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

Back in March, the World Health Organisation’s report on the origin of the COVID-19 pandemic coronavirus confirmed something that had long been widely presumed. Since the pandemic began, there has been an enormous virus hunt in China.

The purpose of this hunt has been to find the viruses intermediate between SARS-CoV-2 and its coronavirus relatives found in bats (Luk et al., 2019).

The closest known wild relative of SARS-CoV-2 was found by Zheng-li Shi of the Wuhan Institute of Virology (WIV) in a bat in central Yunnan province, China. This virus, called RaTG13, is 96.1% similar to SARS-CoV-2. This genetic difference (3.9%) corresponds to about 1150 nucleotide differences between the two viruses; i.e. it is quite a large gap. Finding intermediate viruses would solve two puzzles. One is geographical: By what means or in what host animal(s) did the virus get to Wuhan? The second is genetic: what viruses were the evolutionary intermediates between RaTG13 and SARS-CoV-2?