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Open AccessArticle

Genomic Diversity and Hotspot Mutations in 30,983 SARS-CoV-2 Genomes: Moving Toward a Universal Vaccine for the “Confined Virus”?

1
Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco
2
Medical Biotechnology Center, Moroccan Foundation for Science, Innovation & Research (MAScIR), Rabat 10100, Morocco
3
Faculty of Medicine, Mohammed VI University of Health Sciences (UM6SS), Casablanca 82403, Morocco
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Riad Laboratory, City Center Hay Riad, Rabat 10112, Morocco
5
Biotechnology Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Rabat 10101, Morocco
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Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat 10000, Morocco
7
International School of Public Health, Mohammed VI University of Health Sciences (UM6SS), Casablanca 82403, Morocco
8
Laboratory of Human Pathologies Biology, Faculty of Sciences, Mohammed V University, Rabat 10000, Morocco
9
Emergency Department, Military Hospital Mohammed V, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10112, Morocco
*
Authors to whom correspondence should be addressed.
These authors contributed equally.
Pathogens 2020, 9(10), 829; https://doi.org/10.3390/pathogens9100829
Received: 30 July 2020 / Revised: 30 September 2020 / Accepted: 1 October 2020 / Published: 10 October 2020
(This article belongs to the Special Issue SARS-CoV Infections)
The COVID-19 pandemic has been ongoing since its onset in late November 2019 in Wuhan, China. Understanding and monitoring the genetic evolution of the virus, its geographical characteristics, and its stability are particularly important for controlling the spread of the disease and especially for the development of a universal vaccine covering all circulating strains. From this perspective, we analyzed 30,983 complete SARS-CoV-2 genomes from 79 countries located in the six continents and collected from 24 December 2019, to 13 May 2020, according to the GISAID database. Our analysis revealed the presence of 3206 variant sites, with a uniform distribution of mutation types in different geographic areas. Remarkably, a low frequency of recurrent mutations has been observed; only 169 mutations (5.27%) had a prevalence greater than 1% of genomes. Nevertheless, fourteen non-synonymous hotspot mutations (>10%) have been identified at different locations along the viral genome; eight in ORF1ab polyprotein (in nsp2, nsp3, transmembrane domain, RdRp, helicase, exonuclease, and endoribonuclease), three in nucleocapsid protein, and one in each of three proteins: Spike, ORF3a, and ORF8. Moreover, 36 non-synonymous mutations were identified in the receptor-binding domain (RBD) of the spike protein with a low prevalence (<1%) across all genomes, of which only four could potentially enhance the binding of the SARS-CoV-2 spike protein to the human ACE2 receptor. These results along with intra-genomic divergence of SARS-CoV-2 could indicate that unlike the influenza virus or HIV viruses, SARS-CoV-2 has a low mutation rate which makes the development of an effective global vaccine very likely. View Full-Text
Keywords: COVID-19; SARS-CoV-2; genomic diversity; divergence; hotspot mutations; spike protein; vaccine COVID-19; SARS-CoV-2; genomic diversity; divergence; hotspot mutations; spike protein; vaccine
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MDPI and ACS Style

Alouane, T.; Laamarti, M.; Essabbar, A.; Hakmi, M.; Bouricha, E.M.; Chemao-Elfihri, M.W.; Kartti, S.; Boumajdi, N.; Bendani, H.; Laamarti, R.; Ghrifi, F.; Allam, L.; Aanniz, T.; Ouadghiri, M.; El Hafidi, N.; El Jaoudi, R.; Benrahma, H.; Attar, J.E.; Mentag, R.; Sbabou, L.; Nejjari, C.; Amzazi, S.; Belyamani, L.; Ibrahimi, A. Genomic Diversity and Hotspot Mutations in 30,983 SARS-CoV-2 Genomes: Moving Toward a Universal Vaccine for the “Confined Virus”? Pathogens 2020, 9, 829. https://doi.org/10.3390/pathogens9100829

AMA Style

Alouane T, Laamarti M, Essabbar A, Hakmi M, Bouricha EM, Chemao-Elfihri MW, Kartti S, Boumajdi N, Bendani H, Laamarti R, Ghrifi F, Allam L, Aanniz T, Ouadghiri M, El Hafidi N, El Jaoudi R, Benrahma H, Attar JE, Mentag R, Sbabou L, Nejjari C, Amzazi S, Belyamani L, Ibrahimi A. Genomic Diversity and Hotspot Mutations in 30,983 SARS-CoV-2 Genomes: Moving Toward a Universal Vaccine for the “Confined Virus”? Pathogens. 2020; 9(10):829. https://doi.org/10.3390/pathogens9100829

Chicago/Turabian Style

Alouane, Tarek; Laamarti, Meriem; Essabbar, Abdelomunim; Hakmi, Mohammed; Bouricha, El M.; Chemao-Elfihri, M. W.; Kartti, Souad; Boumajdi, Nasma; Bendani, Houda; Laamarti, Rokia; Ghrifi, Fatima; Allam, Loubna; Aanniz, Tarik; Ouadghiri, Mouna; El Hafidi, Naima; El Jaoudi, Rachid; Benrahma, Houda; Attar, Jalil E.; Mentag, Rachid; Sbabou, Laila; Nejjari, Chakib; Amzazi, Saaid; Belyamani, Lahcen; Ibrahimi, Azeddine. 2020. "Genomic Diversity and Hotspot Mutations in 30,983 SARS-CoV-2 Genomes: Moving Toward a Universal Vaccine for the “Confined Virus”?" Pathogens 9, no. 10: 829. https://doi.org/10.3390/pathogens9100829

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