Global patterns in coronavirus diversity

Anthony, Simon J., Johnson, Christine K., Greig, Denise J., Kramer, Sarah, Che, Xiaoyu, Wells, Heather, Hicks, Allison L., Joly, Damien O., Wolfe, Nathan D., Daszak, Peter, Karesh, William, Lipkin, W.I., Morse, Stephen S., PRECICT Consortium, , Mazet, Jonna A.K., and Goldstein, Tracey (2017) Global patterns in coronavirus diversity. Virus Evolution, 3 (1). vex012.

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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.

Item ID: 65356
Item Type: Article (Research - C1)
ISSN: 2057-1577
Keywords: coronavirus; viral ecology; bat; evolution
Copyright Information: (C) The Author 2017. Published by Oxford University Press.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properlycited.For commercial re-use, please contact journals.permissions@oup.com
Additional Information:

Paul Horwood is a member of the PREDICT Consortium.

Funders: United States Agency for International Development (USAID)
Projects and Grants: USAID Emerging Pandemic Threats PREDICT project (cooperative agreement number GHN-A-OO-09-00010-00)
Date Deposited: 07 Jan 2021 22:11
FoR Codes: 30 AGRICULTURAL, VETERINARY AND FOOD SCIENCES > 3009 Veterinary sciences > 300914 Veterinary virology @ 100%
SEO Codes: 97 EXPANDING KNOWLEDGE > 970107 Expanding Knowledge in the Agricultural and Veterinary Sciences @ 100%
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