The SARS-CoV-2-like virus found in captive pangolins from Guangdong should be better sequenced

Viruses closely related to SARS-CoV-2, which is the virus responsible of the Covid-19 pandemic, were sequenced in several Sunda pangolins (Manis javanica) seized in the Guangdong and Guangxi provinces of China between 2017 and 2019^1-3. These viruses belong to two lineages: one from Guangdong (GD/P) and the other from Guangxi (GX/P). TheGD/Pviruses are particularly intriguing as the amino-acid sequence of the receptor binding domain of the spike protein is very similar to that of the human SARS-CoV-2 virus (97.4%)². This characteristic suggests thatGD/Pviruses are capable of binding human ACE2 receptor and may therefore be able to mediate infection of human cells. Whereas all sixGX/Pgenomes were deposited as annotated sequences in GenBank, none of the twoGD/Pgenomes assembled in previous studies^2,3are currently available. To overcome this absence, I assembled these genomes from the Sequence Read Archive (SRA) data available for SARS-CoV-2-like viruses detected in five captive pangolins from Guangdong. I found the genome assemblies ofGD/Pvirus of poor quality, having high levels of missing data. Additionally, unexpected reads in the Illumina sequencing data were identified. TheGD/P2Sdataset²contains reads that are identical to SARS-CoV-2, suggesting either the coexistence of two SARS-CoV-2-like viruses in the same pangolin or contamination by the human virus. In the four otherGD/Pdatasets¹many mitochondrial reads from pangolin were identified, as well as from three other species, namely, human, mouse and tiger. Importantly, I only identified three polymorphic nucleotide sites between the fiveGD/Psequences. Such low levels of polymorphism may reasonably be accounted for by sequencing errors alone, thus raising the possibility that the five pangolins seized in Guangdong in March 2019 were infected by the same virus strain, most probably during their captivity.