Classification HIV is a member of the
genus Lentivirus, part of the family
Retroviridae. Lentiviruses have many
morphologies and
biological properties in common. Many species are infected by lentiviruses, which are characteristically responsible for long-duration illnesses with a long
incubation period. Lentiviruses are transmitted as
single-stranded, positive-
sense,
enveloped RNA viruses. Upon entry into the target cell, the viral
RNA genome is converted (reverse transcribed) into double-stranded
DNA by a virally encoded enzyme,
reverse transcriptase, that is transported along with the viral genome in the virus particle. The resulting viral DNA is then imported into the
cell nucleus and integrated into the cellular DNA by a virally encoded enzyme,
integrase, and host
co-factors. Once integrated, the virus may become
latent, allowing the virus and its host cell to avoid detection by the immune system, for an indeterminate amount of time. The virus can remain dormant in the human body for up to ten years after primary infection; during this period the virus does not cause symptoms. Alternatively, the integrated viral DNA may be
transcribed, producing new RNA genomes and viral proteins, using host cell resources, that are packaged and released from the cell as new virus particles that will begin the replication cycle anew. Two types of HIV have been characterized: HIV-1 and HIV-2. HIV-1 is the virus that was initially discovered and termed both lymphadenopathy associated virus (LAV) and human T-lymphotropic virus 3 (HTLV-III). HIV-1 is more
virulent and more
infective than HIV-2, and is the cause of the majority of HIV infections globally. The lower infectivity of HIV-2, compared to HIV-1, implies that fewer of those exposed to HIV-2 will be infected per exposure. Due to its relatively poor capacity for transmission, HIV-2 is largely confined to
West Africa. Both HIV-1 and HIV-2 have gained an additional classification according to the
International Committee on Taxonomy of Viruses, with the change being approved in 2020, to belong to the species called "
Lentivirus humimdef1" and "
Lentivirus humimdef2" for HIV-1 and HIV-2 respectively.
Structure and genome HIV is similar in structure to other retroviruses. It is roughly spherical with a diameter of about 120
nm, around 100,000 times smaller in volume than a
red blood cell. It is composed of two copies of positive-
sense single-stranded RNA that codes for the virus' nine
genes enclosed by a ovoidal
capsid composed of 2,000 copies of the viral protein
p24. The single-stranded RNA is tightly bound to nucleocapsid proteins, p7, and enzymes needed for the development of the virion such as
reverse transcriptase,
proteases,
ribonuclease and
integrase. A matrix composed of the viral protein p17 surrounds the capsid ensuring the integrity of the virion particle. The envelope protein, encoded by the HIV
env gene, allows the virus to attach to target cells and fuse the viral envelope with the target
cell's membrane releasing the viral contents into the cell and initiating the infectious cycle. Over half of the mass of the trimeric envelope spike is N-linked
glycans. The density is high as the glycans shield the underlying viral protein from neutralisation by antibodies. This is one of the most densely glycosylated molecules known and the density is sufficiently high to prevent the normal maturation process of glycans during biogenesis in the endoplasmic and Golgi apparatus. The majority of the glycans are therefore stalled as immature 'high-mannose' glycans not normally present on human glycoproteins that are secreted or present on a cell surface. The unusual processing and high density means that almost all broadly neutralising antibodies that have so far been identified (from a subset of patients that have been infected for many months to years) bind to, or are adapted to cope with, these envelope glycans. The molecular structure of the viral spike has now been determined by
X-ray crystallography and
cryogenic electron microscopy. These advances in structural biology were made possible due to the development of stable
recombinant forms of the viral spike by the introduction of an intersubunit
disulphide bond and an
isoleucine to
proline mutation (
radical replacement of an amino acid) in gp41. The so-called SOSIP
trimers not only reproduce the antigenic properties of the native viral spike, but also display the same degree of immature glycans as presented on the native virus. Recombinant trimeric viral spikes are promising vaccine candidates as they display less non-neutralising
epitopes than recombinant monomeric gp120, which act to suppress the immune response to target epitopes. The RNA genome consists of at least seven structural landmarks (
LTR,
TAR,
RRE, PE, SLIP, CRS, and INS), and nine genes (
gag,
pol, and
env,
tat,
rev,
nef,
vif,
vpr,
vpu, and sometimes a tenth
tev, which is a fusion of
tat,
env and
rev), encoding 19 proteins. Three of these genes,
gag,
pol, and
env, contain information needed to make the structural proteins for new virus particles. The
rev protein (p19) is involved in shuttling RNAs from the nucleus and the cytoplasm by binding to the
RRE RNA element. The
vif protein (p23) prevents the action of
APOBEC3G (a cellular protein that
deaminates cytidine to
uridine in the single-stranded viral DNA and/or interferes with reverse transcription). The
vpr protein (p14) arrests
cell division at
G2/M. The
nef protein (p27) down-regulates
CD4 (the major viral receptor), as well as the
MHC class I and
class II molecules.
