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Postans M, Pacchiarini N, Song J, Cottrell S, Williams C, Beazer A, Moore C, Connor TR, Williams C. Evaluating the risk of SARS-CoV-2 reinfection with the Omicron or Delta variant in Wales, UK. PLoS One 2024; 19:e0309645. [PMID: 39240934 PMCID: PMC11379141 DOI: 10.1371/journal.pone.0309645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 08/16/2024] [Indexed: 09/08/2024] Open
Abstract
Recent studies suggest an increased risk of reinfection with the SARS-CoV-2 Omicron variant compared with previous variants, potentially due to an increased ability to escape immunity specific to older variants, high antigenic divergence of Omicron from earlier virus variants as well as its altered cell entry pathway. The present study sought to investigate epidemiological evidence for differential SARS-CoV-2 reinfection intervals and incidence rates for the Delta versus Omicron variants within Wales. Reinfections in Wales up to February 2022 were defined using genotyping and whole genome sequencing. The median inter-infection intervals for Delta and Omicron were 226 and 192 days, respectively. An incidence rate ratio of 2.17 for reinfection with Omicron compared to Delta was estimated using a conditional Poisson model, which accounted for several factors including sample collection date, age group, area of residence, vaccination and travel status. These findings are consistent with an increased risk of reinfection with the Omicron variant, and highlight the value of monitoring emerging variants that have the potential for causing further waves of cases.
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Affiliation(s)
- Mark Postans
- Communicable Disease Surveillance Centre (CDSC), Public Health Wales, Cardiff, Wales, United Kingdom
| | - Nicole Pacchiarini
- Communicable Disease Surveillance Centre (CDSC), Public Health Wales, Cardiff, Wales, United Kingdom
| | - Jiao Song
- Communicable Disease Surveillance Centre (CDSC), Public Health Wales, Cardiff, Wales, United Kingdom
| | - Simon Cottrell
- Communicable Disease Surveillance Centre (CDSC), Public Health Wales, Cardiff, Wales, United Kingdom
| | - Catie Williams
- Pathogen Genomics Unit, Public Health Wales, Cardiff, Wales, United Kingdom
| | - Andrew Beazer
- Pathogen Genomics Unit, Public Health Wales, Cardiff, Wales, United Kingdom
| | - Catherine Moore
- Wales Specialist Virology Centre, Microbiology, Public Health Wales, Cardiff, Wales, United Kingdom
| | - Thomas R Connor
- Pathogen Genomics Unit, Public Health Wales, Cardiff, Wales, United Kingdom
- Cardiff University School of Biosciences, Cardiff University, Wales, United Kingdom
| | - Christopher Williams
- Communicable Disease Surveillance Centre (CDSC), Public Health Wales, Cardiff, Wales, United Kingdom
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2
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Maen A, Gok Yavuz B, Mohamed YI, Esmail A, Lu J, Mohamed A, Azmi AS, Kaseb M, Kasseb O, Li D, Gocio M, Kocak M, Selim A, Ma Q, Kaseb AO. Individual ingredients of NP-101 (Thymoquinone formula) inhibit SARS-CoV-2 pseudovirus infection. Front Pharmacol 2024; 15:1291212. [PMID: 38379905 PMCID: PMC10876831 DOI: 10.3389/fphar.2024.1291212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/15/2024] [Indexed: 02/22/2024] Open
Abstract
Thymoquinone TQ, an active ingredient of Nigella Sativa, has been shown to inhibit COVID-19 symptoms in clinical trials. Thymoquinone Formulation (TQF or NP-101) is developed as a novel enteric-coated medication derivative from Nigella Sativa. TQF consists of TQ with a favorable concentration and fatty acids, including palmitic, oleic, and linoleic acids. In this study, we aimed to investigate the roles of individual ingredients of TQF on infection of SARS-CoV-2 variants in-vitro, by utilizing Murine Leukemia Virus (MLV) based pseudovirus particles. We demonstrated that NP-101, TQ, and other individual ingredients, including oleic, linoleic, and palmitic acids inhibited SARS-CoV-2 infection in the MLV-based pseudovirus model. A large, randomized phase 2 study of NP-101 is planned in outpatient COVID-19 patients.
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Affiliation(s)
- Abdelrahim Maen
- Section of GI Oncology, Houston Methodist Neal Cancer Center, Houston, TX, United States
- Weill Cornell Medical College, New York, NY, United States
- Cockrell Center for Advanced Therapeutic Phase I Program, Houston Methodist Research Institute, Houston, TX, United States
| | - Betul Gok Yavuz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Yehia I. Mohamed
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Abdullah Esmail
- Section of GI Oncology, Houston Methodist Neal Cancer Center, Houston, TX, United States
| | - Jianming Lu
- Codex BioSolutions Inc., Rockville, MD, United States
| | - Amr Mohamed
- Seidman Cancer Center, Case Western University, Multidisciplinary NET Treatment, Cleveland, OH, United States
| | - Asfar S. Azmi
- School of Medicine, Wayne State University, Detroit, MI, United States
| | - Mohamed Kaseb
- Novatek Pharmaceuticals, Inc., Houston, TX, United States
| | - Osama Kasseb
- Novatek Pharmaceuticals, Inc., Houston, TX, United States
| | - Dan Li
- Department of Hematopoietic Biology and Malignancy, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Michelle Gocio
- Novatek Pharmaceuticals, Inc., Houston, TX, United States
| | - Mehmet Kocak
- Department of Biostatistics and Medical Informatics, International School of Medicine, Istanbul Medipol University, Istanbul, Türkiye
| | - Abdelhafez Selim
- Philadelphia College of Osteopathic Medicine (PCOM), Philadelphia, PA, United States
| | - Qing Ma
- Department of Hematopoietic Biology and Malignancy, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ahmed O. Kaseb
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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Scheuermann SE, Goff K, Rowe LA, Beddingfield BJ, Maness NJ. Real-Time Analysis of SARS-CoV-2-Induced Cytolysis Reveals Distinct Variant-Specific Replication Profiles. Viruses 2023; 15:1937. [PMID: 37766343 PMCID: PMC10537736 DOI: 10.3390/v15091937] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/31/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
The ability of each new SARS-CoV-2 variant to evade host humoral immunity is the focus of intense research. Each variant may also harbor unique replication capabilities relevant for disease and transmission. Here, we demonstrate a new approach to assessing viral replication kinetics using real-time cell analysis (RTCA). Virus-induced cell death is measured in real time as changes in electrical impedance through cell monolayers while images are acquired at defined intervals via an onboard microscope and camera. Using this system, we quantified replication kinetics of five clinically important viral variants: WA1/2020 (ancestral), Delta, and Omicron subvariants BA.1, BA.4, and BA.5. Multiple measures proved useful in variant replication comparisons, including the elapsed time to, and the slope at, the maximum rate of cell death. Important findings include significantly weaker replication kinetics of BA.1 by all measures, while BA.5 harbored replication kinetics at or near ancestral levels, suggesting evolution to regain replicative capacity, and both an altered profile of cell killing and enhanced fusogenicity of the Delta variant. Together, these data show that RTCA is a robust method to assess replicative capacity of any given SARS-CoV-2 variant rapidly and quantitatively, which may be useful in assessment of newly emerging variants.
