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Cross-species transmission (CST), also called interspecies transmission, host jump, or spillover, is the transmission of an infectious
pathogen In biology, a pathogen ( el, πάθος, "suffering", "passion" and , "producer of") in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a ger ...
, such as a
virus A virus is a wikt:submicroscopic, submicroscopic infectious agent that replicates only inside the living Cell (biology), cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and ...
, between hosts belonging to different
species In biology, a species is the basic unit of Taxonomy (biology), classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of ...
. Once introduced into an individual of a new host species, the pathogen may cause disease for the new host and/or acquire the ability to infect other individuals of the same species, allowing it to spread through the new host population. The phenomenon is most commonly studied in
virology Virology is the scientific study of biological viruses. It is a subfield of microbiology that focuses on their detection, structure, classification and evolution, their methods of infection and exploitation of host cells for reproduction, th ...
, but cross-species transmission may also occur with
bacterial Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...
pathogens or other types of microorganisms. Steps involved in the transfer of pathogens to new hosts include contact between the pathogen and the host; the successful
infection An infection is the invasion of tissues by pathogens, their multiplication, and the reaction of host tissues to the infectious agent and the toxins they produce. An infectious disease, also known as a transmissible disease or communicable d ...
of an initial individual host, which may lead to amplification and an
outbreak In epidemiology, an outbreak is a sudden increase in occurrences of a disease when cases are in excess of normal expectancy for the location or season. It may affect a small and localized group or impact upon thousands of people across an entire ...
; and the adaptation of the pathogen, within either the original or new host, which may render it capable of spreading efficiently between individuals in populations of the new host. The concept is important in understanding and controlling
emerging infectious disease An emerging infectious disease (EID) is an infectious disease whose incidence has increased recently (in the past 20 years), and could increase in the near future. The minority that are capable of developing efficient transmission between human ...
s in humans, especially those caused by viruses. Most viral diseases of humans are zoonotic in origin, having been historically transmitted to human populations from various animal species; examples include
SARS Severe acute respiratory syndrome (SARS) is a viral respiratory disease of zoonotic origin caused by the severe acute respiratory syndrome coronavirus (SARS-CoV or SARS-CoV-1), the first identified strain of the SARS coronavirus species, '' s ...
,
Ebola Ebola, also known as Ebola virus disease (EVD) and Ebola hemorrhagic fever (EHF), is a viral hemorrhagic fever in humans and other primates, caused by ebolaviruses. Symptoms typically start anywhere between two days and three weeks after bec ...
,
swine flu Swine influenza is an infection caused by any of several types of swine influenza viruses. Swine influenza virus (SIV) or swine-origin influenza virus (S-OIV) refers to any strain of the influenza family of viruses that is endemic in pigs. As ...
,
rabies Rabies is a viral disease that causes encephalitis in humans and other mammals. Early symptoms can include fever and tingling at the site of exposure. These symptoms are followed by one or more of the following symptoms: nausea, vomiting, vio ...
, and
avian influenza Avian influenza, known informally as avian flu or bird flu, is a variety of influenza caused by viruses adapted to birds.
. The exact mechanisms which facilitate cross-species transmission vary by pathogen, and even for common diseases are often poorly understood. It is believed that viruses with high mutation rates are able to rapidly adapt to new hosts and thereby overcome host-specific immunological defenses, allowing their continued transmission. A host shifting event occurs when a strain that was previously zoonotic begins to circulate exclusively among the new host species. Pathogen transfer is most likely to occur between species which are frequently in close contact with each other. It can also occur indirectly between species with less frequent contact if facilitated by an intermediary species; for example, a
reservoir A reservoir (; from French ''réservoir'' ) is an enlarged lake behind a dam. Such a dam may be either artificial, built to store fresh water or it may be a natural formation. Reservoirs can be created in a number of ways, including control ...
species may transfer the virus to a
vector Vector most often refers to: *Euclidean vector, a quantity with a magnitude and a direction *Vector (epidemiology), an agent that carries and transmits an infectious pathogen into another living organism Vector may also refer to: Mathematic ...
species, which in turn transfers the virus to humans. The degree of phylogenetic relatedness between host species also influences the likelihood that a pathogen is transmitted between them, likely because of the similarity of the hosts' immunological defenses; for example, most human zoonotic transmissions come from other species of mammals. Pathogens of more distantly related species, on the other hand, such as plant viruses, may not be capable of infecting humans at all. Other factors influencing transmission rates include geographic proximity and intraspecies behaviors. Due to
climate change In common usage, climate change describes global warming—the ongoing increase in global average temperature—and its effects on Earth's climate system. Climate change in a broader sense also includes previous long-term changes to ...
and land use expansion, the risk of viral spillover is predicted to significantly increase.


