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Kim BK, Choi WS, Jeong JH, Oh S, Park JH, Yun YS, Min SC, Kang DH, Kim EG, Ryu H, Kim HK, Baek YH, Choi YK, Song MS. A Rapid Method for Generating Infectious SARS-CoV-2 and Variants Using Mutagenesis and Circular Polymerase Extension Cloning. Microbiol Spectr 2023; 11:e0338522. [PMID: 36877070 PMCID: PMC10100849 DOI: 10.1128/spectrum.03385-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 02/12/2023] [Indexed: 03/07/2023] Open
Abstract
The appearance of SARS-CoV-2 variants in late 2020 raised alarming global public health concerns. Despite continued scientific progress, the genetic profiles of these variants bring changes in viral properties that threaten vaccine efficacy. Thus, it is critically important to investigate the biologic profiles and significance of these evolving variants. In this study, we demonstrate the application of circular polymerase extension cloning (CPEC) to the generation of full-length clones of SARS-CoV-2. We report that, combined with a specific primer design scheme, this yields a simpler, uncomplicated, and versatile approach for engineering SARS-CoV-2 variants with high viral recovery efficiency. This new strategy for genomic engineering of SARS-CoV-2 variants was implemented and evaluated for its efficiency in generating point mutations (K417N, L452R, E484K, N501Y, D614G, P681H, P681R, Δ69-70, Δ157-158, E484K+N501Y, and Ins-38F) and multiple mutations (N501Y/D614G and E484K/N501Y/D614G), as well as a large truncation (ΔORF7A) and insertion (GFP). The application of CPEC to mutagenesis also allows the inclusion of a confirmatory step prior to assembly and transfection. This method could be of value in the molecular characterization of emerging SARS-CoV-2 variants as well as the development and testing of vaccines, therapeutic antibodies, and antivirals. IMPORTANCE Since the first emergence of the SARS-CoV-2 variant in late 2020, novel variants have been continuously introduced to the human population, causing severe public health threats. In general, because these variants acquire new genetic mutation/s, it is critical to analyze the biological function of viruses that such mutations can confer. Therefore, we devised a method that can construct SARS-CoV-2 infectious clones and their variants rapidly and efficiently. The method was developed based on a PCR-based circular polymerase extension cloning (CPEC) combined with a specific primer design scheme. The efficiency of the newly designed method was evaluated by generating SARS-CoV-2 variants with single point mutations, multiple point mutations, and a large truncation and insertion. This method could be of value for the molecular characterization of emerging SARS-CoV-2 variants and the development and testing of vaccines and antiviral agents.
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Affiliation(s)
- Beom Kyu Kim
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Won-Suk Choi
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Ju Hwan Jeong
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Sol Oh
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Ji-Hyun Park
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Yu Soo Yun
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Seong Cheol Min
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Da Hyeon Kang
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Eung-Gook Kim
- Department of Biochemistry, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Hojin Ryu
- Department of Biological Sciences and Biotechnology, College of Natural Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Hye Kwon Kim
- Department of Biological Sciences and Biotechnology, College of Natural Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Yun Hee Baek
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Young Ki Choi
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Min-Suk Song
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
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Jimenez Ruiz JA, Lopez Ramirez C, Lopez-Campos JL. Spike protein of SARS-CoV-2 Omicron variant: An in-silico study evaluating spike interactions and immune evasion. Front Public Health 2022; 10:1052241. [PMID: 36523581 PMCID: PMC9746896 DOI: 10.3389/fpubh.2022.1052241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/03/2022] [Indexed: 11/30/2022] Open
Abstract
Background The fundamentals of the infectivity and immune evasion of the SARS-CoV-2 Omicron variant are not yet fully understood. Here, we carried out an in-silico study analyzing the spike protein, the protein electrostatic potential, and the potential immune evasion. Methods The analysis was based on the structure of the spike protein from two SARS-CoV-2 variants, the original Wuhan and the Botswana (Omicron). The full-length genome sequences and protein sequences were obtained from databanks. The interaction of the spike proteins with the human Angiotensin Converting Enzyme 2 (ACE2) receptor was evaluated through the open-source software. The Immune Epitope Database was used to analyze the potential immune evasion of the viruses. Results Our data show that the Omicron spike protein resulted in 37 amino acid changes. The physicochemical properties of the spike had changed, and the electrostatic potentials differed between both variants. This resulted in a decrease in protein interactions, which does not establish a greater interaction with the ACE2 receptor. These changes compromise key receptor-binding motif residues in the SARS-CoV-2 spike protein that interact with neutralizing antibodies and ACE2. Conclusions These mutations appear to confer enhanced properties of infectivity. The Omicron variant appears to be more effective at evading immune responses.