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Affiliation(s)
- Sarah E. Scheuermann
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA; (S.E.S.); (K.G.); (L.A.R.)
| | - Kelly Goff
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA; (S.E.S.); (K.G.); (L.A.R.)
| | - Lori A. Rowe
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA; (S.E.S.); (K.G.); (L.A.R.)
| | - Brandon J. Beddingfield
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA; (S.E.S.); (K.G.); (L.A.R.)
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Nicholas J. Maness
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA; (S.E.S.); (K.G.); (L.A.R.)
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
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4
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Sobkowiak B, Haghmaram P, Prystajecky N, Zlosnik JEA, Tyson J, Hoang LMN, Colijn C. The utility of SARS-CoV-2 genomic data for informative clustering under different epidemiological scenarios and sampling. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105484. [PMID: 37531976 DOI: 10.1016/j.meegid.2023.105484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/25/2023] [Accepted: 07/30/2023] [Indexed: 08/04/2023]
Abstract
OBJECTIVES Clustering pathogen sequence data is a common practice in epidemiology to gain insights into the genetic diversity and evolutionary relationships among pathogens. We can find groups of cases with a shared transmission history and common origin, as well as identifying transmission hotspots. Motivated by the experience of clustering SARS-CoV-2 cases using whole genome sequence data during the COVID-19 pandemic to aid with public health investigation, we investigated how differences in epidemiology and sampling can influence the composition of clusters that are identified. METHODS We performed genomic clustering on simulated SARS-CoV-2 outbreaks produced with different transmission rates and levels of genomic diversity, along with varying the proportion of cases sampled. RESULTS In single outbreaks with a low transmission rate, decreasing the sampling fraction resulted in multiple, separate clusters being identified where intermediate cases in transmission chains are missed. Outbreaks simulated with a high transmission rate were more robust to changes in the sampling fraction and largely resulted in a single cluster that included all sampled outbreak cases. When considering multiple outbreaks in a sampled jurisdiction seeded by different introductions, low genomic diversity between introduced cases caused outbreaks to be merged into large clusters. If the transmission and sampling fraction, and diversity between introductions was low, a combination of the spurious break-up of outbreaks and the linking of closely related cases in different outbreaks resulted in clusters that may appear informative, but these did not reflect the true underlying population structure. Conversely, genomic clusters matched the true population structure when there was relatively high diversity between introductions and a high transmission rate. CONCLUSION Differences in epidemiology and sampling can impact our ability to identify genomic clusters that describe the underlying population structure. These findings can help to guide recommendations for the use of pathogen clustering in public health investigations.
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Affiliation(s)
| | - Pouya Haghmaram
- Department of Mathematics, Simon Fraser University, Burnaby, Canada
| | - Natalie Prystajecky
- BC Centre for Disease Control Public Health Laboratory, BC Centre for Disease Control, Vancouver, Canada; Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Canada
| | - James E A Zlosnik
- BC Centre for Disease Control Public Health Laboratory, BC Centre for Disease Control, Vancouver, Canada
| | - John Tyson
- BC Centre for Disease Control Public Health Laboratory, BC Centre for Disease Control, Vancouver, Canada
| | - Linda M N Hoang
- BC Centre for Disease Control Public Health Laboratory, BC Centre for Disease Control, Vancouver, Canada; Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Canada
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, Canada
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Gupta A, Basu R, Bashyam MD. Assessing the evolution of SARS-CoV-2 lineages and the dynamic associations between nucleotide variations. Access Microbiol 2023; 5:acmi000513.v3. [PMID: 37601437 PMCID: PMC10436015 DOI: 10.1099/acmi.0.000513.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 02/20/2023] [Indexed: 08/22/2023] Open
Abstract
Despite seminal advances towards understanding the infection mechanism of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), it continues to cause significant morbidity and mortality worldwide. Though mass immunization programmes have been implemented in several countries, the viral transmission cycle has shown a continuous progression in the form of multiple waves. A constant change in the frequencies of dominant viral lineages, arising from the accumulation of nucleotide variations (NVs) through favourable selection, is understandably expected to be a major determinant of disease severity and possible vaccine escape. Indeed, worldwide efforts have been initiated to identify specific virus lineage(s) and/or NVs that may cause a severe clinical presentation or facilitate vaccination breakthrough. Since host genetics is expected to play a major role in shaping virus evolution, it is imperative to study the role of genome-wide SARS-CoV-2 NVs across various populations. In the current study, we analysed the whole genome sequence of 3543 SARS-CoV-2-infected samples obtained from the state of Telangana, India (including 210 from our previous study), collected over an extended period from April 2020 to October 2021. We present a unique perspective on the evolution of prevalent virus lineages and NVs during this period. We also highlight the presence of specific NVs likely to be associated favourably with samples classified as vaccination breakthroughs. Finally, we report genome-wide intra-host variations at novel genomic positions. The results presented here provide critical insights into virus evolution over an extended period and pave the way to rigorously investigate the role of specific NVs in vaccination breakthroughs.
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Affiliation(s)
- Asmita Gupta
- Laboratory of Molecular Oncology, Centre of DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Reelina Basu
- Laboratory of Molecular Oncology, Centre of DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Murali Dharan Bashyam
- Laboratory of Molecular Oncology, Centre of DNA Fingerprinting and Diagnostics, Hyderabad, India
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6
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Tolbert WD, Chen Y, Sun L, Benlarbi M, Ding S, Manickam R, Pangaro E, Nguyen DN, Gottumukkala S, Côté M, Gonzalez FJ, Finzi A, Tehrani ZR, Sajadi MM, Pazgier M. The molecular basis of the neutralization breadth of the RBD-specific antibody CoV11. Front Immunol 2023; 14:1178355. [PMID: 37334379 PMCID: PMC10272436 DOI: 10.3389/fimmu.2023.1178355] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/16/2023] [Indexed: 06/20/2023] Open
Abstract
SARS-CoV-2, the virus behind the COVID-19 pandemic, has changed over time to the extent that the current virus is substantially different from what originally led to the pandemic in 2019-2020. Viral variants have modified the severity and transmissibility of the disease and continue do so. How much of this change is due to viral fitness versus a response to immune pressure is hard to define. One class of antibodies that continues to afford some level of protection from emerging variants are those that closely overlap the binding site for angiotensin-converting enzyme 2 (ACE2) on the receptor binding domain (RBD). Some members of this class that were identified early in the course of the pandemic arose from the VH 3-53 germline gene (IGHV3-53*01) and had short heavy chain complementarity-determining region 3s (CDR H3s). Here, we describe the molecular basis of the SARS-CoV-2 RBD recognition by the anti-RBD monoclonal antibody CoV11 isolated early in the COVID-19 pandemic and show how its unique mode of binding the RBD determines its neutralization breadth. CoV11 utilizes a heavy chain VH 3-53 and a light chain VK 3-20 germline sequence to bind to the RBD. Two of CoV11's four heavy chain changes from the VH 3-53 germline sequence, T h r F W R H 1 28 to Ile and S e r C D R H 1 31 to Arg, and some unique features in its CDR H3 increase its affinity to the RBD, while the four light chain changes from the VK 3-20 germline sequence sit outside of the RBD binding site. Antibodies of this type can retain significant affinity and neutralization potency against variants of concern (VOCs) that have diverged significantly from original virus lineage such as the prevalent omicron variant. We also discuss the mechanism by which VH 3-53 encoded antibodies recognize spike antigen and show how minimal changes to their sequence, their choice of light chain, and their mode of binding influence their affinity and impact their neutralization breadth.
