VIRUS
WHAT IS VIRUS?
FOUNDING OF VIRUS.
INTRODUCTION
Following on from the discovery of the tobacco mosaic virus in 1892 and the foot-and-mouth disease virus in 1898, the first ‘filterable agent’ to be discovered in humans was the yellow fever virus in 1901 [1]. New species of the human virus are still being identified, at a rate of three or four per year (see below), and viruses make up over two-thirds of all new human pathogens [2], a highly significant over-representation given that most human pathogen species are bacteria, fungi or helminths. These new viruses differ wildly in their importance, ranging from the rare and mild illness due to Menangle virus to the devastating public health impact of HIV-1.
In this paper, we take an ecological approach to studying the diversity of human viruses (defined as viruses for which there is evidence of natural infection of humans). First, we describe and analyze temporal, geographical and taxonomic patterns in the discovery of human viruses (§2). We then consider the processes by which new human viruses emerge (§3). There are a number of definitions of ‘emergence’ [3]; here, we are interested in all stages of the process by which a virus shifts from not infecting humans at all to becoming a major human pathogen. As experiences with HIV-1 and new variants of influenza A (and also with novel animal pathogens such as canine parvovirus [4]) show, this shift can occur rapidly, over time scales of decades, years or even months.
Of course, not all newly identified human virus species are ‘new’ in the sense that they have only recently started to infect humans; many of them have been present in humans for a considerable time but have only recently been recognized (see [2] for a more detailed discussion). Moreover, we recognize that ‘species’ itself is an imprecise designation, especially for viruses such as influenza A where different serotypes can have very different epidemiologies and health impacts. Indeed, the demarcation between genus, species complex, species and serotype (or other designations of sub-specific variation) can be somewhat arbitrary. Nonetheless, a study of currently recognized ‘species’ is a natural starting point for attempts to characterize and interpret patterns of virus diversity.
VIRUS DIVERSITY
Survey of human viruses
As a starting point for our survey, we used a previously published database (see [5]) obtained by systematically searching the primary scientific literature up to and including 2005 for reports of human infection with recognized virus species, using species as defined by the International Committee on Taxonomy of Viruses (ICTV) [6]. The list of viruses was updated if either a new species that can infect humans had been described in the literature and also recognized by the ICTV, if a known species had been found in humans for the first time, or if there had been a change in species classifications by the ICTV (notably for the human papillomaviruses and the vesicular stomatitis viruses).
The year of discovery was taken to be the year of publication of the first report of human infection. The place of discovery was determined from the original report and recorded as the location of the diagnostic laboratory or, in the few instances where this was not clear, the address of the first author of the report. We did not attempt to locate the case itself, as this information was often lacking.
We obtained a list of 219 ICTV-recognized virus species that have been reported to infect humans. 23 virus families were represented by species on this list.
Major developments in the technology of virus discovered.
| year | technology |
|---|---|
| 1890s | filtration |
| 1929 | complement fixation |
| 1948 | tissue culture |
| 1970s | monoclonal antibodies |
| 1985 | polymerase chain reaction (PCR) |
| 2000s | high throughput sequencing |
New virus families
The discovery curve for virus families is shown in figure 1b. Here, a family is included on the date of the first published report of human infection by a virus species from that family. There is too little data (n = 23) for detailed statistical analysis, but the figure does suggest a possible decrease in the rate of discovery, implying that the pool of undiscovered families may be relatively modest (see [5]).
Strikingly, no new families have been added to the list since 1988, the longest such interval on record. However, several viruses (specifically Torque Teno (TT) virus, TT mini virus and TT midi virus) newly reported since 1988 remain unassigned to a family.
It should also be noted that there are three virus families that, although they do not contain any known human virus species, do contain species that infect other mammals: Arteriviridae (several species including simian hemorrhagic fever virus); Asfarviridae (African swine fever virus); Circoviridae (including mammal infecting circoviruses as well as gyrovirus which infects chickens). This suggests that the list of families containing human viruses may not yet be complete
Discovered of virus
Discovered of virus
| virus name | family |
|---|---|
| human bocavirus | Parvoviridae |
| parvovirus 4 | Parvoviridae |
| KI polyomavirus | Polyomaviridae |
| Melaka virus | Reoviridae |
| WU polyomavirus | Polyomaviridae |
| astrovirus MLB1 | Astroviridae |
| Bundibugyo ebolavirus | Filoviridae |
| human bocavirus 2 | Parvoviridae |
| human cosaviruses A-D | Picornaviridae |
| human cosavirus E1 | Picornaviridae |
| astrovirus VA1 | Astroviridae |
| human papilloma virus 116 | Papillomaviridae |
| klassevirus | Picornaviridae |
| Lujo virus | Arenaviridae |
CONCLUSIONS
The lines of evidence described earlier combine to suggest the following tentative model of the emergence process for novel human viruses. First, humans are constantly exposed to a huge diversity of viruses, though those of other mammals (and perhaps birds) are of greatest importance. Moreover, these viruses are very genetically diverse and new genotypes, strains, and species evolve rapidly (over periods of years or decades). A fraction of these viruses (both existing and newly evolved) are capable of infecting humans
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