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subsection</span> </button> <ul id="toc-Prevalence_and_control-sublist" class="vector-toc-list"> <li id="toc-Between_non-human_primates_and_humans" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Between_non-human_primates_and_humans"> <div class="vector-toc-text"> <span class="vector-toc-numb">1.1</span> <span>Between non-human primates and humans</span> </div> </a> <ul id="toc-Between_non-human_primates_and_humans-sublist" class="vector-toc-list"> </ul> </li> </ul> </li> <li id="toc-Predicting_and_preventing_transmission_between_species" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#Predicting_and_preventing_transmission_between_species"> <div class="vector-toc-text"> <span class="vector-toc-numb">2</span> <span>Predicting and preventing transmission between species</span> </div> </a> <ul id="toc-Predicting_and_preventing_transmission_between_species-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Analysis" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#Analysis"> <div class="vector-toc-text"> <span class="vector-toc-numb">3</span> <span>Analysis</span> </div> </a> <button aria-controls="toc-Analysis-sublist" class="cdx-button cdx-button--weight-quiet cdx-button--icon-only vector-toc-toggle"> <span class="vector-icon mw-ui-icon-wikimedia-expand"></span> <span>Toggle Analysis subsection</span> </button> <ul id="toc-Analysis-sublist" class="vector-toc-list"> <li id="toc-Phylogeny" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Phylogeny"> <div class="vector-toc-text"> <span class="vector-toc-numb">3.1</span> <span>Phylogeny</span> </div> </a> <ul id="toc-Phylogeny-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Most_parsimonious_reconstruction_(MPR)" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Most_parsimonious_reconstruction_(MPR)"> <div class="vector-toc-text"> <span class="vector-toc-numb">3.2</span> <span>Most parsimonious reconstruction (MPR)</span> </div> </a> <ul id="toc-Most_parsimonious_reconstruction_(MPR)-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Using_genetic_markers" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Using_genetic_markers"> <div class="vector-toc-text"> <span class="vector-toc-numb">3.3</span> <span>Using genetic markers</span> </div> </a> <ul id="toc-Using_genetic_markers-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Bayesian_analysis" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Bayesian_analysis"> <div class="vector-toc-text"> <span class="vector-toc-numb">3.4</span> <span>Bayesian analysis</span> </div> </a> <ul id="toc-Bayesian_analysis-sublist" class="vector-toc-list"> </ul> </li> </ul> </li> <li id="toc-See_also" 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0;overflow:hidden;width:238px;border-collapse:collapse;font-size:88%;line-height:1.25em}.mw-parser-output .ambox-speedy{border-left:10px solid #b32424;background-color:#fee7e6}.mw-parser-output .ambox-delete{border-left:10px solid #b32424}.mw-parser-output .ambox-content{border-left:10px solid #f28500}.mw-parser-output .ambox-style{border-left:10px solid #fc3}.mw-parser-output .ambox-move{border-left:10px solid #9932cc}.mw-parser-output .ambox-protection{border-left:10px solid #a2a9b1}.mw-parser-output .ambox .mbox-text{border:none;padding:0.25em 0.5em;width:100%}.mw-parser-output .ambox .mbox-image{border:none;padding:2px 0 2px 0.5em;text-align:center}.mw-parser-output .ambox .mbox-imageright{border:none;padding:2px 0.5em 2px 0;text-align:center}.mw-parser-output .ambox .mbox-empty-cell{border:none;padding:0;width:1px}.mw-parser-output .ambox .mbox-image-div{width:52px}@media(min-width:720px){.mw-parser-output .ambox{margin:0 10%}}@media print{body.ns-0 .mw-parser-output .ambox{display:none!important}}</style><table class="box-Technical plainlinks metadata ambox ambox-style ambox-technical" role="presentation"><tbody><tr><td class="mbox-image"><div class="mbox-image-div"><span typeof="mw:File"><span><img alt="" src="//upload.wikimedia.org/wikipedia/en/thumb/f/f2/Edit-clear.svg/40px-Edit-clear.svg.png" decoding="async" width="40" height="40" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/en/thumb/f/f2/Edit-clear.svg/60px-Edit-clear.svg.png 1.5x, //upload.wikimedia.org/wikipedia/en/thumb/f/f2/Edit-clear.svg/80px-Edit-clear.svg.png 2x" data-file-width="48" data-file-height="48" /></span></span></div></td><td class="mbox-text"><div class="mbox-text-span">This article's lead section <b>may be too technical for most readers to understand</b>.<span class="hide-when-compact"> Please <a class="external text" href="https://en.wikipedia.org/w/index.php?title=Cross-species_transmission&action=edit">help improve it</a> to <a href="/wiki/Wikipedia:Make_technical_articles_understandable" title="Wikipedia:Make technical articles understandable">make it understandable to non-experts</a>, without removing the technical details.</span> <span class="date-container"><i>(<span class="date">August 2022</span>)</i></span><span class="hide-when-compact"><i> (<small><a href="/wiki/Help:Maintenance_template_removal" title="Help:Maintenance template removal">Learn how and when to remove this message</a></small>)</i></span></div></td></tr></tbody></table> <p><b>Cross-species transmission</b> (<b>CST</b>), also called <b>interspecies transmission</b>, <b>host jump</b>, or <b>spillover</b>, is the <a href="/wiki/Transmission_(medicine)" class="mw-redirect" title="Transmission (medicine)">transmission</a> of an infectious <a href="/wiki/Pathogen" title="Pathogen">pathogen</a>, such as a <a href="/wiki/Virus" title="Virus">virus</a>, between <a href="/wiki/Host_(biology)" title="Host (biology)">hosts</a> belonging to different <a href="/wiki/Species" title="Species">species</a>. 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.<sup id="cite_ref-Childs_1-0" class="reference"><a href="#cite_note-Childs-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup> The phenomenon is most commonly studied in <a href="/wiki/Virology" title="Virology">virology</a>, but cross-species transmission may also occur with <a href="/wiki/Bacterial" class="mw-redirect" title="Bacterial">bacterial</a> pathogens or other types of microorganisms.<sup id="cite_ref-Benavides_2-0" class="reference"><a href="#cite_note-Benavides-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> </p><p>Steps involved in the transfer of pathogens to new hosts include contact between the pathogen and the host; the successful <a href="/wiki/Infection" title="Infection">infection</a> of an initial individual host, which may lead to amplification and an <a href="/wiki/Outbreak" class="mw-redirect" title="Outbreak">outbreak</a>; and the <a href="/wiki/Adaptation" title="Adaptation">adaptation</a> 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.<sup id="cite_ref-Parrish_3-0" class="reference"><a href="#cite_note-Parrish-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup> The concept is important in understanding and controlling <a href="/wiki/Emerging_infectious_disease" title="Emerging infectious disease">emerging infectious diseases</a> in humans, especially those caused by viruses. Most viral diseases of humans are <a href="/wiki/Zoonotic" class="mw-redirect" title="Zoonotic">zoonotic</a> in origin, having been historically transmitted to human populations from various animal species; examples include <a href="/wiki/SARS" title="SARS">SARS</a>, <a href="/wiki/Ebola" title="Ebola">Ebola</a>, <a href="/wiki/Swine_flu" class="mw-redirect" title="Swine flu">swine flu</a>, <a href="/wiki/Rabies" title="Rabies">rabies</a>, and <a href="/wiki/Avian_influenza" title="Avian influenza">avian influenza</a>.<sup id="cite_ref-Faria_4-0" class="reference"><a href="#cite_note-Faria-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> </p><p>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 <a href="/wiki/Immunological_defense" class="mw-redirect" title="Immunological defense">immunological defenses</a>, 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.<sup id="cite_ref-Haven_5-0" class="reference"><a href="#cite_note-Haven-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup> </p><p>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 <a href="/wiki/Natural_reservoir" title="Natural reservoir">reservoir</a> species may transfer the virus to a <a href="/wiki/Vector_(epidemiology)" class="mw-redirect" title="Vector (epidemiology)">vector</a> species, which in turn transfers the virus to humans.<sup id="cite_ref-Wang2019_6-0" class="reference"><a href="#cite_note-Wang2019-6"><span class="cite-bracket">[</span>6<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Fagre2019_7-0" class="reference"><a href="#cite_note-Fagre2019-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup> 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 <a href="/wiki/Plant_virus" title="Plant virus">plant viruses</a>, may not be capable of infecting humans at all. Other factors influencing transmission rates include geographic proximity and intraspecies behaviors.