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Affiliation(s)
- William D. Tolbert
- Infectious Disease Division, Department of Medicine of Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Yaozong Chen
- Infectious Disease Division, Department of Medicine of Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Lulu Sun
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Mehdi Benlarbi
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Shilei Ding
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada
| | - Rohini Manickam
- Infectious Disease Division, Department of Medicine of Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Emily Pangaro
- Infectious Disease Division, Department of Medicine of Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Dung N. Nguyen
- Infectious Disease Division, Department of Medicine of Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Suneetha Gottumukkala
- Infectious Disease Division, Department of Medicine of Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology, and Centre for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, Canada
| | - Frank J. Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Andrés Finzi
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Zahra R. Tehrani
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Mohammad M. Sajadi
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Medicine, Baltimore Veterans Health Administration (VA) Medical Center, Baltimore, MD, United States
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine of Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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AlMalki FA, Albukhaty S, Alyamani AA, Khalaf MN, Thomas S. The relevant information about the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using the five-question approach (when, where, what, why, and how) and its impact on the environment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:61430-61454. [PMID: 35175517 PMCID: PMC8852932 DOI: 10.1007/s11356-022-18868-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 01/21/2022] [Indexed: 05/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is regarded as a threat because it spreads quickly across the world without requiring a passport or establishing an identity. This tiny virus has wreaked havoc on people's lives, killed people, and created psychological problems all over the world. The viral spike protein (S) significantly contributes to host cell entry, and mutations associated with it, particularly in the receptor-binding protein (RBD), either facilitate the escape of virus from neutralizing antibodies or enhance its transmission by increasing the affinity for cell entry receptor, angiotensin-converting enzyme 2 (ACE2). The initial variants identified in Brazil, South Africa, and the UK have spread to various countries. On the other hand, new variants are being detected in India and the USA. The viral genome and proteome were applied for molecular detection techniques, and nanotechnology particles and materials were utilized in protection and prevention strategies. Consequently, the SARS-CoV-2 pandemic has resulted in extraordinary scientific community efforts to develop detection methods, diagnosis tools, and effective antiviral drugs and vaccines, where prevailing academic, governmental, and industrial institutions and organizations continue to engage themselves in large-scale screening of existing drugs, both in vitro and in vivo. In addition, COVID-19 pointed on the possible solutions for the environmental pollution globe problem. Therefore, this review aims to address SARS-CoV-2, its transmission, where it can be found, why it is severe in some people, how it can be stopped, its diagnosis and detection techniques, and its relationship with the environment.
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Affiliation(s)
- Faizah A AlMalki
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Kingdom of Saudi Arabia.
| | - Salim Albukhaty
- Deptartment of Chemistry, College of Science, University of Misan, Maysan, 62001, Iraq
| | - Amal A Alyamani
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Kingdom of Saudi Arabia
| | - Moayad N Khalaf
- Deptartment of Chemistry, College of Science, University of Basrah, Basrah, Iraq
| | - Sabu Thomas
- Centre for Nanoscience and Nanotechnology, Mahatma Gandhi University, Kottayam, Kerala, 686 560, India
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Bakkas J, Hanine M, Chekry A, Gounane S, de la Torre Díez I, Lipari V, López NMM, Ashraf I. SARSMutOnto: An Ontology for SARS-CoV-2 Lineages and Mutations. Viruses 2023; 15:v15020505. [PMID: 36851719 PMCID: PMC9967353 DOI: 10.3390/v15020505] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/04/2023] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
Mutations allow viruses to continuously evolve by changing their genetic code to adapt to the hosts they infect. It is an adaptive and evolutionary mechanism that helps viruses acquire characteristics favoring their survival and propagation. The COVID-19 pandemic declared by the WHO in March 2020 is caused by the SARS-CoV-2 virus. The non-stop adaptive mutations of this virus and the emergence of several variants over time with characteristics favoring their spread constitute one of the biggest obstacles that researchers face in controlling this pandemic. Understanding the mutation mechanism allows for the adoption of anticipatory measures and the proposal of strategies to control its propagation. In this study, we focus on the mutations of this virus, and we propose the SARSMutOnto ontology to model SARS-CoV-2 mutations reported by Pango researchers. A detailed description is given for each mutation. The genes where the mutations occur and the genomic structure of this virus are also included. The sub-lineages and the recombinant sub-lineages resulting from these mutations are additionally represented while maintaining their hierarchy. We developed a Python-based tool to automatically generate this ontology from various published Pango source files. At the end of this paper, we provide some examples of SPARQL queries that can be used to exploit this ontology. SARSMutOnto might become a 'wet bench' machine learning tool for predicting likely future mutations based on previous mutations.
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Affiliation(s)
- Jamal Bakkas
- LAPSSII Laboratory, Graduate School of Technology, Cadi Ayyad University, Safi 46000, Morocco
| | - Mohamed Hanine
- Department of Telecommunications, Networks, and Informatics, LTI Laboratory, ENSA, Chouaib Doukkali University, Eljadida 24000, Morocco
| | - Abderrahman Chekry
- LAPSSII Laboratory, Graduate School of Technology, Cadi Ayyad University, Safi 46000, Morocco
| | - Said Gounane
- MIMSC Laboratory, Graduate School of Technology, Cadi Ayyad University, Essaouira 44000, Morocco
| | - Isabel de la Torre Díez
- Department of Signal Theory and Communications and Telematic Engineering, University of Valladolid, Paseo de Belén, 15, 47011 Valladolid, Spain
| | - Vivian Lipari
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, Isabel Torres 21, 39011 Santander, Spain
- Department of Project Management, Universidad Internacional Iberoamericana Campeche, Mexico City 24560, Mexico
- Fundación Universitaria Internacional de Colombia Bogotá, Bogotá 11001, Colombia
| | - Nohora Milena Martínez López
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, Isabel Torres 21, 39011 Santander, Spain
- Research Group on Foods, Nutritional Biochemistry and Health Universidad Internacional Iberoamericana, Arecibo, PR 00613, USA
- Research Group on Foods, Nutritional Biochemistry and Health Universidade Internacional do Cuanza, Cuito EN250, Angola
| | - Imran Ashraf
- Department of Information and Communication Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
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Vukovikj M, Boshevska G, Janchevska E, Buzharova T, Preshova A, Simova M, Peshnacka A, Kocinski D, Kuzmanovska G, Memeti S, Gjorgoski I. In-depth genetic characterization of the SARS-CoV-2 pandemic in a two-year frame in North Macedonia using second and third generation sequencing technologies. FRONTIERS IN VIROLOGY 2023. [DOI: 10.3389/fviro.2022.1064882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a persistent negative impact on both the public health and the global economy. To comprehend the origin, transmission routes and discover the mutations that alter the virus’s transmissibility and pathogenicity, full-length SARS-CoV-2 genomes have to be molecularly characterized. Focusing on a two-year time frame (2020-2021), we provide an in-depth virologic and epidemiological overview of the SARS-CoV-2 pandemic in the Republic of North Macedonia by assessing the frequency and distribution of the circulating SARS-CoV-2 variants. Using genetic characterization and phylogenetic analysis we shed light on the molecular evolution of the virus as well as test for a possible connection between specific SARS-CoV-2 haplotypes and the severity of the clinical symptoms. Our results show that one fifth (21.51%) of the tested respiratory samples for SARS-CoV-2 were positive. A noticeable trend in the incidence and severity of the COVID-19 infections was observed in the 60+ age group between males and females. Of the total number of positive cases, the highest incidence of SARS-CoV-2 was noticed in 60+ males (4,170.4/100,000), with a statistically significant (0,0001) difference between the two sexes. Additionally, a 1.8x increase in male mortality and consequentially significantly higher number of death cases was observed compared to females of the same age group (0.001). A total of 327 samples were sequenced in the period March 2020 - August 2021, showing the temporal distribution of SARS-CoV-2 variants circulating in North Macedonia. The phylogenetic analysis showed that most of the viral genomes were closely related and clustered in four distinctive lineages, B.1, B.1.1.7, B.1.351 and B.1.617.2. A statistically significant difference was observed in the 2C_1 haplotype (p=0.0013), where 10.5% of the patients were hospitalized due to severe clinical condition. By employing genetic sequencing, coupled with epidemiological investigations, we investigated viral distribution patterns, identified emerging variants and detected vaccine breakthrough infections. The present work is the first molecular study giving a comprehensive overview of the genetic landscape of circulating SARS-CoV-2 viruses in North Macedonia in a period of two years.
