Wildlife as a Source of SARS-CoV-2 Evolution- A Review

Muhammad Altaf1* Arshad Mahmood Abbasi2, Muhammad Shoaib Amjad3, Sadia Naseer1 and Muhammad Umair4

1Department of Zoology, Women University of Azad Jammu and Kashmir, Bagh, Pakistan

2Department of Environment Sciences, COMSATS University Islamabad, Abbottabad Campus 22060, Pakistan

3Department of Botany, Women University of Azad Jammu and Kashmir, Bagh, Pakistan

4School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China

ABSTRACT

Coronavirus consists of single-stranded, enveloped and RNA virus, largest genome among all RNA viruses and has 4 proteins i.e. envelope, spike, nucleocapsid and membrane. Coronaviruses are classified into 4 genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus and Deltacoronavirus. Betacoronavirus most probably originated from bats and the virus may have jumped to avian species and evolved as Deltacoronavirus group. The avian coronaviruses jumped among other avian species, giving rise to Gammacoronavirus from Deltacoronavirus, while Betacoronavirus may have given rise to Alphacoronavirus. It is known that SARS-CoV-2 belongs to Betacoronavirus. This most similar virus is verified in bat and Malayan Pangolin. Analysis showed that SARS-CoV-2 most probably originated by recombination of both bat and pangolin viruses. Viral protein seroconversion and viral specific nucleotide positive documented in all COVID-19 patients tested provides confirmation of a link between the presence of this virus and the disease.

Article Information

Received 10 May 2020

Revised 30 July 2020

Accepted 10 November 2020

Available online 22 March 2022

(early access)

Published 24 April 2022

Authors’ Contribution

MA designed the stusy and wrote the article. MSA and SN helped in data collection. AMA and MU critically analyzed this article.

Key words

Zoonoses, COVID-19, Bats, Pangolin, SARS-CoV-2

DOI: https://dx.doi.org/10.17582/journal.pjz/20200510100555

* Corresponding author: altaf_mughal450@yahoo.com

0030-9923/2022/0004-1899 $ 9.00/0

Copyright 2022 by the authors. Licensee Zoological Society of Pakistan.

This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).

INTRODUCTION

Coronaviruses consist of 4 proteins i.e. envelope, spike, nucleocapsid and membrane (Tidona and Darai, 2011; Scientific American, 2020), single-stranded and RNA virus. Coronaviruses have the largest genome sequence among all RNA viruses. Coronaviruses infect different animal species including human (WHO, 2020).

Coronaviruses belong to order Nidovirales, family Coronaviridae, subfamily Coronavirinae. Coronaviruses have the largest RNA genome, ranging from 25-33 kilobases (Woo et al., 2009). On the basis of cluster analysis coronaviruses are classified into following genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus and Deltacoronavirus (Woo et al., 2009; King et al., 2012).

Alphacoronavirus belongs to subfamily Coronavirinae, and has unique characteristics as a distinctive kind of nsp1, different in sequence and size from betacoronavirus nsp1 (nonstructural RNA-binding protein 1) and not counterpart in gammacoronaviruses, and has ORF3, ORF3b and ORF3c in TGEV (transmissible gastroenteritis virus) and αmp (alphacoronavirus membrane protein). Alphacoronaviruses are monophyletic of viruses as compared with all coronaviruses group (King et al., 2012). Following species of alphacoronaviruses are recorded till now i.e. Human coronavirus 229E (HCoV-229E), Alphacoronavirus-1, Miniopterus bat coronavirus 1(Mi-BatCoV-1), Porcine epidemic diarrea virus (PEDV), Miniopterus bat coronavirus HKU8 (Mi-BatCoV-HKU8), Scotophilus bat coronavirus 512 (Sc-BatCoV-512), Rhinolophus bat coronavirus HKU2 (Rh-BatCoV-HKU2), Harbor seal coronavirus 1, Ferret coronavirus (FrCoV) and Mink coronavirus (MiCoV) (Tidona and Darai, 2011; Saey, 2013; de Barros et al., 2019).

Betacoronaviruses are monophyletic, the only well-known feature that would set them separate from other species of coronaviruses is their differnt nsp1 (i.e. nonstructural RNA-binding protein 1), different in sequence and size from alphacoronavirus nsp1 and not equal in the other groups of coronaviruses (King et al., 2012). Following species of Betacoronaviruses are recorded till now i.e. Betacoronavirus 1, Murine coronavirus, Human coronavirus HKU-1 (HCoV-HKU1), Rousettus bat coronavirus HKU9 (Ro-BatCoV-HKU9), Pipistrellus bat coronavirus HKU5 (Pi-BatCoV-HKU5), SARS coronavirus (SARS-CoV), MERS coronavirus MERS-CoV, Tylonycteris bat coronavirus HKU4 (Ty-BatCoV-HKU4) and SARS-CoV-2, (Tidona and Darai, 2011).