<sup id="cite_ref-Parrish_3-1" class="reference"><a href="#cite_note-Parrish-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup> Due to <a href="/wiki/Climate_change" title="Climate change">climate change</a> and habitat loss owing to land use expansion,<sup id="cite_ref-8" class="reference"><a href="#cite_note-8"><span class="cite-bracket">[</span>8<span class="cite-bracket">]</span></a></sup> the risk of viral spillover is predicted to significantly increase.<sup id="cite_ref-Carlson_9-0" class="reference"><a href="#cite_note-Carlson-9"><span class="cite-bracket">[</span>9<span class="cite-bracket">]</span></a></sup> </p> <meta property="mw:PageProp/toc" /> <div class="mw-heading mw-heading2"><h2 id="Prevalence_and_control">Prevalence and control</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Cross-species_transmission&action=edit&section=1" title="Edit section: Prevalence and control"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Cross-species transmission is the most significant cause of disease emergence in humans and other species. <sup class="noprint Inline-Template Template-Fact" style="white-space:nowrap;">[<i><a href="/wiki/Wikipedia:Citation_needed" title="Wikipedia:Citation needed"><span title="This claim needs references to reliable sources. (October 2021)">citation needed</span></a></i>]</sup> <a href="/wiki/Wildlife" title="Wildlife">Wildlife</a> <a href="/wiki/Zoonotic" class="mw-redirect" title="Zoonotic">zoonotic</a> diseases of microbial origin are also the most common group of human emerging diseases, and CST between wildlife and <a href="/wiki/Livestock" title="Livestock">livestock</a> has appreciable economic impacts in agriculture by reducing livestock productivity and imposing export restrictions.<sup id="cite_ref-Benavides_2-1" class="reference"><a href="#cite_note-Benavides-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> This makes CST of major concern for <a href="/wiki/Public_health" title="Public health">public health</a>, <a href="/wiki/Agriculture" title="Agriculture">agriculture</a>, and <a href="/wiki/Wildlife_management" title="Wildlife management">wildlife management</a>.<sup class="noprint Inline-Template Template-Fact" style="white-space:nowrap;">[<i><a href="/wiki/Wikipedia:Citation_needed" title="Wikipedia:Citation needed"><span title="This claim needs references to reliable sources. (January 2023)">citation needed</span></a></i>]</sup> </p><p>The authors of a study on the <a href="/wiki/Bubonic_plague" title="Bubonic plague">bubonic plague</a> in <a href="/wiki/Oran" title="Oran">Oran</a> stress that the disease "is primarily a <a href="/w/index.php?title=Bacterial_zoonosis&action=edit&redlink=1" class="new" title="Bacterial zoonosis (page does not exist)">bacterial zoonosis</a> affecting <a href="/wiki/Rodents" class="mw-redirect" title="Rodents">rodents</a>. It is caused by <i><a href="/wiki/Yersinia_pestis" title="Yersinia pestis">Yersinia pestis</a></i> and is transmitted from animal to animal by <a href="/wiki/Fleas" class="mw-redirect" title="Fleas">fleas</a>. Humans usually become infected through the bite of an infected <b>rodent flea</b>." The sanitary control measure instituted by the <a href="/w/index.php?title=Public_health_authority&action=edit&redlink=1" class="new" title="Public health authority (page does not exist)">public health authority</a> was chemical in nature: "Intra- and peridomestic spraying with <a href="/wiki/Permethrin" title="Permethrin">permethrin</a> was conducted. <a href="/wiki/Deltamethrin" title="Deltamethrin">Deltamethrin</a> 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."<sup id="cite_ref-bertherat03_10-0" class="reference"><a href="#cite_note-bertherat03-10"><span class="cite-bracket">[</span>10<span class="cite-bracket">]</span></a></sup> </p><p>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, <a href="/wiki/Avian_flu" class="mw-redirect" title="Avian flu">avian flu</a>, <a href="/wiki/Ebola" title="Ebola">Ebola</a>, <a href="/wiki/Monkeypox" class="mw-redirect" title="Monkeypox">monkeypox</a>, and <a href="/wiki/Hanta_virus" class="mw-redirect" title="Hanta virus">Hanta viruses</a>.<sup id="cite_ref-11" class="reference"><a href="#cite_note-11"><span class="cite-bracket">[</span>11<span class="cite-bracket">]</span></a></sup> 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.<sup id="cite_ref-Crosby_12-0" class="reference"><a href="#cite_note-Crosby-12"><span class="cite-bracket">[</span>12<span class="cite-bracket">]</span></a></sup> There is a risk of this phenomenon occurring with <a href="/wiki/Morbillivirus" title="Morbillivirus">morbilliviruses</a> as they can readily cross species barriers.<sup id="cite_ref-Crosby_12-1" class="reference"><a href="#cite_note-Crosby-12"><span class="cite-bracket">[</span>12<span class="cite-bracket">]</span></a></sup> CST can also have a significant effect on produce industries. Genotype VI-<a href="/wiki/Avian_paramyxovirus" class="mw-redirect" title="Avian paramyxovirus">Avian paramyxovirus</a> serotype 1 (GVI-PMV1) is a virus that arose through cross-species transmission events from <a href="/wiki/Galliformes" title="Galliformes">Galliformes</a> (i.e. <a href="/wiki/Chicken" title="Chicken">chicken</a>) to <a href="/wiki/Columbiformes" class="mw-redirect" title="Columbiformes">Columbiformes</a>, and has become prevalent in the <a href="/wiki/Poultry_industry" class="mw-redirect" title="Poultry industry">poultry industry</a>.<sup id="cite_ref-Chong_13-0" class="reference"><a href="#cite_note-Chong-13"><span class="cite-bracket">[</span>13<span class="cite-bracket">]</span></a></sup> </p><p>CST of <a href="/wiki/Rabies" title="Rabies">rabies</a> virus variants between many different species populations is a major concern of <a href="/wiki/Wildlife_management" title="Wildlife management">wildlife management</a>. Introduction of these variants into non-reservoir animals increases the risk of human exposures and threatens current advances toward rabies control.<sup id="cite_ref-Wallace_14-0" class="reference"><a href="#cite_note-Wallace-14"><span class="cite-bracket">[</span>14<span class="cite-bracket">]</span></a></sup> </p><p>Many pathogens are thought to have host specialization, which explains the maintenance of distinct <a href="/wiki/Strain_(biology)" title="Strain (biology)">strains</a> in host species.<sup id="cite_ref-Haven_5-1" class="reference"><a href="#cite_note-Haven-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup> 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.<sup id="cite_ref-Haven_5-2" class="reference"><a href="#cite_note-Haven-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup> Original hosts usually have low death rates when infected with a pathogen, with <a href="/wiki/Death_(science)" class="mw-redirect" title="Death (science)">fatality</a> rates tending to be much higher in new hosts<sup id="cite_ref-Chen_15-0" class="reference"><a href="#cite_note-Chen-15"><span class="cite-bracket">[</span>15<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Between_non-human_primates_and_humans">Between non-human primates and humans</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Cross-species_transmission&action=edit&section=2" title="Edit section: Between non-human primates and humans"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Further information: <a href="/wiki/Human-to-primate_transmission" title="Human-to-primate transmission">Human-to-primate transmission</a></div> <p>Due to the close relation of <a href="/wiki/Nonhuman_primate" class="mw-redirect" title="Nonhuman primate">nonhuman primates</a> (NHP) and <a href="/wiki/Human" title="Human">humans</a>, disease transmission between NHP and humans is relatively common and can become a major public health concern. Diseases such as <a href="/wiki/HIV" title="HIV">HIV</a> and human <a href="/wiki/Adenovirus" class="mw-redirect" title="Adenovirus">adenoviruses</a> have been associated with NHP interactions.<sup id="cite_ref-Hoppe_16-0" class="reference"><a href="#cite_note-Hoppe-16"><span class="cite-bracket">[</span>16<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Lemey_17-0" class="reference"><a href="#cite_note-Lemey-17"><span class="cite-bracket">[</span>17<span class="cite-bracket">]</span></a></sup> </p><p>In places where contact between humans and NHPs is frequent, precautions are often taken to prevent disease transmission. <a href="/wiki/Simian_foamy_virus" class="mw-redirect" title="Simian foamy virus">Simian foamy viruses</a> (SFV) is an <a href="/wiki/Enzootic" title="Enzootic">enzootic</a> <a href="/wiki/Retrovirus" title="Retrovirus">retrovirus</a> that has high rates of cross-species transmission and has been known to affect humans bitten by infected NHPs.<sup id="cite_ref-Mouinga_18-0" class="reference"><a href="#cite_note-Mouinga-18"><span class="cite-bracket">[</span>18<span class="cite-bracket">]</span></a></sup> It has caused health concerns in places like Indonesia where visitors at monkey temples can contract SFV from temple macaques (<i><a href="/wiki/Macaca_fascicularis" class="mw-redirect" title="Macaca fascicularis">Macaca fascicularis</a></i>).