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Affiliation(s)
- Jose A. Jimenez Ruiz
- Research Group on Electronic Technology and Industrial Computing (TIC-150) at the University of Seville, Seville, Spain
| | - Cecilia Lopez Ramirez
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Jose Luis Lopez-Campos
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
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A Comparative Study of the Plasma Chemokine Profile in COVID-19 Patients Infected with Different SARS-CoV-2 Variants. Int J Mol Sci 2022; 23:ijms23169058. [PMID: 36012323 PMCID: PMC9409001 DOI: 10.3390/ijms23169058] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/04/2022] [Accepted: 08/10/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Infection caused by SARS-CoV-2 mostly affects the upper and lower respiratory tracts and causes symptoms ranging from the common cold to pneumonia with acute respiratory distress syndrome. Chemokines are deeply involved in the chemoattraction, proliferation, and activation of immune cells within inflammation. It is crucial to consider that mutations within the virion can potentially affect the clinical course of SARS-CoV-2 infection because disease severity and manifestation vary depending on the genetic variant. Our objective was to measure and assess the different concentrations of chemokines involved in COVID-19 caused by different variants of the virus. METHODS We used the blood plasma of patients infected with different variants of SARS-CoV-2, i.e., the ancestral Wuhan strain and the Alpha, Delta, and Omicron variants. We measured the concentrations of 11 chemokines in the samples: CCL2/MCP-1, CCL3/MIP-1α, CCL4/MIP-1β, CCL7/MCP-3, CCL11/Eotaxin, CCL22/MDC, CXCL1/GROα, CXCL8/IL-8, CXCL9/MIG, CXCL10/IP-10, and CX3CL1/Fractalkine. RESULTS We noted a statistically significant elevation in the concentrations of CCL2/MCP-1, CXCL8/IL-8, and CXCL1/IP-10 independently of the variant, and a drop in the CCL22/MDC concentrations. CONCLUSIONS The chemokine concentrations varied significantly depending on the viral variant, leading us to infer that mutations in viral proteins play a role in the cellular and molecular mechanisms of immune responses.
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Tarry H, Vézina V, Bailey J, Lopes L. Political orientation, moral foundations, and COVID-19 social distancing. PLoS One 2022; 17:e0267136. [PMID: 35749535 PMCID: PMC9232135 DOI: 10.1371/journal.pone.0267136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 04/01/2022] [Indexed: 11/21/2022] Open
Abstract
During the COVID-19 pandemic, governments have advocated numerous social distancing measures, and compliance with these has likely saved millions of lives globally. In an online sample drawn from the U.S. and Canada (N = 209), participants completed measures of political orientation, moral foundations, and COVID-19 social distancing attitudes and behaviours. A more left-wing political orientation, and greater endorsement of the individualizing moral foundations were significantly related to more positive social distancing attitudes, and greater self-reported compliance with relevant restrictions. A more right-wing political orientation, and greater endorsement of the binding and economic liberty foundations were associated with less positive attitudes and reduced compliance. In a series of mediation analyses, the relationships between political orientation and various social distancing measures were significantly mediated by variations in participants' moral foundations, particularly their endorsement of economic liberty and the individualizing foundations. Further data indicated that the perceived persuasiveness of messages based on each moral foundation advocating for continued social distancing was significantly related to both participants' moral values and their political orientation. Findings are discussed in terms of understanding politicized differences around social distancing as partly reflecting differential valuation of the moral foundations, and in creating effective public health messaging regarding compliance.
