Host switch

All diseases have an origin. Some disease circulate in human populations and are already known to epidemiologists, but evolution of the disease can result in a new strain of this disease emerging that makes it stronger - for example, multi-drug resistant tuberculosis. In other cases, diseases can be discovered that have not previously been observed or studied. These can emerge due to host switch events allowing the pathogen to evolve to become human-adapted and are only discovered due to an infection outbreak.

A pathogen that switches host emerges as a new form of the virus capable of circulating within a new population. Diseases that emerge in this sense can occur more often through human over exposure to the wildlife. This can be as a result of urbanisation, deforestation, destruction of wildlife habitats and changes to agricultural practise. The more exposure humans have to the wild, the more spillover infections occur and pathogens are exposed to human-specific selection pressures. The pathogen is therefore driven towards specific-specific adaptation and is more likely to gain the necessary mutations to jump the species barrier and become human-infective.

The problem with diseases emerging in new species is that the host population will be immunologically naïve. This means that the host has never been previously exposed to the pathogen and has no pre-existing antibodies or protection from the infection. This make host switching dangerous and can result in more pathogenic infections. The pathogen is not adapted to surviving in this new host and this imbalance of coevolutionary history may result in aggressive infections. However, this balance must be brought under control for the pathogen to maintain its infection in the new host and not burn through the population.

Influenza
Influenza virus has an 8 segment genome encapsulated within the viral matrix surrounded by the viral capsule containing the hemaglutinnin and neuraminidase proteins.
Virus classification
Group:	Group V ((−)ssRNA)
Family:	Orthomyxoviridae
Genus:	Alphainfluenzavirus
Species:	Influenza a virus

Influenza - also known as the flu - is one of the most well-known viruses that continues to pose a huge burden on today's health care systems and is the most common cause of human respiratory infections.[10] Influenza is an example of how a virus can continuously jump the species barrier in multiple isolated instances over time creating different human infecting strains circulating our populations - for example, H1N1, H5N1 and H7N9. These host switch events create pandemic strains that eventually transition into seasonal flu that annually circulates in the human population in colder months.

Influenza A viruses (IAVs) are classified by two defining proteins. These proteins are present in all influenza viral strains but small differences allow for differentiation of new strains. These identifiers are:

• hemagglutinin (HA)
• neuraminidase (NA)

IAVs naturally exist in wild birds without causing disease or symptoms. These birds, especially waterfowl and shore birds, are the reservoir host of the majority of IAVs with these HA and NA protein antigens.[11] From these animals, the virus spills into other species (e.g. pigs, humans, dogs [10]) creating smaller scale infections until the virus has acquired significant mutations to spread and maintain itself in another species. The RNA polymerase enzyme of influenza has low level accuracy due to a lack of a proofreading mechanism and therefore has a high error rate in terms of genetic replication.[10] Because of this, influenza has the capacity to mutate frequently dependent of the current selection pressures and has the capability to adapt to surviving in different host species.

Comparing IAVs in birds and humans, one of the main barriers to host switching is the type of cells the virus can recognise and bind to (cell tropism) in order to initiate infection and viral replication. An avian influenza virus is adapted to binding to the gastrointestinal tract of birds.[11] In bird populations, the virus is shed from the excretory system into the water and ingested by other birds to colonise their guts. This is not the case in humans as influenza, in this species, produces a respiratory infection. The virus here binds to respiratory tissue and is transmitted through breathing, talking and coughing, therefore the virus has to adapt in order to switch to the human host from avian populations. Additionally, the respiratory tract is mildly acidic and so the virus must also mutate to overcome these conditions in order to successfully colonise mammalian lungs and respiratory tracts. Acidic conditions are a trigger for viral uncoating as it is normally a sign the virus has penetrated a cell, however premature uncoating will result in virus exposure to the immune system leading killing of the virus.[12]

IAVs binds to host cells using the HA protein. These proteins recognise sialic acid that reside on the terminal regions of external glycoproteins on host cell membranes. However, HA proteins have different specificities for isomers of sialic acid depending on which species the IAV is adapted for. IAVs adapted for birds recognise α2-3 sialic acid isomers whereas human adapted IAV HAs bind to α2-6 isomers.[10] These are the isomers of sialic acid mostly present in the regions of the host that each IAVs infected respectively - i.e. the gastrointestinal tract of birds and the respiratory tract of humans. Therefore, in order to commit to a host switch, the HA specificity must mutate to the substrate receptors of the new host.