<sup id="cite_ref-Engel_19-0" class="reference"><a href="#cite_note-Engel-19"><span class="cite-bracket">[</span>19<span class="cite-bracket">]</span></a></sup> TMAdV (<a href="/wiki/Titi_monkey_adenovirus" title="Titi monkey adenovirus">titi monkey adenovirus</a>) is a highly divergent, sharing <57% <a href="/wiki/Pairwise_comparison_(psychology)" title="Pairwise comparison (psychology)">pairwise</a> nucleotide identity with other adenoviruses, NHP virus that had a high fatality rate (83%) in monkeys and is capable of spreading through human hosts.<sup id="cite_ref-Chen_15-1" class="reference"><a href="#cite_note-Chen-15"><span class="cite-bracket">[</span>15<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="Predicting_and_preventing_transmission_between_species">Predicting and preventing transmission between species</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Cross-species_transmission&action=edit&section=3" title="Edit section: Predicting and preventing transmission between species"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>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.<sup id="cite_ref-Faria_4-1" class="reference"><a href="#cite_note-Faria-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> This has resulted in the use of different <a href="/wiki/Statistical_model" title="Statistical model">statistical models</a> for the analysis of CST. Some of these include risk-analysis models,<sup id="cite_ref-Parrish2_20-0" class="reference"><a href="#cite_note-Parrish2-20"><span class="cite-bracket">[</span>20<span class="cite-bracket">]</span></a></sup> single rate dated tip (SRDT) models,<sup id="cite_ref-Lemey_17-1" class="reference"><a href="#cite_note-Lemey-17"><span class="cite-bracket">[</span>17<span class="cite-bracket">]</span></a></sup> and phylogenetic diffusion models.<sup id="cite_ref-Faria_4-2" class="reference"><a href="#cite_note-Faria-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> The study of the <a href="/wiki/Genome" title="Genome">genomes</a> of pathogens involved in CST events is very useful in determining their origin and fate.<sup id="cite_ref-Faria_4-3" class="reference"><a href="#cite_note-Faria-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> This is because a pathogens <a href="/wiki/Genetic_diversity" title="Genetic diversity">genetic diversity</a> and <a href="/wiki/Mutation" title="Mutation">mutation</a> 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.<sup id="cite_ref-Chen_15-2" class="reference"><a href="#cite_note-Chen-15"><span class="cite-bracket">[</span>15<span class="cite-bracket">]</span></a></sup> A change in genomic structure could cause a pathogen that has a narrow host range to become capable of exploiting a wider host range.<sup id="cite_ref-Haven_5-3" class="reference"><a href="#cite_note-Haven-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup> <a href="/wiki/Genetic_distance" title="Genetic distance">Genetic distance</a> between different species, geographical range, and other interaction barriers will also influence cross-species transmission.<sup id="cite_ref-Faria_4-4" class="reference"><a href="#cite_note-Faria-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> </p><p>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.<sup id="cite_ref-Engel_19-1" class="reference"><a href="#cite_note-Engel-19"><span class="cite-bracket">[</span>19<span class="cite-bracket">]</span></a></sup> </p><p>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.<sup id="cite_ref-21" class="reference"><a href="#cite_note-21"><span class="cite-bracket">[</span>21<span class="cite-bracket">]</span></a></sup> </p><p>Detecting CST and estimating its rate based on prevalence data is challenging.<sup id="cite_ref-Benavides_2-2" class="reference"><a href="#cite_note-Benavides-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> Due to these difficulties, <a href="/wiki/Computational" class="mw-redirect" title="Computational">computational</a> methods are used to analyse CST events and the pathogens associated with them. The explosive development of <a href="/wiki/Molecular" class="mw-redirect" title="Molecular">molecular</a> techniques has opened new possibilities for using phylogenetic analysis of pathogen genetics to infer <a href="/wiki/Epidemiological" class="mw-redirect" title="Epidemiological">epidemiological</a> parameters.<sup id="cite_ref-Benavides_2-3" class="reference"><a href="#cite_note-Benavides-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> 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 <a href="/wiki/Cell_biology" title="Cell biology">cellular</a> <a href="/wiki/Assay" title="Assay">assays</a> and <a href="/wiki/Phylogenetic" class="mw-redirect" title="Phylogenetic">phylogenetic</a> comparisons to support a role for TRIM5α, the product of the TRIM5 gene, in suppressing interspecies transmission and emergence of retroviruses in nature.<sup id="cite_ref-Kirmaier_22-0" class="reference"><a href="#cite_note-Kirmaier-22"><span class="cite-bracket">[</span>22<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="Analysis">Analysis</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Cross-species_transmission&action=edit&section=4" title="Edit section: Analysis"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <div class="mw-heading mw-heading3"><h3 id="Phylogeny">Phylogeny</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Cross-species_transmission&action=edit&section=5" title="Edit section: Phylogeny"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The comparison of genomic data is very important for the study of cross-species transmission. <a href="/wiki/Phylogenetic_analysis" class="mw-redirect" title="Phylogenetic analysis">Phylogenetic analysis</a> 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<sup id="cite_ref-Parrish2_20-1" class="reference"><a href="#cite_note-Parrish2-20"><span class="cite-bracket">[</span>20<span class="cite-bracket">]</span></a></sup> </p><p>Alternative hosts can also potentially have a critical role in the evolution and diffusion of a pathogen.<sup id="cite_ref-Allison_23-0" class="reference"><a href="#cite_note-Allison-23"><span class="cite-bracket">[</span>23<span class="cite-bracket">]</span></a></sup> When a pathogen crosses species it often acquires new characteristics that allow it to breach host barriers.<sup id="cite_ref-Parrish2_20-2" class="reference"><a href="#cite_note-Parrish2-20"><span class="cite-bracket">[</span>20<span class="cite-bracket">]</span></a></sup> Different pathogen variants can have very different effects on host species.<sup id="cite_ref-Allison_23-1" class="reference"><a href="#cite_note-Allison-23"><span class="cite-bracket">[</span>23<span class="cite-bracket">]</span></a></sup> 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.<sup id="cite_ref-Chen_15-3" class="reference"><a href="#cite_note-Chen-15"><span class="cite-bracket">[</span>15<span class="cite-bracket">]</span></a></sup> A useful strategy for investigating the history of epidemics caused by pathogen transmission combines <a href="/wiki/Molecular_clock" title="Molecular clock">molecular clock</a> analysis, to estimate the timescale of the epidemic, and <a href="/wiki/Coalescent_theory" title="Coalescent theory">coalescent theory</a>, to infer the <a href="/wiki/Demographic" class="mw-redirect" title="Demographic">demographic</a> history of the pathogen.<sup id="cite_ref-Lemey_17-2" class="reference"><a href="#cite_note-Lemey-17"><span class="cite-bracket">[</span>17<span class="cite-bracket">]</span></a></sup> When constructing phylogenies, computer databases and tools are often used. Programs, such as <a href="/wiki/BLAST_(biotechnology)" title="BLAST (biotechnology)">BLAST</a>, are used to annotate pathogen sequences, while databases like <a href="/wiki/GenBank" title="GenBank">GenBank</a> 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.<sup id="cite_ref-24" class="reference"><a href="#cite_note-24"><span class="cite-bracket">[</span>24<span class="cite-bracket">]</span></a></sup> Single rate dated tip (SRDT) models, for example, allows for estimates of <a href="https://en.wiktionary.org/wiki/time_scale" class="extiw" title="wikt:time scale">timescale</a> under a phylogenetic tree.<sup id="cite_ref-Lemey_17-3" class="reference"><a href="#cite_note-Lemey-17"><span class="cite-bracket">[</span>17<span class="cite-bracket">]</span></a></sup> Models for CST prediction will vary depending on what parameters need to be accounted for when constructing the model.