HIV strains. For instance, while CCR5 expression is restricted to a small memory/activated CD4 T cell subset, CXCR4 is present on upwards of 90% of all CD4 T cells. 88-90 Historically the growth of X4 strains in vitro has been characterised by the presence of syncytial cells, which are formed by the fusion of multiple infected cells and can be observed by light microscopy. This classification, however, is largely based on the relative expression of CXCR4 on T cell lines used in these assays. The expression of CCR5 expression to similar levels as CXCR4 can readily result in the formation of syncytia when using R5 strains that replicate at similar levels. Indeed the mechanistic basis of syncytial formation is the level of HIV envelope expressed on the infected donor cells and the HIV receptor expression (CD4 and CCR5 or CXCR4) on the neighbouring recipient cell. This scenario is largely based on the replication of the virus within the donor cell and indicative of overall viral production. Indeed investigators have demonstrated the spontaneous formation of syncytia in cell lines that are exposed to high titer virus. 91
Importantly the knowledge of the role of CD4 and associated chemokine receptors led to a new area in HIV therapeutics. A number of small molecules that block binding of HIV to either CCR5 and CXCR4 has been described. Two randomised, placebo-controlled clinical trials (known as MOTIVATE 1 and 2)using the CCR5 inhibitor maraviroc have demonstrated, in conjunction with present optimised therapies, greater virological and immunological efficacy profiles compared to placebo only control. However this was in the context of participants having only detectable R5 HIV. 92, 93 X4-specific chemokine receptor inhibitors also exist, the first generation AMD3100 and the second generation AMD11070. Curiously AMD3100 was discovered in anti-HIV drug screens prior to the knowledge that chemokine receptors work in concert with CD4 to allow HIV entry. 94, 95 Initial trials in humans using the bioavailable AMD11070 CXCR4 inhibitor observed positive virological outcomes, but further development of this drug class has been delayed due to observations of liver damage in animal models. 96
The pre-integration complex
The genetic information of HIV is contained within an RNA genome. Following infection of a new host cell, the RNA genome is first reverse transcribed into single-stranded DNA that is then further transcribed to double-stranded DNA. These two polymerase steps are performed by viral reverse transcriptase, which is co-packaged in the viral particle. Self-priming of the single-stranded RNA and DNA and removal of the transcribed RNA strand occur by a complex series of steps dependent upon interactions between the viral LTR and host-cell enzymes. The double-stranded DNA genome forms a complex with host-cell and viral proteins (including matrix, integrase and Vpr) that is actively transported to the nucleus. 97, 98
During the early steps of the HIV-1 replication cycle, the virus counteracts specific host proteins that have evolved to limit retroviral replication. Two key host cell factors that influence early viral events are i) a protein called human tripartite motif 5 alpha (TRIM5alpha) and ii) sterile alpha motif (SAM) domain and Histidine- Aspartic (HD) domain-containing protein 1 (SAMHD1). TRIM5alpha acts in the early steps of HIV-1 replication cycle, soon after the entry process and before reverse transcription. 99 TRIM5alpha restricts retroviral infection by specifically recognising HIV-1 capsid and promoting its rapid, premature disassembly. 100, 101 TRIM5alpha from rhesus macaques and African green monkeys inhibit HIV-1 replication, whereas the human homologue is inactive against SIV and HIV-1, leading to the susceptibility of human cells to both viruses. For SAMHD1, the primary mode of action was initially hypothesised to be by cleaving nucleotides needed for efficient HIV reverse transcription and subsequent integration. This action is particularly apparent in resting cells like macrophages, dendritic cells and resting CD4 T cells, where there is already a limited nucleotide pool. However recent studies have observed SAMHD1 to also act on HIV RNA and restrict HIV infection through RNase activity 102 and it is presently unclear whether it is the RNase activity combined with dNTPase activity that combines to restrict HIV infection. Observations by Ryoo and colleagues 102 currently support RNase activity only, but require further independent confirmation.
