The diversity of human RNA viruses

Abstract

We still cannot answer the very basic question "how many kinds of RNA viruses are there?" even for those that infect humans. It is often suggested that there remains a large number of viruses in humans that we have not yet discovered or recognised, and that there is a much larger and rapidly evolving pool of potential new viruses in mammalian and avian reservoirs that humans are continually being exposed to. However, a careful examination of discovery rates of new human RNA virus species, genera and families challenges this view, raising the possibility that the diversity is much more limited. Moreover, there is some evidence that the cast of human viruses is dynamic, with existing viruses disappearing (at least from humans) and new viruses appearing (perhaps evolving) over timescales of decades. Most of these new viruses, however, remain rare; only a small (but highly significant) minority are capable of spreading extensively through human populations.

Keywords: biodiversity; discovery curve; emergence; evolution; loss; nucleotide sequences; species; surveillance; zoonosis.

Figure 1

RNA virus discovery curves: the cumulative number of RNA virus species (blue), genera (red) and families (green) found in humans between 1901 and 2006. Taxa are those used in the 9^th ICTV report [9]. Adapted from [7].

Figure 2

Taxonomic diversity of human RNA viruses. A) Numbers of species per genus for all 47 currently recognised genera. B) Numbers of genera per family for all 17 currently recognised families. Taxa are those used in the 9^th ICTV report [9]. Adapted from [7].

Figure 3

Sensitivity of species diversity estimator to changes in the numbers of recognised genera and families. A) Expected number of as yet undiscovered species (vertical axis) as a function of number of recognised genera (horizontal axis) and families (increasing from 15 to 25 as indicated by arrow). Expectations given the currently recognised numbers (47 and 17 respectively) and plausible upper limits (60 and 20) are shown (black circles). B) Expected number of as yet undiscovered species as a function of a scaling factor. The scaling factor has a central value of 2 (dotted vertical line) corresponding to the assumption that species scale to genera as genera scale to family [2]. Values >2 indicate that families actually contain more genera than is currently recognised and values <2 that they contain fewer. The lower curve corresponds to the observed 47 genera and 17 families and the upper curve to the plausible estimate of 60 and 20 respectively.