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Review
. 2023 Aug 21;9(9):e19345.
doi: 10.1016/j.heliyon.2023.e19345. eCollection 2023 Sep.

SARS-CoV-2 prevalence in domestic and wildlife animals: A genomic and docking based structural comprehensive review

Affiliations
Review

SARS-CoV-2 prevalence in domestic and wildlife animals: A genomic and docking based structural comprehensive review

Tuhin Das et al. Heliyon. .

Abstract

The SARS-CoV-2 virus has been identified as the infectious agent that led to the COVID-19 pandemic, which the world has seen very recently. Researchers have linked the SARS-CoV-2 outbreak to bats for the zoonotic spread of the virus to humans. Coronaviruses have a crown-like shape and positive-sense RNA nucleic acid. It attaches its spike glycoprotein to the host angiotensin-converting enzyme 2 (ACE2) receptor. Coronavirus genome comprises 14 ORFs and 27 proteins, spike glycoprotein being one of the most critical proteins for viral pathogenesis. Many mammals and reptiles, including bats, pangolins, ferrets, snakes, and turtles, serve as the principal reservoirs for this virus. But many experimental investigations have shown that certain domestic animals, including pigs, chickens, dogs, cats, and others, may also be able to harbor this virus, whether they exhibit any symptoms. These animals act as reservoirs for SARS-CoV, facilitating its zoonotic cross-species transmission to other species, including humans. In this review, we performed a phylogenetic analysis with multiple sequence alignment and pairwise evolutionary distance analysis, which revealed the similarity of ACE2 receptors in humans, chimpanzees, domestic rabbits, house mice, and golden hamsters. Pairwise RMSD analysis of the spike protein from some commonly reported SARS-CoV revealed that bat and pangolin coronavirus shared the highest structural similarity with human coronavirus. In a further experiment, molecular docking confirmed a higher affinity of pig, bat, and pangolin coronavirus spike proteins' affinity to the human ACE2 receptor. Such comprehensive structural and genomic analysis can help us to forecast the next likely animal source of these coronaviruses that may infect humans. To combat these zoonotic illnesses, we need a one health strategy that considers the well-being of people and animals and the local ecosystem.

Keywords: Mammals and reptiles; Molecular docking; One health strategy; Phylogenetic analysis; RMSD analysis; SARS-CoV-2.

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Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Fig. 1
Fig. 1
Structure of SARS-CoV-2 showing significant components of the virus particle.
Fig. 2
Fig. 2
Genome-wide arrangement of all proteins of SARS-CoV-2 as modeled by Zhang lab [90].
Fig. 3
Fig. 3
Mechanism of viral replication inside the host cell.
Fig. 4
Fig. 4
Potential animals hosts of SARS-CoV-2.
Fig. 5
Fig. 5
Phylogenetic analysis of the angiotensin-converting enzyme 2 (ACE2) receptor gene sequence in different mammals, including humans. The ACE2 sequences were downloaded from the NCBI nucleotide database (https://www.ncbi.nlm.nih.gov/nuccore). The tree was generated using the ggtree package, and the multiple sequence alignment (MSA) was generated using the MSA package in R, with each color in the MSA representing a nucleotide.
Fig. 6
Fig. 6
Dendrogram and heatmap depicting pairwise distance of the ACE2 gene sequence among animals, including humans. The sequence of ACE2 coding genes was downloaded from the NCBI nucleotide database (https://www.ncbi.nlm.nih.gov/nuccore). The pairwise distance matrix was calculated using the Tamura-Nei model with a gamma parameter (α) of 1.00 for rate variation among sites. Analyses were conducted using MEGA X software, and the heat map visualization with dendrogram analysis was performed using ‘Heatmap with Dendrogram’ in OriginLab 2021 pro.
Fig. 7
Fig. 7
Protein-protein docking simulating interaction, (A) 1R42-4F5C:C; (B) 1R42-6QFY:A; (C) 1R42-6BFU:A; (D) 1R42-6JX7:A; (E) 1R42-4H14:A; (F) 1R42-7DRV:C; (G) 1R42-6JHY:A; (H) 1R42-7BBH:A.
Fig. 8
Fig. 8
Pairwise RMSD values among different animals' spike glycoprotein structure of coronavirus.
Fig. 9
Fig. 9
Superimposed spike glycoprotein structure of coronavirus among human, pangolin and bat.

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