Integration and transcription
The double-stranded HIV genome is then either integrated into the host-cell genome by means of DNA splicing, performed by the viral integrase, or forms stable DNA circles.103 In the context of chromosomal integration, this process is not random, as recent studies have observed preferential HIV DNA integration in active transcriptional sites within infected cells.104 The integrated form of HIV is known as the provirus and takes the form shown in Figure HIV life cycle, with identical LTR copies flanking the coding regions. Proviral DNA is replicated as part of the normal cell genome and may persist in this form for long periods and through many rounds of mitotic cell division. Furthermore integration into long-lived resting CD4 T cells provides challenges in HIV cure attempts, as the virus in these cell types in typically latent.
The 5’ end of the LTR now functions as a promoter, regulating the production of RNA transcripts dependent on the presence of host-cell transcription factors (such as promoter-specific transcription factor, SP1, and nuclear factor - kappa beta) and the viral protein Tat. 105 The transcribed HIV RNA molecules may either be spliced in preparation for translation of viral proteins, or exported from the nucleus in an unspliced form for packaging into newly produced virions. Nuclear export of spliced RNA is assisted by the viral protein Rev.
HIV assembly and release
For full viral assembly, HIV transcription and subsequent translation must reach a critical threshold for viral assembly to occur. 106 One common misconception with respect to HIV latency is the complete lack of HIV transcription and translation in all latently infected cells. For instance, latency in resting CD4 T cells can also exist where low levels of detectable viral RNA and proteins are present, but at a level that does not lead to assembly and production of fully assembled and infectious virions.
Once a threshold of viral protein production is reached, viral proteins that are destined for virions are recruited and assembled at the plasma membrane. 106 Not all virally produced proteins are incorporated with assembling virions, with the dominant virion-associated proteins expressed as either a fusion protein with the structural protein HIV Gag (i.e. HIV Gag-Pol) or are able to non-covalently associate with HIV Gag (e.g. HIV Vpr). For post translational events, HIV Gag exists as a monomer and oligomerisation of HIV Gag triggers the exposure of a myristoylation motif that binds to the membrane-enriched lipid called phosphatidylinositol 4,5-bisphosphate. While HIV Gag oligomerisation can proceed when expressed in isolation, it can also be triggered by viral RNA binding largely through the NC domain of Gag, 107 thus ensuring viral inocula have a greater propensity to bud from the cell membrane with its genetic cargo.
Oligomerisation of HIV Gag at the plasma membrane leads to the formation of what is known as the immature viral shell, primarily consisting of repeating Gag polyprotein hexamers. 108 A partially intact spherical shell is hypothesised to leave the membrane, with the aid of scission from the membrane through the Gag-specific recruitment of cellular proteins involved in the endosomal sorting complexes required for transport (ESCRT) complex, that effectively acts as molecular scissors to liberate virions from the membrane.
Shortly after leaving the membrane, HIV protease is activated and culminates in the sequential cleavage of Gag and Gag-Pol proteins. This process, commonly referred to as viral maturation, is marked by condensation of a large pool of HIV capsid, that leads to encapsulating many viral proteins including HIV RNA-bound NC within the conical shaped viral core.