Prevalence and control

Cross-species transmission is the most significant cause of disease emergence in humans and other species.
Wildlife Wildlife refers to undomesticated animal species, but has come to include all organisms that grow or live wild in an area without being introduced by humans. Wildlife was also synonymous to game: those birds and mammals that were hunted f ...
zoonotic diseases of microbial origin are also the most common group of human emerging diseases, and CST between wildlife and
livestock Livestock are the domesticated animals raised in an agricultural setting to provide labor and produce diversified products for consumption such as meat, eggs, milk, fur, leather, and wool. The term is sometimes used to refer solely to anima ...
has appreciable economic impacts in agriculture by reducing livestock productivity and imposing export restrictions. This makes CST of major concern for
public health Public health is "the science and art of preventing disease, prolonging life and promoting health through the organized efforts and informed choices of society, organizations, public and private, communities and individuals". Analyzing the det ...
,
agriculture Agriculture or farming is the practice of cultivating plants and livestock. Agriculture was the key development in the rise of sedentary human civilization, whereby farming of domesticated species created food surpluses that enabled peop ...
, and
wildlife management Wildlife management is the management process influencing interactions among and between wildlife, its habitats and people to achieve predefined impacts. It attempts to balance the needs of wildlife with the needs of people using the best availab ...
. The authors of a study on the
bubonic plague Bubonic plague is one of three types of plague caused by the plague bacterium ('' Yersinia pestis''). One to seven days after exposure to the bacteria, flu-like symptoms develop. These symptoms include fever, headaches, and vomiting, as ...
in Oran stress that the disease "is primarily a bacterial zoonosis affecting
rodents Rodents (from Latin , 'to gnaw') are mammals of the order Rodentia (), which are characterized by a single pair of continuously growing incisors in each of the upper and lower jaws. About 40% of all mammal species are rodents. They are na ...
. It is caused by ''
Yersinia pestis ''Yersinia pestis'' (''Y. pestis''; formerly '' Pasteurella pestis'') is a gram-negative, non-motile, coccobacillus bacterium without spores that is related to both '' Yersinia pseudotuberculosis'' and '' Yersinia enterocolitica''. It is a facu ...
'' and is transmitted from animal to animal by
fleas Flea, the common name for the order Siphonaptera, includes 2,500 species of small flightless insects that live as external parasites of mammals and birds. Fleas live by ingesting the blood of their hosts. Adult fleas grow to about long, a ...
. Humans usually become infected through the bite of an infected rodent flea." The sanitary control measure instituted by the public health authority was chemical in nature: "Intra- and peridomestic spraying with
permethrin Permethrin is a medication and an insecticide. As a medication, it is used to treat scabies and lice. It is applied to the skin as a cream or lotion. As an insecticide, it can be sprayed onto clothing or mosquito nets to kill the insects tha ...
was conducted. Deltamethrin was dusted on the tracks and around the burrows of rodents located in a radius of 10 km around the dwelling of the patients. Uncontrolled killing of rats was prohibited." A large proportion of viral pathogens that have emerged recently in humans are considered to have originated from various animal species. This is shown by several recent epidemics such as,
avian flu Avian influenza, known informally as avian flu or bird flu, is a variety of influenza caused by viruses adapted to birds.Ebola Ebola, also known as Ebola virus disease (EVD) and Ebola hemorrhagic fever (EHF), is a viral hemorrhagic fever in humans and other primates, caused by ebolaviruses. Symptoms typically start anywhere between two days and three weeks after bec ...
,
monkeypox Monkeypox (also called mpox by the WHO) is an infectious viral disease that can occur in humans and some other animals. Symptoms include fever, swollen lymph nodes, and a rash that forms blisters and then crusts over. The time from exposur ...
, and
Hanta virus ''Orthohantavirus'' is a genus of single-stranded, enveloped, negative-sense RNA viruses in the family '' Hantaviridae'' within the order '' Bunyavirales''. Members of this genus may be called orthohantaviruses or simply hantaviruses. Orthohant ...
es. There is evidence to suggest that some diseases can potentially be re-introduced to human populations through animal hosts after they have been eradicated in humans. There is a risk of this phenomenon occurring with morbilliviruses as they can readily cross species barriers. CST can also have a significant effect on produce industries. Genotype VI-
Avian paramyxovirus ''Avulavirinae'' is a subfamily of viruses in the family '' Paramyxoviridae''. Members of the subfamily are collectively known as avulaviruses. All members of the subfamily primarily infect birds. ''Avulavirinae'' was previously recognized as the ...
serotype 1 (GVI-PMV1) is a virus that arose through cross-species transmission events from
Galliformes Galliformes is an order of heavy-bodied ground-feeding birds that includes turkeys, chickens, quail, and other landfowl. Gallinaceous birds, as they are called, are important in their ecosystems as seed dispersers and predators, and are ofte ...
(i.e.
chicken The chicken (''Gallus gallus domesticus'') is a domestication, domesticated junglefowl species, with attributes of wild species such as the grey junglefowl, grey and the Ceylon junglefowl that are originally from Southeastern Asia. Rooster ...
) to Columbiformes, and has become prevalent in the poultry industry. CST of
rabies Rabies is a viral disease that causes encephalitis in humans and other mammals. Early symptoms can include fever and tingling at the site of exposure. These symptoms are followed by one or more of the following symptoms: nausea, vomiting, vio ...
virus variants between many different species populations is a major concern of
wildlife management Wildlife management is the management process influencing interactions among and between wildlife, its habitats and people to achieve predefined impacts. It attempts to balance the needs of wildlife with the needs of people using the best availab ...
. Introduction of these variants into non-reservoir animals increases the risk of human exposures and threatens current advances toward rabies control. Many pathogens are thought to have host specialization, which explains the maintenance of distinct strains in host species. Pathogens would have to overcome their host specificity to cross to a new host species. Some studies have argued that host specializations may be exaggerated, and pathogens are more likely to exhibit CST than previously thought. Original hosts usually have low death rates when infected with a pathogen, with
fatality Fatality may refer to: * Fatality (''Mortal Kombat''), a finishing move, originated in the ''Mortal Kombat'' series of fighting games * Fatality (comics), a character published by DC Comics * Fatal1ty, the screen name of professional electronic s ...
rates tending to be much higher in new hosts