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Affiliation(s)
- Hammond Tarry
- Department of Psychology, Kwantlen Polytechnic University, Surrey, British Columbia, Canada
| | - Valérie Vézina
- Department of Political Science, Kwantlen Polytechnic University, Surrey, British Columbia, Canada
| | - Jacob Bailey
- Student Research Assistant, Kwantlen Polytechnic University, Surrey, British Columbia, Canada
| | - Leah Lopes
- Student Research Assistant, Kwantlen Polytechnic University, Surrey, British Columbia, Canada
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Goguet E, Powers JH, Olsen CH, Tribble DR, Davies J, Illinik L, Jackson-Thompson BM, Hollis-Perry M, Maiolatesi SE, Pollett S, Duplessis CA, Wang G, Ramsey KF, Reyes AE, Alcorta Y, Wong MA, Ortega O, Parmelee E, Lindrose AR, Moser M, Samuels EC, Coggins SA, Graydon E, Robinson S, Campbell W, Malloy AMW, Voegtly LJ, Arnold CE, Cer RZ, Malagon F, Bishop-Lilly KA, Burgess TH, Broder CC, Laing ED, Mitre E. Prospective Assessment of Symptoms to Evaluate Asymptomatic SARS-CoV-2 Infections in a Cohort of Health Care Workers. Open Forum Infect Dis 2022; 9:ofac030. [PMID: 35198647 PMCID: PMC8860153 DOI: 10.1093/ofid/ofac030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The frequency of asymptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is unclear and may be influenced by how symptoms are evaluated. In this study, we sought to determine the frequency of asymptomatic SARS-CoV-2 infections in a prospective cohort of health care workers (HCWs). METHODS A prospective cohort of HCWs, confirmed negative for SARS-CoV-2 exposure upon enrollment, were evaluated for SARS-CoV-2 infection by monthly analysis of SARS-CoV-2 antibodies as well as referral for polymerase chain reaction testing whenever they exhibited symptoms of coronavirus disease 2019 (COVID-19). Participants completed the standardized and validated FLU-PRO Plus symptom questionnaire scoring viral respiratory disease symptom intensity and frequency at least twice monthly during baseline periods of health and each day they had any symptoms that were different from their baseline. RESULTS Two hundred sixty-three participants were enrolled between August 25 and December 31, 2020. Through February 28, 2021, 12 participants were diagnosed with SARS-CoV-2 infection. Symptom analysis demonstrated that all 12 had at least mild symptoms of COVID-19, compared with baseline health, near or at time of infection. CONCLUSIONS These results suggest that asymptomatic SARS-CoV-2 infection in unvaccinated, immunocompetent adults is less common than previously reported. While infectious inoculum doses and patient factors may have played a role in the clinical manifestations of SARS-CoV-2 infections in this cohort, we suspect that the high rate of symptomatic disease was due primarily to participant attentiveness to symptoms and collection of symptoms in a standardized, prospective fashion. These results have implications for studies that estimate SARS-CoV-2 infection prevalence and for public health measures to control the spread of this virus.
