Epidemiology
1.1. Origins
The human immunodeficiency virus (HIV) comes from the Genus Lentivirus and belongs to the family Reteroviridae, but is more commonly known as a retrovirus, characterised by having an RNA based genome [1]. HIV originated from the simian immunodeficiency virus (SIV) found in non-human primates (NHPs) such as monkeys, chimpanzees and apes. SIV was transmitted to chimpanzees after they hunted and ate two smaller species of monkeys which resulted in two different strains of SIV joining together to form SIVcpz; a strain of SIV that could infect humans [2].
There are two types of HIV, HIV-1 and HIV-2, both are part of the lentivirus subgroup of retroviruses but are distantly related from one another [3]. HIV-2, a much slower and less transmissible virus type was discovered to be transmitted from sooty mangabey monkeys and is mostly confined to the region of West Africa. The more prevalent HIV-1 virus, transmitted from apes, contains four subgroups that represent three distinct transmission events [6]. Three of these subgroups M (majority), O (outliers) and N (non-M/non-O) originated from chimpanzees and the fourth subgroup P originated from gorillas [4]. These subgroups are characterized through their transmissibility and virulence based on the sequence identity of the two viral genes env and gag [1].
1.2. Clades
Group M is the major subgroup responsible for the HIV pandemic, and is made up of numerous clades that are predominant in different parts of the world. Clade B predominates most through Western Europe, Australia and the Americas, whereas clades A, C, D and E are most predominant in developing countries such as sub-Saharan Africa and Asia [1]. The diversity in clades is due to the genetic composition of the viral genome; as a consequence of the error-prone viral reverse transcriptase that produces a very high mutation rate [4].
2. Structure and function
2.1. HIV-1 Virion Structure
HIV-1 virions are very complex in structure but the overall components are very typical for a retrovirus. Each viral particle has a spherical morphology, and is between 100-120nm in diameter [5]. They consist of a lipid bilayer membrane that is acquired upon maturation and budding from the infected cell, that acts as an envelope for the nucleocapsid which itself encloses the viral genome and all the replication machinery; a viral protease, reverse transcriptase and integrase (see figure 1) [3][5]. The HIV-1 genome is RNA based, consisting of two identical ssRNA molecules per virus particle approximately 9.7kb in length [5]. The viral genome encodes for several gene products that are essential for viral stability, entry into host and replication (see table 1).
2.2. Envelope Glycoprotein
The envelope glycoproteins gp41 and gp120 may be one of the most important structural features of the HIV-1 particle, as they act as the viral cell surface receptors, and have been the target of many broadly neutralising antibody vaccine attempts. Together they are responsible for the recognition of suitable target cells and the fusion of the viral envelope with the target cell’s plasma membrane to allow entry into host cells [3]. gp41 and gp120 are originally synthesized as a 845-870 amino acid (160 kDa) precursor polypeptide, gp160, in the rough endoplasmic reticulum, where high-mannose sugar chains are added to form the mature protein [7][8]. gp160 exists as trimer and is subsequently transported to the Golgi apparatus to undergo enzymatic cleavage by the viral protease, resulting in the non-covalently attached envelope glycoprotein gp120 and the transmembrane glycoprotein gp41 (see figure 2) [7][8][9].
The envelope glycoprotein gp120 possesses certain characteristics that help mask HIV-1 from the host’s immune cells [8]. gp120 is covered in complex carbohydrates which are then heavily glycosylated (a post-translational modification) in the Golgi by the addition of complex non-immunogenic sugars, preventing recognition by host antibodies [7][10]. In addition, this glycoprotein also confers sequence variability in specific immunodominant domains [8].
3. Transmission
Transmission of HIV-1 occurs as a result of exposure to viral particles contaminating blood, blood products or bodily secretion such as vaginal fluid or semen [21]. Some of the most prevalent methods of transmission include sexual transmission, sharing of needles, breast-feeding and sometimes HIV-1 can be transmitted from mother-to-child in the womb via the placenta [14].
For transmission to occur these secretions, contaminated with HIV-1 particles, must come into direct contact with a mucosal membrane, damaged tissue surfaces or be directly injected into the bloodstream (via a needle). HIV-1 transmission occurs most via receptive anal sex, followed by vaginal sex [22].
However, regardless of the mode of transmission, the probability that infection will occur has a (broadly) direct correlation with the concentration of HIV-1 in the secretion (viral load) [21]. Therefore, it has been shown by multiple studies that a subject is at higher risk during the acute phase of infection, while the virus is rapidly replicating, when viral load is much higher compared later on during infection when the virus is more latent [14][23].