Gammacoronavirus genome organization, morphology and gene composition, replication or biology is different from other coronaviruses. Viruses of the species Avian coronavirus not have an nsp1 (i.e. nonstructural RNA- binding protein 1) (King et al., 2012). Following species of Gammacoronaviruses are recorded till now i.e. Avian coronavirus, Asian leopard cat coronavirus (ALCCoV), Beluga Whale coronavirus SW1 (BWCoVSW1), Black-headed gull coronavirus, Chinese ferret badger coronavirus Guanxi/2006 (CFBCoVGuanxi/2006), Glaucous gull coronavirus, Glaucouswinged gull coronavirus, Pintail coronavirus PBA-124, Rock sandpiper coronavirus, Brent goose coronavirus, Snow goose coronavirus and Western sandpiper coronavirus.

Analysis of complete genome explained that the Deltacoronavirus groups have relatively smallest genomes (e.g. 25.421 to 26.674 kilobases) among all groups of coronaviruses. Delta coronaviruses have one papain-like protease domain in nsp3 (i.e. non-structural protein 3), NS6 located between M and N genes (King et al., 2011; Woo et al., 2012). Following species of Deltacoronavirus are recorded till now i.e. Bulbul coronavirus HKU11, Wigeon coronavirus HKU20, Munia coronavirus HKU13, Porcine coronavirus HKU15, Night heron coronavirus HKU19, White-eye coronavirus HKU16, Thrush coronavirus HKU12, Common moorhen coronavirus HKU21, Magpie robin coronavirus HKU18 and Sparrow coronavirus HKU17 (King et al., 2011; Woo et al., 2012).

Betacoronavirus most probably originated from bats species at nearly 3300 BC and virus may be jumped to avian species and evolved as Deltacoronavirus group at about 3000 BC. The avian coronaviruses jumped among other avian species, giving rise to Gammacoronavirus from Deltacoronavirus about 2800 BC. While Betacoronavirus may jumped among other mammals and evolved as Alphacoronavirus approximately 2400 BC. This evolution lineage shown in (Fig. 1 and Table I) and Woo et al. (2012) analysis evolutionary lineage with molecular clock analysis (MCA).

SARS CORONAVIRUSES-2

At the end of 2019, unique pneumonia was documented in Wuhan, China and might be transferred from wild animals to human and human to human. SARS-Cov-2 was observed as different and new coronavirus and has close phylogenetic relation with SARS-like coronaviruses (Fig. 2). This disease was diagnosed with novel coronavirus (SARS-Cov-2). Jiang et al. (2020) and Xu et al. (2020) also noted that the pathogen was at that time identified as a SARS-Cov-2 belonging to lineage SARS-CoV. Wu et al. (2020) analysis showed that phylogenetic comparison recognized 380 amino acid changeovers between SARS-Cov-2 and SARS, which may have caused functional and

pathogenic divergence of SARS-Cov-2. Paraskevis et al. (2020) demonstrate proof that the SARS-Cov-2 is not-mosaic consisting in approximately half of its genome of a lineage within the Betacoronavirus. These genomic characteristics showed their potential virulence in humans.

Adaptation and mutation have driven the co-evolution of coronaviruses and animals, for thousands of years (Woo et al., 2012). Two coronaviruses i.e. severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) were recognized to reason mild disease, like common cold, before 2003. At the end of 2019, the appearance of SARS-CoV-2 in China has originated, new virus has 95% similarity to SARS-CoV and spike in SARS-CoV-2 gene, the most different region among whole genome. SARS-CoV-2 has high transmissibility and low pathogenicity as compared to SARS-CoV. Research showed that SARS-CoV-2 may be evolved from the bat (Paraskevis et al., 2020) and Malayan Pangolin (Lam et al., 2020), but later analysis of SARS-CoV-2 showed that recombination actions were probable to happen in pangolin-bat-origin-coronaviruses either in human, bat or pangolin (Fig. 3) (Zhang et al., 2020).

Table I. Classification of Coronaviruses, mode of transmission, hosts and diseases.

Zhou et al. (2020) noted Viral protein seroconversion and viral specific nucleotide positive documented in all patients tested provides confirmation of a link between the presence of this virus and the disease. Owing to shortage of specific treatment and considering the relatedness between SARS-CoV as well as SARS-CoV-2, some drugs and pre-clinical vaccine against SARS-CoV probably can be applied to this virus.

The mode is transmission is aerosol from bats to human, and human to human (Table I). Chen et al. (2020) observed that SARS-CoV-2 is more likely to impact aged males with multiple coexisting diseases, and can result in severe and fatal respiratory diseases e.g. acute respiratory distress syndrome.

CONCLUSIONS

It is concluded that Betacoronavirus is most probably originated first from bats species and virus may be jumped to other species and evolved as Deltacoronavirus, Gammacoronavirus and Alphacoronavirus. SARS-CoV-2 is belongs to genus Betacoronavirus, and has close phylogenetic relation with SARS-like coronaviruses. Adaptation and Mutation have driven the co-evolution of coronaviruses and animals. Two coronaviruses belong to genus Betacoronavirus i.e. severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) were recognized to reason mild disease, like common cold, before 2003. At the end of 2019, SARS-CoV-2 in China has originated, new virus has 95% similarity to SARS-CoV and spike in SARS-CoV-2 gene, the most different region among whole genome. SARS-CoV-2 has high transmissibility and low pathogenicity as compared to SARS-CoV. Genomic analysis showed recombination actions were probable to happen in pangolin-bat-origin-coronaviruses either in human, bat or pangolin.

Statement of conflict of interest

The authors have declared no conflict of interest.

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