Abstract
Since its emergence in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been spreading remarkably fast worldwide. Effective countermeasures require the rapid development of data and tools to monitor its spread and better understand immunogenic profile. However, limited information is available about the tools and target of the immune responses to SARS-CoV-2. In this study, we excogitated a new approach for analyzing phylogenetic relationships by using the whole prototype proteome sequences. Phylogenetic analysis on the whole prototype proteome sequences showed that SARS-CoV-2 was a direct descendant of Bat-CoV and was closely related to Pangolin-CoV, Bat-SL-CoV, and SARS-CoV. The pairwise comparison of SARS-CoV-2 with Bat-CoV showed an unusual replacement of the motif consisting of seven amino acids (NNLDSKV) within the spike protein of SARS-CoV-2. The replaced motif in the spike protein of SARS-CoV-2 was found in 12 other species, including a conserved surface protein of a malaria-causing pathogen, Plasmodium malariae. We further identified the T and B cell epitope sequence homology of SARS-CoV-2 spike protein with conserved surface protein of P. malariae using the Immune Epitope Database and Analysis Resource (IEDB). The shared immunodominant epitopes may provide immunity against SARS-CoV-2 infection to those previously infected with P. malariae.
Highlights
Coronaviruses (CoVs) are the predominant cause of the common cold widely present in nature with a broad spectrum of hosts
We further identified the T and B cell epitope sequence homology of SARS-CoV-2 spike protein with conserved surface protein of P. malariae using the Immune Epitope Database and Analysis Resource (IEDB)
3.1 Comparison of the whole prototype proteomes of coronaviruses to SARSCoV-2 revealed the phylogeny without showing ambiguity
Summary
Coronaviruses (CoVs) are the predominant cause of the common cold widely present in nature with a broad spectrum of hosts. The genomes of CoVs consist of a single-stranded, positive RNA of 26,000–32,000 base pairs and a variable number (from 6 to 11) of open reading frames [2]. Because of their considerable size with the characteristics of the RNA genomes, CoVs can frequently mutate to escape their natural hosts, causing severe diseases in humans. Outbreaks of SARS-CoV in 2003 and MERS-CoV in 2012 are well-known examples. Another severe pathogenic novel coronavirus, SARS-CoV-2, has emerged and caused a global pandemic [3,4]
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