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Affiliation(s)
- Emilie Goguet
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - John H Powers
- Clinical Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Cara H Olsen
- Department of Preventive Medicine & Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - David R Tribble
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine & Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Julian Davies
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine & Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Luca Illinik
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine & Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Belinda M Jackson-Thompson
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Monique Hollis-Perry
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, Maryland, USA
| | - Santina E Maiolatesi
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, Maryland, USA
| | - Simon Pollett
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine & Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Christopher A Duplessis
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, Maryland, USA
| | - Gregory Wang
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, Maryland, USA
- General Dynamics Information Technology, Falls Church, Virginia, USA
| | - Kathleen F Ramsey
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, Maryland, USA
- General Dynamics Information Technology, Falls Church, Virginia, USA
| | - Anatalio E Reyes
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, Maryland, USA
- General Dynamics Information Technology, Falls Church, Virginia, USA
| | - Yolanda Alcorta
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, Maryland, USA
- General Dynamics Information Technology, Falls Church, Virginia, USA
| | - Mimi A Wong
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, Maryland, USA
- General Dynamics Information Technology, Falls Church, Virginia, USA
| | - Orlando Ortega
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine & Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Edward Parmelee
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine & Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Alyssa R Lindrose
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Matthew Moser
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Emily C Samuels
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Si’Ana A Coggins
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Elizabeth Graydon
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Sara Robinson
- Division of Infectious Diseases, Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - Wesley Campbell
- Division of Infectious Diseases, Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - Allison M W Malloy
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Logan J Voegtly
- Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, Maryland, USA
- Leidos, Reston, Virginia, USA
| | - Catherine E Arnold
- Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, Maryland, USA
- Defense Threat Reduction Agency, Fort Belvoir, Virginia, USA
| | - Regina Z Cer
- Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, Maryland, USA
| | - Francisco Malagon
- Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, Maryland, USA
- Leidos, Reston, Virginia, USA
| | - Kimberly A Bishop-Lilly
- Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, Maryland, USA
| | - Timothy H Burgess
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine & Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Christopher C Broder
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Eric D Laing
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Edward Mitre
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
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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. ENVIRONMENTAL RESEARCH 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] [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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Hofman P, Bordone O, Chamorey E, Benzaquen J, Schiappa R, Lespinet-Fabre V, Lanteri E, Brest P, Mograbi B, Maniel C, Tanga V, Allegra M, Salah M, Fayada J, Boutros J, Leroy S, Heeke S, Hofman V, Marquette CH, Ilié M. Setting-Up a Rapid SARS-CoV-2 Genome Assessment by Next-Generation Sequencing in an Academic Hospital Center (LPCE, Louis Pasteur Hospital, Nice, France). Front Med (Lausanne) 2022; 8:730577. [PMID: 35087842 PMCID: PMC8787061 DOI: 10.3389/fmed.2021.730577] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/08/2021] [Indexed: 11/13/2022] Open
Abstract
Introduction: Aside from the reverse transcription-PCR tests for the diagnosis of the COVID-19 in routine clinical care and population-scale screening, there is an urgent need to increase the number and the efficiency for full viral genome sequencing to detect the variants of SARS-CoV-2. SARS-CoV-2 variants assessment should be easily, rapidly, and routinely available in any academic hospital. Materials and Methods: SARS-CoV-2 full genome sequencing was performed retrospectively in a single laboratory (LPCE, Louis Pasteur Hospital, Nice, France) in 103 SARS-CoV-2 positive individuals. An automated workflow used the Ion Ampliseq SARS-CoV-2 panel on the Genexus Sequencer. The analyses were made from nasopharyngeal swab (NSP) (n = 64) and/or saliva (n = 39) samples. All samples were collected in the metropolitan area of the Nice city (France) from September 2020 to March 2021. Results: The mean turnaround time between RNA extraction and result reports was 30 h for each run of 15 samples. A strong correlation was noted for the results obtained between NSP and saliva paired samples, regardless of low viral load and high (>28) Ct values. After repeated sequencing runs, complete failure of obtaining a valid sequencing result was observed in 4% of samples. Besides the European strain (B.1.160), various variants were identified, including one variant of concern (B.1.1.7), and different variants under monitoring. Discussion: Our data highlight the current feasibility of developing the SARS-CoV-2 next-generation sequencing approach in a single hospital center. Moreover, these data showed that using the Ion Ampliseq SARS-CoV-2 Assay, the SARS-CoV-2 genome sequencing is rapid and efficient not only in NSP but also in saliva samples with a low viral load. The advantages and limitations of this setup are discussed.