Nef also interacts with
SH3 domains. The
vpu protein (p16) influences the release of new virus particles from infected cells. Macrophage-tropic (M-tropic) strains of HIV-1, or non-
syncytia-inducing strains (NSI; now called R5 viruses) use the
β-chemokine receptor,
CCR5, for entry and are thus able to replicate in both macrophages and CD4+ T cells. This CCR5 co-receptor is used by almost all primary HIV-1 isolates regardless of viral genetic subtype. Indeed, macrophages play a key role in several critical aspects of HIV infection. They appear to be the first cells infected by HIV and perhaps the source of HIV production when CD4+ cells become depleted in the patient. Macrophages and microglial cells are the cells infected by HIV in the
central nervous system. In the
tonsils and
adenoids of HIV-infected patients, macrophages fuse into multinucleated
giant cells that produce huge amounts of virus. T-tropic strains of HIV-1, or
syncytia-inducing strains (SI; now called X4 viruses Dual-tropic HIV-1 strains are thought to be transitional strains of HIV-1 and thus are able to use both CCR5 and CXCR4 as co-receptors for viral entry. The
α-chemokine
SDF-1, a
ligand for CXCR4, suppresses replication of T-tropic HIV-1 isolates. It does this by
down-regulating the expression of CXCR4 on the surface of HIV target cells. M-tropic HIV-1 isolates that use only the CCR5 receptor are termed R5; those that use only CXCR4 are termed X4, and those that use both, X4R5. However, the use of co-receptors alone does not explain viral tropism, as not all R5 viruses are able to use CCR5 on macrophages for a productive infection which probably constitute a
reservoir that maintains infection when CD4+ T cell numbers have declined to extremely low levels. Some people are resistant to certain strains of HIV. For example, people with the
CCR5-Δ32 mutation are resistant to infection by the R5 virus, as the mutation leaves HIV unable to bind to this co-receptor, reducing its ability to infect target cells.
Sexual intercourse is the major mode of HIV transmission. Both X4 and R5 HIV are present in the
seminal fluid, which enables the virus to be transmitted from a male to his
sexual partner. The virions can then infect numerous cellular targets and disseminate into the whole organism. However, a selection process leads to a predominant transmission of the R5 virus through this pathway, hypothesized to be because some variants may more easily infect cells when entering the body, or because some variants replicate more efficiently after initial infection and become the dominant variant in blood. In patients infected with subtype B HIV-1, there is often a co-receptor switch in late-stage disease and T-tropic variants that can infect a variety of T cells through CXCR4. These variants then replicate more aggressively with heightened virulence that causes rapid T cell depletion, immune system collapse, and opportunistic infections that mark the advent of AIDS. HIV-positive patients acquire an enormously broad spectrum of opportunistic infections, which was particularly problematic prior to the onset of
HAART therapies; however, the same infections are reported among HIV-infected patients examined post-mortem following the onset of antiretroviral therapies. HIV-2 is much less pathogenic than HIV-1 and is restricted in its worldwide distribution to
West Africa. The adoption of "accessory genes" by HIV-2 and its more
promiscuous pattern of co-receptor usage (including CD4-independence) may assist the virus in its adaptation to avoid innate restriction factors present in host cells. Adaptation to use normal cellular machinery to enable transmission and productive infection has also aided the establishment of HIV-2 replication in humans. A survival strategy for any infectious agent is not to kill its host, but ultimately become a
commensal organism. Having achieved a low pathogenicity, over time, variants that are more successful at transmission will be selected.
Replication cycle Entry to the cell The HIV virion enters
macrophages and CD4+
T cells by the
adsorption of
glycoproteins on its surface to receptors on the target cell followed by fusion of the
viral envelope with the target cell membrane and the release of the HIV capsid into the cell. Entry to the cell begins through interaction of the trimeric envelope complex (
gp160 spike) on the HIV viral envelope and both
CD4 and a chemokine co-receptor (generally either
CCR5 or
CXCR4, but others are known to interact) on the target cell surface. The gp160 spike contains binding domains for both CD4 and chemokine receptors. DCs are one of the first cells encountered by the virus during sexual transmission. They are currently thought to play an important role by transmitting HIV to T cells when the virus is captured in the
mucosa by DCs. HIV-1 entry, as well as entry of many other retroviruses, has long been believed to occur exclusively at the plasma membrane. More recently, however, productive infection by
pH-independent,
clathrin-mediated endocytosis of HIV-1 has also been reported and was recently suggested to constitute the only route of productive entry.
