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

Pathogens

Rachid Mentag¹  Lahcen Belyamani²  Chakib Nejjari³  Saaid Amzazi⁴  Rokia Laamarti⁵  Mouna Ouadghiri⁶  Mohammed Hakmi⁶  Fatima Ghrifi⁶  Tarek Alouane⁶  Meriem Laamarti⁶  Abdelomunim Essabbar⁶  Nasma Boumajdi⁶  Loubna Allam⁶  Azeddine Ibrahimi⁶  Rachid El Jaoudi⁶  ElMehdi Bouricha⁶  Souad Kartti⁶  Naima El Hafidi⁶  Houda Bendani⁶  Tarik Aanniz⁶  M.W. Chemao-Elfihri⁶  Laila Sbabou⁷  Houda Benrahma⁸  JalilEl Attar⁹ 

[1] Biotechnology Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Rabat 10101, Morocco;Emergency Department, Military Hospital Mohammed V, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10112, Morocco;International School of Public Health, Mohammed VI University of Health Sciences (UM6SS), Casablanca 82403, Morocco;Laboratory of Human Pathologies Biology, Faculty of Sciences, Mohammed V University, Rabat 10000, Morocco;Medical Biotechnology Center, Moroccan Foundation for Science, Innovation & Research (MAScIR), Rabat 10100, Morocco;Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat 10100, Morocco;Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat 10000, Morocco;National Reference Laboratory, Mohammed VI University of Health Sciences (UM6SS), Casablanca 82403, Morocco;Riad Laboratory, City Center Hay Riad, Rabat 10112, Morocco;

关键词: COVID-19;    SARS-CoV-2;    genomic diversity;    divergence;    hotspot mutations;    spike protein;   

DOI  :  10.3390/pathogens9100829

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown