Global patterns in coronavirus diversity

Abstract

Since the emergence of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle East Respiratory Syndrom Coronavirus (MERS-CoV) it has become increasingly clear that bats are important reservoirs of CoVs. Despite this, only 6% of all CoV sequences in GenBank are from bats. The remaining 94% largely consist of known pathogens of public health or agricultural significance, indicating that current research effort is heavily biased towards describing known diseases rather than the ‘pre-emergent’ diversity in bats. Our study addresses this critical gap, and focuses on resource poor countries where the risk of zoonotic emergence is believed to be highest. We surveyed the diversity of CoVs in multiple host taxa from twenty countries to explore the factors driving viral diversity at a global scale. We identified sequences representing 100 discrete phylogenetic clusters, ninety-one of which were found in bats, and used ecological and epidemiologic analyses to show that patterns of CoV diversity correlate with those of bat diversity. This cements bats as the major evolutionary reservoirs and ecological drivers of CoV diversity. Co-phylogenetic reconciliation analysis was also used to show that host switching has contributed to CoV evolution, and a preliminary analysis suggests that regional variation exists in the dynamics of this process. Overall our study represents a model for exploring global viral diversity and advances our fundamental understanding of CoV biodiversity and the potential risk factors associated with zoonotic emergence.

When bats go viral: negative framings in virological research imperil bat conservation

“…Although we acknowledge that bats may represent an important share of natural virus reservoirs (Anthony et al 2017, Maxmen 2017, Olival et al 2017) that might eventually pose danger to people, we remain firm in asserting that the risk of virus transmission from bats to humans is small (Kingston 2016, Anthony et al 2017, an aspect that is worryingly neglected in most virological bat-related publications. Moreover, the fact that an increasing number of virus outbreaks is largely attributable to human encroachment in natural areas (Buttke et al 2015, Terraube et al 2017) is rarely publicised.…”

A Comparative Analysis of Viral Richness and Viral Sharing in Cave-Roosting Bats

“…Specific clades of viruses are often primarily associated with closely related bat taxa; for example, the SARS coronaviruses are primarily found in the genus Rhinolophus, which includes a number of cave-roosting species [23,24]. Other viral groups appear to be shared more widely across bat taxa with varying ecological and life-history traits, particularly generalist viruses such as lyssaviruses and mosquito-borne flaviviruses [25].…”

“…Standardized field surveillance in targeted sites are beginning to fill these gaps [23]. Our calculated spatial variables rely on an assumption that viral distribution extends across a species' entire geographic range [11,68], although pathogen distribution is likely more constrained to certain bat populations or habitat fragments.…”

Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species

“…Again, over eons, bats have evolved to cope with these challenges, often leading to survival despite viral exposure (for a comprehensive list of viruses detected in bats, see 54). Epidemiological studies and field surveys suggest viruses circulate in wild bat populations (12,55) without causing the great morbidity or mortality observed as a result of viral spillovers into humans (Table 1) (14,56). Although the processes through which bats manage to clear viral infections remain poorly understood, possible explanations for the resilience of individual bats to these infections include not only heightened immune function but modulation of inflammation and mechanisms of repair (16).…”

“…Without bats, it is estimated that the United States would spend more than $3 billion a year on pesticides alone (10). Bats are suspected reservoirs for some of the deadliest viral diseases [e.g., Ebola, SARS (severe acute respiratory syndrome), rabies, and MERS (Middle East respiratory syndrome coronavirus); [11][12][13][14], but they appear to be asymptomatic and survive these infections. This suggests that bats have evolved unique immune systems, and potentially the solution to better tolerate these pathogens may lie in uncovering how bats limit their immunopathology upon infection (15,16).…”