While the above description outlines the specific role of the major structural protein, HIV Gag, other viral proteins perform a variety of roles to subvert normal cellular function and facilitate viral replication (Table 1). Much about these processes remains poorly understood. Vpr acts to alter host-cell transcription and arrests infected cells at the G2/M phase of cell division. 109 Nef induces downregulation of the CD4 receptor and MHC class I molecules.55, 57, 110 Vpu promotes degradation of CD4 in the endoplasmic reticulum and counteracts an interferon-induced restriction factor known as tetherin, which acts by tethering and preventing the release of newly formed HIV particles from the plasma membrane. 68 Vif is necessary for subsequent efficient infectivity of the newly produced viral particles 70, 111 and counteracts cytidine deaminases (enzymes present especially in macrophages and T cells) that are naturally occurring host defence mechanisms against retroviruses. These proteins include APOBEC3G and APOBEC3F and are degraded by HIV. 111
HIV transmission and biomedical prevention
Recent failures and successes of biomedical prevention in conjunction with the studies of HIV discordant couples (i.e. where one partner is positive and the other negative and thus at risk of acquisition from a known donor), have led to seminal contributions which give us a greater understanding of how HIV is spread person to person. Biomedical prevention in the form of topical microbicides (essentially lubricants that can kill or inhibit HIV) over the past decade has evolved from using formulations consisting of spermicidal detergents through to gel formulations containing the same or similar ingredients as current antiretroviral therapies.112 The first clinical trials using the spermicidal detergent noxanol-9 (N-9) showed increased incidence of HIV transmission 113 and following trials using polyanion-based gels showed either enhanced or limited effects.67, 114 However, these trials did provide important evidence about how the virus was spread. For instance, the use of N-9 and its deleterious effects on the genital mucosa illustrated how primary mucosal barriers were essential for blocking the incoming virions. The combined knowledge of the early microbicide (including polyanions) trials also demonstrated that the maintenance of good reproductive health further strengthened these primary barriers and thus limited the numbers of people contracting HIV through sexual transmission. The more recent studies using microbicides with antiretrovirals, 115 combined with studies on pre-exposure antiretroviral treatment for recipients and treatment as prevention in HIV positive donors also emphasised that there is a clear window during HIV transmission that can be targeted at the recipient and donor level. 116 One of the most successful trials in this latter context was HPTN 052. In this trial of HIV serodiscordant couples, the treatment of the partner with infection led to a reduction in HIV transmission events of 96%. 116 Thus successful control of viral load in the donor, as is the case with limiting mother-to-child HIV transmission, 117 is indeed paramount in limiting the spread between people.
While these prevention strategies gave broad insights into HIV transmission and its prevention, the studies of early HIV acquisition in HIV discordant couples provided the viral genetic footprint that is needed for a virus to cross hosts. The study of the genetic makeup of HIV strains that are the first detected during infection pointed to an extreme bottleneck where only the fittest virus is transmitted. 118 Curiously, the genetic diversity of transmitting strains is reflected in the ease with which the virus can infect. For instance there is greater genetic diversity in HIV founder strains that are transmitted from male to female compared to female-to-male transmitting viruses. In addition those recipients with additional risk factors such as sexually transmitted infection (STI) further relax the genetic bottleneck of the virus and allow a more diverse viral population to pass rather than a stringently defined transmitting strain. 118, 119 While the genetic makeup of the incoming virions in the early stages of HIV transmission is now mapped in large cohorts at fine detail with near whole HIV genomes, understanding the actual biological phenotype of the transmitting strain is still under consideration. 118, 120-127 Recent studies by Carlson and colleagues point to the transmitting strain being the fittest virus, 118 that is, the virus that makes it across the mucosa and has the ability to sustain early and robust viral replication before the mounting of the acquired immune response. While most researchers point to changes in the HIV envelope, it is rather the overall genetic makeup of the virus that dictates the fitness of virus in vivo. As to whether the HIV envelope in a transmitting strain has a preference for HIV targets, in vitro assays suggest the founder viruses rely on high levels of CD4 and thus on having a preference for CD4 T cells. 120, 125, 128 That said, the appearance of HIV within the brain is largely mediated through macrophage infections and thus the clear-cut distinction that transmitting strains preferentially infect CD4 T cells rather than other known HIV targets like dendritic cells and macrophages is still a topic of debate. Even if founder strains did preferentially target CD4 T cells, we must note that other HIV reservoirs, like macrophages and dendritic cells, do exist in vivo and must be taken into context for the overall pathogenesis in vivo (whether that be during the acute or chronic stages of disease).
The taxonomy of HIV and the primate immunodeficiency viruses
HIV is subdivided into two very broad types: HIV-1 and HIV-2 (Figure The molecular phylogeny of primate immunodeficiency viruses). HIV-1 is by far the most common and broadly distributed HIV type, accounting for most of HIV infections worldwide. HIV-2 is genetically closer to SIV strains than HIV-1 and as a consequence HIV-2 can be refractory towards certain HIV-1 reverse transcriptase and HIV protease inhibitors. The pathogenicity of HIV-2 in vivo is far less than HIV-1.129 HIV-2 also has a limited global prevalence (estimated between 1 to 2 million cases worldwide) with restriction primarily to areas within West Africa.