Replication and transcription of the HIV
genome into
double-stranded DNA Shortly after the viral capsid enters the cell, an
enzyme called
reverse transcriptase liberates the positive-sense single-stranded
RNA genome from the attached viral proteins and copies it into a
complementary DNA (cDNA) molecule. The process of reverse transcription is extremely error-prone, and the resulting mutations may cause
drug resistance or allow the virus to evade the body's immune system. The reverse transcriptase also has ribonuclease activity that degrades the viral RNA during the synthesis of cDNA, as well as DNA-dependent DNA polymerase activity that creates a
sense DNA from the
antisense cDNA. Together, the cDNA and its complement form a double-stranded viral DNA that is then transported into the
cell nucleus. The integration of the viral DNA into the host cell's
genome is carried out by another viral enzyme called
integrase. This means that those cells most likely to be targeted, entered and subsequently killed by HIV are those actively fighting infection. During viral replication, the integrated DNA
provirus is
transcribed into RNA. The full-length genomic RNAs (gRNA) can be packaged into new viral particles in a
pseudodiploid form. The selectivity in the packaging is explained by the structural properties of the dimeric conformer of the gRNA. The gRNA dimer is characterized by a tandem three-way junction within the gRNA monomer, in which the SD and AUG
hairpins, responsible for splicing and translation respectively, are sequestered and the DIS (dimerization initiation signal) hairpin is exposed. The formation of the gRNA dimer is mediated by a 'kissing' interaction between the DIS hairpin loops of the gRNA monomers. At the same time, certain guanosine residues in the gRNA are made available for binding of the nucleocapsid (NC) protein leading to the subsequent virion assembly. The labile gRNA dimer has been also reported to achieve a more stable conformation following the NC binding, in which both the DIS and the U5:AUG regions of the gRNA participate in extensive base pairing. RNA can also be
processed to produce mature
messenger RNAs (mRNAs). In most cases, this processing involves
RNA splicing to produce mRNAs that are shorter than the full-length genome. Which part of the RNA is removed during RNA splicing determines which of the HIV protein-coding sequences is translated. Mature HIV mRNAs are exported from the nucleus into the
cytoplasm, where they are
translated to produce HIV proteins, including
Rev. As the newly produced Rev protein is produced it moves to the nucleus, where it binds to full-length, unspliced copies of virus RNAs and allows them to leave the nucleus. Some of these full-length RNAs function as mRNAs that are translated to produce the structural proteins Gag and Env. Gag proteins bind to copies of the virus RNA genome to package them into new virus particles. HIV-1 and HIV-2 appear to package their RNA differently. HIV-1 will bind to any appropriate RNA. HIV-2 will preferentially bind to the mRNA that was used to create the Gag protein itself.
Recombination Two RNA genomes are encapsidated in each HIV-1 particle (see
Structure and genome of HIV). Upon infection and replication catalyzed by reverse transcriptase, recombination between the two genomes can occur. Recombination occurs as the single-strand, positive-sense RNA genomes are reverse transcribed to form DNA. During reverse transcription, the nascent DNA can switch multiple times between the two copies of the viral RNA. This form of recombination is known as copy-choice. Recombination events may occur throughout the genome. Anywhere from two to 20 recombination events per genome may occur at each replication cycle, and these events can rapidly shuffle the genetic information that is transmitted from parental to progeny genomes. Recombination may also contribute, in principle, to overcoming the immune defenses of the host. Yet, for the adaptive advantages of genetic variation to be realized, the two viral genomes packaged in individual infecting virus particles need to have arisen from separate progenitor parental viruses of differing genetic constitution. It is unknown how often such mixed packaging occurs under natural conditions. Bonhoeffer
et al. suggested that template switching by reverse transcriptase acts as a repair process to deal with breaks in the single-stranded RNA genome. In addition, Hu and Temin Thus, the HIV genome may be vulnerable to
oxidative damage, including breaks in the single-stranded RNA. For HIV, as well as for viruses in general, successful infection depends on overcoming host defense strategies that often include production of genome-damaging reactive oxygen species. Thus, Michod
et al. suggested that recombination by viruses is an adaptation for repair of genome damage, and that recombinational variation is a byproduct that may provide a separate benefit.
