Table 1.
Distribution of SARS-CoV-2 related viruses in bats and pangolins.
Fig 1.
Spatial distribution of SARS-CoV-2 related viruses reported in horseshoe bat species in the world.
A. SC2r-CoV reported in bat species in the world; B. SC1r-CoV reported in bat species in the world.
Fig 2.
Possible evolution and transmission pathways of SARS-CoV-2 and its related virus at animal-human- ecosystem interface.
Table 2.
Natural infection of SARS-CoV-2 in animal.
Fig 3.
Spatial distribution of SARS-CoV-2 in domestic and wild animals in the world.
Fig 4.
Phylogenetic analysis of SARS-CoV-2 related viruses retrieved from bat and pangolin.
Here, blue dots denote SARS-like CoV, SARS-CoV-2 and SARS-CoV-2 like CoV viruses, green and pink dotes denotes SARS-CoV and Wuhan-Hu-1 viruses respectively.
Fig 5.
Phylogenetic analysis of SARS-CoV-2 sequences from domestic and wild animals.
Blue dots denote sequences detect in domestic and wild animals. Pink dots = indicate Wuhan-Hu-1 sequence.
Fig 6.
Phylogenetic analysis of SARS-CoV-2 and representative sequences of alpha, beta, delta, lambda, mu, gamma CoV sequences.
Blue dots denote Alpha sequences, lime (Gamma), maroon (Delta), teal (Beta), lambda (Navy), green (Mu). Red dots indicate Wuhan-Hu-1 sequence.
Fig 7.
Phylogenetic analysis of SARS-CoV-2 sequences from minks.
Lime dots denote sequences from American mink whereas blue dots denote sequences from European mink. Star (*) indicates mink variant mutation in spike protein (Spike_Y453F) reported in mink and humans.
Fig 8.
SimPlot was used to compare the genomes of SARS-CoV-2 and comparable viruses.
The RatTG13 CoV genome (green) and the consensus genomes of the GX Pangolin CoV (red), Gu Pangolin CoV (gray), Bat BANAL-103 (lime), Bat RShSTT200 (blue), Bat RaTG13 (violet) and Bat RpYN06 (teal) groups are shown beside the Wuhan SARS-CoV-2 2020 reference genome. The RB domain, as well as gene limitations for ORF1ab, S, ORF3a, E, M, ORF6, ORF7a, ORF7b, ORF8, N, and ORF10, is displayed at the top of the image. Distinct colors reflect different groups of sequences integrated in SimPlot analysis, corresponding to species groupings in the entire genome phylogeny depicted in panel.
Fig 9.
Gene-by-gene SimPlot similarity analysis of the Wuhan SARS-CoV-2 2020 reference genome against the GX Pangolin CoV (red), Gu Pangolin CoV (gray), Bat BANAL-103 (lime), Bat RShSTT200 (blue), Bat RaTG13 (violet), and Bat RpYN06 (pink) consensus genomes.
Similarity plots are shown for the genes ORF1ab, M, ORF3a, N, ORF7a, and S, showing the most significant overlaps between the sequences as mentioned above.
Table 3.
The recombination test outcomes for Wuhan SARS-CoV-2, RaTG13, Pangolin Gx CoV P5L, Pangolin Gu CoV SM44, Bat BANAL-103, Bat RShSTT200, and Bat RpYN06 gene and complete genome sequences.
Fig 10.
Clade diversity of SARS-CoV-2 in different animal species.
Fig 11.
Lineage diversity of SARS-CoV-2 among different animal species.
Fig 12.
Frequency of specific mutation points at the amino acid level in spike protein of SARS-CoV-2 in different animal species.
Fig 13.
Frequency of specific mutation points at the amino acid level in spike protein of SARS-CoV-2 in American mink.
Fig 14.
Genomic mutation analysis of animals originated SARS-CoV-2.
Genomic mutation analysis of SARS-CoV-2 strains identified. >> ↑ and marking indicating the mutational changes among 12 SARS-CoV-2 (EPI_ISL_408514 is not included due to Nil mutation) strain studied in this study in comparison with the reference strain NC_045512.2.