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

Tuhin Das; Suranjana Sikdar; Md Helal Uddin Chowdhury; Khandakar Jannatul Nyma; Md Adnan

doi:10.1016/j.heliyon.2023.e19345

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

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

Authors

Tuhin Das¹, Suranjana Sikdar¹, Md Helal Uddin Chowdhury², Khandakar Jannatul Nyma¹, Md Adnan^{3

4}

Affiliations

¹ Department of Microbiology, University of Chittagong, Chattogram, 4331, Bangladesh.
² Ethnobotany and Pharmacognosy Lab, Department of Botany, University of Chittagong, Chattogram, 4331, Bangladesh.
³ Department of Molecular Pharmaceutics, University of Utah, Salt Lake City, 84112, United States.
⁴ Department of Pharmacy, International Islamic University Chittagong, Chattogram, 4318, Bangladesh.

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.

Publication types

Review