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Affiliation(s)
- Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France.,Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France.,Team 4, Institute of Research on Cancer and Aging (IRCAN), CNRS INSERM, Centre Antoine-Lacassagne, Université Côte d'Azur, Nice, France
| | - Olivier Bordone
- Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France.,Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France
| | - Emmanuel Chamorey
- Epidemiology and Biostatistics Unit, Centre Antoine-Lacassagne, Université Côte d'Azur, Nice, France
| | - Jonathan Benzaquen
- Team 4, Institute of Research on Cancer and Aging (IRCAN), CNRS INSERM, Centre Antoine-Lacassagne, Université Côte d'Azur, Nice, France.,Department of Pulmonary Medicine and Oncology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France
| | - Renaud Schiappa
- Epidemiology and Biostatistics Unit, Centre Antoine-Lacassagne, Université Côte d'Azur, Nice, France
| | - Virginie Lespinet-Fabre
- Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France.,Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France
| | - Elisabeth Lanteri
- Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France
| | - Patrick Brest
- Team 4, Institute of Research on Cancer and Aging (IRCAN), CNRS INSERM, Centre Antoine-Lacassagne, Université Côte d'Azur, Nice, France
| | - Baharia Mograbi
- Team 4, Institute of Research on Cancer and Aging (IRCAN), CNRS INSERM, Centre Antoine-Lacassagne, Université Côte d'Azur, Nice, France
| | - Charlotte Maniel
- Department of Pulmonary Medicine and Oncology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France
| | - Virginie Tanga
- Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France.,Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France
| | - Maryline Allegra
- Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France.,Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France
| | - Myriam Salah
- Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France
| | - Julien Fayada
- Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France
| | - Jacques Boutros
- Department of Pulmonary Medicine and Oncology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France
| | - Sylvie Leroy
- Department of Pulmonary Medicine and Oncology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France
| | - Simon Heeke
- Department of Thoracic H&N Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, United States
| | - Véronique Hofman
- Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France.,Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France.,Team 4, Institute of Research on Cancer and Aging (IRCAN), CNRS INSERM, Centre Antoine-Lacassagne, Université Côte d'Azur, Nice, France
| | - Charles-Hugo Marquette
- Team 4, Institute of Research on Cancer and Aging (IRCAN), CNRS INSERM, Centre Antoine-Lacassagne, Université Côte d'Azur, Nice, France.,Department of Pulmonary Medicine and Oncology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France
| | - Marius Ilié
- Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France.,Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France.,Team 4, Institute of Research on Cancer and Aging (IRCAN), CNRS INSERM, Centre Antoine-Lacassagne, Université Côte d'Azur, Nice, France
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8
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Gao R, Zu W, Liu Y, Li J, Li Z, Wen Y, Wang H, Yuan J, Cheng L, Zhang S, Zhang Y, Zhang S, Liu W, Lan X, Liu L, Li F, Zhang Z. Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis. Virulence 2021; 12:1209-1226. [PMID: 34030593 PMCID: PMC8158041 DOI: 10.1080/21505594.2021.1911477] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/28/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022] Open
Abstract
New SARS-CoV-2 mutants have been continuously indentified with enhanced transmission ever since its outbreak in early 2020. As an RNA virus, SARS-CoV-2 has a high mutation rate due to the low fidelity of RNA polymerase. To study the single nucleotide polymorphisms (SNPs) dynamics of SARS-CoV-2, 158 SNPs with high confidence were identified by deep meta-transcriptomic sequencing, and the most common SNP type was C > T. Analyses of intra-host population diversity revealed that intra-host quasispecies' composition varies with time during the early onset of symptoms, which implicates viral evolution during infection. Network analysis of co-occurring SNPs revealed the most abundant non-synonymous SNP 22,638 in the S glycoprotein RBD region and 28,144 in the ORF8 region. Furthermore, SARS-CoV-2 variations differ in an individual's respiratory tissue (nose, throat, BALF, or sputum), suggesting independent compartmentalization of SARS-CoV-2 populations in patients. The positive selection analysis of the SARS-CoV-2 genome uncovered the positive selected amino acid G251V on ORF3a. Alternative allele frequency spectrum (AAFS) of all variants revealed that ORF8 could bear alternate alleles with high frequency. Overall, the results show the quasispecies' profile of SARS-CoV-2 in the respiratory tract in the first two months after the outbreak.
