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 takenAlternative 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 analysis, to estimate the timescale of the epidemic, and coalescent theory, to infer the demographic 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 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.
Cross-species transmission (CST), also called interspecies transmission, host jump, or spillover, is the transmission of an infectious pathogen, such as a virus, between hosts belonging to different species. 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, but cross-species transmission may also occur with bacterial 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 of an initial individual host, which may lead to amplification and an outbreak; 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 diseases 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, Ebola, swine flu, rabies, and avian influenza.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.