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10
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Yakoubi A, Dhafer CEB. Advanced Plasmonic Nanoparticle-Based Techniques for the Prevention, Detection, and Treatment of Current COVID-19. PLASMONICS (NORWELL, MASS.) 2022; 18:311-347. [PMID: 36588744 PMCID: PMC9786532 DOI: 10.1007/s11468-022-01754-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/20/2022] [Indexed: 06/16/2023]
Abstract
Coronavirus is an ongoing global pandemic caused by severe acute respiratory syndrome coronavirus 2. Coronavirus disease 2019 known as COVID-19 is the worst pandemic since World War II. The outbreak of COVID-19 had a significant repercussion on the health, economy, politics, and environment, making coronavirus-related issues more complicated and becoming one of the most challenging pandemics of the last century with deadly outcomes and a high rate of the reproduction number. There are thousands of different types - or variants - of COVID circulating across the world. Viruses mutate all the time; it emphasizes the critical need for the designing of efficient vaccines to prevent virus infection, early and fast diagnosis, and effective antiviral and protective therapeutics. In this regard, the use of nanotechnology offers new opportunities for the development of novel strategies in terms of prevention, diagnosis, and treatment of COVID-19. This review presents an outline of the platforms developed using plasmonic nanoparticles in the detection, treatment, and prevention of SARS-CoV-2. We select the best strategies in each of these approaches. The properties of metallic plasmon NPs and their relevance in the development of novel point-of-care diagnosis approaches for COVID-19 are highlighted. Also, we discuss the current challenges and the future perspectives looking towards the clinical translation and the commercial aspects of nanotechnology and plasmonic NP-based diagnostic tools and therapy to fight COVID-19 pandemic. The article could be of significance for researchers dedicated to developing suitable plasmonic detection tools and therapy approaches for COVID-19 viruses and future pandemics.
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Affiliation(s)
- Afef Yakoubi
- Laboratory of Hetero-organic Compounds and Nanostructured Materials, Chemistry Department, Faculty of Sciences Bizerte, University of Carthage, LR 18 ES11, 7021 Bizerte, Tunisia
| | - Cyrine El Baher Dhafer
- Chemistry Department College of Science, Jouf University, P.O Box: 2014, Sakaka, Saudi Arabia
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11
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Dhawan M, Sharma A, Priyanka, Thakur N, Rajkhowa TK, Choudhary OP. Delta variant (B.1.617.2) of SARS-CoV-2: Mutations, impact, challenges and possible solutions. Hum Vaccin Immunother 2022; 18:2068883. [PMID: 35507895 PMCID: PMC9359381 DOI: 10.1080/21645515.2022.2068883] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/04/2022] [Accepted: 04/18/2022] [Indexed: 12/24/2022] Open
Abstract
Since commencement of COVID-19 pandemic, several SARS-CoV-2 variants have emerged amid containment efforts via vaccination. The Delta variant (B.1.617.2), discovered in October 2020, was designated as a VOC by the WHO on May 11, 2021. The enhanced transmissibility of Delta variant has been associated with critical mutations such as D614G, L452R, P681R, and T478K in the S-protein. The increased affinity of the S-protein and ACE2 has been postulated as a key reason for decreased vaccine efficacy. As per evidence, the Delta variant possesses increased transmissibility and decreased vaccine efficacy compared to other VOCs like Alpha and Beta. This has led to concerns regarding the acquisition of novel mutations in the Delta variant and outbreaks in vulnerable communities, including vaccinated people. In this mini-review of Delta variant, we have explained its evolution and characteristics, the impact of spike mutations on infectivity and immune evasion, and measures to combat future outbreaks.
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Affiliation(s)
- Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana, India
- Trafford College, Altrincham, Manchester, UK
| | - Abhilasha Sharma
- Department of Life Science, University School of Sciences, Gujarat University, Ahmedabad, India
| | - Priyanka
- Independent Researcher, 07, Type IV Quarter, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, Mizoram, India
| | - Nanamika Thakur
- Department of Medical Lab Technology, Faculty of Allied and Healthcare Sciences, GNA University, Phagwara, Punjab, India
| | - Tridib Kumar Rajkhowa
- Department of Veterinary Pathology, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, Mizoram, India
| | - Om Prakash Choudhary
- Department of Veterinary Anatomy and Histology, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, Mizoram, India
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Li H, Arcalas C, Song J, Rahmati M, Park S, Koyanagi A, Lee SW, Yon DK, Shin JI, Smith L. Genetics, structure, transmission, epidemiology, immune response, and vaccine efficacies of the SARS‐CoV‐2 Delta variant: A comprehensive review. Rev Med Virol 2022; 33:e2408. [PMID: 36420676 DOI: 10.1002/rmv.2408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 10/29/2022] [Accepted: 11/02/2022] [Indexed: 11/25/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant (B.1.617.2) was the predominant variant behind the surges of COVID-19 in the United States, Europe, and India in the second half of 2021. The information available regarding the defining mutations and their effects on the structure, transmission, and vaccine efficacy of SARS-CoV-2 is constantly evolving. With waning vaccine immunity and relaxation of social distancing policies across the globe driving the increased spread of the Delta variant, there is a great need for a resource aggregating the most recent information for clinicians and researchers concerning the Delta variant. Accordingly, this narrative review comprehensively reviews the genetics, structure, epidemiology, clinical course, and vaccine efficacy of the Delta variant. Comparison with the omicron variant is also discussed. The Delta variant is defined by 15 mutations in the Spike protein, most of which increase affinity for the ACE-2 receptor or enhance immune escape. The Delta variant causes similar symptoms to prototypical COVID-19, but it is more likely to be severe, with a greater inflammatory phenotype and viral load. The reproduction number is estimated to be approximately twice the prototypical strains present during the early pandemic, and numerous breakthrough infections have been reported. Despite studies demonstrating breakthrough infection and reduced antibody neutralisation, full vaccination effectively reduces the likelihood of severe illness and hospitalisation.