<sup class="noprint Inline-Template Template-Fact" style="white-space:nowrap;">[<i><a href="/wiki/Wikipedia:Citation_needed" title="Wikipedia:Citation needed"><span title="This claim needs references to reliable sources. (January 2023)">citation needed</span></a></i>]</sup> </p> <div class="mw-heading mw-heading3"><h3 id="Most_parsimonious_reconstruction_(MPR)"><span id="Most_parsimonious_reconstruction_.28MPR.29"></span>Most parsimonious reconstruction (MPR)</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Cross-species_transmission&action=edit&section=6" title="Edit section: Most parsimonious reconstruction (MPR)"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/wiki/Occam%27s_razor" title="Occam's razor">Parsimony</a> is the principle in which one chooses the simplest scientific explanation that fits the evidence. In terms of building phylogenetic trees, the best <a href="/wiki/Hypothesis" title="Hypothesis">hypothesis</a> 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 <a href="/wiki/Ecological" class="mw-redirect" title="Ecological">ecological</a> and <a href="/wiki/Evolutionary" class="mw-redirect" title="Evolutionary">evolutionary</a> hypotheses.<sup id="cite_ref-Cunningham_25-0" class="reference"><a href="#cite_note-Cunningham-25"><span class="cite-bracket">[</span>25<span class="cite-bracket">]</span></a></sup> This method can be used in CST studies to estimate the number of character changes that exist between pathogens in relation to their host.<sup id="cite_ref-Benavides_2-4" class="reference"><a href="#cite_note-Benavides-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> 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 <a href="/wiki/Animal_migration" title="Animal migration">migrate</a> regionally are important for spreading viruses through population networks.<sup id="cite_ref-26" class="reference"><a href="#cite_note-26"><span class="cite-bracket">[</span>26<span class="cite-bracket">]</span></a></sup> </p><p>Despite the success of parsimony reconstructions, research suggests they are often sensitive and can sometimes be prone to bias in complex models.<sup id="cite_ref-Cunningham_25-1" class="reference"><a href="#cite_note-Cunningham-25"><span class="cite-bracket">[</span>25<span class="cite-bracket">]</span></a></sup> 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.<sup id="cite_ref-Cunningham_25-2" class="reference"><a href="#cite_note-Cunningham-25"><span class="cite-bracket">[</span>25<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Using_genetic_markers">Using genetic markers</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Cross-species_transmission&action=edit&section=7" title="Edit section: Using genetic markers"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Two methods of measuring genetic variation, <a href="/wiki/Variable_number_tandem_repeat" title="Variable number tandem repeat">variable number tandem repeats</a> (VNTRs) and <a href="/wiki/Single_nucleotide_polymorphism" class="mw-redirect" title="Single nucleotide polymorphism">single nucleotide polymorphisms</a> (SNPs), have been very beneficial to the study of bacterial transmission.<sup id="cite_ref-Benavides_2-5" class="reference"><a href="#cite_note-Benavides-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> VNTRs, due to the low cost and high mutation rates, make them particularly useful to detect genetic differences in recent <a href="/wiki/Outbreak" class="mw-redirect" title="Outbreak">outbreaks</a>, 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.<sup id="cite_ref-Benavides_2-6" class="reference"><a href="#cite_note-Benavides-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> However, it can be difficult for these methods to accurately simulate CSTs everts. Estimates of CST based on <a href="/wiki/Phylogeny" class="mw-redirect" title="Phylogeny">phylogenies</a> 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.<sup id="cite_ref-Benavides_2-7" class="reference"><a href="#cite_note-Benavides-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> 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, <a href="/wiki/Stochasticity" class="mw-redirect" title="Stochasticity">stochasticity</a>, 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.<sup id="cite_ref-Benavides_2-8" class="reference"><a href="#cite_note-Benavides-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> </p><p>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.<sup id="cite_ref-Benavides_2-9" class="reference"><a href="#cite_note-Benavides-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> 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.<sup id="cite_ref-Benavides_2-10" class="reference"><a href="#cite_note-Benavides-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> 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 <a href="/wiki/Likelihood" class="mw-redirect" title="Likelihood">Likelihood</a> approaches that require an estimation of the mutation rate.<sup id="cite_ref-Benavides_2-11" class="reference"><a href="#cite_note-Benavides-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> 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<sup id="cite_ref-Benavides_2-12" class="reference"><a href="#cite_note-Benavides-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Bayesian_analysis">Bayesian analysis</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Cross-species_transmission&action=edit&section=8" title="Edit section: Bayesian analysis"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Bayesian frameworks are a form of maximum likelihood-based analyses and can be very effective in cross-species transmission studies. <a href="/wiki/Bayesian_inference" title="Bayesian inference">Bayesian inference</a> 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 <a href="/wiki/RNA_virus" title="RNA virus">RNA viruses</a>.<sup id="cite_ref-Benavides_2-13" class="reference"><a href="#cite_note-Benavides-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> 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.<sup id="cite_ref-LemeyP_27-0" class="reference"><a href="#cite_note-LemeyP-27"><span class="cite-bracket">[</span>27<span class="cite-bracket">]</span></a></sup> </p><p>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 <a href="/wiki/Biogeographical" class="mw-redirect" title="Biogeographical">biogeographical</a> history reconstruction from genetic data.<sup id="cite_ref-LemeyP_27-1" class="reference"><a href="#cite_note-LemeyP-27"><span class="cite-bracket">[</span>27<span class="cite-bracket">]</span></a></sup> 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.<sup id="cite_ref-R_28-0" class="reference"><a href="#cite_note-R-28"><span class="cite-bracket">[</span>28<span class="cite-bracket">]</span></a></sup> 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 <a href="/wiki/Gorilla" title="Gorilla">gorilla</a> and <a href="/wiki/Common_chimpanzee" class="mw-redirect" title="Common chimpanzee">chimpanzee</a> origin for the viral species, aiding prevention efforts.<sup id="cite_ref-Hoppe_16-1" class="reference"><a href="#cite_note-Hoppe-16"><span class="cite-bracket">[</span>16<span class="cite-bracket">]</span></a></sup> 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.<sup id="cite_ref-Hoppe_16-2" class="reference"><a href="#cite_note-Hoppe-16"><span class="cite-bracket">[</span>16<span class="cite-bracket">]</span></a></sup> </p><p>Phylogenetic diffusion models are frequently used for phylogeographic analyses, with the inference of host jumping becoming of increasing interest.<sup id="cite_ref-Faria_4-5" class="reference"><a href="#cite_note-Faria-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> 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.<sup id="cite_ref-Faria_4-6" class="reference"><a href="#cite_note-Faria-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> 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.<sup id="cite_ref-Faria_4-7" class="reference"><a href="#cite_note-Faria-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> One study on rabies in bats showed geographical range overlap is a modest predictor for CST, but not for host shifts.<sup id="cite_ref-Faria_4-8" class="reference"><a href="#cite_note-Faria-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> This highlights how Bayesian inferences in models can be used for CST analysis.