4. Pathology of HIV-1
Understanding the pathophysiology of HIV-1 is a crucial concept in the development of vaccine prospects. This is because understanding the development of the disease from the initial infection process to replication of the viral genome and eventually budding of the mature virus particle can give insights to potential targets for specific therapies that may prevent HIV-1 infection or progression.
4.1. Viral Entry into Host Cells
HIV-1 gains entry into host cells through the fusion of the viral membrane with the target cell membrane [12]. Fusion of the cell membranes is mediated by the recognition and binding of its gp120 surface glycoprotein to the CD4 receptor found on CD4+ T-cells and certain sentinel cells [1]. The gp120 and CD4 interaction results in a conformational change of the HIV-1 surface glycoprotein exposing a binding site for specific chemokine co-receptors [9].
The chemokine co-receptor that is used to gain entry depends on the type of cell that the virus is infecting. HIV-1 strains can be separated into two groups based on their cell tropism; macrophage-tropic (M-tropic, also known as R5 viruses), use CCR5 to mediate entry into macrophages and primary T-cells (M-tropic lines have a higher sexual transmissibility), and T-cell line-tropic (T-tropic, also known as X4 viruses), that use CXCR4 to mediate entry into mainly CD4+ T-cells [12][13]. Upon binding to the chemokine co-receptor gp41 binds to heparin sulphate that is located on the host plasma membrane, triggering the fusion of the two membranes [1]. After fusion of viral and host membranes the viral capsid containing the viral genome an replicative machinery is released into the cytoplasm of the host cell [3][5].
During the acute phase of infection it is the M-tropic virus that predominates but later on as the chronic phase takes over both M-tropic and T-tropic viruses are recovered [1]. Studies have also shown that a mutation in the coding region of the CCR5 gene (a 32-bp deletion) provides protection against M-tropic strains of HIV-1 [14].
4.2. Viral Replication
Once the viral capsid is in the cytoplasm, the viral RNA genome and viral proteins are released [1]. The viral core is disassembled, stripped and converted to a reverse transcription complex (RTC) by certain cellular factors along with the viral proteins MA, Nef and Vif [5][15]. The heterodimeric viral reverse transcriptase then proceeds to reverse transcribe the two strands of viral RNA into complimentary DNA (cDNA) [15]. Upon synthesis of the cDNA, it is subsequently transported into the nucleus with the aid of two viral proteins Vpr and Vif. Vif is thought to assist in the nuclear translocation of the cDNA, whereas Vpr helps direct the pre-integration complex (PIC) to the nucleus (during reverse transcription the viral genome stays associated to the RTC but during nuclear translocation it becomes associated with the PIC)[1][5][15].
After the cDNA arrives in the nucleus, as a part of the PIC, it is integrated into the host cell genome through an integration reaction that is catalysed by the viral integrase [15]. Following integration, the first round of pro-viral transcription is carried out by the cellular RNA polymerase resulting in multiple viral mRNAs that encode specific proteins (see table 2). These mRNA transcripts are then translated into their constitutive proteins [1][15].
4.3. Assembly and Budding
Following translation of the mRNA transcripts into viral proteins, assembly of the virus particle can begin. The Gag precursor protein, pr55, is one of the most important proteins in the assembly process, as it contains determinants that target it to the plasma membrane of the infected host cell. Once at the plasma membrane Gag, associates with other Gag molecules (Gag-Gag interactions), which promotes assembly of progeny virions through encapsidating the viral genome and recruitment of the Env glycoproteins [15]. The Env precursor protein gp160 is transported to the cell surface via the secretory pathway (during transportation through the Golgi, the viral protease cleaves gp160 into gp41 and gp120). Directly after cleavage the transmembrane gp41 anchors the Env complex (gp41 non-covalently attached to gp120) to the membrane via its cytoplasmic tail domain [15].
To finally bud from the infected cell, retroviruses like HIV-1 encode particular sequences, L domains (late domain, referring to the late stage in replication) that stimulate particle release; this L domain is encoded in Gag. To undergo successful budding Nef, Env and Vpu are involved in this process to down-regulate expression of CD4 so that there are no interactions between the surface glycoprotein gp120 and CD4. Vpu has also been found to produce ion conductive pores that enhance viral release [5]. To acquire the viral envelope the capsid proteins (p24) condense and surround the viral genome towards the inner surface of the plasma membrane, resulting in the nucleocapsid being encapsulated in the envelope as it buds through the plasma membrane [3].
