Analysis of the spike proteins suggest pangolin as an intermediate host of COVID-19 (SARS-CoV-2)

Raza, S.; Navid, M. T.; Zahir, W.; Khan, MuhammadNabeel Awais M.; Yaqub, T.; Rabbani, M.; Rashid, M.; Saddick, S.; Rasheed, M. A.

The novel coronavirus (SARS-CoV-2) is a third member of its group that has introduced public health catastrophes around the globe. Since, its emergence in Wuhan, China by December 2019, SARS-CoV-2 infected millions of human population along with many casualties globally. The transmission potential of SARS-CoV-2 between humans has already been studied. Despite this transmission in human population, the primary origin of SARS-CoV-2 has been linked with bats by the help of an intermediate (secondary) host. This study was assumed to investigate the possible secondary or intermediate host to shuttle down the SARS-CoV-2 transmission and further to mitigate future pandemics. The antigenic surface/spike (S) protein was used for the structural and genomic analysis through currently available computer assisted technology. For the In-silico analysis, 43 sequences of S-protein of coronaviruses originated in various species were retrieved from nucleotide database of NCBI. These sequences were matched to find any similarities/differences by employing pairwise and multiple sequence alignment. The phylogenetic analysis was conducted to observe the relation among different species through MEGA software. Finally, comparative analysis for structures of S-protein (superimposition) was done with reference structure by using UCSF Chimera software. The results of this study expressed maximum match of S-protein sequences of human coronavirus with Bat and with Pangolin sequences respectively. The Phylogenetic analysis between Bat and Pangolin showed that SARS-CoV-2 transmitted from bats to humans possibly through the intermediate host of Pangolin.