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Affiliation(s)
- Han Li
- University of Florida College of Medicine Gainesville Florida USA
| | | | - Junmin Song
- Keimyung University School of Medicine Daegu Republic of Korea
| | - Masoud Rahmati
- Department of Physical Education and Sport Sciences Faculty of Literature and Human Sciences Lorestan University Khoramabad Iran
| | - Seoyeon Park
- Yonsei University College of Medicine Seoul Republic of Korea
| | - Ai Koyanagi
- Parc Sanitari Sant Joan de Deu/CIBERSAM Fundacio Sant Joan de Deu Universitat de Barcelona Sant Boi de Llobregat, Barcelona Spain
- ICREA (Catalan Institution for Research and Advanced Studies) Barcelona Spain
| | - Seung Won Lee
- Department of Precision Medicine Sungkyunkwan University School of Medicine Suwon Republic of Korea
| | - Dong Keon Yon
- Center for Digital Health, Medical Science Research Institute Kyung Hee University College of Medicine Seoul Republic of Korea
- Department of Pediatrics Kyung Hee University Medical Center Kyung Hee University College of Medicine Seoul Republic of Korea
| | - Jae Il Shin
- Department of Pediatrics Yonsei University College of Medicine Seoul Republic of Korea
| | - Lee Smith
- Centre for Health, Performance, and Wellbeing Anglia Ruskin University Cambridge UK
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13
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Wang J, Ma T, Ding S, Xu K, Zhang M, Zhang Z, Dai Q, Tao S, Wang H, Cheng X, He M, Du X, Feng Z, Yang H, Wang R, Xie C, Xu Y, Liu L, Chen X, Li C, Wu W, Ye S, Yang S, Fan H, Zhou N, Ding J. Dynamic characteristics of a COVID-19 outbreak in Nanjing, Jiangsu province, China. Front Public Health 2022; 10:933075. [PMID: 36483256 PMCID: PMC9723226 DOI: 10.3389/fpubh.2022.933075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 09/21/2022] [Indexed: 12/13/2022] Open
Abstract
Objectives Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage B.1.617.2 (also named the Delta variant) was declared as a variant of concern by the World Health Organization (WHO). This study aimed to describe the outbreak that occurred in Nanjing city triggered by the Delta variant through the epidemiological parameters and to understand the evolving epidemiology of the Delta variant. Methods We collected the data of all COVID-19 cases during the outbreak from 20 July 2021 to 24 August 2021 and estimated the distribution of serial interval, basic and time-dependent reproduction numbers (R0 and Rt), and household secondary attack rate (SAR). We also analyzed the cycle threshold (Ct) values of infections. Results A total of 235 cases have been confirmed. The mean value of serial interval was estimated to be 4.79 days with the Weibull distribution. The R0 was 3.73 [95% confidence interval (CI), 2.66-5.15] as estimated by the exponential growth (EG) method. The Rt decreased from 4.36 on 20 July 2021 to below 1 on 1 August 2021 as estimated by the Bayesian approach. We estimated the household SAR as 27.35% (95% CI, 22.04-33.39%), and the median Ct value of open reading frame 1ab (ORF1ab) genes and nucleocapsid protein (N) genes as 25.25 [interquartile range (IQR), 20.53-29.50] and 23.85 (IQR, 18.70-28.70), respectively. Conclusions The Delta variant is more aggressive and transmissible than the original virus types, so continuous non-pharmaceutical interventions are still needed.
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Affiliation(s)
- Junjun Wang
- Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China,Chinese Field Epidemiology Training Program, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Tao Ma
- Department of Acute Infectious Diseases Control and Prevention, Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Songning Ding
- Department of Acute Infectious Diseases Control and Prevention, Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Ke Xu
- Department of Acute Infectious Diseases Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Min Zhang
- Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Zhong Zhang
- Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Qigang Dai
- Department of Acute Infectious Diseases Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Shilong Tao
- Jiangning District Center for Disease Control and Prevention, Nanjing, China
| | - Hengxue Wang
- Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Xiaoqing Cheng
- Chinese Field Epidemiology Training Program, Chinese Center for Disease Control and Prevention, Beijing, China,Department of Acute Infectious Diseases Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Min He
- Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Xuefei Du
- Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Zhi Feng
- Jiangning District Center for Disease Control and Prevention, Nanjing, China
| | - Huafeng Yang
- Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Rong Wang
- Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Chaoyong Xie
- Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Yuanyuan Xu
- Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Li Liu
- Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Xupeng Chen
- Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Chen Li
- Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Wen Wu
- Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Sheng Ye
- Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Sheng Yang
- Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Huafeng Fan
- Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Nan Zhou
- Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China,*Correspondence: Jie Ding
| | - Jie Ding
- Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China,Nan Zhou
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14
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Zaman K, Shete AM, Mishra SK, Kumar A, Reddy MM, Sahay RR, Yadav S, Majumdar T, Pandey AK, Dwivedi GR, Deval H, Singh R, Behera SP, Kumar N, Patil S, Kumar A, Dudhmal M, Joshi Y, Shukla A, Gawande P, Kavathekar A, Kumar N, Kumar V, Kumar K, Singh RS, Kumar M, Tiwari S, Verma A, Yadav PD, Kant R. Omicron BA.2 lineage predominance in severe acute respiratory syndrome coronavirus 2 positive cases during the third wave in North India. Front Med (Lausanne) 2022; 9:955930. [PMID: 36405589 PMCID: PMC9666497 DOI: 10.3389/fmed.2022.955930] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 10/03/2022] [Indexed: 01/25/2023] Open
Abstract
Background Recent studies on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reveal that Omicron variant BA.1 and sub-lineages have revived the concern over resistance to antiviral drugs and vaccine-induced immunity. The present study aims to analyze the clinical profile and genome characterization of the SARS-CoV-2 variant in eastern Uttar Pradesh (UP), North India. Methods Whole-genome sequencing (WGS) was conducted for 146 SARS-CoV-2 samples obtained from individuals who tested coronavirus disease 2019 (COVID-19) positive between the period of 1 January 2022 and 24 February 2022, from three districts of eastern UP. The details regarding clinical and hospitalized status were captured through telephonic interviews after obtaining verbal informed consent. A maximum-likelihood phylogenetic tree was created for evolutionary analysis using MEGA7. Results The mean age of study participants was 33.9 ± 13.1 years, with 73.5% accounting for male patients. Of the 98 cases contacted by telephone, 30 (30.6%) had a travel history (domestic/international), 16 (16.3%) reported having been infected with COVID-19 in past, 79 (80.6%) had symptoms, and seven had at least one comorbidity. Most of the sequences belonged to the Omicron variant, with BA.1 (6.2%), BA.1.1 (2.7%), BA.1.1.1 (0.7%), BA.1.1.7 (5.5%), BA.1.17.2 (0.7%), BA.1.18 (0.7%), BA.2 (30.8%), BA.2.10 (50.7%), BA.2.12 (0.7%), and B.1.617.2 (1.3%) lineages. BA.1 and BA.1.1 strains possess signature spike mutations S:A67V, S:T95I, S:R346K, S:S371L, S:G446S, S:G496S, S:T547K, S:N856K, and S:L981F, and BA.2 contains S:V213G, S:T376A, and S:D405N. Notably, ins214EPE (S1- N-Terminal domain) mutation was found in a significant number of Omicron BA.1 and sub-lineages. The overall Omicron BA.2 lineage was observed in 79.5% of women and 83.2% of men. Conclusion The current study showed a predominance of the Omicron BA.2 variant outcompeting the BA.1 over a period in eastern UP. Most of the cases had a breakthrough infection following the recommended two doses of vaccine with four in five cases being symptomatic. There is a need to further explore the immune evasion properties of the Omicron variant.