5. Pathophysiology of HIV-1
The pathophysiology of HIV-1 infection also uproots vital information that can aid in the development of an HIV-1 vaccine. Through knowing the development of the disease and how it causes this wide scale depletion of CD4+ T-cells allows researchers to identify potential mechanisms of the virus that could be exploited to cease further progression to AIDS.
The entire infection process of HIV-1 can be characterized by a four step progression that results in the development of AIDs [11].
1) The early and rapid infection of memory CD4+ T-cells, followed by their initial depletion, (known as the acute phase of infection).
2) Chronic activation of the immune system and further depletion of memory CD4+ T-cells along with the CD4+ T-cell pools, (known as the chronic phase of infection).
3) Destruction of the lymph nodes micro-environment, (compromises CD4+ homeostasis).
4) Suppression of thymic output, (affects CD4+ T-cell reconstitution).
To map the course of HIV infection, non-human primates (NHP) are infected with the non-human Simian Immunodeficiency Virus (SIV) which leads to the development of an AIDS-like disease. The infection of NHPs, in particular macaques with SIV, allows researchers to study the immunological event s that take place throughout infection with this HIV like disease.
5.1. Acute Phase of infection
The acute phase of infection occurs normally within the first few weeks after initial infection with the virus and is best characterized by the wide scale infection and depletion of CD4+ T-cells [18]. Upon infection at mucosal surfaces, immature dendritic cells (DCs) are the first line of defence against further penetration of the mucosal lamina [17]. Dendritic cells play an important role in the fight against the infection. HIV-1 binds to DCs via C-type lectin binding receptors, which is followed by the migration of the DCs to the draining lymph nodes where the viral particle is presented to CD4+ helper T-cells, resulting in HIV-specific immune responses [17][19]. Immune activation against HIV-1 is like a double edged sword; on the one hand studies have shown activation of HIV-1 specific CD8+ cytotoxic T-cells (mediated by the CD4+ helper T-cells) provides some sort of control against the rapidly replicating virus [17]. However, activation of the immune system results in the proliferation and differentiation of central memory and naïve CD4+ T-cells to CD4+ effector memory T-cells; providing more targets for the virus to infect [16].
Studies using SIV infected macaques have shown that the earliest targets of the HIV-1 virus are mucosal CCR5+ CD4+ memory T-cells (CD4+ T-cells expressing CCR5 as the co-receptor for HIV-1 were shown to predominantly be infected during the acute phase of infection, with CXCR4+ CD4+ T-cells developing during the chronic phase towards the end of infection; this is known as cell tropism) [11][16]. The mucosal-associated lymphoid tissue (MALT) is where the majority of CCR5+ CD4+ memory T-cells exist [17]. During the early stages of infection it has been shown that up to 60% of all memory CD4+ T-cells are infected, with 80% of them eventually being destroyed by fas-induced apoptosis shortly after infection [10][11]. The homeostatic properties of the immune system then signal the pools of naïve and central memory T-cells to proliferate and differentiate into more effector memory CD4+ T-cells to replace and regenerate the depleted mucosal environments [16].
5.2. Chronic Phase of infection
The chronic phase of HIV-1 infection is much longer lived, with the end result being the development of AIDS. It can be characterized by the repeated cycle that is the depletion of CD4+ effector memory T-cells, followed by the proliferation of central memory CD4+ T-cells (from the naive T-cell pool) into effector memory CD4+ T-cells [18][19]. Constant repetition of this cycle eventually drains and consumes the pools of naïve and resting memory cells (disrupts homeostatic properties), as well as being responsible for the destruction in lymph node architecture and suppression of thymic output [17].
The slow homeostatic failure within the immune system may fall down to limitations in the intrinsic or extrinsic abilities of the central memory/naïve CD4+ T-cells to self-renew (or to keep the balance between self-renewal and differentiation into effector memory CD4+ T-cells) [16].
Another mechanism that is accountable for CD4+ T-cell depletion is the disturbance of lymph node architecture [16]. Peripheral lymph nodes are organized in a certain way structural to generate an immunological response (production of CD4+/CD8+ T-cells) through the promotion of interactions between antigens, lymphocytes and cytokines. Destruction of the architecture arises from the repeated inflammation and tissue remodelling that is associated with local innate and adaptive immune responses [11].
The final mechanism that contributes to the overall depletion of CD4+ T-cells is the suppression of thymic output. Recent findings have indicated that infection by HIV indirectly inhibits proliferation of thymocytes, which therefore reduces the overall flux from central memory/naïve T-cells to effector-differentiated memory T-cells [11].