World distribution of mammalian coronaviruses: One reason the pandemic started in Wuhan

It's currently fashionable in many US circles to speculate that Covid-19 started in a Wuhan lab. But according to this 2017 paper, more coronaviruses are to be found in the regions around Wuhan than much of the rest of the world. The next SARS will also likely start in Asia, or perhaps Africa. That could have happened with or without help of a lab, and without a lab seems more likely at the moment.

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ABSTRACT

Global patterns in coronavirus diversity

Simon J. Anthony, Christine K. Johnson, Denise J. Greig, Sarah Kramer, Xiaoyu Che, Heather Wells, Allison L. Hicks, Damien O. Joly, Nathan D. Wolfe, Peter Daszak

Virus Evolution, Volume 3, Issue 1, January 2017, vex012, https://doi.org/10.1093/ve/vex012

Published: 12 June 2017

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.