Between non-human primates and humans

Due to the close relation of
nonhuman primate Primates are a diverse order of mammals. They are divided into the strepsirrhines, which include the lemurs, galagos, and lorisids, and the haplorhines, which include the tarsiers and the simians (monkeys and apes, the latter including humans ...
s (NHP) and
human Humans (''Homo sapiens'') are the most abundant and widespread species of primate, characterized by bipedalism and exceptional cognitive skills due to a large and complex brain. This has enabled the development of advanced tools, culture, ...
s, disease transmission between NHP and humans is relatively common and can become a major public health concern. Diseases such as
HIV The human immunodeficiency viruses (HIV) are two species of '' Lentivirus'' (a subgroup of retrovirus) that infect humans. Over time, they cause acquired immunodeficiency syndrome (AIDS), a condition in which progressive failure of the immu ...
and human
adenovirus Adenoviruses (members of the family ''Adenoviridae'') are medium-sized (90–100 nm), nonenveloped (without an outer lipid bilayer) viruses with an icosahedral nucleocapsid containing a double-stranded DNA genome. Their name derives from t ...
es have been associated with NHP interactions. In places where contact between humans and NHPs is frequent, precautions are often taken to prevent disease transmission. Simian foamy viruses (SFV) is an
enzootic Enzootic is the non-human equivalent of endemic and means, in a broad sense, "belonging to" or "native to", "characteristic of", or "prevalent in" a particular geography, race, field, area, or environment; native to an area or scope. It also has ...
retrovirus A retrovirus is a type of virus that inserts a DNA copy of its RNA genome into the DNA of a host cell that it invades, thus changing the genome of that cell. Once inside the host cell's cytoplasm, the virus uses its own reverse transcriptase ...
that has high rates of cross-species transmission and has been known to affect humans bitten by infected NHPs. It has caused health concerns in places like Indonesia where visitors at monkey temples can contract SFV from temple macaques ('' Macaca fascicularis''). TMAdV ( titi monkey adenovirus) is a highly divergent, sharing <57% pairwise nucleotide identity with other adenoviruses, NHP virus that had a high fatality rate (83%) in monkeys and is capable of spreading through human hosts.