<sup class="noprint Inline-Template Template-Fact" style="white-space:nowrap;">[<i><a href="/wiki/Wikipedia:Citation_needed" title="Wikipedia:Citation needed"><span title="This claim needs references to reliable sources. (January 2023)">citation needed</span></a></i>]</sup> </p> <div class="mw-heading mw-heading2"><h2 id="See_also">See also</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Cross-species_transmission&action=edit&section=9" title="Edit section: See also"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <ul><li><a href="/wiki/Mathematical_modelling_of_infectious_disease" class="mw-redirect" title="Mathematical modelling of infectious disease">Mathematical modelling of infectious disease</a></li> <li><a href="/wiki/Reverse_zoonosis" title="Reverse zoonosis">Reverse zoonosis</a></li> <li><a href="/wiki/Spillover_infection" title="Spillover infection">Spillover infection</a></li> <li><a href="/wiki/Vector_(epidemiology)" class="mw-redirect" title="Vector (epidemiology)">Vector</a></li> <li><a href="/wiki/Zoonosis" title="Zoonosis">Zoonosis</a></li> <li><a href="/wiki/Feline_zoonosis" title="Feline zoonosis">Feline zoonosis</a></li></ul> <div class="mw-heading mw-heading2"><h2 id="References">References</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Cross-species_transmission&action=edit&section=10" title="Edit section: References"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <style data-mw-deduplicate="TemplateStyles:r1239543626">.mw-parser-output .reflist{margin-bottom:0.5em;list-style-type:decimal}@media screen{.mw-parser-output .reflist{font-size:90%}}.mw-parser-output .reflist .references{font-size:100%;margin-bottom:0;list-style-type:inherit}.mw-parser-output .reflist-columns-2{column-width:30em}.mw-parser-output .reflist-columns-3{column-width:25em}.mw-parser-output .reflist-columns{margin-top:0.3em}.mw-parser-output .reflist-columns ol{margin-top:0}.mw-parser-output .reflist-columns li{page-break-inside:avoid;break-inside:avoid-column}.mw-parser-output .reflist-upper-alpha{list-style-type:upper-alpha}.mw-parser-output .reflist-upper-roman{list-style-type:upper-roman}.mw-parser-output .reflist-lower-alpha{list-style-type:lower-alpha}.mw-parser-output .reflist-lower-greek{list-style-type:lower-greek}.mw-parser-output .reflist-lower-roman{list-style-type:lower-roman}</style><div class="reflist reflist-columns references-column-width reflist-columns-2"> <ol class="references"> <li id="cite_note-Childs-1"><span class="mw-cite-backlink"><b><a href="#cite_ref-Childs_1-0">^</a></b></span> <span class="reference-text"><style data-mw-deduplicate="TemplateStyles:r1238218222">.mw-parser-output cite.citation{font-style:inherit;word-wrap:break-word}.mw-parser-output .citation q{quotes:"\"""\"""'""'"}.mw-parser-output .citation:target{background-color:rgba(0,127,255,0.133)}.mw-parser-output .id-lock-free.id-lock-free a{background:url("//upload.wikimedia.org/wikipedia/commons/6/65/Lock-green.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-limited.id-lock-limited a,.mw-parser-output .id-lock-registration.id-lock-registration a{background:url("//upload.wikimedia.org/wikipedia/commons/d/d6/Lock-gray-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-subscription.id-lock-subscription a{background:url("//upload.wikimedia.org/wikipedia/commons/a/aa/Lock-red-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .cs1-ws-icon a{background:url("//upload.wikimedia.org/wikipedia/commons/4/4c/Wikisource-logo.svg")right 0.1em center/12px no-repeat}body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-free a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-limited a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-registration a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-subscription a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .cs1-ws-icon a{background-size:contain;padding:0 1em 0 0}.mw-parser-output .cs1-code{color:inherit;background:inherit;border:none;padding:inherit}.mw-parser-output .cs1-hidden-error{display:none;color:var(--color-error,#d33)}.mw-parser-output .cs1-visible-error{color:var(--color-error,#d33)}.mw-parser-output .cs1-maint{display:none;color:#085;margin-left:0.3em}.mw-parser-output .cs1-kern-left{padding-left:0.2em}.mw-parser-output .cs1-kern-right{padding-right:0.2em}.mw-parser-output .citation .mw-selflink{font-weight:inherit}@media screen{.mw-parser-output .cs1-format{font-size:95%}html.skin-theme-clientpref-night .mw-parser-output .cs1-maint{color:#18911f}}@media screen and (prefers-color-scheme:dark){html.skin-theme-clientpref-os .mw-parser-output .cs1-maint{color:#18911f}}</style><cite id="CITEREFChildsMackenzieRicht2007" class="citation cs2">Childs JE, Mackenzie JE, Richt JE (2007), <i>Wildlife and Emerging Zoonotic Diseases: The Biology, Circumstances and Consequences of Cross-Species Transmission</i>, Current Topics in Microbiology and Immunology, vol. 315, Springer-Verlag Berlin Heidelberg: Springer Science+Business Media, pp. 129–134, <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1007%2F978-3-540-70962-6">10.1007/978-3-540-70962-6</a>, <a href="/wiki/ISBN_(identifier)" class="mw-redirect" title="ISBN (identifier)">ISBN</a> <a href="/wiki/Special:BookSources/978-3-540-70961-9" title="Special:BookSources/978-3-540-70961-9"><bdi>978-3-540-70961-9</bdi></a></cite><span 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(2009), "Bayesian Phylogeography Finds Its Roots", <i>PLOS Comput Biol</i>, <b>5</b> (9): e1000520, <a href="/wiki/Bibcode_(identifier)" class="mw-redirect" title="Bibcode (identifier)">Bibcode</a>:<a rel="nofollow" class="external text" href="https://ui.adsabs.harvard.edu/abs/2009PLSCB...5E0520L">2009PLSCB...5E0520L</a>, <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://doi.org/10.1371%2Fjournal.pcbi.1000520">10.1371/journal.pcbi.1000520</a></span>, <a href="/wiki/PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2740835">2740835</a></span>, <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/19779555">19779555</a></cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=PLOS+Comput+Biol&rft.atitle=Bayesian+Phylogeography+Finds+Its+Roots&rft.volume=5&rft.issue=9&rft.pages=e1000520&rft.date=2009&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC2740835%23id-name%3DPMC&rft_id=info%3Apmid%2F19779555&rft_id=info%3Adoi%2F10.1371%2Fjournal.pcbi.1000520&rft_id=info%3Abibcode%2F2009PLSCB...5E0520L&rft.aulast=Lemey&rft.aufirst=P&rft.au=Rambaut%2C+A&rft.au=Drummoond%2C+AJ&rft.au=Suchard%2C+MA&rfr_id=info%3Asid%2Fen.wikipedia.org%3ACross-species+transmission" class="Z3988"></span></span> </li> <li id="cite_note-R-28"><span class="mw-cite-backlink"><b><a href="#cite_ref-R_28-0">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFRonquist2004" class="citation cs2">Ronquist F (2004), <a rel="nofollow" class="external text" href="http://www.nrm.se/download/18.42129f1312d951207af800041642/1367705015783/Ronquist_TREE_2004.pdf">"Bayesian inference of character evolution"</a> <span class="cs1-format">(PDF)</span>, <i>Trends in Ecology & Evolution</i>, <b>19</b> (9): 475–481, <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1016%2Fj.tree.2004.07.002">10.1016/j.tree.2004.07.002</a>, <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/16701310">16701310</a></cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Trends+in+Ecology+%26+Evolution&rft.atitle=Bayesian+inference+of+character+evolution&rft.volume=19&rft.issue=9&rft.pages=475-481&rft.date=2004&rft_id=info%3Adoi%2F10.1016%2Fj.tree.2004.07.002&rft_id=info%3Apmid%2F16701310&rft.aulast=Ronquist&rft.aufirst=F&rft_id=http%3A%2F%2Fwww.nrm.se%2Fdownload%2F18.42129f1312d951207af800041642%2F1367705015783%2FRonquist_TREE_2004.pdf&rfr_id=info%3Asid%2Fen.wikipedia.org%3ACross-species+transmission" class="Z3988"></span></span> </li> </ol></div> <div class="mw-heading mw-heading2"><h2 id="External_links">External links</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Cross-species_transmission&action=edit&section=11" title="Edit section: External links"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <ul><li><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFTheo_Kypraios" class="citation web cs1">Theo Kypraios. <a rel="nofollow" class="external text" href="https://www.academia.edu/5221812">"A Gentle Tutorial in Bayesian Statistics"</a> (PDF)<span class="reference-accessdate">. Retrieved <span class="nowrap">10 July</span> 2020</span>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=unknown&rft.btitle=A+Gentle+Tutorial+in+Bayesian+Statistics&rft.au=Theo+Kypraios&rft_id=https%3A%2F%2Fwww.academia.edu%2F5221812&rfr_id=info%3Asid%2Fen.wikipedia.org%3ACross-species+transmission" class="Z3988"></span></li> <li><a rel="nofollow" class="external text" href="http://bayesmodels.com/">Bayesian modeling book</a> and examples available for downloading.</li> <li><a href="https://en.wikiversity.org/wiki/Bayesian_statistics" class="extiw" title="v:Bayesian statistics">Bayesian statistics</a> at Wikiversity</li> <li><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFSmith2022" class="citation web cs1"><a href="/wiki/Tara_C._Smith" title="Tara C. Smith">Smith TC</a> (2022-04-27). <a rel="nofollow" class="external text" href="https://www.quantamagazine.org/what-happens-when-we-give-animals-our-diseases-20220427/">"What Happens When We Give Animals Our Diseases?"</a>. <i><a href="/wiki/Quanta_Magazine" title="Quanta Magazine">Quanta Magazine</a></i>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=unknown&rft.jtitle=Quanta+Magazine&rft.atitle=What+Happens+When+We+Give+Animals+Our+Diseases%3F&rft.date=2022-04-27&rft.aulast=Smith&rft.aufirst=Tara+C.