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Affiliation(s)
- Rongsui Gao
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Wenhong Zu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Yang Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Junhua Li
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China
| | - Zeyao Li
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Yanling Wen
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Haiyan Wang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Jing Yuan
- Department of Infectious Diseases, Shenzhen Third People’s Hospital, National Clinical Research Center for Infectious Disease, Shenzhen, Guangdong Province, China
| | - Lin Cheng
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Shengyuan Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Yu Zhang
- National Supercomputing Center in Shenzhen (Shenzhen Cloud Computing Center), Shenzhen, China
| | - Shuye Zhang
- Shanghai Public Health Clinical Center, Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Weilong Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Xun Lan
- Department of Basic Medical Sciences at School of Medicine, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Lei Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Feng Li
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
- Shenzhen Research Center for Communicable Disease Diagnosis and Treatment of Chinese Academy of Medical Science, Shenzhen, Guangdong Province, China
- Guangdong Key Laboratory for Anti-infection Drug Quality Evaluation, Shenzhen, Guangdong Province, China
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9
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Kim DY, Shinde SK, Lone S, Palem RR, Ghodake GS. COVID-19 Pandemic: Public Health Risk Assessment and Risk Mitigation Strategies. J Pers Med 2021; 11:1243. [PMID: 34945715 PMCID: PMC8707584 DOI: 10.3390/jpm11121243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/17/2021] [Accepted: 11/22/2021] [Indexed: 12/17/2022] Open
Abstract
A newly emerged respiratory viral disease called severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is also known as pandemic coronavirus disease (COVID-19). This pandemic has resulted an unprecedented global health crisis and devastating impact on several sectors of human lives and economies. Fortunately, the average case fatality ratio for SARS-CoV-2 is below 2%, much lower than that estimated for MERS (34%) and SARS (11%). However, COVID-19 has a much higher transmissibility rate, as evident from the constant increase in the count of infections worldwide. This article explores the reasons behind how COVID-19 was able to cause a global pandemic crisis. The current outbreak scenario and causes of rapid global spread are examined using recent developments in the literature, epidemiological features relevant to public health awareness, and critical perspective of risk assessment and mitigation strategies. Effective pandemic risk mitigation measures have been established and amended against COVID-19 diseases, but there is still much scope for upgrading execution and coordination among authorities in terms of organizational leadership's commitment and diverse range of safety measures, including administrative control measures, engineering control measures, and personal protective equipment (PPE). The significance of containment interventions against the COVID-19 pandemic is now well established; however, there is a need for its effective execution across the globe, and for the improvement of the performance of risk mitigation practices and suppression of future pandemic crises.
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Affiliation(s)
- Dae-Young Kim
- Department of Biological and Environmental Science, Dongguk University-Seoul, 32 Dongguk-ro, Ilsandong-gu, Goyang-si 10326, Gyeonggi-do, Korea; (D.-Y.K.); (S.K.S.)
| | - Surendra Krushna Shinde
- Department of Biological and Environmental Science, Dongguk University-Seoul, 32 Dongguk-ro, Ilsandong-gu, Goyang-si 10326, Gyeonggi-do, Korea; (D.-Y.K.); (S.K.S.)
| | - Saifullah Lone
- Interdisciplinary Division for Renewable Energy and Advanced Materials (iDREAM), National Institute of Technology (NIT), Srinagar 190006, India;
| | - Ramasubba Reddy Palem
- Department of Medical Biotechnology, Dongguk University-Seoul, 32 Dongguk-ro, Ilsandong-gu, Goyang-si 10326, Gyeonggi-do, Korea;
| | - Gajanan Sampatrao Ghodake
- Department of Biological and Environmental Science, Dongguk University-Seoul, 32 Dongguk-ro, Ilsandong-gu, Goyang-si 10326, Gyeonggi-do, Korea; (D.-Y.K.); (S.K.S.)
