A Strategy To Estimate Unknown Viral Diversity in Mammals

Abstract

The majority of emerging zoonoses originate in wildlife, and many are caused by viruses. However, there are no rigorous estimates of total viral diversity (here termed “virodiversity”) for any wildlife species, despite the utility of this to future surveillance and control of emerging zoonoses. In this case study, we repeatedly sampled a mammalian wildlife host known to harbor emerging zoonotic pathogens (the Indian Flying Fox, Pteropus giganteus) and used PCR with degenerate viral family-level primers to discover and analyze the occurrence patterns of 55 viruses from nine viral families. We then adapted statistical techniques used to estimate biodiversity in vertebrates and plants and estimated the total viral richness of these nine families in P. giganteus to be 58 viruses. Our analyses demonstrate proof-of-concept of a strategy for estimating viral richness and provide the first statistically supported estimate of the number of undiscovered viruses in a mammalian host. We used a simple extrapolation to estimate that there are a minimum of 320,000 mammalian viruses awaiting discovery within these nine families, assuming all species harbor a similar number of viruses, with minimal turnover between host species. We estimate the cost of discovering these viruses to be ~$6.3 billion (or ~$1.4 billion for 85% of the total diversity), which if annualized over a 10-year study time frame would represent a small fraction of the cost of many pandemic zoonoses.

Random sampling of the Central European bat fauna reveals the existence of numerous hitherto unknown adenoviruses

“…In a recent study aiming at the assessment of viral diversity of mammals, numerous novel viruses including AdVs were found in the Indian flying fox (Pteropus giganteus) (Anthony et al, 2013). The authors described an AdV almost identical to BtAdV-1 (AB303301) (with a single silent mutation on the short pol fragment), which was detected in the closely related species (Ryukyu flying fox, Pteropus dasymallus yayeyamae, Maeda et al, 2008).…”

Novel bat adenoviruses with an extremely large E3 gene

“…However, most bat viruses reported are RNA viruses and were identified by nucleic acid detection. Previously, we and other investigators have demonstrated the high prevalence and great genetic diversity of AdVs in different bat species by PCR screening (Anthony et al, 2013;Casas et al, 2010;Chen et al, 2012;Li et al, 2010;Lima et al, 2013;Vidovszky et al, 2015). Given that over 1000 bat species are known worldwide (Simmons, 2005), the prevalence and number of bat AdV types need to be further investigated.…”

Isolation of multiple novel paramyxoviruses from pteropid bat urine

“…Detection of viral nucleic acid by PCR to identify viruses in bats represents the most common method employed in published studies. Several groups have also used nextgeneration sequencing platforms to identify most, if not all, of the viruses in a target species of bat, termed the 'bat virome' (Anthony et al, 2013;Baker et al, 2013a;Donaldson et al, 2010;Ge et al, 2012;Li et al, 2010). However, determining the zoonotic and pathogenic potential of these agents is very difficult based on sequence information alone.…”