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Phylogeographic Mapping Of Coronaviruses Pinpoints Direct Progenitor Of SARS-CoV-2 As Originating From China

Phylogeographic Mapping of Newly Discovered Coronaviruses Pinpoints the Direct Progenitor of SARS-CoV-2 as Originating from Mojiang, China

by Jonathan Latham, PhD and Allison Wilson, PhD

Synopsis: Many scientists are now openly considering whether a lab leak best explains the origin of SARS-CoV-2. But it is frequently also suggested in the media that the data ‘hasn’t changed’, only people’s opinions. This is far from the truth. One data set that has grown substantively since the pandemic broke out is the number of wild virus relatives of SARS-CoV-2. In all, twelve isolates have now been described, ten obtained from bats and two from pangolins. All 12 isolates were found in Asia. These viruses constitute what we know of the SARS-CoV-2 reservoir population in its bat hosts. For most of these viruses both their sampling location and their genetic similarity to SARS-CoV-2 are known. We therefore conducted a phylogeographic analysis of these viruses. It revealed that the SARS-CoV-2-related viruses form a coherent group with a geographically ordered genetic structure. Because of this geographic ordering the location from which human SARS-CoV-2 originated, i.e. the locality where its direct ancestor jumped from the bat reservoir, could be identified with high confidence. Using two different approaches, which gave the same result, this location was determined to be a comparatively small region of south-central Yunnan, China.

Positively locating the jump from bats represents an advance with major implications for understanding the origin of SARS-CoV-2. While a south-central Yunnan source does not rule out either a lab or a zoonotic origin in principle, the result compels all candidate hypotheses to incorporate a plausible link with that locality. Indeed, some well-known origin theories are clearly not compatible with this and therefore appear to be non-viable. Perhaps even more importantly, a south-central Yunnan origin is a highly suggestive finding because, at the centre of that region is the Mojiang mine. This mine has been the focus of most lab origin theories. In particular, the Mojiang Miners Passage theory, which posits that SARS-CoV-2 derives from tissue samples taken from miners who were infected in a novel coronavirus outbreak in 2012, specifically predicts that Mojiang in south-central Yunnan was the site where the jump from bats occurred. For these reasons, this new analysis should transform the origins debate about COVID-19.

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