Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins

Abstract

The outbreak of COVID-19 poses unprecedent challenges to global health 1 . The new coronavirus, SARS-CoV-2, shares high sequence identity to SARS-CoV and a bat coronavirus RaTG13 2 . While bats may be the reservoir host for various coronaviruses 3,4 , whether SARS-CoV-2 has other hosts remains ambiguous. In this study, one coronavirus isolated from a Malayan pangolin showed 100%, 98.6%, 97.8% and 90.7% amino acid identity with SARS-CoV-2 in the E, M, N and S genes, respectively. In particular, the receptor-binding domain within the S protein of the Pangolin-CoV is virtually identical to that of SARS-CoV-2, with one noncritical amino acid difference. Results of comparative genomic analysis suggest that SARS-CoV-2 might have originated from the recombination of a Pangolin-CoV-like virus with a Bat-CoV-RaTG13-like virus. The Pangolin-CoV was detected in 17 of 25 Malayan pangolins analyzed. Infected pangolins showed clinical signs and histological changes, and circulating antibodies against Pangolin-CoV reacted with the S protein of SARS-CoV-2. The isolation of a coronavirus that is highly related to SARS-CoV-2 in pangolins suggests that they have the potential to act as the intermediate host of SARS-CoV-2. The newly identified coronavirus in the most-trafficked mammal could represent a future threat to public health if wildlife trade is not effectively controlled.As coronaviruses (CoVs) are common in mammals and birds 5 , we used the whole genome sequence of SARS-CoV-2 (WHCV; GenBank accession No. MN908947) in a Blast search of SARS-relate CoV (SARSr-CoV) sequences in available mammalian and avian viromic, metagenomic, and transcriptomic data. This led to the identification of 34 highly related contigs in a set of pangolin viral metagenomes (Extended

Binding Ability Prediction between Spike Protein and Human ACE2 Reveals the Adaptive Strategy of SARS-CoV-2 in Humans

“…Some studies show the stability and viability of SARS-CoV-2 are higher than SARS-CoV generally in both aerosol environments and objects surfaces 24 , which indicates SARS-CoV-2 might adapt to human transmission better while MERS and SARS-CoV failed to do so 6,9,23,25 . Same with other studies 1,2,11,26 , we found all SARS-CoV-2 in our analysis were sister taxon with a coronavirus from horseshoe bat (RaTG13) which highly suspected as the natural reservoir host of coronavirus 17,26 and the similarity between SARS-CoV-2 and SARS-bat is high as 96.12%. Meanwhile, the coronavirus isolated from pangolins also were detected 91.02% identical with SARS-CoV-2 at the nucleotide level, which makes people think pangolins might be a potential intermediate host between the natural reservoir and human beings.…”

Single-cell screening of SARS-CoV-2 target cells in pets, livestock, poultry and wildlife

“…SRAS-CoV-2 like coronavirus has been isolated from pangolin, and SARS-CoV-2 was proposed to origin from the recombination of a pangolin coronavirus with a bat coronavirus 6,7 . Cat is also a suspected intermediate host, as human-to-cat and cat-to-cat transmission of SARS-CoV-2 have been reported 9,10 .…”

“…The bat has been proposed to be the original host of SARS-CoV-2 5 , however, the transmission from bats to humans requires some intermediate hosts. Several studies have linked pangolins, cats, dogs and hamsters with SARS-CoV-2 infection and transmission [6][7][8][9][10][11][12] , indicating the potential widespread prevalence across animals, which would post potential threats to humans. The identification of the origin of this virus and its path to becoming a deadly human pathogen is needed to understand how such processes occur in nature and identify ways we can prevent the onset of these types of global crises in the future.…”

Unveiling diffusion pattern and structural impact of the most invasive SARS-CoV-2 spike mutation

“…This likely facilitates the site recognition by the protease and promotes the subsequent cleavage, leading to an increased rate of spike protein priming. As the furin-like cleavage site an evolutionary novelty in SARS-CoV-2 as compared to its close CoVs relative (Andersen et al 2020, Xiao et al 2020, and given its crucial role for efficient cell-cell transmission (Hoffman et al 2020a and 2020b), our results argue for a refined efficiency of this infection mechanism in the G614 variant.…”

“…1B-C). This site has been observed, though with different amino acid sequences, in distantly related CoVs, like MERS-CoV and HKU1-CoV, but not in those viruses that are the most closely related to SARS-CoV-2 (Coutard et al 2020, Andersen et al 2020, Xiao et al 2020.…”