Fig 1.
Sequence similarity between SARS-CoV-2 proteins and positive sense ssRNA virus families.
Results of sequence similarity searches for 25 SARS-CoV-2 RefSeq proteins against positive strand ssRNA viruses are shown as scatter plots. X axis in each graph shows the maximum score obtained for each protein query. Y axis in each graph shows the highest negative log E-value obtained for each protein query. Black labels show the name of SARS-CoV-2 protein. Red labels show the name of the protein from the relevant ssRNA virus family. The name of virus species with sequence similarity is included in S4 Table in S1 File. Abbreviations: NSP, non-structural protein; RdRp, RNA-dependent RNA polymerase.
Fig 2.
Sequence similarity between SARS-CoV-2 proteins and negative sense ssRNA virus families.
Results of similarity searches for 25 SARS-CoV-2 RefSeq proteins against negative strand ssRNA viruses are shown as scatter plots. X axis in each graph shows the maximum score obtained for each protein query. Y axis in each graph shows the highest negative log E-value obtained for each protein query. Black labels show the name of SARS-CoV-2 protein. Red labels show the name of the protein from the relevant ssRNA virus family. The name of virus species with sequence similarity is included in S5 Table in S1 File.
Fig 3.
Overlay plots for SARS-CoV2’s most significant protein similarities with non-coronavirus ssRNA viruses.
Score-negative log E value for various SARS-CoV-2 proteins against positive sense ssRNA virus families (a) and negative sense ssRNA virus families (b). For each protein query, only the highest score-negative log E value pair is shown.
Fig 4.
Spike-Fusion protein similarity region on spike protein.
SARS-CoV-2 spike schematic model with paramyxovirus sequence similarity region shown with pale blue bar (residues 810 to 1098) (a). Corresponding area is shown in red on SARS-CoV-2 spike 3D structure (b). Delta-BLAST result for SARS-CoV-2 spike protein versus Avian metaavulavirus 20 fusion protein, which showed the highest score-negative E value in Delta-BLAST searches (c).
Fig 5.
SARS-CoV-2 spike protein similarity with pathogenic human paramyxoviruses.
The result of similarity searches between SARS-CoV-2 spike protein versus different human paramyxoviruses. The X axis shows maximum score for each protein query and the Y axis shows negative log E value for each protein query. Dot colors and legend show different genera of paramyxoviruses.
Fig 6.
Spike similarity between different variants of SARS-CoV-2 and different subgroups of coronaviruses versus fusion protein of paramyxoviruses.
Sequence similarity between VOI and VOC variants of SARS-CoV-2 with fusion proteins of Paramyxoviruses (a). AM20 is avian metaavulavirus 20. CM is Canine morbillivirus. Spike similarity of alpha (blue dots) and beta (red dots) coronaviruses with fusion proteins of Paramyxoviruses (b). The X axis shows maximum score and the Y axis shows negative log of E value in each graph.
Fig 7.
Distribution of B cell and T cell epitopes as well MHC binding peptides inside spike-fusion similarity region.
Experimentally verified B cell epitopes (a), T cell epitopes (B) and MHC binding peptides (c) which matched substrings of SARS-CoV2 spike protein were obtained from IEDB and aligned with SARS-CoV2 spike protein to determine their distribution across the area.
Fig 8.
Phylogenetic tree of ssRNA viruses.
Phylogenetic tree of representative members of positive sense strand ssRNA viruses (i.e. Picornaviridae, Caliciviridae, Coronaviridae, Flaviviridae and Togaviridae) and negative sense strand ssRNA viruses (i.e. Orthomyxoviridae, Paramyxoviridae, Filoviridae, Rhabdoviridae) was drawn based on viral RdRP protein sequences. Virus name abbreviations: BC tibro, Bas-Congo tibrovirus; BVDV1, Bovine viral diarrhea virus 1; EEEV, Eastern equine encephalitis virus; L Cueva, Lloviu cuevavirus; PEDV, Porcine epidemic diarrhea virus; Pr-nor, Primate norovirus; Semliki F, Semliki Forest virus; VHS, Viral hemorrhagic septicemia virus; VSV, Vesicular stomatitis Indiana virus; WEEV, Western equine encephalitis virus.