Predicting and preventing transmission between species

Prediction and monitoring are important for the study of CSTs and their effects. However, factors that determine the origin and fate of cross-species transmission events remain unclear for the majority of human pathogens. This has resulted in the use of different
statistical model A statistical model is a mathematical model that embodies a set of statistical assumptions concerning the generation of sample data (and similar data from a larger population). A statistical model represents, often in considerably idealized form, ...
s for the analysis of CST. Some of these include risk-analysis models, single rate dated tip (SRDT) models, and phylogenetic diffusion models. The study of the
genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ...
s of pathogens involved in CST events is very useful in determining their origin and fate. This is because a pathogens
genetic diversity Genetic diversity is the total number of Genetics, genetic characteristics in the genetic makeup of a species, it ranges widely from the number of species to differences within species and can be attributed to the span of survival for a species. ...
and
mutation In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA or viral replication, m ...
rate are key factors in determining if it can transmit across multiple hosts. This makes it important for the genomes of transmission species to be partially or completely sequenced. A change in genomic structure could cause a pathogen that has a narrow host range to become capable of exploiting a wider host range.
Genetic distance Genetic distance is a measure of the genetic divergence between species or between populations within a species, whether the distance measures time from common ancestor or degree of differentiation. Populations with many similar alleles have s ...
between different species, geographical range, and other interaction barriers will also influence cross-species transmission. One approach to risk assessment analysis of CST is to develop risk-analysis models that break the ‘‘process’’ of disease transmission into parts. Processes and interactions that could lead to cross-species disease transmission are explicitly described as a hypothetical infection chain. Data from laboratory and field experiments are used to estimate the probability of each component, expected natural variation, and margins of error. Different types of CST research would require different analysis pathways to meet their needs. A study on identification of viruses in bats that could spread to other mammals used the workflow: sequencing of genomic samples → “cleaning” of raw reads → elimination of host reads and eukaryotic contaminants → de novo assembly of the remaining reads → annotation of viral contigs → molecular detection of specific viruses → phylogenetic analysis → interpretation of data. Detecting CST and estimating its rate based on prevalence data is challenging. Due to these difficulties, computational methods are used to analyse CST events and the pathogens associated with them. The explosive development of
molecular A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bioch ...
techniques has opened new possibilities for using phylogenetic analysis of pathogen genetics to infer
epidemiological Epidemiology is the study and analysis of the distribution (who, when, and where), patterns and determinants of health and disease conditions in a defined population. It is a cornerstone of public health, and shapes policy decisions and evide ...
parameters. This provides some insight into the origins of these events and how they could be addressed. Methods of CST prevention are currently using both biological and computational data. An example of this is using both cellular
assay An assay is an investigative (analytic) procedure in laboratory medicine, mining, pharmacology, environmental biology and molecular biology for qualitatively assessing or quantitatively measuring the presence, amount, or functional activity of ...
s and
phylogenetic In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups o ...
comparisons to support a role for TRIM5α, the product of the TRIM5 gene, in suppressing interspecies transmission and emergence of retroviruses in nature.


Analysis


Phylogeny

The comparison of genomic data is very important for the study of cross-species transmission.
Phylogenetic analysis In biology Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of cells that pro ...
is used to compare genetic variation in both pathogens associated with CST and the host species that they infect. Taken together, it is possible to infer what allowed a pathogen to crossover to a new host (i.e. mutation in a pathogen, change in host susceptibility) and how this can be prevented in the future. If the mechanisms a pathogens uses to initially enter a new species are well characterized and understood a certain level of risk control and prevention can be obtained. In contact, a poor understanding of pathogens, and their associated diseases, makes it harder for preventive measures to be taken Alternative hosts can also potentially have a critical role in the evolution and diffusion of a pathogen. When a pathogen crosses species it often acquires new characteristics that allow it to breach host barriers. Different pathogen variants can have very different effects on host species. Thus it can be beneficial to CST analysis to compare the same pathogens occurring in different host species. Phylogenetic analysis can be used to track a pathogens history through different species populations. Even if a pathogen is new and highly divergent, phylogenetic comparison can be very insightful. A useful strategy for investigating the history of epidemics caused by pathogen transmission combines
molecular clock The molecular clock is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleo ...
analysis, to estimate the timescale of the epidemic, and
coalescent theory Coalescent theory is a model of how alleles sampled from a population may have originated from a common ancestor. In the simplest case, coalescent theory assumes no recombination, no natural selection, and no gene flow or population structu ...
, to infer the
demographic Demography () is the statistical study of populations, especially human beings. Demographic analysis examines and measures the dimensions and dynamics of populations; it can cover whole societies or groups defined by criteria such as edu ...
history of the pathogen. When constructing phylogenies, computer databases and tools are often used. Programs, such as BLAST, are used to annotate pathogen sequences, while databases like
GenBank The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a part ...
provide information about functions based on the pathogens genomic structure. Trees are constructed using computational methods such as MPR or Bayesian Inference, and models are created depending on the needs of the study. Single rate dated tip (SRDT) models, for example, allows for estimates of timescale under a phylogenetic tree. Models for CST prediction will vary depending on what parameters need to be accounted for when constructing the model.


