An Ecological Framework of the Human Virome Provides Classification of Current Knowledge and Identifies Areas of Forthcoming Discovery

Parker, Michael T.

The key characteristic of pathogenic viruses is that they cause an acute disease in which the host either lives or dies, with the virus simply using it as a vessel to move to the next host. In these interactions, hosts typically mount strong immune responses and literally fight for their lives. This is not to say that all pathogenic infections are deadly or resolved immediately, since the degree of pathogenicity and time to resolution vary widely, as will be discussed in following sections. Rather, the virus-host interactions classified here as "pathogenic" represent perturbations of homeostasis for which the only resolution is that one side must prevail. Either the host completely clears its body of the virus, or it succumbs to infection. While this sounds like a poor transmission strategy, history has shown it can be quite effective, as long as the proper trade-offs are satisfied (see The Parasitic Virome, above). Influenza virus is a prime example of the success of a pathogenic strategy. Most humans can expect to be infected with at least one influenza virus per year, and in general they will observe a fairly robust set of symptoms including, but not limited to, fever, chills, headache, nasal congestion, and coughing [40] . While infection can be severe and even cause death, this is typically limited to hosts in an immunocompromised state, as selective pressure typically drives virus evolution to less virulence [41] . In general, virus is shed one to two days after infection, with symptoms usually presenting one day later, ensuring that a person shedding virus will be out and about among currently uninfected individuals [42] . Severe symptoms may be due to viral replication and destruction of tissue; however, over-reaction of the immune system is often the cause [41] . This is exemplified by secondary bacterial pneumonia where blooms of pathogenic and/or commensal bacteria can result in severe disease or death [38] [39] [40] [41] . However, by the time a person has become ill, they have likely spread the virus by direct contact with an uninfected individual, contaminated fomites, or aerosolized respiratory droplets [46] .