Are pangolins the intermediate host of the 2019 novel coronavirus (SARS-CoV-2)?

Abstract

The outbreak of a novel corona Virus Disease 2019 (COVID-19) in the city of Wuhan, China has resulted in more than 1.7 million laboratory confirmed cases all over the world. Recent studies showed that SARS-CoV-2 was likely originated from bats, but its intermediate hosts are still largely unknown. In this study, we assembled the complete genome of a coronavirus identified in 3 sick Malayan pangolins. The molecular and phylogenetic analyses showed that this pangolin coronavirus (pangolin-CoV-2020) is genetically related to the SARS-CoV-2 as well as a group of bat coronaviruses but do not support the SARS-CoV-2 emerged directly from the pangolin-CoV-2020. Our study suggests that pangolins are natural hosts of Betacoronaviruses. Large surveillance of coronaviruses in pangolins could improve our understanding of the spectrum of coronaviruses in pangolins. In addition to conservation of wildlife, minimizing the exposures of humans to wildlife will be important to reduce the spillover risks of coronaviruses from wild animals to humans.

Fig 1. Genomic comparison of pangolin-CoV-2020, SARS-CoV-2, and other coronaviruses.

A) Similarity plot based on the full-length genome sequence of SARS-CoV-2. Full-length genome sequences of Bat-CoV-RaTG13, Bat-CoV-ZXC21, SARS-CoV, Bat-CoV-ZC45, MERS-CoV, and pangolin-CoV-2020 were used as subject sequences. The green line indicates MERS-CoV, the dark blue line indicates SARS-CoV, the grey line indicates Bat-CoV-ZXC21, the yellow line indicates Bat-CoV-ZC45, the orange line indicates pangolin-CoV-2020, while the light blue line indicates Bat-CoV-RaTG13; B) Phylogenetic analyses of whole genome sequences depicting the evolutionary relationship among SARS-CoV-2, pangolin-CoV-2020, and other coronaviruses from different hosts. The phylogenies were estimated using the MrBayes approach employing the GTR+I+G nucleotide substitution model.

Fig 2. Genetic analyses of the spike (S) surface glycoprotein of pangolin-CoV-2020, SARS-CoV-2, and other coronaviruses.

A) Similarity plot based on the spike surface glycoprotein amino acid and nucleotide sequence of SARS-CoV-2. Bat-CoV-RaTG13, Bat-CoV-ZXC21, Bat-CoV-ZC45, SARS-CoV, and pangolin-CoV-2020 were used as subject sequences. The green lines indicate SARS-CoV, the grey lines indicate Bat-CoV-ZXC21, the yellow lines indicate Bat-CoV-ZC45, the orange lines indicate pangolin-CoV-2020, while the light blue lines indicate Bat-CoV-RaTG13; B) Phylogenetic analysis of S gene sequences depicting the evolutionary relationship among SARS-CoV-2, pangolin-CoV-2020, and other coronaviruses from different hosts. The phylogenies were estimated using MrBayes approach employing the GTR+I+G nucleotide substitution model.

Fig 3. Amino acid sequence alignment of the spike (S) surface glycoprotein of the pangolin-CoV-2020 with SARS-CoV-2 and Bat-CoV-RaTG13.

Previously identified critical ACE2-binding residues are in the blue box. An arginine in the core structure that interacts with glycan is displayed within the red box.