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10
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The microbiome in atopic patients and potential modifications in the context of the severe acute respiratory syndrome coronavirus 2 pandemic. Curr Opin Allergy Clin Immunol 2021; 21:245-251. [PMID: 33769313 DOI: 10.1097/aci.0000000000000738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
PURPOSE OF REVIEW Data regarding the effects of coronavirus disease 2019 (COVID-19) on host-microbiome alteration and subsequent effects on susceptibility and clinical course of COVID-19, especially in atopic patients, are currently limited. Here, we review the studies regarding the microbiome of atopic patients with other respiratory infections and discuss the potential role of probiotics as therapeutic targets for COVID-19 to decrease its susceptibility and severity of COVID-19. RECENT FINDINGS Respiratory tract virus infection affects the gut and airway microbiome structures and host's immune function. Diverse factors in atopic diseases affect the airway and gut microbiome structures, which are expected to negatively influence host health. However, response to respiratory virus infection in atopic hosts depends on the preexisting microbiome and immune responses. This may explain the inconclusiveness of the effects of COVID-19 on the susceptibility, morbidity, and mortality of patients with atopic diseases. Beneficial probiotics may be a therapeutic adjuvant in COVID-19 infection as the beneficial microbiome can decrease the viral load in the early phase of respiratory virus infection and improve the morbidity and mortality. SUMMARY Application of probiotics can be a potential adjuvant treatment in respiratory virus infection to improve host immune responses and disturbed microbiome structures in atopic patients. Further related studies involving COVID-19 are warranted in near future.
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11
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Randomness for Nucleotide Sequences of SARS-CoV-2 and Its Related Subfamilies. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2020; 2020:8819942. [PMID: 33273962 PMCID: PMC7683162 DOI: 10.1155/2020/8819942] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/23/2020] [Accepted: 11/05/2020] [Indexed: 01/15/2023]
Abstract
The origin and evolution of SARS-CoV-2 has been an important issue in tackling COVID-19. Research on these topics would enhance our knowledge of this virus and help us develop vaccines or predict its paths of mutations. There are many theoretical and clinical researches in this area. In this article, we devise a structural metric which directly measures the structural differences between any two nucleotide sequences. In order to explore the mechanisms of how the evolution works, we associate the nucleotide sequences of SARS-CoV-2 and its related families with the degrees of randomness. Since the distances between randomly generated nucleotide sequences are very concentrated around a mean with low variance, they are qualified as good candidates for the fundamental reference. Such reference could then be applied to measure the randomness of other Coronaviridae sequences. Our findings show that the relative randomness ratios are very consistent and concentrated. This result indicates their randomness is very stable and predictable. The findings also reveal the evolutional behaviours between the Coronaviridae and all its subfamilies.