Assembly and release of an infected
macrophage. The HIV virions have been marked with a green
fluorescent tag and then viewed under a fluorescent microscope. The final step of the viral cycle, assembly of new HIV-1 virions, begins at the
plasma membrane of the host cell. The Env polyprotein (gp160) goes through the
endoplasmic reticulum and is transported to the
Golgi apparatus where it is
cleaved by
furin resulting in the two HIV envelope glycoproteins,
gp41 and
gp120. These are transported to the plasma membrane of the host cell where gp41 anchors gp120 to the membrane of the infected cell. The Gag (p55) and Gag-Pol (p160) polyproteins also associate with the inner surface of the plasma membrane along with the HIV genomic RNA as the forming virion begins to bud from the host cell. The budded virion is still immature as the
gag polyproteins still need to be cleaved into the actual matrix, capsid and nucleocapsid proteins. This cleavage is mediated by the packaged viral protease and can be inhibited by antiretroviral drugs of the
protease inhibitor class. The various structural components then assemble to produce a mature HIV virion. Only mature virions are then able to infect another cell.
Spread within the body The classical process of infection of a cell by a virion can be called "cell-free spread" to distinguish it from a more recently recognized process called "cell-to-cell spread". In cell-free spread (see figure), virus particles bud from an infected T cell, enter the blood or
extracellular fluid and then infect another T cell following a chance encounter. Secondly, an
antigen-presenting cell (APC), such as a macrophage or dendritic cell, can transmit HIV to T cells by a process that either involves productive infection (in the case of macrophages) or capture and transfer of virions
in trans (in the case of dendritic cells). Whichever pathway is used, infection by cell-to-cell transfer is reported to be much more efficient than cell-free virus spread. A number of factors contribute to this increased efficiency, including polarised virus budding towards the site of cell-to-cell contact, close apposition of cells, which minimizes fluid-phase
diffusion of virions, and clustering of HIV entry receptors on the target cell towards the contact zone. The many dissemination mechanisms available to HIV contribute to the virus' ongoing replication in spite of anti-retroviral therapies.
Genetic variability of the SIV and HIV HIV differs from many viruses in that it has very high
genetic variability. This diversity is a result of its fast
replication cycle, with the generation of about 1010 virions every day, coupled with a high
mutation rate of approximately 3 × 10−5 per
nucleotide base per cycle of replication and
recombinogenic properties of reverse transcriptase. Some estimates put HIV's mutation rate as high as 4.1 × 10−3 substitutions per base pair, making HIV the microbe with the highest mutation rate known by far. A 2014 study estimated that about 15−20% of all HIV mutations are due to recombination, numbering roughly 1.35 × 10−3 recombination events per nucleotide (REPN) per replication cycle. This complex scenario leads to the generation of many variants of HIV in a single infected patient in the course of one day. which is present at high levels in the host's blood, but evokes only a mild immune response, does not cause the development of simian AIDS, and does not undergo the extensive mutation and recombination typical of HIV infection in humans. In contrast, when these strains infect species that have not adapted to SIV ("heterologous" or similar hosts such as
rhesus or
cynomologus macaques), the animals develop AIDS and the virus generates
genetic diversity similar to what is seen in human HIV infection.
Chimpanzee SIV (SIVcpz), the closest genetic relative of HIV-1, is associated with increased mortality and AIDS-like symptoms in its natural host. SIVcpz appears to have been transmitted relatively recently to chimpanzee and human populations, so their hosts have not yet adapted to the virus. Three groups of HIV-1 have been identified on the basis of differences in the envelope (
env) region: M, N, and O. Group M is the most prevalent and is subdivided into eight subtypes (or
clades), based on the whole genome, which are geographically distinct. The most prevalent are subtypes B (found mainly in North America and Europe), A and D (found mainly in Africa), and C (found mainly in Africa and Asia); these subtypes form branches in the
phylogenetic tree representing the lineage of the M group of HIV-1.
Co-infection with distinct subtypes gives rise to circulating recombinant forms (CRFs). In 2000, the last year in which an analysis of global subtype prevalence was made, 47.2% of infections worldwide were of subtype C, 26.7% were of subtype A/CRF02_AG, 12.3% were of subtype B, 5.3% were of subtype D, 3.2% were of CRF_AE, and the remaining 5.3% were composed of other subtypes and CRFs. Most HIV-1 research is focused on subtype B; few laboratories focus on the other subtypes. The existence of a fourth group, "P", has been hypothesised based on a virus isolated in 2009. The strain is apparently derived from
gorilla SIV (SIVgor), first isolated from
western lowland gorillas in 2006. == Diagnosis ==