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Affiliation(s)
- Kamran Zaman
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Anita M Shete
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology Pune (ICMR-NIV Pune), Pune, India
| | - Shailendra Kumar Mishra
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Abhinendra Kumar
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology Pune (ICMR-NIV Pune), Pune, India
| | - Mahendra M Reddy
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Rima R Sahay
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology Pune (ICMR-NIV Pune), Pune, India
| | - Shailendra Yadav
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Triparna Majumdar
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology Pune (ICMR-NIV Pune), Pune, India
| | - Ashok K Pandey
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Gaurav Raj Dwivedi
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Hirawati Deval
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Rajeev Singh
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Sthita Pragnya Behera
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Niraj Kumar
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Savita Patil
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology Pune (ICMR-NIV Pune), Pune, India
| | - Ashish Kumar
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Manisha Dudhmal
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology Pune (ICMR-NIV Pune), Pune, India
| | - Yash Joshi
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology Pune (ICMR-NIV Pune), Pune, India
| | - Aishwarya Shukla
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Pranita Gawande
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology Pune (ICMR-NIV Pune), Pune, India
| | - Asif Kavathekar
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Nalin Kumar
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Vijay Kumar
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Kamlesh Kumar
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Ravi Shankar Singh
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Manoj Kumar
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Shashikant Tiwari
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
| | - Ajay Verma
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology Pune (ICMR-NIV Pune), Pune, India
| | - Pragya D Yadav
- Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology Pune (ICMR-NIV Pune), Pune, India
| | - Rajni Kant
- Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India
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Iyer P, Chino T, Ojcius DM. Infection of the oral cavity with SARS-CoV-2 variants: Scope of salivary diagnostics. FRONTIERS IN ORAL HEALTH 2022; 3:1001790. [PMID: 36389278 PMCID: PMC9659966 DOI: 10.3389/froh.2022.1001790] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 10/05/2022] [Indexed: 01/24/2023] Open
Abstract
Coronaviruses, including SARS-CoV-2, have caused pandemics in the past two decades. The most prevalent SARS-CoV-2 variants of concern can re-infect individuals who have been previously infected with other variants or had protection from vaccines targeting the original SARS-CoV-2 variant. Given the high risk of transmission of coronavirus via aerosols produced during dental procedures, it is important to understand the future risk of coronavirus infection for oral health professionals and to diagnose quickly early stages of outbreaks. Testing of saliva for coronavirus may be the least invasive and most convenient method for following the outbreak at the individual and community level. This review will describe strategies for diagnosis of coronavirus in saliva.
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Affiliation(s)
- Parvati Iyer
- Department of Diagnostic Sciences, University of the Pacific, Arthur Dugoni School of Dentistry, San Francisco, CA, United States
| | - Takahiro Chino
- Department of Biomedical Sciences, University of the Pacific Arthur A. Dugoni School of Dentistry, San Francisco, CA, United States
| | - David M. Ojcius
- Department of Biomedical Sciences, University of the Pacific Arthur A. Dugoni School of Dentistry, San Francisco, CA, United States
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Ao Z, Ouyang MJ, Olukitibi TA, Warner B, Vendramelli R, Truong T, Meilleur C, Zhang M, Kung S, Fowke KR, Kobasa D, Yao X. A Recombinant VSV-Based Bivalent Vaccine Effectively Protects against Both SARS-CoV-2 and Influenza A Virus Infection. J Virol 2022; 96:e0133722. [PMID: 36069551 PMCID: PMC9517730 DOI: 10.1128/jvi.01337-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 12/03/2022] Open
Abstract
COVID-19 and influenza are both highly contagious respiratory diseases that have been serious threats to global public health. It is necessary to develop a bivalent vaccine to control these two infectious diseases simultaneously. In this study, we generated three attenuated replicating recombinant vesicular stomatitis virus (rVSV)-based vaccine candidates against both SARS-CoV-2 and influenza viruses. These rVSV-based vaccines coexpress SARS-CoV-2 Delta spike protein (SP) bearing the C-terminal 17 amino acid (aa) deletion (SPΔC) and I742A point mutation, or the SPΔC with a deletion of S2 domain, or the RBD domain, and a tandem repeat harboring four copies of the highly conserved influenza M2 ectodomain (M2e) that fused with the Ebola glycoprotein DC-targeting/activation domain. Animal immunization studies have shown that these rVSV bivalent vaccines induced efficient humoral and cellular immune responses against both SARS-CoV-2 SP and influenza M2 protein, including high levels of neutralizing antibodies against SARS-CoV-2 Delta and other variant SP-pseudovirus infections. Importantly, immunization of the rVSV bivalent vaccines effectively protected hamsters or mice against the challenges of SARS-CoV-2 Delta variant and lethal H1N1 and H3N2 influenza viruses and significantly reduced respiratory viral loads. Overall, this study provides convincing evidence for the high efficacy of this bivalent vaccine platform to be used and/or easily adapted to produce new vaccines against new or reemerging SARS-CoV-2 variants and influenza A virus infections. IMPORTANCE Given that both COVID-19 and influenza are preferably transmitted through respiratory droplets during the same seasons, it is highly advantageous to develop a bivalent vaccine that could simultaneously protect against both COVID-19 and influenza. In this study, we generated the attenuated replicating recombinant vesicular stomatitis virus (rVSV)-based vaccine candidates that target both spike protein of SARS-Cov-2 Delta variant and the conserved influenza M2 domain. Importantly, these vaccine candidates effectively protected hamsters or mice against the challenges of SARS-CoV-2 Delta variant and lethal H1N1 and H3N2 influenza viruses and significantly reduced respiratory viral loads.