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12
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Caccuri F, Zani A, Messali S, Giovanetti M, Bugatti A, Campisi G, Filippini F, Scaltriti E, Ciccozzi M, Fiorentini S, Caruso A. A persistently replicating SARS-CoV-2 variant derived from an asymptomatic individual. J Transl Med 2020; 18:362. [PMID: 32967693 PMCID: PMC7509824 DOI: 10.1186/s12967-020-02535-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 09/15/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Since the first outbreak of SARS-CoV-2, the clinical characteristics of the Coronavirus Disease 2019 (COVID-19) have been progressively changed. Data reporting a viral intra-host and inter-host evolution favouring the appearance of mild SARS-CoV-2 strains are since being accumulating. To better understand the evolution of SARS-CoV-2 pathogenicity and its adaptation to the host, it is therefore crucial to investigate the genetic and phenotypic characteristics of SARS-CoV-2 strains circulating lately in the epidemic. METHODS Nasopharyngeal swabs have been analyzed for viral load in the early (March 2020) and late (May 2020) phases of epidemic in Brescia, Italy. Isolation of SARS-CoV-2 from 2 high viral load specimens identified on March 9 (AP66) and on May 8 (GZ69) was performed on Vero E6 cells. Amount of virus released was assessed by quantitative PCR. Genotypic characterization of AP66 and GZ69 was performed by next generation sequencing followed by an in-depth in silico analysis of nucleotide mutations. RESULTS The SARS-CoV-2 GZ69 strain, isolated in May from an asymptomatic healthcare worker, showed an unprecedented capability of replication in Vero E6 cells in the absence of any evident cytopathic effect. Vero E6 subculturing, up to passage 4, showed that SARS-CoV-2 GZ69 infection was as productive as the one sustained by the cytopathic strain AP66. Whole genome sequencing of the persistently replicating SARS-CoV-2 GZ69 has shown that this strain differs from the early AP66 variant in 9 nucleotide positions (C2939T; C3828T; G21784T; T21846C; T24631C; G28881A; G28882A; G28883C; G29810T) which lead to 6 non-synonymous substitutions spanning on ORF1ab (P892S; S1188L), S (K74N; I95T) and N (R203K, G204R) proteins. CONCLUSIONS Identification of the peculiar SARS-CoV-2 GZ69 strain in the late Italian epidemic highlights the need to better characterize viral variants circulating among asymptomatic or paucisymptomatic individuals. The current approach could unravel the ways for future studies aimed at analyzing the selection process which favours viral mutations in the human host.
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Affiliation(s)
- Francesca Caccuri
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
| | - Alberto Zani
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
| | - Serena Messali
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
| | - Marta Giovanetti
- Flavivirus Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio De Janeiro, Brazil
| | - Antonella Bugatti
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
| | - Giovanni Campisi
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
| | - Federica Filippini
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
| | - Erika Scaltriti
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Simona Fiorentini
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
| | - Arnaldo Caruso
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy.
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13
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Funk CD, Laferrière C, Ardakani A. A Snapshot of the Global Race for Vaccines Targeting SARS-CoV-2 and the COVID-19 Pandemic. Front Pharmacol 2020; 11:937. [PMID: 32636754 PMCID: PMC7317023 DOI: 10.3389/fphar.2020.00937] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 06/09/2020] [Indexed: 01/08/2023] Open
Abstract
A novel coronavirus SARS-CoV-2 causing Coronavirus disease 2019 (COVID-19) has entered the human population and has spread rapidly around the world in the first half of 2020 causing a global pandemic. The virus uses its spike glycoprotein receptor-binding domain to interact with host cell angiotensin-converting enzyme 2 (ACE2) sites to initiate a cascade of events that culminate in severe acute respiratory syndrome in some individuals. In efforts to curtail viral spread, authorities initiated far-reaching lockdowns that have disrupted global economies. The scientific and medical communities are mounting serious efforts to limit this pandemic and subsequent waves of viral spread by developing preventative vaccines and repurposing existing drugs as potential therapies. In this review, we focus on the latest developments in COVID-19 vaccine development, including results of the first Phase I clinical trials and describe a number of the early candidates that are emerging in the field. We seek to provide a balanced coverage of the seven main platforms used in vaccine development that will lead to a desired target product profile for the "ideal" vaccine. Using tales of past vaccine discovery efforts that have taken many years or that have failed, we temper over exuberant enthusiasm with cautious optimism that the global medical community will reach the elusive target to treat COVID-19 and end the pandemic.
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Affiliation(s)
- Colin D. Funk
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Craig Laferrière
- Scientific Research Division, Novateur Ventures Inc., Vancouver, BC, Canada
| | - Ali Ardakani
- Scientific Research Division, Novateur Ventures Inc., Vancouver, BC, Canada
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