The differences between HIV types 1 and 2 reflect their distinct zoonotic origin.130 HIV-1 is most similar to SIV strains isolated from chimpanzees and HIV-2 to those from the sooty mangabey. HIV-2 results in a less virulent infection than HIV-1, with generally lower viral loads, lower rates of vertical transmission and slower progression of the disease in an individual with the infection. 130-133
Figure The molecular phylogeny of primate immunodeficiency viruses
Note: An unrooted phylogenetic tree estimated using an alignment of the envelope gene (gp160). HIV is classified into types 1 and 2, the latter co-segregating with simian immunodeficiency virus (SIV ) strains from sooty mangabey and the former with those from chimpanzee indicating probable distinct zoonotic origins. HIV forms three groups: M, N and O. Group M contain the nine subtypes and further circulating recombinant forms that contribute to the overwhelming majority of HIV infections worldwide. (In this analysis of envelope, CRF01_AE is the only circulating recombinant strain included. The scale bar indicates 10% nucleotide sequence divergence.
HIV-1 is divided into three quite distinct lineages: groups M, N and O. Again, the worldwide distribution of these groups is not equal: group M (for Main) strains are substantially more common in the global epidemic than the group O (Outlier) strains, which are largely confined to Africa, with sporadic cases reported elsewhere. The group N (non-M, non-O) strains have only been isolated in Cameroon. 134
Subtypes and circulating recombinant forms
There are currently nine subtypes that are consistently identified as different subtypes regardless of the genomic region analysed (Figure 1.4). Additionally, several recombinant forms of the virus, the genomes of which are made up of different regions from distinct subtypes, have been separately classified as circulating recombinant forms (CRFs).
Figure Phylogeny of HIV subtype M envelope gene
Note: A tree based on an alignment of envelope gene sequences (gp120 portion) from reference-subtype strains currently recommended by the Los Alamos National Laboratory (USA) HIV Sequence Database. Group M strains are clearly segregated into subtypes A to K (without I and with the further subdivision of subtype F into sub-subtypes F1 and F2). The tree topology is star shaped, indicating a shared common ancestor and roughly equal divergence times for these strains.
The subtypes and CRFs show strong patterns of distribution in the global pandemic. Western countries, including Australia, continue to have an epidemic that is almost exclusively subtype B in all risk groups. Thailand originally showed a sharp segregation of subtypes between risk groups, with heterosexual transmission largely due to CRF01-AE, and injecting drug use (IDU) transmission due to subtype B; since then CRF01-AE has come to predominate in all risk groups.135-137 India and South Africa are experiencing explosive epidemics of subtype C.138, 139 All HIV subtypes described to date have also been detected in sub-Saharan Africa.
HIV subtype A/E was first described in Thailand as a new subtype E. Subsequent analysis of the entire genome of this form showed it to be a recombinant between subtypes A (that is most prevalent in Africa) and subtype E (that is unique). Isolates of this strain were then termed subtype A/E. As this strain is so prevalent in Asia, it was among the first to be renamed under the new nomenclature of CRFs. It is now referred to as HIV CRF01-AE.
A further refinement in the subtype classification has been made recently to distinguish strains that form distinct groups within subtypes, but are not sufficiently different to warrant classification as a novel subtype. A detailed description of the most recent HIV taxonomy has been published by the Los Alamos National Laboratory (USA) HIV Sequence Database and is continuously updated on the Laboratory’s database website.