In the final stages of infection, the HA proteins are cleaved to activate the virus.[10] Certain hemagglutinin subtypes (H5 and H7) have the capacity to obtain additional mutations. These exist at the HA activation cleavage site which changes the HA specificity. This results in a broadening of the range of protease enzymes that can bind to and activate the virus. Therefore, this makes the virus more pathogenic and can make IAV infections more aggressive.[10]

Successfully binding to different host tissue is not the only requirement of host switch for influenza A. The influenza genome is replicated using the virus RNA-dependent RNA polymerase but it must adapt to use host specific cofactors in order to function.[13] The polyermase is a heterotrimeric complex and consists of 3 major domains: PB1, PB2 and PA. Each plays their own role in replication of the viral genome but PB2 is an important factor in the host range barrier as it interacts with host cap proteins.[10] Specifically, residue 627 of the PB2 unit shows to play a defining role in the host switch from avian to human adapted influenza strains. In IAVs, the residue at position 627 is glutamic acid (E) whereas in mammal infecting influenza, this residue is mutated to lysine (K).[13][14] Therefore, the virus must undergo a E627K mutation in order to perform a mammalian host switch. This region surrounding residue 627 forms a cluster protruding from the enzyme core. With lysine, this PB2 surface region can form a basic patch enabling host cofactor interaction, whereas the glutamic acid residue found in IAVs disrupt this basic region and subsequent interactions.[13]

The cellular protein ANP32A has been shown to account for contrasting levels of avian influenza interaction efficiency with different host species.[13][15] The key difference between ANP32A is that the avian form contains an additional 33 amino acids than the mammalian form.[15] When mammals cells are infected with avian IAVs, the polymerase enzyme efficiency is sub-optimal as the avian virus is not adapted to surviving in mammalian cells. However, when that mammalian cell contains the avian ANP32A protein, viral replication is mostly restored,[15] showing that the ANP32A is likely to positively interact and optimise the polymerase action. Mutations in the PB2 making the influenza mammal-adapted allow for the interaction between the viral polymerase and the mammalian ANP32A protein and therefore essential for the host switch.

There are many factor that determine a successful influenza host switch from avian to a mammalian host:

• Stability in the mildly acidic mammalian respiratory tract
• Recognition of mammalian sialic acid by HA receptors
• PB2 E627K mutation in the viral polymerase to allow for interaction with mammalian ANP32A for optimal viral replication

Each factor has a role to play and so the virus must acquire them all in order to undergo the host switch. This is a complex process and requires time for the virus to sufficiently adapt and mutate. Once each mutation has been achieved, the virus can infect human populations and has the potential to reach pandemic levels. However, this is dependent on virulence and rate of transmission and host switching will change these parameters of viral infection.

HIV
The human immunodeficiency viruses (both HIV1 and HIV2) exhibited evolutionary switches from non-human primates to humans.
Virus classification
Group:	Group VII (dsDNA-RT)
Family:	Retroviridae
Subfamily:	Orthoretrovirinae
Genus:	Lentivirus
Species:	HIV-1 and HIV-2

HIV is the human immunodeficiency virus and attacks cells of the immune system depleting the body's defence against incoming pathogens. In particular, HIV infects CD4⁺ T helper lymphocytes, a cell involved in the organisation and coordination of the immune response. This means that the body can recognise incoming pathogens but cannot trigger their defences against them.[16] When HIV sufficiently diminishes the immune system, it causes a condition known as acquired immunodeficiency syndrome or AIDS characterised by severe weight loss, fever, swollen lymph nodes and susceptibility to other severe infections [17]

