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Hassan SS, Basu P, 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 MM, Lal A, Chauhan G, Baetas-da-Cruz W, Sherchan SP, Uversky VN. Periodically aperiodic pattern of SARS-CoV-2 mutations underpins the uncertainty of its origin and evolution. Environ Res 2022; 204:112092. [PMID: 34562480 PMCID: PMC8457672 DOI: 10.1016/j.envres.2021.112092] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 05/20/2023]
Abstract
Various lineages of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) have contributed to prolongation of the Coronavirus Disease 2019 (COVID-19) pandemic. Several non-synonymous mutations in SARS-CoV-2 proteins have generated multiple SARS-CoV-2 variants. In our previous report, we have shown that an evenly uneven distribution of unique protein variants of SARS-CoV-2 is geo-location or demography-specific. However, the correlation between the demographic transmutability of the SARS-CoV-2 infection and mutations in various proteins remains unknown due to hidden symmetry/asymmetry in the occurrence of mutations. This study tracked how these mutations are emerging in SARS-CoV-2 proteins in six model countries and globally. In a geo-location, considering the mutations having a frequency of detection of at least 500 in each SARS-CoV-2 protein, we studied the country-wise percentage of invariant residues. Our data revealed that since October 2020, highly frequent mutations in SARS-CoV-2 have been observed mostly in the Open Reading Frame (ORF) 7b and ORF8, worldwide. No such highly frequent mutations in any of the SARS-CoV-2 proteins were found in the UK, India, and Brazil, which does not correlate with the degree of transmissibility of the virus in India and Brazil. However, we have found a signature that SARS-CoV-2 proteins were evolving at a higher rate, and considering global data, mutations are detected in the majority of the available amino acid locations. Fractal analysis of each protein's normalized factor time series showed a periodically aperiodic emergence of dominant variants for SARS-CoV-2 protein mutations across different countries. It was noticed that certain high-frequency variants have emerged in the last couple of months, and thus the emerging SARS-CoV-2 strains are expected to contain prevalent mutations in the ORF3a, membrane, and ORF8 proteins. In contrast to other beta-coronaviruses, SARS-CoV-2 variants have rapidly emerged based on demographically dependent mutations. Characterization of the periodically aperiodic nature of the demographic spread of SARS-CoV-2 variants in various countries can contribute to the identification of the origin of SARS-CoV-2.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, 721140, West Bengal, India.
| | - Pallab Basu
- School of Physics, University of the Witwatersrand, Johannesburg, Braamfontein 2000, 721140, South Africa.
| | - 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 & Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia, San Vicente Mártir, Valencia 46001, 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 Cîencias Bioĺogicas, 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 (CiRA), 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 M Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, BT52 1SA, Northern Ireland, 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 Léon, 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.
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA, 70112, USA.
| | - Vladimir N Uversky
- Department of Molecular Medicine and 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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Brandt D, Simunovic M, Busche T, Haak M, Belmann P, Jünemann S, Schulz T, Klages LJ, Vinke S, Beckstette M, Pohl E, Scherer C, Sczyrba A, Kalinowski J. Multiple Occurrences of a 168-Nucleotide Deletion in SARS-CoV-2 ORF8, Unnoticed by Standard Amplicon Sequencing and Variant Calling Pipelines. Viruses 2021; 13:1870. [PMID: 34578452 PMCID: PMC8518987 DOI: 10.3390/v13091870] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/20/2022] Open
Abstract
Genomic surveillance of the SARS-CoV-2 pandemic is crucial and mainly achieved by amplicon sequencing protocols. Overlapping tiled-amplicons are generated to establish contiguous SARS-CoV-2 genome sequences, which enable the precise resolution of infection chains and outbreaks. We investigated a SARS-CoV-2 outbreak in a local hospital and used nanopore sequencing with a modified ARTIC protocol employing 1200 bp long amplicons. We detected a long deletion of 168 nucleotides in the ORF8 gene in 76 samples from the hospital outbreak. This deletion is difficult to identify with the classical amplicon sequencing procedures since it removes two amplicon primer-binding sites. We analyzed public SARS-CoV-2 sequences and sequencing read data from ENA and identified the same deletion in over 100 genomes belonging to different lineages of SARS-CoV-2, pointing to a mutation hotspot or to positive selection. In almost all cases, the deletion was not represented in the virus genome sequence after consensus building. Additionally, further database searches point to other deletions in the ORF8 coding region that have never been reported by the standard data analysis pipelines. These findings and the fact that ORF8 is especially prone to deletions, make a clear case for the urgent necessity of public availability of the raw data for this and other large deletions that might change the physiology of the virus towards endemism.
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Affiliation(s)
- David Brandt
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.B.); (M.S.); (T.B.); (M.H.); (P.B.); (S.J.); (T.S.); (L.J.K.); (S.V.); (M.B.); (A.S.)
| | - Marina Simunovic
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.B.); (M.S.); (T.B.); (M.H.); (P.B.); (S.J.); (T.S.); (L.J.K.); (S.V.); (M.B.); (A.S.)
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.B.); (M.S.); (T.B.); (M.H.); (P.B.); (S.J.); (T.S.); (L.J.K.); (S.V.); (M.B.); (A.S.)
| | - Markus Haak
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.B.); (M.S.); (T.B.); (M.H.); (P.B.); (S.J.); (T.S.); (L.J.K.); (S.V.); (M.B.); (A.S.)
| | - Peter Belmann
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.B.); (M.S.); (T.B.); (M.H.); (P.B.); (S.J.); (T.S.); (L.J.K.); (S.V.); (M.B.); (A.S.)
- Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Sebastian Jünemann
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.B.); (M.S.); (T.B.); (M.H.); (P.B.); (S.J.); (T.S.); (L.J.K.); (S.V.); (M.B.); (A.S.)
- Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Tizian Schulz
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.B.); (M.S.); (T.B.); (M.H.); (P.B.); (S.J.); (T.S.); (L.J.K.); (S.V.); (M.B.); (A.S.)
- Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Levin Joe Klages
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.B.); (M.S.); (T.B.); (M.H.); (P.B.); (S.J.); (T.S.); (L.J.K.); (S.V.); (M.B.); (A.S.)
| | - Svenja Vinke
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.B.); (M.S.); (T.B.); (M.H.); (P.B.); (S.J.); (T.S.); (L.J.K.); (S.V.); (M.B.); (A.S.)
| | - Michael Beckstette
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.B.); (M.S.); (T.B.); (M.H.); (P.B.); (S.J.); (T.S.); (L.J.K.); (S.V.); (M.B.); (A.S.)
- Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Ehmke Pohl
- Department of Biosciences, Durham University, Durham DH1 3LE, UK;
| | - Christiane Scherer
- Evangelisches Klinikum Bethel, Institut für Laboratoriumsmedizin, Mikrobiologie und Hygiene, 33617 Bielefeld, Germany;
- Universitätsklinikum OWL der Universität Bielefeld, 33615 Bielefeld, Germany
| | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.B.); (M.S.); (T.B.); (M.H.); (P.B.); (S.J.); (T.S.); (L.J.K.); (S.V.); (M.B.); (A.S.)
- Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.B.); (M.S.); (T.B.); (M.H.); (P.B.); (S.J.); (T.S.); (L.J.K.); (S.V.); (M.B.); (A.S.)
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