&rft_id=https%3A%2F%2Fwww.quantamagazine.org%2Fwhat-happens-when-we-give-animals-our-diseases-20220427%2F&rfr_id=info%3Asid%2Fen.wikipedia.org%3ACross-species+transmission" class="Z3988"></span></li></ul> <div class="navbox-styles"><style data-mw-deduplicate="TemplateStyles:r1129693374">.mw-parser-output .hlist dl,.mw-parser-output .hlist ol,.mw-parser-output .hlist ul{margin:0;padding:0}.mw-parser-output .hlist dd,.mw-parser-output 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href="/wiki/Template:Concepts_in_infectious_disease" title="Template:Concepts in infectious disease"><abbr title="View this template">v</abbr></a></li><li class="nv-talk"><a href="/wiki/Template_talk:Concepts_in_infectious_disease" title="Template talk:Concepts in infectious disease"><abbr title="Discuss this template">t</abbr></a></li><li class="nv-edit"><a href="/wiki/Special:EditPage/Template:Concepts_in_infectious_disease" title="Special:EditPage/Template:Concepts in infectious disease"><abbr title="Edit this template">e</abbr></a></li></ul></div><div id="Concepts_in_infectious_disease_(Outline)" style="font-size:114%;margin:0 4em">Concepts in <a href="/wiki/Infection" title="Infection">infectious disease</a> (<a href="/wiki/Outline_of_infectious_disease_concepts" title="Outline of infectious disease concepts">Outline</a>)</div></th></tr><tr><th scope="row" class="navbox-group" style="width:1%">Determinants</th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"></div><table class="nowraplinks navbox-subgroup" style="border-spacing:0"><tbody><tr><th scope="row" class="navbox-group" style="width:1%;text-align:left;"><a href="/wiki/Pathogen" title="Pathogen">Agent</a></th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Biofilm#Infectious_diseases" title="Biofilm">Biofilm</a></li> <li><a href="/wiki/Germ_theory_of_disease" title="Germ theory of disease">Germ theory of disease</a></li> <li><a href="/wiki/Infectivity" title="Infectivity">Infectivity</a> <ul><li><a href="/wiki/Minimal_infective_dose" title="Minimal infective dose">Infectious dose</a></li></ul></li> <li><a href="/wiki/Pathogenicity" class="mw-redirect" title="Pathogenicity">Pathogenicity</a> <ul><li><a href="/wiki/Attack_rate" title="Attack rate">Attack rate</a></li></ul></li> <li><a href="/wiki/Quorum_sensing" title="Quorum sensing">Quorum sensing</a></li> <li><a href="/wiki/Virulence" title="Virulence">Virulence</a> <ul><li><a href="/wiki/Endotoxin" class="mw-redirect" title="Endotoxin">Endotoxin</a></li> <li><a href="/wiki/Exotoxin" title="Exotoxin">Exotoxin</a></li> <li><a href="/wiki/Case_fatality_rate" title="Case fatality rate">Case fatality rate</a></li> <li><a href="/wiki/Virulence_factor" title="Virulence factor">factors</a></li></ul></li> <li><a href="/wiki/Antimicrobial_resistance" title="Antimicrobial resistance">Antimicrobial resistance</a> <ul><li><a href="/wiki/Drug_resistance" title="Drug resistance">Drug resistance</a></li> <li><a href="/wiki/Horizontal_gene_transfer" title="Horizontal gene transfer">Horizontal gene transfer</a></li> <li><a href="/wiki/Multidrug-resistant_bacteria" title="Multidrug-resistant bacteria">Multidrug-resistant bacteria</a></li></ul></li> <li><a href="/wiki/Host_tropism" title="Host tropism">Host tropism</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%;text-align:left;"><a href="/wiki/Host_(biology)" title="Host (biology)">Host</a></th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Burn#Complications" title="Burn">Burn</a></li> <li><a href="/wiki/Comorbidity" title="Comorbidity">Comorbidity</a></li> <li><a href="/wiki/Diabetic_foot_infection" title="Diabetic foot infection">Diabetes</a></li> <li><a href="/wiki/Host%E2%80%93pathogen_interaction" title="Host–pathogen interaction">Host–pathogen interaction</a></li> <li><a href="/wiki/Immune_response" title="Immune response">Immune response</a> <ul><li><a href="/wiki/Immunodeficiency" title="Immunodeficiency">Immunodeficiency</a></li> <li><a href="/wiki/Immunosuppression" title="Immunosuppression">Immunosuppression</a></li></ul></li> <li><a href="/wiki/Microbial_symbiosis_and_immunity" title="Microbial symbiosis and immunity">Microbiome health</a></li> <li><a href="/wiki/Opportunistic_infection" title="Opportunistic infection">Opportunistic infection</a></li> <li><a href="/wiki/Risk_of_infection" title="Risk of infection">Risk of infection</a></li> <li><a href="/wiki/Susceptible_individual" title="Susceptible individual">Susceptible individual</a> <ul><li>Age</li> <li>Gender</li> <li>Nutrition status</li> <li>Vaccination status</li> <li>Genetic predisposition</li> <li>Behavioral/lifestyle factors <ul><li><a href="/wiki/Health_effects_of_tobacco#infection" title="Health effects of tobacco">Smoking</a></li></ul></li> <li>Pregnancy</li> <li>Stress levels</li></ul></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%;text-align:left;"><a href="/wiki/Environmental_epidemiology" title="Environmental epidemiology">Environment</a></th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/WASH" title="WASH">Access to water, sanitation and hygiene</a></li> <li>Air quality</li> <li>Biodiversity loss</li> <li><a href="/wiki/Climate_change_and_infectious_diseases" title="Climate change and infectious diseases">Climate change</a></li> <li>Climate zones <ul><li><a href="/wiki/El_Ni%C3%B1o#Health_and_social_impacts" class="mw-redirect" title="El Niño">El Niño</a></li> <li><a href="/wiki/Tropical_disease#Relation_of_climate_to_tropical_diseases" title="Tropical disease">Tropical diseases</a></li></ul></li> <li><a href="/wiki/Globalization_and_disease" title="Globalization and disease">Commerce</a></li> <li><a href="/wiki/Deforestation#Health_effects" title="Deforestation">Deforestation</a></li> <li><a href="/wiki/Disease_ecology" title="Disease ecology">Ecology</a></li> <li><a href="/wiki/Humidity#Human_health" title="Humidity">Humidity</a></li> <li><a href="/wiki/Needle_sharing" title="Needle sharing">Injection drug use</a></li> <li>Natural disaster <ul><li><a href="/wiki/Flood#Health_effects" title="Flood">Flood</a></li></ul></li> <li><a href="/wiki/Zoonosis#Farming,_ranching_and_animal_husbandry" title="Zoonosis">Poultry and livestock</a></li> <li><a href="/wiki/Diseases_of_poverty" title="Diseases of poverty">Poverty</a></li> <li><a href="/wiki/Travel_medicine" title="Travel medicine">Travel</a></li> <li><a href="/wiki/Urbanization#Infections" title="Urbanization">Urbanization</a></li> <li><a href="/wiki/Vector_control" title="Vector control">Vector control</a></li> <li><a href="/wiki/Conflict_epidemiology" title="Conflict epidemiology">War and conflict</a></li></ul> </div></td></tr></tbody></table><div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="/wiki/Transmission_(medicine)" class="mw-redirect" title="Transmission (medicine)">Transmission</a></th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"></div><table class="nowraplinks navbox-subgroup" style="border-spacing:0"><tbody><tr><th id="Basic_concepts" scope="row" class="navbox-group" style="width:1%;text-align:left;">Basic <br />concepts</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Asymptomatic_carrier" title="Asymptomatic carrier">Asymptomatic carrier</a></li> <li><a href="/wiki/Infection#Pathophysiology" title="Infection">Chain of infection</a></li> <li><a href="/wiki/Fomite" title="Fomite">Fomite</a></li> <li><a href="/wiki/Host_(biology)" title="Host (biology)">Host</a></li> <li><a href="/wiki/Incubation_period" title="Incubation period">Incubation period</a></li> <li><a href="/wiki/Index_case" title="Index case">Index case</a></li> <li><a href="/wiki/Infectious_period" title="Infectious period">Infectious period</a></li> <li><a href="/wiki/Latent_period_(epidemiology)" title="Latent period (epidemiology)">Latent period</a></li> <li><a href="/wiki/Natural_reservoir" title="Natural reservoir">Natural reservoir</a></li> <li><a href="/wiki/Opportunistic_infection" title="Opportunistic infection">Opportunistic infection</a></li> <li><a href="/wiki/Subclinical_infection" title="Subclinical infection">Silent/Subclinical infection</a></li> <li><a href="/wiki/Superinfection" title="Superinfection">Superinfection</a></li> <li><a href="/wiki/Super-spreader" class="mw-redirect" title="Super-spreader">Super-spreader</a></li> <li><a href="/wiki/Viral_load" title="Viral load">Viral load</a></li> <li><a href="/wiki/Window_period" title="Window period">Window period</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%;text-align:left;">Modes</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"></div><table class="nowraplinks navbox-subgroup" style="border-spacing:0"><tbody><tr><th scope="row" class="navbox-group" style="width:1%;text-align:left;">Endogenous</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li>Endogenous overgrowth</li> <li><a href="/wiki/Human_microbiome#Disease_and_death" title="Human microbiome">Normal flora overgrowth</a></li> <li><a href="/wiki/Virus_latency" title="Virus latency">Endogenous reactivation</a></li> <li>Microbial translocation</li> <li>Endogenous seeding</li> <li><a href="/wiki/Biofilm" title="Biofilm">Biofilm</a> formation</li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%;text-align:left;">Exogenous</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"></div><table class="nowraplinks navbox-subgroup" style="border-spacing:0"><tbody><tr><th scope="row" class="navbox-group" style="width:1%;text-align:left;"><a class="mw-selflink selflink">Cross-species</a></th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Spillover_infection" title="Spillover infection">Spillover infection</a></li> <li><a href="/wiki/Vector_(epidemiology)" class="mw-redirect" title="Vector (epidemiology)">Vector</a></li> <li><a href="/wiki/Zoonosis" title="Zoonosis">Zoonosis</a></li> <li><a