Most parsimonious reconstruction (MPR)

Parsimony Parsimony refers to the quality of economy or frugality in the use of resources. Parsimony may also refer to * The Law of Parsimony, or Occam's razor, a problem-solving principle ** Maximum parsimony (phylogenetics), an optimality criterion in p ...
is the principle in which one chooses the simplest scientific explanation that fits the evidence. In terms of building phylogenetic trees, the best
hypothesis A hypothesis (plural hypotheses) is a proposed explanation for a phenomenon. For a hypothesis to be a scientific hypothesis, the scientific method requires that one can testable, test it. Scientists generally base scientific hypotheses on prev ...
is the one that requires the fewest evolutionary changes. Using parsimony to reconstruct ancestral character states on a phylogenetic tree is a method for testing
ecological Ecology () is the study of the relationships between living organisms, including humans, and their biophysical environment, physical environment. Ecology considers organisms at the individual, population, community (ecology), community, ecosy ...
and
evolutionary Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation t ...
hypotheses. This method can be used in CST studies to estimate the number of character changes that exist between pathogens in relation to their host. This makes MPR useful for tracking a CST pathogen to its origins. MPR can also be used to the compare traits of host species populations. Traits and behaviours within a population could make them more susceptible to CST. For example, species which
migrate Migration, migratory, or migrate may refer to: Human migration * Human migration, physical movement by humans from one region to another ** International migration, when peoples cross state boundaries and stay in the host state for some minimum le ...
regionally are important for spreading viruses through population networks. Despite the success of parsimony reconstructions, research suggests they are often sensitive and can sometimes be prone to bias in complex models. This can cause problems for CST models that have to consider many variables. Alternatives methods, such as maximum likelihood, have been developed as an alternative to parsimony reconstruction.


Using genetic markers

Two methods of measuring genetic variation,
variable number tandem repeat A variable number tandem repeat (or VNTR) is a location in a genome where a short nucleotide sequence is organized as a tandem repeat. These can be found on many chromosomes, and often show variations in length (number of repeats) among individ ...
s (VNTRs) and single nucleotide polymorphisms (SNPs), have been very beneficial to the study of bacterial transmission. VNTRs, due to the low cost and high mutation rates, make them particularly useful to detect genetic differences in recent
outbreak In epidemiology, an outbreak is a sudden increase in occurrences of a disease when cases are in excess of normal expectancy for the location or season. It may affect a small and localized group or impact upon thousands of people across an entire ...
s, and while SNPs have a lower mutation rate per locus than VNTRs, they deliver more stable and reliable genetic relationships between isolates. Both methods are used to construct phylogenies for genetic analysis, however, SNPs are more suitable for studies on phylogenies contraction. However, it can be difficult for these methods to accurately simulate CSTs everts. Estimates of CST based on
phylogenies A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...
made using the VNTR marker can be biased towards detecting CST events across a wide range of the parameters. SNPs tend to be less biased and variable in estimates of CST when estimations of CST rates are low and a low number of SNPs is used. In general, CST rate estimates using these methods are most reliable in systems with more mutations, more markers, and high genetic differences between introduced strains. CST is very complex and models need to account for a lot of parameters to accurately represent the phenomena. Models that oversimplify reality can result in biased data. Multiple parameters such as number of mutations accumulated since introduction, stochasticity, the genetic difference of strains introduced, and the sampling effort can make unbiased estimates of CST difficult even with whole-genome sequences, especially if sampling is limited, mutation rates are low, or if pathogens were recently introduced. More information on the factors that influence CST rates is needed for the contraction of more appropriate models to study these events. The process of using genetic markers to estimate CST rates should take into account several important factors to reduce bias. One is that the phylogenetic tree constructed in the analysis needs to capture the underlying epidemiological process generating the tree. The models need to account for how the genetic variability of a pathogen influences a disease in a species, not just general differences in genomic structure. Two, the strength of the analysis will depend on the amount of mutation accumulated since the pathogen was introduced in the system. This is due to many models using the number of mutations as an indicator of CST frequency. Therefore, efforts are focused on estimating either time since the introduction or the substitution rate of the marker (from laboratory experiments or genomic comparative analysis). This is important not only when using the MPR method but also for
Likelihood The likelihood function (often simply called the likelihood) represents the probability of random variable realizations conditional on particular values of the statistical parameters. Thus, when evaluated on a given sample, the likelihood funct ...
approaches that require an estimation of the mutation rate. Three, CST will also affect disease prevalence in the potential host, so combining both epidemiological time series data with genetic data may be an excellent approach to CST study