HIV is a type of lentivirus of which two types are known to cause AIDS: HIV-1 and HIV-2,[16][18] both of which jumped into the human population from numerous cross-species transmission events by the equivalent disease in primates known as simian immunodeficiency virus (SIV). SIVs are found in many different primate species, including chimpanzees and mandrills found in sub-Saharan Africa, and for the most part are largely non pathogenic[18] HIV-1 and HIV-2 having similar features but are antigenically different and so are classed as different types of HIV.[18] Most transmission events are unsuccessful in switching its host, however in the context of HIV-1, four distinct forms emerged categorised as groups M, N, O and P of which group M is associated with pandemic HIV-1 and accounts for the majority of global cases. Each type is proposed to have emerged through bush-meat hunting and the exposure to the body fluids of infected primates,[18] including blood.

Host-specific selection pressures would bring about a change in the viral proteome of HIVs to suit the new host and therefore these regions would not be conserved when compared to SIVs. Through these viral proteomic comparisons, the viral matrix protein Gag-30 was identified as having differing amino acids at position 30. This amino acid is conserved as a methionine in SIVs but mutated to an arginine or lysine in HIV-1 groups M, N and O,[18][19] suggesting a strong selection pressure in the new host. This observation was supported by other data including the fact that this mutation was reversed when HIV-1 was used to infect primates meaning that the arginine or lysine converted back to the methionine originally observed in SIVs.[19] This reinforces the idea of the strong, opposing host-specific selection pressure between humans and primates. Additionally, it was observed that methionine containing viruses replicated more efficiently in primates and arginine/lysine containing viruses in humans.[19] This is evidence of the reason behind the mutation (optimal levels of replication in host CD4⁺ T lymphocytes), however the exact function and action of the position 30 amino acid is unknown.

Nef and Vpu proteins interact with different regions of tetherin. Nef proteins from SIV interact with the cytoplasmic domain due to the presence of the additional 33 amino acids found in primates. However, these extra amino acids are not present in human tetherin and so in HIV, the Vpu protein instead interacts with the conserved transmembrane domain of tetherin.

Tetherin is a defence protein in the innate immune response whose production is activation by interferon. Tetherin specifically inhibits the infective capabilities of HIV-1 by blocking its release from the cells it infects.[20] This prevents the virus from leaving to infect more cells and halts the progression of the infection giving the host defences time to destroy the viral-infected cells. Adapted viruses tend to have countermeasures to defend themselves against tetherin normally through degradation through specific regions of the protein. These anti-tetherin techniques are different between SIVs and HIV-1 showing that tetherin interaction is a host range restriction that must be overcome to enable a primate-human host switch. SIVs use the Nef protein to remove tetherin from the cell membrane whereas HIV-1 uses the Vpu protein degrade the defence protein.[18]

Tetherin is a conserved viral-defence mechanism across species but its exact sequence and structure shows some differences. The regions making up tetherin include the cytoplasmic region, transmembrane region, a coiled-coiled extracellular domain and a GPI anchor;[18] however, human tetherin defers to other primates by having a deletion in the cytoplasmic region.[21] This incomplete cytoplasmic domain renders Nef proteins found in SIVs ineffective as an anti-tetherin response in humans and so in order to switch from non-human primates to a human host, the SIV must activate the Vpu protein which instead blocks tetherin through interaction with the conserved transmembrane region.[21]

The two factors that are involved in the host range barrier for SIV to HIV viruses are:

• Gag-30 protein - specifically the amino acid at position 30
• The use of Nef or Vpu proteins as an anti-tetherin defence

Only a SIV virus containing both mutations of the Gag-30 protein and acquisition of the Vpu anti-tetherin protein will be able to undergo a host switch from primates to humans and become a HIV. This evolutionary adaptations allows the virus to acquire optimal levels of polymerase action in human infected cells and the ability to prevent destruction of the virus by tetherin.