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Affiliation(s)
- Zhujun Ao
- Laboratory of Molecular Human Retrovirology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Maggie J. Ouyang
- Laboratory of Molecular Human Retrovirology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Titus A. Olukitibi
- Laboratory of Molecular Human Retrovirology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Bryce Warner
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Robert Vendramelli
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Thang Truong
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Courtney Meilleur
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Manli Zhang
- Department of Immunology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sam Kung
- Department of Immunology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Keith R. Fowke
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Darwyn Kobasa
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Xiaojian Yao
- Laboratory of Molecular Human Retrovirology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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17
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Sayeed MA, Ferdous J, Saha O, Islam S, Choudhury SD, Abedin J, Hassan MM, Islam A. Transmission Dynamics and Genomic Epidemiology of Emerging Variants of SARS-CoV-2 in Bangladesh. Trop Med Infect Dis 2022; 7:197. [PMID: 36006289 PMCID: PMC9414541 DOI: 10.3390/tropicalmed7080197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022] Open
Abstract
With the progression of the global SARS-CoV-2 pandemic, the new variants have become more infectious and continue spreading at a higher rate than pre-existing ones. Thus, we conducted a study to explore the epidemiology of emerging variants of SARS-CoV-2 that circulated in Bangladesh from December 2020 to September 2021, representing the 2nd and 3rd waves. We collected new cases and deaths per million daily data with the reproduction rate. We retrieved 928 SARS-CoV-2 sequences from GISAID and performed phylogenetic tree construction and mutation analysis. Case counts were lower initially at the end of 2020, during January-February and April-May 2021, whereas the death toll reached the highest value of 1.587 per million on the first week of August and then started to decline. All the variants (α, β, δ, η) were prevalent in the capital city, Dhaka, with dispersion to large cities, such as Sylhet and Chattogram. The B.1.1.25 lineage was prevalent during December 2020, but the B.1.617.2/δ variant was later followed by the B.1.351/β variant. The phylogeny revealed that the various strains found in Bangladesh could be from numerous countries. The intra-cluster and inter-cluster communication began in Bangladesh soon after the virus arrived. The prominent amino acid substitution was D614G from December 2020 to July 2021 (93.5 to 100%). From February-April, one of the VOC's important mutations, N501Y substitution, was also estimated at 51.8%, 76.1%, and 65.1% for the α, β and γ variants, respectively. The γ variant's unique mutation K417T was detected only at 1.8% in February. Another frequent mutation was P681R, a salient feature of the δ variant, detected in June (88.2%) and July (100%). Furthermore, only one γ variant was detected during the entire second and third wave, whereas no η variant was observed in this period. This rapid growth in the number of variants identified across Bangladesh shows virus adaptation and a lack of strict quarantine, prompting periodic genomic surveillance to foresee the spread of new variants, if any, and to take preventive measures as soon as possible.
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Affiliation(s)
- Md. Abu Sayeed
- EcoHealth Alliance New York, New York, NY 10018, USA
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh
| | - Jinnat Ferdous
- EcoHealth Alliance New York, New York, NY 10018, USA
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh
| | - Otun Saha
- Department of Microbiology, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Shariful Islam
- EcoHealth Alliance New York, New York, NY 10018, USA
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh
| | - Shusmita Dutta Choudhury
- EcoHealth Alliance New York, New York, NY 10018, USA
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh
| | - Josefina Abedin
- EcoHealth Alliance New York, New York, NY 10018, USA
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh
| | - Mohammad Mahmudul Hassan
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram 4225, Bangladesh
- Queensland Alliance for One Health Sciences, School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia
| | - Ariful Islam
- EcoHealth Alliance New York, New York, NY 10018, USA
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh
- Centre for Integrative Ecology, School of Life and Environmental Science, Deakin University, Melbourne, VIC 3216, Australia
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18
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Ochoa-Azze R, Chang-Monteagudo A, Climent-Ruiz Y, Macías-Abraham C, Valenzuela-Silva C, de Los Ángeles García-García M, Jerez-Barceló Y, Triana-Marrero Y, Ruiz-Villegas L, Dairon Rodríguez-Prieto L, Guerra-Chaviano PP, Sánchez-Ramírez B, Hernández-García T, Orosa-Vázquez I, Díaz-Hernández M, Chiodo F, Calcagno A, Ghisetti V, Rodríguez-Acosta M, Noa-Romero E, Enríquez-Puertas J, Ortega-León D, Valdivia-Álvarez I, Delahanty-Fernández A, Palenzuela-Díaz A, Rodríguez-Noda L, González-Mugica R, Valdés-Balbín Y, García-Rivera D, Verez-Bencomo V. Safety and immunogenicity of the FINLAY-FR-1A vaccine in COVID-19 convalescent participants: an open-label phase 2a and double-blind, randomised, placebo-controlled, phase 2b, seamless, clinical trial. THE LANCET. RESPIRATORY MEDICINE 2022; 10:785-795. [PMID: 35691295 PMCID: PMC9183216 DOI: 10.1016/s2213-2600(22)00100-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/15/2022] [Accepted: 03/15/2022] [Indexed: 12/26/2022]
Abstract
BACKGROUND A phase 1, clinical trial to evaluate FINLAY-FR-1A vaccine in COVID-19 convalescent individuals was completed. Here, we report results of the phase 2, clinical trial. METHODS We studied 450 convalescent participants with a history of asymptomatic, mild, or moderate COVID-19 at the National Institute of Hematology and Immunology and the National Centre for Sexual Education in Havana, Cuba. The study included adults aged 19-78 years who had recovered from COVID-19 and had had a negative PCR test at least 2 months before the initiation of the study. Phase 2 was done sequentially in two stages. The first stage to assess safety comprised an open, non-controlled phase 2a study in participants aged 60-78 years who received a single dose of the FINLAY-FR-1A vaccine (50 μg of recombinant dimeric receptor binding domain [RBD]). The second stage comprised the placebo-controlled, double-blind, phase 2b trial in participants aged 19-78 years, where participants were randomly assigned (4:1) into two groups: an experimental group vaccinated with a single dose of the FINLAY-FR-1A vaccine, and a control (placebo) group injected with vaccine excipient. The primary outcomes were safety, evaluated 28 days after vaccination by the occurrence of serious adverse events in all participants, and successful immune response, assessed by neutralising antibody ELISA, and defined as half-maximal surrogate virus neutralisation titres of 250 or more. Secondary endpoints included vaccine immunogenicity assessed by ELISA anti-RBD and live-virus neutralisation test. All randomly assigned participants were included in the safety analysis (safety population), and immunogenicity was evaluated in participants without study interruptions (per-protocol population). The trial is registered with the Cuban Public Registry of Clinical Trials, RPCEC00000366-En and WHO-ICTRP and is complete. FINDINGS From April 9, 2021, to April 17, 2021, 663 COVID-19 convalescent participants were enrolled in the study; 213 participants did not meet the selection criteria and 450 volunteers were recruited. 20 participants aged 60-78 years were included in the open, single-group, phase 2a study and 430 participants were randomly assigned to the experimental (n=344) or control groups (n=86) in the phase 2b study of participants aged 19-78 years. 19 (95%) of 20 phase 2a volunteers achieved a successful immune response after vaccination. No vaccine-associated serious adverse events were reported in the whole study population. Minor adverse events were found, the most common being pain at the injection site (105 [29%] of 364 in the intervention group; 13 [15%] of 86 in the placebo group). A successful immune response was found in 289 (81%) of 358 participants 28 days after vaccination. The vaccine elicited a greater than 31-times increase in anti-RBD-IgG antibodies compared with prevaccination rates, and the seroconversion rate was 302 (84%) of 358 on day 28 after vaccination; the geometric mean titres of live-virus neutralisation test increased from 15·4 (95% CI 10·3-23·2) to 400·3 (272·4-588·1) and high response was found against alpha, beta, and delta variants of concern. INTERPRETATION A single dose of the FINLAY-FR-1A vaccine against SARS-CoV-2 strengthened the pre-existing natural immunity, with excellent safety profile. FUNDING Cuba's Ministry of Science, Technology, and Environment.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Fabrizio Chiodo
- Finlay Vaccine Institute, Atabey, Playa, Havana, Cuba; Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Vrije Universiteit Amsterdam, Netherlands and Institute of Biomolecular Chemistry, National Research Council, Pozzuoli, Napoli, Italy
| | - Andrea Calcagno
- Unit of Infectious Diseases, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Valeria Ghisetti
- Laboratory of Microbiology and Virology, Amedeo di Savoia Hospital, ASL, Turin, Italy
| | | | - Enrique Noa-Romero
- Research Centre of Civil Defence, San José de las Lajas, Mayabeque, Cuba
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19
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Pondé RAA. Physicochemical effect of the N501Y, E484K/Q, K417N/T, L452R and T478K mutations on the SARS-CoV-2 spike protein RBD and its influence on agent fitness and on attributes developed by emerging variants of concern. Virology 2022; 572:44-54. [PMID: 35580380 PMCID: PMC9096574 DOI: 10.1016/j.virol.2022.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/26/2022] [Accepted: 05/06/2022] [Indexed: 01/17/2023]
Abstract
The spike protein comprises one of the main structural components of SARS-CoV-2 because it is directly involved in the infection process and viral transmission, and also because of its immunogenic properties, as an inducer of the protective antibodies production and as a vaccine component. The occurrence of mutations in this region or in other the virus genome regions, comprises a natural phenomenon in its evolution. However, they also occur due to the selective immune pressure, to which the agent is continuously subjected, especially in the spike protein immunodominant regions, such as the RBD. Mutations in the spike protein can change the virus' fitness, increasing its affinity for target cells, its transmissibility and its virulence. In addition, these mutations can giving it the potential ability to evade the protective antibodies action obtained from convalescent sera or vaccine origin, as well as those used in therapy, which may favor the virus expansion and compromise the infection control. Five mutations N501Y, E484K/Q, K417N/T, L452R and T478K, located in the spike protein RBD, have had a greater impact because they are associated with new attributes developed by the virus, which characterize the emerging variants of concern (VOCs) of SARS-Cov-2 identified so far. The occurrence of these mutations induces complex physicochemical effects that can alter the spike protein's structure and its function, which in turn, lead to changes in the agents' fitness. This manuscript discusses the attributes of VOCs associated with the physicochemical effects caused by the aforementioned mutations.