href="/wiki/Reverse_zoonosis" title="Reverse zoonosis">Reverse zoonosis</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%;text-align:left;"><a href="/wiki/Human-to-human_transmission" title="Human-to-human transmission">Human-to-human</a><br />/Cross-infection</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Contagious_disease" title="Contagious disease">Contagious disease</a></li> <li>Source <ul><li><a href="/wiki/Hospital-acquired_infection" title="Hospital-acquired infection">Nosocomial/Hospital</a></li> <li><a href="/wiki/Iatrogenesis" title="Iatrogenesis">Iatrogenic/Medical care</a></li></ul></li> <li>Generational difference <ul><li><a href="/wiki/Vertically_transmitted_infection" title="Vertically transmitted infection">Vertical/Congenital</a> <ul><li>Prenatal</li> <li>Perinatal</li> <li><a href="/wiki/Neonatal_infection" title="Neonatal infection">Neonatal</a></li></ul></li> <li><a href="/wiki/Transmission_(medicine)#Horizontal_transmission" class="mw-redirect" title="Transmission (medicine)">Horizontal</a></li></ul></li> <li><a href="/wiki/Breakthrough_infection" title="Breakthrough infection">Breakthrough infection</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%;text-align:left;">Environment-<br />to-human</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Sapronosis" title="Sapronosis">Sapronosis</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%;text-align:left;">Routes</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"></div><table class="nowraplinks navbox-subgroup" style="border-spacing:0"><tbody><tr><th scope="row" class="navbox-group" style="width:1%;text-align:left;">Respiratory</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Airborne_disease" class="mw-redirect" title="Airborne disease">Air</a></li> <li><a href="/wiki/Bioaerosol" title="Bioaerosol">Bioaerosol</a> <ul><li><a href="/wiki/Aerosol-generating_procedure" title="Aerosol-generating procedure">Aerosol-generating procedure</a></li></ul></li> <li><a href="/wiki/Dental_aerosol" title="Dental aerosol">Dental aerosol</a></li> <li><a href="/wiki/Respiratory_droplet#Role_in_disease_transmission" title="Respiratory droplet">Respiratory droplet</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%;text-align:left;">Linked to<br />Vascular system</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Blood-borne_disease" title="Blood-borne disease">Blood-borne disease</a></li> <li>Percutaneous inoculation <ul><li><a href="/wiki/Injection_(medicine)#Infection" title="Injection (medicine)">Injection site</a></li> <li><a href="/wiki/Intravenous_therapy#Infection_and_inflammation" title="Intravenous therapy">Intravenous line</a></li> <li>Insect bite</li> <li><a href="/wiki/Animal_bite#Infection" title="Animal bite">Animal bite</a></li></ul></li> <li>Surgical intervention <ul><li><a href="/wiki/Postoperative_wounds#Infection" title="Postoperative wounds">Postoperative wound</a></li> <li><a href="/wiki/Surgical_site_infection" title="Surgical site infection">Surgical site infection</a></li></ul></li> <li>Vector-borne <ul><li><a href="/wiki/Mosquito-borne_disease" title="Mosquito-borne disease">Mosquito</a></li> <li><a href="/wiki/Tick-borne_disease" title="Tick-borne disease">Tick</a></li></ul></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%;text-align:left;">Gastrointestinal</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Foodborne_illness" title="Foodborne illness">Food</a> <ul><li><a href="/wiki/Food_contaminant" title="Food contaminant">Contamination</a></li></ul></li> <li><a href="/wiki/Breastfeeding_contraindications" title="Breastfeeding contraindications">Breastmilk</a></li> <li><a href="/wiki/Waterborne_disease" title="Waterborne disease">Water</a></li> <li><a href="/wiki/Fecal%E2%80%93oral_route" title="Fecal–oral route">Feces</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%;text-align:left;">Cutaneous</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Burn#Complications" title="Burn">Burn</a></li> <li><a href="/wiki/Fomite" title="Fomite">Fomite</a></li> <li><a href="/wiki/Soil-transmitted_helminthiasis" title="Soil-transmitted helminthiasis">Soil</a></li> <li>Open <a href="/wiki/Wound" title="Wound">wound</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%;text-align:left;">Genitourinary</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Sexually_transmitted_infection" title="Sexually transmitted infection">Sex</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%;text-align:left;">Trans-placental</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li>Prenatal</li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%;text-align:left;">Cervico-vaginal</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li>Perinatal</li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%;text-align:left;">Other</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Eye_disease" title="Eye disease">Ocular (Eye) mucosal membrane</a></li></ul> </div></td></tr></tbody></table><div></div></td></tr></tbody></table><div></div></td></tr></tbody></table><div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%;text-align:left;"><a href="/wiki/Mathematical_modelling_of_infectious_disease" class="mw-redirect" title="Mathematical modelling of infectious disease">Modelling</a></th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Agent-based_model_in_biology#Bacteria_aggregation_leading_to_biofilm_formation" title="Agent-based model in biology">Agent-based model</a></li> <li><a href="/wiki/Animal_disease_model" title="Animal disease model">Animal disease model</a></li> <li><a href="/wiki/Attack_rate" title="Attack rate">Attack rate</a></li> <li><a href="/wiki/Basic_reproduction_number" title="Basic reproduction number">Basic reproduction number</a></li> <li><a href="/wiki/Compartmental_models_in_epidemiology" title="Compartmental models in epidemiology">Compartmental models in epidemiology</a></li> <li><a href="/wiki/Critical_community_size" title="Critical community size">Critical community size</a></li> <li><a href="/wiki/Force_of_infection" title="Force of infection">Force of infection</a></li> <li><a href="/wiki/Herd_immunity" title="Herd immunity">Herd immunity</a></li> <li><a href="/wiki/Infection_rate" title="Infection rate">Infection rate</a></li> <li><a href="/wiki/Artificial_intelligence_in_healthcare" title="Artificial intelligence in healthcare">Machine learning</a></li> <li><a href="/wiki/Multiplicity_of_infection" title="Multiplicity of infection">Multiplicity of infection</a></li> <li><a href="/wiki/Serial_interval" title="Serial interval">Serial interval</a></li> <li><a href="/wiki/WAIFW_matrix" title="WAIFW matrix">WAIFW matrix</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%;text-align:left;">Occurrence<br />in population</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Disease_cluster" title="Disease cluster">Cluster</a></li> <li><a href="/wiki/Endemic_(epidemiology)" title="Endemic (epidemiology)">Endemic</a></li> <li><a href="/wiki/Epidemic" title="Epidemic">Epidemic</a> <ul><li><a href="/wiki/Epidemic_curve" title="Epidemic curve">Curve</a></li> <li><a href="/wiki/Farr%27s_laws" title="Farr's laws">Farr's laws</a></li></ul></li> <li><a href="/wiki/Holoendemic" title="Holoendemic">Holoendemic</a></li> <li><a href="/wiki/Hyperendemic" title="Hyperendemic">Hyperendemic</a></li> <li><a href="/wiki/Incidence_(epidemiology)" title="Incidence (epidemiology)">Incidence</a></li> <li><a href="/wiki/Inequality_in_disease" title="Inequality in disease">Inequality</a></li> <li><a href="/wiki/Mesoendemic" class="mw-redirect" title="Mesoendemic">Mesoendemic</a></li> <li><a href="/wiki/Disease_outbreak" title="Disease outbreak">Outbreak</a></li> <li><a href="/wiki/Pandemic" title="Pandemic">Pandemic</a></li> <li><a href="/wiki/Prevalence" title="Prevalence">Prevalence</a></li> <li><a href="/wiki/Epidemic#Seasonality" title="Epidemic">Seasonality</a></li> <li><a href="/wiki/Spatial_epidemiology" title="Spatial epidemiology">Geographic distribution</a></li> <li><a href="/wiki/Sporadic_disease" title="Sporadic disease">Sporadic</a></li> <li><a href="/wiki/Syndemic" title="Syndemic">Syndemic</a></li> <li><a href="/wiki/Twindemic" title="Twindemic">Twindemic</a></li></ul> </div></td></tr></tbody></table><div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Anatomical <br />location</th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li>Respiratory <ul><li><a href="/wiki/Upper_respiratory_tract_infection" title="Upper respiratory tract infection">Ear-Nose-Throat/Upper respiratory tract</a></li> <li><a href="/wiki/Lower_respiratory_tract_infection" title="Lower respiratory tract infection">Chest/Lower respiratory tract</a></li></ul></li> <li><a href="/wiki/Gastrointestinal_infection" class="mw-redirect" title="Gastrointestinal infection">Gastrointestinal</a> <ul><li><a href="/wiki/Intestinal_infectious_diseases" title="Intestinal infectious diseases">Intestinal</a></li></ul></li> <li>Genitourinary</li> <li>Nervous system</li> <li><a href="/wiki/Skin_infection" title="Skin infection">Skin</a></li> <li>Soft