The global pandemic of HIV
The number of individuals with the infection at the end of 2013 reached 35.3 million of which 17.7 million were women and 3.3 million were children under the age of 15 years. The improved access to antiretroviral treatment (in 2012, around 9.7 million people living with HIV had access to antiretroviral therapy in low- and middle-income countries), the implementation of prevention programs and the development of low-cost testing for early detection appear to be having an impact on the HIV epidemic in many countries. For instance total new HIV infections fell by 33% in 2012 compared to estimates in 2001. New HIV infections among adults and adolescents decreased by 50% or more in 26 countries between 2001 and 2012. In addition new HIV infections among children have declined by 52% over the same 2001 to 2012 period. AIDS-related deaths have fallen by 30% since the peak in 2005.140
Source: Joint United Nations Programme on HIV/AIDS 2014
Source: Joint United Nations Programme on HIV/AIDS 2014
North America and Western and Central Europe
The number of people living with HIV in North America and Western and Central Europe reached an estimated 2.3 million in 2013. Approximately 54% of these cases are from the USA. The majority of new infections in 2011 were attributed to the USA (approximately 50 000 of a total of 88 000 newly diagnosed cases). In the USA, sexual activity among men who have sex with men (MSM) is still the main mode of HIV transmission accounting for approximately 63% of new HIV infections in the USA, while IDU and unprotected paid sex represent the minority of new transmission cases.
The rates of diagnosed HIV cases doubled between 2000 and 2009 in Bulgaria, the Czech Republic, Hungary, Lithuania, Slovakia and Slovenia. In contrast, the number of people newly diagnosed with HIV decreased by more than 20% in Latvia, Portugal and Romania. Over the same period there was an increase by more than 50% in Germany and the United Kingdom; antiretroviral treatment within this region remains a challenge. In the USA the late diagnosis of HIV, poor treatment adherence and high levels of early treatment discontinuation contribute to avoidable HIV-related deaths. Whereas in western and central Europe people at risk are not being tested for HIV. Lack of testing is problematic in terms of treatment, and for the potential effect on increased levels of HIV transmission.
Asia, the Pacific and Australia
There were an estimated 350 000 (220 000 – 550 000) new HIV infections in Asia and the Pacific in 2012, a decline of 26% since 2001. In most countries in Asia and the Pacific, sex workers and their clients, MSM, transgender people and people who inject drugs represent the populations most affected by the epidemic. In 2012, 1.25 million were accessing antiretroviral treatment (51% [43-63%]). In the Asia-Pacific region,12 countries account for more than 90% of people living with HIV and more than 90% of new HIV infections: Cambodia, China, India, Indonesia, Malaysia, Myanmar, Nepal, Pakistan, Papua New Guinea, the Philippines, Thailand and Vietnam. Australia’s closest neighbour Papua New Guinea, although with a total of 32 000 people with HIV infection, has observed a decline in new HIV infections of over 50% since 2001 and a 31% decrease between 2005 to 2013. Presently over 40% have access to antiretroviral treatment.
In Australia 1236 cases of HIV infection were newly diagnosed in 2013, similar to levels in 2012 when the number of cases was the highest in Australia since the early 1990s. The annual number of new HIV diagnoses has gradually increased over the past 14 years, from 724 diagnoses in 1999. As in the USA, the dominant form of transmission is MSM accounting for over 70% of new cases in 2013. In 2013 between 13 200 and 19 500 were receiving antiretroviral treatment and had undetectable levels of HIV, corresponding to 49–73% of all people with HIV and 57–84% of people with diagnosed HIV infection. Australian figures cited and respective updates can be found at: https://kirby.unsw.edu.au/surveillance/Annual-Surveillance-Reports.
Around 24.7 million or nearly 70% of all people living with HIV worldwide live in Sub-Saharan Africa (58% of them women). There were 1.5 million [1.3 million–1.6 million] new HIV infections in sub-Saharan Africa in 2013. However, new infections are declining. There was a 33% drop in new HIV infections among all ages in the region between 2005 and 2013. Previously this area also had the lowest prevalence of antiretroviral treatment. Fortunately, successive increases in antiretroviral treatment have occurred, especially over the last 3 years, with 2012 recording an increase in 1.7 million people on treatment. Collectively 37% people in this region now have access to treatment. In addition 68% were receiving effective drug regimens to prevent mother-to child transmission in 2013. Access to antiretroviral treatment has related directly to a reduction in HIV-related deaths in this region. For instance, in South African over the period 2005 to 2013 there was a 48% reduction of HIV-related deaths. The limited uptake of antiretroviral treatment in Nigeria has unchanged the rate of HIV-related deaths in 2005 compared to 2013.
