A comparative phylogenomic analysis of SARS-CoV-2 strains reported from non-human mammalian species and environmental sa
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A comparative phylogenomic analysis of SARS‑CoV‑2 strains reported from non‑human mammalian species and environmental samples Aziz Ul‑Rahman1,2,4 · Muhammad Abu Bakr Shabbir2 · Muhammad Waqar Aziz2 · Saima Yaqub2 · Asif Mehmood3 · Muhammad Asif Raza1 · Muhammad Zubair Shabbir4 Received: 10 April 2020 / Accepted: 29 September 2020 © Springer Nature B.V. 2020
Abstract Coronaviruses (CoVs) infect a wide range of domestic and wild mammals. These viruses have a potential and tendency to cross-species barriers and infect humans. Novel human coronavirus 2019-nCoV (hCoV-19) emerged from Wuhan, China, and has caused a global pandemic. Genomic features of SARS-CoV-2 may attribute inter-species transmission and adaptation to a novel host, and therefore is imperative to explicate the evolutionary dynamics of the viral genome and its propensity for differential host selection. We conducted an in silico analysis of all the coding gene sequences of SARS-CoV-2 strains (n = 39) originating from a range of non-human mammalian species, including pangolin, bat, dog, cat, tiger, mink, mouse, and the environmental samples such as wastewater, air and surface samples from the door handle and seafood market. Compared to the reference SARS-CoV-2 strain (MN908947; Wuhan-Hu-1), phylogenetic and comparative residue analysis revealed the circulation of three variants, including hCoV-19 virus from humans and two hCoV-19-related precursors from bats and pangolins. A lack of obvious differences as well as a maximum genetic homology among dog-, cat-, tiger-, mink-, mouse-, bat- and pangolin-derived SARS-CoV-2 sequences suggested a likely evolution of these strains from a common ancestor. Several residue substitutions were observed in the receptor-binding domain (RBD) of the spike protein, concluding a promiscuous nature of the virus for host species where genomic alternations may be required for the adaptation to novel host/s. However, such speculation needs in vitro investigations to unleash the influence of substitutions towards species-jump and disease pathogenesis. Keywords Novel coronavirus · SARS-CoV-2 · Non-human mammalian sequences · Phylogenomic analysis · Residue substitutions · Species-jump
Introduction Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11033-020-05879-5) contains supplementary material, which is available to authorized users. * Aziz Ul‑Rahman [email protected] 1
Faculty of Veterinary and Animal Sciences, Muhammad Nawaz Shareef University of Agriculture, Multan 66000, Pakistan
2
Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore 54600, Pakistan
3
Veterinary Research Institute, Zarar Shaheed road, Lahore 54000, Pakistan
4
Quality Operations Laboratory, University of Veterinary and Animal Sciences, Outfall road, Lahore 54600, Pakistan
Coronaviruses (CoVs) have been identified from a diverse range of birds and mammals, including humans [1, 2]. Most of the emerging CoVs, those have infected humans, are
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