The virology team @PasteurCambodia has screened 400+ archived samples of wild animals incl. different bat species, and found a positive SARS-like signal in rectal swabs of 2 Rhinolophus shameli bats from 2010. 2/7
mNGS & phylogenetic analysis revealed a virus closely related to SARS-CoV-2. It consistently branches with SARS-CoV-2 and RaTG13 in most of the genome, aside of a small portion corresponding to the spike N terminal domain (more divergent). 3/7
The location is the big surprise. R. Shameli bats are only found in Southeast Asia iucnredlist.org/species/19566/… , which indicates that the SARS-CoV-2 lineage is more geographically widespread than previously understood. 4/7
The Mekong river links the Yunnan, where RaTG13 and RmYN02 were found, and Southeast Asia, and some species of bats have a wide range of circulation that encompasses all these areas 5/7
Interestingly, Manis Javanica (pangolins) are also from Southeast Asia. More sampling efforts in that area could help us better understand the coronaviruses diversity and range of circulation! 6/7
The sequences were deposited on GISAID last week (just after verification) and the raw NGS data will be on ENA in 24h. 7/7
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We’ve prepared a short report on the early introductions and spread of #SARS-CoV-2 in the northern regions of France doi.org/10.1101/2020.0…. Find some key messages below. #COVID19 (1/9)
Several early introductions to France do not appear to have led to further spread likely due to effective contact tracing and isolation. (2/9)
Most sequences from France are spread out in the diversity of clade G (@GISAID nomenclature). This represents local circulation with possibly multiple introductions, and one export to Algeria. (3/9)