Move towards an HIV cure
Present limitations on therapeutic driven cures
The persistence of HIV in the face of antiretroviral treatment reflects the complex nature of the target: the human immune system. Our acquired immune system relies on the persistence of long-lived memory CD4 T cells that can be activated upon future pathogenic exposure. Analogous to an acquired immune response, HIV can establish a latent reservoir within this latter CD4 memory T cell type and thus persist for long periods of time (estimated to be several decades with current half life estimates of 44 months).141
Cure strategies aimed at purging HIV reservoirs
Several approaches to eradicate reservoirs of HIV by clinical treatment have attempted to use latency reversing agents (LRAs) in an HIV cure strategy known as ‘shock and kill’. That is, in patients undergoing antiretroviral treatment, the dormant virus in resting memory CD4 T cells would be rendered ‘awake’ and while these cells are replicating virus they would succumb to the action of virus-specific cytolytic T lymphocytes, but would not further spread virus due to the presence of effective antiretroviral therapy. The most prominent and current LRAs being used in clinical trials are derived from the class of histone deacetylase inhibitors (summarised at http://www.hdacis.com/index.html). The LRA approach has yet to definitively demonstrate functional or complete HIV cure and is still the focus of current clinical research.
The Berlin patient and HIV gene therapy
The only known example of a person to be cured of HIV is the Berlin patient.142, 143 In this setting, the patient had HIV infection for over 10 years and underwent treatment for acute myeloid leukaemia. The treatment consisted of chemotherapy, antithymocyte globulin, total body irradiation and finally a haematopoietic stem cell transplantation from a donor with a homozygous delta 32 mutation in the HIV coreceptor CCR5 (this mutation is well known to confer protection against R5 HIV isolates). Currently 5 years off therapy, the Berlin patient still has undetectable levels of HIV using current detection methodology. Given the complicated nature of treatment for this patient, it has been difficult to assess what level of treatment led to this phenotype. Two other patients, known as Boston patient A and Boston patient B, have undergone similar haematopoietic stem cell transplantation regimes, but with donors that carry the wild type form of CCR5. 144 Both Boston patients had rebound viral loads at 84 days and 225 days post HIV therapy interruption.145 Thus the process of stem cell transplantation may indeed need a donor with a homozygous delta 32 mutation or mimic to create an analogous situation to that of the Berlin patient.
The low frequency of donors who carry homozygous delta 32 mutation in the HIV coreceptor CCR5 has made the Berlin patient approach difficult in the context of overall feasibility.146 The hope is that gene therapy treatment of cells within patients with HIV infection might render cells ex vivo resistant to HIV infection, thereby not only mimicking those of the stem cell donor used in the Berlin patient, but also dealing with issues of graft versus host disease (as the genetically manipulated cells are derived from the same patient). Advancement in gene therapy techniques that can render donor cells resistant to HIV range from: lowering CCR5 expression levels; 147-152 expression of peptides that inhibit the HIV fusion reaction; 147, 152, 153 and post entry manipulation that can transcriptionally silence the virus and thus keep it permanently in a dormant state. 154-156 Treatment may also consist of combination approaches, for example, current clinical trials are underway that use both reduction CCR5 and expression of HIV fusion inhibiting peptides (http://www.businesswire.com/news/home/20150527005387/en#.VZDZGUZfcoS). While the latter gene therapies have great potential, delivery of the genetic information to the right cells still provides issues in terms of feasibility. Peripheral CD4 T cells for instance are notoriously difficult at taking on the genetic information using existing transduction techniques. 157
Footnote: Robert Oelrichs is a staff member of the International Bank for Reconstruction and Development/The World Bank. The findings, interpretations and conclusions presented in this article do not necessarily reflect the views of the Executive Directors of the World Bank or the Governments they represent.
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