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Evolutionary Trajectory for the Emergence of Novel Coronavirus SARS-CoV-2

1
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources of Guangxi University, Nanning 530005, China
2
Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus 57000, Pakistan
3
College of Pharmacy, South Central University for Nationalities, Wuhan 430074, China
*
Authors to whom correspondence should be addressed.
Pathogens 2020, 9(3), 240; https://doi.org/10.3390/pathogens9030240
Received: 3 March 2020 / Revised: 18 March 2020 / Accepted: 21 March 2020 / Published: 23 March 2020
(This article belongs to the Section Animal Pathogens)
Over the last two decades, the world experienced three outbreaks of coronaviruses with elevated morbidity rates. Currently, the global community is facing emerging virus SARS-CoV-2 belonging to Betacoronavirus, which appears to be more transmissible but less deadly than SARS-CoV. The current study aimed to track the evolutionary ancestors and different evolutionary strategies that were genetically adapted by SARS-CoV-2. Our whole-genome analysis revealed that SARS-CoV-2 was the descendant of Bat SARS/SARS-like CoVs and bats served as a natural reservoir. SARS-CoV-2 used mutations and recombination as crucial strategies in different genomic regions including the envelop, membrane, nucleocapsid, and spike glycoproteins to become a novel infectious agent. We confirmed that mutations in different genomic regions of SARS-CoV-2 have specific influence on virus reproductive adaptability, allowing for genotype adjustment and adaptations in rapidly changing environments. Moreover, for the first time we identified nine putative recombination patterns in SARS-CoV-2, which encompass spike glycoprotein, RdRp, helicase and ORF3a. Six recombination regions were spotted in the S gene and are undoubtedly important for evolutionary survival, meanwhile this permitted the virus to modify superficial antigenicity to find a way from immune reconnaissance in animals and adapt to a human host. With these combined natural selected strategies, SARS-CoV-2 emerged as a novel virus in human society. View Full-Text
Keywords: SARS-CoV-2; SARS-CoV; phylogeny; genomic structure; evolutionary strategies; mutations; recombination or reassortment SARS-CoV-2; SARS-CoV; phylogeny; genomic structure; evolutionary strategies; mutations; recombination or reassortment
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Rehman, S.; Shafique, L.; Ihsan, A.; Liu, Q. Evolutionary Trajectory for the Emergence of Novel Coronavirus SARS-CoV-2. Pathogens 2020, 9, 240.

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