Bayesian analysis

Bayesian frameworks are a form of maximum likelihood-based analyses and can be very effective in cross-species transmission studies. Bayesian inference of character evolution methods can account for phylogenetic tree uncertainty and more complex scenarios, with models such as the character diffusion model currently being developed for the study of CST in
RNA virus An RNA virus is a virusother than a retrovirusthat has ribonucleic acid (RNA) as its genetic material. The nucleic acid is usually single-stranded RNA ( ssRNA) but it may be double-stranded (dsRNA). Notable human diseases caused by RNA viruse ...
es. A Bayesian statistical approach presents advantages over other analyses for tracking CST origins. Computational techniques allow integration over an unknown phylogeny, which cannot be directly observed, and unknown migration process, which is usually poorly understood. The Bayesian frameworks are also well suited to bring together different kinds of information. The BEAST software, which has a strong focus on calibrated phylogenies and genealogies, illustrates this by offering a large number of complementary evolutionary models including substitution models, demographic and relaxed clock models that can be combined into a full probabilistic model. By adding spatial reconstruction, these models create the probability of
biogeographical Biogeography is the study of the distribution of species and ecosystems in geographic space and through geological time. Organisms and biological communities often vary in a regular fashion along geographic gradients of latitude, elevation, ...
history reconstruction from genetic data. This could be useful for determining the origins of cross-species transmissions. The high effectiveness of Bayesian statistical methods has made them instrumental in evolutionary studies. Bayesian ancestral host reconstruction under discrete diffusion models can be used to infer the origin and effects of pathogens associated with CST. One study on Human adenoviruses using Bayesian supported a
gorilla Gorillas are herbivorous, predominantly ground-dwelling great apes that inhabit the tropical forests of equatorial Africa. The genus ''Gorilla'' is divided into two species: the eastern gorilla and the western gorilla, and either four ...
and chimpanzee origin for the viral species, aiding prevention efforts. Despite presumably rare direct contact between sympatric populations of the two species, CST events can occur between them. The study also determined that two independent HAdV-B transmission events to humans occurred and that the HAdV-Bs circulating in humans are of zoonotic origin and have probably affected global health for most of our species lifetime. Phylogenetic diffusion models are frequently used for phylogeographic analyses, with the inference of host jumping becoming of increasing interest. The Bayesian inference approach enables model averaging over several potential diffusion predictors and estimates the support and contribution of each predictor while marginalizing over phylogenetic history. For studying viral CST, the flexibility of the Bayesian statistical framework allows for the reconstruction of virus transmission between different host species while simultaneously testing and quantifying the contribution of multiple ecological and evolutionary influences of both CST spillover and host shifting. One study on rabies in bats showed geographical range overlap is a modest predictor for CST, but not for host shifts. This highlights how Bayesian inferences in models can be used for CST analysis.


See also

*
Mathematical modelling of infectious disease Mathematical models can project how infectious diseases progress to show the likely outcome of an epidemic (including in plants) and help inform public health and plant health interventions. Models use basic assumptions or collected statistics alo ...
* Reverse zoonosis * Spillover infection *
Vector Vector most often refers to: *Euclidean vector, a quantity with a magnitude and a direction *Vector (epidemiology), an agent that carries and transmits an infectious pathogen into another living organism Vector may also refer to: Mathematic ...
*
Zoonosis A zoonosis (; plural zoonoses) or zoonotic disease is an infectious disease of humans caused by a pathogen (an infectious agent, such as a bacterium, virus, parasite or prion) that has jumped from a non-human (usually a vertebrate) to a human. ...
* Feline zoonosis


References


External links

*
Bayesian modeling book
and examples available for downloading. *
Bayesian statistics Bayesian statistics is a theory in the field of statistics based on the Bayesian interpretation of probability where probability expresses a ''degree of belief'' in an event. The degree of belief may be based on prior knowledge about the event, ...
at Wikiversity * {{Concepts in infectious disease Epidemiology Viruses Zoonoses