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Colson P, Chaudet H, Delerce J, Pontarotti P, Levasseur A, Fantini J, La Scola B, Devaux C, Raoult D. Role of SARS-CoV-2 mutations in the evolution of the COVID-19 pandemic. J Infect 2024; 88:106150. [PMID: 38570164 DOI: 10.1016/j.jinf.2024.106150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 03/12/2024] [Accepted: 03/27/2024] [Indexed: 04/05/2024]
Abstract
OBJECTIVES The SARS-CoV-2 pandemic and large-scale genomic surveillance provided an exceptional opportunity to analyze mutations that appeared over three years in viral genomes. Here we studied mutations and their epidemic consequences for SARS-CoV-2 genomes from our center. METHODS We analyzed 61,397 SARS-CoV-2 genomes we sequenced from respiratory samples for genomic surveillance. Mutations frequencies were calculated using Nextclade, Microsoft Excel, and an in-house Python script. RESULTS A total of 22,225 nucleotide mutations were identified, 220 (1.0%) being each at the root of ≥836 genomes, classifying mutations as 'hyperfertile'. Two seeded the European pandemic: P323L in RNA polymerase, associated with an increased mutation rate, and D614G in spike that improved fitness. Most 'hyperfertile' mutations occurred in areas not predicted with increased virulence. Their mean number was 8±6 (0-22) per 1000 nucleotides per gene. They were 3.7-times more frequent in accessory than informational genes (13.8 versus 3.7/1000 nucleotides). Particularly, they were 4.1-times more frequent in ORF8 than in the RNA polymerase gene. Interestingly, stop codons were present in 97 positions, almost only in accessory genes, including ORF8 (21/100 codons). CONCLUSIONS most 'hyperfertile' mutations did not predict emergence of a new epidemic, and some were stop codons indicating the existence of so-named 'non-virulence' genes.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005 Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 Rue Saint-Pierre, 13005 Marseille, France
| | - Hervé Chaudet
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 Rue Saint-Pierre, 13005 Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Vecteurs, Infections Tropicales et Méditerranéennes (VITROME), 27 Boulevard Jean Moulin, 13005 Marseille, France; French Armed Forces Center for Epidemiology and Public Health (CESPA), Camp de Sainte Marthe, Marseille, France
| | - Jérémy Delerce
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005 Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 Rue Saint-Pierre, 13005 Marseille, France
| | - Pierre Pontarotti
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Department of Biological Sciences, Centre National de la Recherche Scientifique (CNRS)-SNC5039, Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005 Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 Rue Saint-Pierre, 13005 Marseille, France
| | - Jacques Fantini
- "Aix-Marseille Université, INSERM UMR UA 16, Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005 Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 Rue Saint-Pierre, 13005 Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Department of Biological Sciences, Centre National de la Recherche Scientifique (CNRS)-SNC5039, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005 Marseille, France.
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Hassan SS, Kodakandla V, Redwan EM, Lundstrom K, Choudhury PP, Serrano-Aroca Á, Azad GK, Aljabali AAA, Palu G, Abd El-Aziz TM, Barh D, Uhal BD, Adadi P, Takayama K, Bazan NG, Tambuwala M, Sherchan SP, Lal A, Chauhan G, Baetas-da-Cruz W, Uversky VN. Non-uniform aspects of the SARS-CoV-2 intraspecies evolution reopen question of its origin. Int J Biol Macromol 2022; 222:972-993. [PMID: 36174872 PMCID: PMC9511875 DOI: 10.1016/j.ijbiomac.2022.09.184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 05/04/2022] [Accepted: 09/20/2022] [Indexed: 12/01/2022]
Abstract
Several hypotheses have been presented on the origin of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) from its identification as the agent causing the current coronavirus disease 19 (COVID-19) pandemic. So far, no solid evidence has been found to support any hypothesis on the origin of this virus, and the issue continue to resurface over and over again. Here we have unfolded a pattern of distribution of several mutations in the SARS-CoV-2 proteins in 24 geo-locations across different continents. The results showed an evenly uneven distribution of the unique protein variants, distinct mutations, unique frequency of common conserved residues, and mutational residues across these 24 geo-locations. Furthermore, ample mutations were identified in the evolutionarily conserved invariant regions in the SARS-CoV-2 proteins across almost all geo-locations studied. This pattern of mutations potentially breaches the law of evolutionary conserved functional units of the beta-coronavirus genus. These mutations may lead to several novel SARS-CoV-2 variants with a high degree of transmissibility and virulence. A thorough investigation on the origin and characteristics of SARS-CoV-2 needs to be conducted in the interest of science and for the preparation of meeting the challenges of potential future pandemics.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, 721140, West Bengal, India.