tissue</li> <li><a href="/wiki/Bone_infection" class="mw-redirect" title="Bone infection">Bone</a></li> <li><a href="/wiki/Joint_infection" class="mw-redirect" title="Joint infection">Joint</a></li> <li>Cardiovascular</li> <li><a href="/wiki/Systemic_disease" title="Systemic disease">Systemic/Generalized</a></li> <li><a href="/wiki/Sepsis" title="Sepsis">Blood</a></li> <li><a href="/wiki/Odontogenic_infection" title="Odontogenic infection">Tooth</a></li> <li><a href="/wiki/Mouth_infection" title="Mouth infection">Mouth</a></li> <li><a href="/wiki/Intra-amniotic_infection" class="mw-redirect" title="Intra-amniotic infection">Fetus</a></li> <li>Eye</li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="/wiki/Infection_prevention_and_control" title="Infection prevention and control">Prevention<br />and Control<br />measures</a></th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"></div><table class="nowraplinks navbox-subgroup" style="border-spacing:0"><tbody><tr><th scope="row" class="navbox-group" style="width:1%;text-align:left;">Pharmaceutical</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Antibiotic" title="Antibiotic">Antibiotic</a> <ul><li><a href="/wiki/Antibiotic_prophylaxis" title="Antibiotic prophylaxis">prophylactic</a></li></ul></li> <li><a href="/wiki/Antifungal" title="Antifungal">Antifungal</a></li> <li><a href="/wiki/Anthelmintic" title="Anthelmintic">Anthelmintic</a> <ul><li><a href="/wiki/Ascaricide" title="Ascaricide">Ascaricide</a></li></ul></li> <li><a href="/wiki/Antimicrobial" title="Antimicrobial">Antimicrobial</a> <ul><li><a href="/wiki/Antimicrobial_stewardship" title="Antimicrobial stewardship">Antimicrobial stewardship</a></li></ul></li> <li><a href="/wiki/Antiseptic" title="Antiseptic">Antiseptic</a></li> <li><a href="/wiki/Antiviral_drug" title="Antiviral drug">Antiviral</a></li> <li><a href="/wiki/Asepsis" title="Asepsis">Asepsis</a></li> <li><a href="/wiki/Combination_therapy" title="Combination therapy">Combination</a></li> <li><a href="/wiki/Pharmacovigilance" title="Pharmacovigilance">Drug safety</a></li> <li><a href="/wiki/Immunization" title="Immunization">Immunization</a></li> <li><a href="/wiki/Immunotherapy" title="Immunotherapy">Immunotherapy</a> <ul><li><a href="/wiki/Monoclonal_antibody_therapy" title="Monoclonal antibody therapy">Monoclonal antibody therapy</a></li></ul></li> <li><a href="/wiki/Inoculation" title="Inoculation">Inoculation</a></li> <li><a href="/wiki/Phage_therapy" title="Phage therapy">Phage therapy</a></li> <li><a href="/wiki/Pre-exposure_prophylaxis" title="Pre-exposure prophylaxis">Pre-exposure prophylaxis</a></li> <li><a href="/wiki/Post-exposure_prophylaxis" title="Post-exposure prophylaxis">Post-exposure prophylaxis</a></li> <li><a href="/wiki/Drug_repositioning" title="Drug repositioning">Repurposed drugs</a></li> <li><a href="/wiki/Vaccination" title="Vaccination">Vaccination</a> <ul><li><a href="/wiki/Vaccine_efficacy" title="Vaccine efficacy">efficacy/effectiveness</a></li> <li><a href="/wiki/Booster_dose" title="Booster dose">booster</a></li> <li><a href="/wiki/Vaccine_resistance" title="Vaccine resistance">resistance</a></li> <li><a href="/wiki/Vaccine-preventable_disease" title="Vaccine-preventable disease">Vaccine-preventable disease</a></li> <li><a href="/wiki/Ring_vaccination" title="Ring vaccination">Ring vaccination</a></li></ul></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%;text-align:left;"><a href="/wiki/Non-pharmaceutical_intervention_(epidemiology)" title="Non-pharmaceutical intervention (epidemiology)">Non-<br />pharmaceutical</a></th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Contact_tracing" title="Contact tracing">Contact tracing</a></li> <li><a href="/wiki/Cordon_sanitaire_(medicine)" title="Cordon sanitaire (medicine)">Cordon sanitaire</a></li> <li><a href="/wiki/Disease_surveillance" title="Disease surveillance">Disease surveillance</a></li> <li><a href="/wiki/Disinfectant" title="Disinfectant">Disinfection</a></li> <li><a href="/wiki/Flattening_the_curve" title="Flattening the curve">Flattening the curve</a></li> <li><a href="/wiki/Hygiene" title="Hygiene">Hygiene</a> <ul><li><a href="/wiki/Food_safety" title="Food safety">Food hygiene</a></li> <li><a href="/wiki/Hand_washing" title="Hand washing">Hand washing</a></li> <li><a href="/wiki/Medical_glove" title="Medical glove">Gloves</a></li></ul></li> <li><a href="/wiki/Isolation_(health_care)" title="Isolation (health care)">Isolation</a> <ul><li><a href="/wiki/Barrier_nursing" title="Barrier nursing">Barrier nursing</a></li></ul></li> <li><a href="/wiki/Stay-at-home_order" title="Stay-at-home order">Lockdown</a></li> <li><a href="/wiki/Notifiable_disease" title="Notifiable disease">Notification</a> <ul><li><a href="/wiki/List_of_notifiable_diseases" title="List of notifiable diseases">list</a></li></ul></li> <li><a href="/wiki/Protective_sequestration" title="Protective sequestration">Protective sequestration</a></li> <li><a href="/wiki/Public_health" title="Public health">Public health</a> <ul><li><a href="/wiki/Community_health" title="Community health">Community health</a> services</li> <li><a href="/wiki/Health_communication" title="Health communication">Health communication</a></li> <li><a href="/wiki/Health_education" title="Health education">Health education</a></li></ul></li> <li><a href="/wiki/Outbreak_response" title="Outbreak response">Outbreak response</a></li> <li><a href="/wiki/Quarantine" title="Quarantine">Quarantine</a></li> <li><a href="/wiki/Source_control_(respiratory_disease)" title="Source control (respiratory disease)">Respiratory source control</a> <ul><li><a href="/wiki/N95_respirator" title="N95 respirator">N95 respirator</a></li> <li><a href="/wiki/Surgical_mask" title="Surgical mask">Surgical mask</a></li> <li><a href="/wiki/Personal_protective_equipment" title="Personal protective equipment">PPE</a></li></ul></li> <li><a href="/wiki/Safe_sex" title="Safe sex">Safe sex</a></li> <li><a href="/wiki/Sanitation" title="Sanitation">Sanitation</a></li> <li><a href="/wiki/Screening_(medicine)" title="Screening (medicine)">Screening</a></li> <li><a href="/wiki/Social_distancing" title="Social distancing">Social distancing</a></li> <li><a href="/wiki/Sterilization_(microbiology)" title="Sterilization (microbiology)">Sterilization</a></li> <li><a href="/wiki/Transmission-based_precautions" title="Transmission-based precautions">Transmission-based precautions</a></li> <li><a href="/wiki/Travel_ban" title="Travel ban">Travel restrictions</a></li> <li><a href="/wiki/Universal_precautions" title="Universal precautions">Universal precautions</a></li> <li><a href="/wiki/Vector_control" title="Vector control">Vector control</a></li> <li><a href="/wiki/Wastewater_surveillance" title="Wastewater surveillance">Wastewater surveillance</a></li> <li>Zoning</li></ul> </div></td></tr></tbody></table><div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="/wiki/Emerging_infectious_disease" title="Emerging infectious disease">Emerging <br />infections</a></th><td class="navbox-list-with-group navbox-list navbox-even hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Antigenic_drift" title="Antigenic drift">Antigenic drift</a></li> <li><a href="/wiki/Antigenic_shift" title="Antigenic shift">Antigenic shift</a></li> <li>Antimicrobial resistance surveillance <ul><li><a href="/wiki/EARS-Net" title="EARS-Net">EARS-Net</a></li></ul></li> <li><a href="/wiki/Biosecurity" title="Biosecurity">Biosecurity</a></li> <li><a href="/wiki/CRISPR" title="CRISPR">CRISPR</a></li> <li><a href="/wiki/Disease_X" title="Disease X">Disease X</a></li> <li><a href="/wiki/Emergent_virus" title="Emergent virus">Emergent virus</a></li> <li><a href="/wiki/Evolutionary_epidemiology" title="Evolutionary epidemiology">Evolutionary epidemiology</a></li> <li><a href="/wiki/Genetic_epidemiology" title="Genetic epidemiology">Genetic epidemiology</a></li> <li><a href="/wiki/Global_Health_Initiatives" title="Global Health Initiatives">Global Health Initiatives</a></li> <li><a href="/wiki/Microbial_phylogenetics" title="Microbial phylogenetics">Microbial phylogenetics</a></li> <li><a href="/wiki/One_Health_Model" title="One Health Model">One Health Model</a></li> <li><a href="/wiki/Reassortment" title="Reassortment">Genomic reassortment</a></li> <li>Re-emerging disease</li> <li><a href="/wiki/Reverse_zoonosis" title="Reverse zoonosis">Reverse zoonosis</a></li> <li><a href="/wiki/Evolutionary_pressure#Antibiotic_resistance" title="Evolutionary pressure">Selection pressure</a></li> <li><a href="/wiki/Synthetic_biology" title="Synthetic biology">Synthetic biology</a></li> <li><a href="/wiki/Viral_phylodynamics" title="Viral phylodynamics">Viral phylodynamics</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Other</th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Discovery_of_disease-causing_pathogens" title="Discovery of disease-causing pathogens">Discovery</a></li> <li><a href="/wiki/Eradication_of_infectious_diseases" title="Eradication of infectious 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