| | - Vaishnavi Kodakandla
- Department of Life sciences, Sophia College For Women, University of Mumbai, Bhulabhai Desai Road, Mumbai 400026, India
| | - Elrashdy M Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, New Borg EL-Arab 21934, Alexandria, Egypt.
| | | | - Pabitra Pal Choudhury
- Indian Statistical Institute, Applied Statistics Unit, 203 B T Road, Kolkata 700108, India
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigacion Traslacional San Alberto Magno, Universidad Cat'olica de Valencia San Vicente Martir, c/Guillem de Castro, 94, 46001 Valencia, Valencia, Spain.
| | | | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University, Faculty of Pharmacy, Irbid 566, Jordan.
| | - Giorgio Palu
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy.
| | - Tarek Mohamed Abd El-Aziz
- Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt; Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3900, USA.
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB, India; Departamento de Geńetica, Ecologia e Evolucao, Instituto de Cíencias Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand
| | - Kazuo Takayama
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 6068507, Japan.
| | - Nicolas G Bazan
- Neuroscience Center of Excellence, School of Medicine, LSU Health New Orleans, New Orleans, LA 70112, USA.
| | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK.
| | - Samendra P Sherchan
- Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln LN6 7TS, UK.
| | - Amos Lal
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, 64849 Monterrey, Nuevo León, Mexico.
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Vladimir N Uversky
- Department of Molecular Medicineand USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny 141700, Russia.
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Luo R, Delaunay‐Moisan A, Timmis K, Danchin A. SARS-CoV-2 biology and variants: anticipation of viral evolution and what needs to be done. Environ Microbiol 2021; 23:2339-2363. [PMID: 33769683 PMCID: PMC8251359 DOI: 10.1111/1462-2920.15487] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 12/14/2022]
Abstract
The global propagation of SARS-CoV-2 and the detection of a large number of variants, some of which have replaced the original clade to become dominant, underscores the fact that the virus is actively exploring its evolutionary space. The longer high levels of viral multiplication occur - permitted by high levels of transmission -, the more the virus can adapt to the human host and find ways to success. The third wave of the COVID-19 pandemic is starting in different parts of the world, emphasizing that transmission containment measures that are being imposed are not adequate. Part of the consideration in determining containment measures is the rationale that vaccination will soon stop transmission and allow a return to normality. However, vaccines themselves represent a selection pressure for evolution of vaccine-resistant variants, so the coupling of a policy of permitting high levels of transmission/virus multiplication during vaccine roll-out with the expectation that vaccines will deal with the pandemic, is unrealistic. In the absence of effective antivirals, it is not improbable that SARS-CoV-2 infection prophylaxis will involve an annual vaccination campaign against 'dominant' viral variants, similar to influenza prophylaxis. Living with COVID-19 will be an issue of SARS-CoV-2 variants and evolution. It is therefore crucial to understand how SARS-CoV-2 evolves and what constrains its evolution, in order to anticipate the variants that will emerge. Thus far, the focus has been on the receptor-binding spike protein, but the virus is complex, encoding 26 proteins which interact with a large number of host factors, so the possibilities for evolution are manifold and not predictable a priori. However, if we are to mount the best defence against COVID-19, we must mount it against the variants, and to do this, we must have knowledge about the evolutionary possibilities of the virus. In addition to the generic cellular interactions of the virus, there are extensive polymorphisms in humans (e.g. Lewis, HLA, etc.), some distributed within most or all populations, some restricted to specific ethnic populations and these variations pose additional opportunities for/constraints on viral evolution. We now have the wherewithal - viral genome sequencing, protein structure determination/modelling, protein interaction analysis - to functionally characterize viral variants, but access to comprehensive genome data is extremely uneven. Yet, to develop an understanding of the impacts of such evolution on transmission and disease, we must link it to transmission (viral epidemiology) and disease data (patient clinical data), and the population granularities of these. In this editorial, we explore key facets of viral biology and the influence of relevant aspects of human polymorphisms, human behaviour, geography and climate and, based on this, derive a series of recommendations to monitor viral evolution and predict the types of variants that are likely to arise.
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Affiliation(s)
- Ruibang Luo
- Department of Computer ScienceThe University of Hong KongBonham RoadPokfulamHong Kong
| | - Agnès Delaunay‐Moisan
- Université Paris‐Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Gif‐sur‐Yvette91198France
| | - Kenneth Timmis
- Institute of MicrobiologyTechnical University of BraunschweigBraunschweigGermany
| | - Antoine Danchin
- Kodikos Labs, Institut Cochin, 24 rue du Faubourg Saint‐JacquesParis75014France
- School of Biomedical Sciences, Li Kashing Faculty of MedicineUniversity of Hong Kong21 Sassoon RoadHong Kong
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