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Affiliation(s)
- R A A Pondé
- State Department of Health SES/Superintendence of Health Surveillance SUVISA/GO, Management of Epidemiological Surveillance-GVE/Coordination of Analysis and Research-CAP, Goiânia, Goiás, Brazil; Laboratory of Human Virology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil.
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20
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Hubler Z, Song X, Norris C, Jani M, Alouani D, Atchley M, Stempak L, Cherian S, Schmotzer C, Sadri N. High-Throughput Adaptable SARS-CoV-2 Screening for Rapid Identification of Dominant and Emerging Regional Variants. Am J Clin Pathol 2022; 157:927-935. [PMID: 34999740 PMCID: PMC8755384 DOI: 10.1093/ajcp/aqab212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 11/16/2021] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant strains can be associated with increased transmissibility, more severe disease, and reduced effectiveness of treatments. To improve the availability of regional variant surveillance, we describe a variant genotyping system that is rapid, accurate, adaptable, and able to detect new low-level variants built with existing hospital infrastructure. METHODS We used a tiered high-throughput SARS-CoV-2 screening program to characterize variants in a supraregional health system over 76 days. Combining targeted reverse transcription-polymerase chain reaction (RT-PCR) and selective sequencing, we screened SARS-CoV-2 reactive samples from all hospitals within our health care system for genotyping dominant and emerging variants. RESULTS The median turnaround for genotyping was 2 days using the high-throughput RT-PCR-based screen, allowing us to rapidly characterize the emerging Delta variant. In our population, the Delta variant is associated with a lower cycle threshold value, lower age at infection, and increased vaccine-breakthrough cases. Detection of low-level and potentially emerging variants highlights the utility of a tiered approach. CONCLUSIONS These findings underscore the need for fast, low-cost, high-throughput monitoring of regional viral sequences as the pandemic unfolds and the emergence of SARS-CoV-2 variants increases. Combining RT-PCR-based screening with selective sequencing allows for rapid genotyping of variants and dynamic system improvement.
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Affiliation(s)
- Zita Hubler
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Xiao Song
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Cameron Norris
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Mehul Jani
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - David Alouani
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Maureen Atchley
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Lisa Stempak
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Sarah Cherian
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Christine Schmotzer
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Navid Sadri
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
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21
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Rajpal VR, Sharma S, Kumar A, Vaishnavi S, Singh A, Sehgal D, Tiwari M, Goel S, Raina SN. Mapping of SARS-CoV-2 spike protein evolution during first and second waves of COVID-19 infections in India. Future Virol 2022. [PMID: 35747327 PMCID: PMC9203035 DOI: 10.2217/fvl-2021-0267] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 05/19/2022] [Indexed: 11/21/2022]
Abstract
Aim: The aim of this study was to investigate the SARS-CoV-2 spike protein evolution during the first and second wave of COVID-19 infections in India. Materials & Methods: Detailed mutation analysis was done in 763 samples taken from GISAID for the ten most affected Indian states between March 2020 to August 2021. Results: The study revealed 242 mutations corresponding to 207 sites. Fifty one novel mutations emerged during the assessment period, including many with higher transmissibility and immune evasion functions. Highest number of mutations per spike protein also rose from 5 (first wave) to 13 (second wave). Conclusion: The study identified mutation-rich and no mutation regions in the spike protein. The conserved spike regions can be useful for designing future diagnostics, vaccines and therapeutics.
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Affiliation(s)
- Vijay Rani Rajpal
- Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India
| | - Shashi Sharma
- Virology Division, Defence Research & Development Establishment, Gwalior, Madhya Pradesh, 474002, India
| | - Avinash Kumar
- Department of Botany, Vinoba Bhave University, Hazaribag, Jharkhand, 825319, India
| | - Samantha Vaishnavi
- Department of Botany, Central University of Jammu, Rahya Suchani (Bagla), Distt. Samba, Jammu and Kashmir, 181143, India
| | - Apekshita Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Sector 125, Noida, Uttar Pradesh, 201313, India
| | - Deepmala Sehgal
- International Maize & Wheat Improvement Center (CIMMYT) Carretera México-Veracruz Km. 45, El Batán, Texcoco, 56237, México
| | - Mughdha Tiwari
- ICMR-National Institute of Occupational Health (ICMR-NIOH), Meghaninagar, Ahmedabad, Gujarat, 380016, India
| | - Shailendra Goel
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Sector 125, Noida, Uttar Pradesh, 201313, India
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22
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Chakraborty C, Sharma AR, Bhattacharya M, Agoramoorthy G, Lee SS. A Paradigm Shift in the Combination Changes of SARS-CoV-2 Variants and Increased Spread of Delta Variant (B.1.617.2) across the World. Aging Dis 2022; 13:927-942. [PMID: 35656100 PMCID: PMC9116911 DOI: 10.14336/ad.2021.1117] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/17/2021] [Indexed: 12/13/2022] Open
Abstract
Since September 2020, the SARS-CoV-2 variants have gained their dominance worldwide, especially in Kenya, Italy, France, the UK, Turkey, Indonesia, India, Finland, Ireland, Singapore, Denmark, Germany, and Portugal. In this study, we developed a model on the frequency of delta variants across 28 countries (R2= 0.1497), displaying the inheritance of mutations during the generation of the delta variants with 123,526 haplotypes. The country-wise haplotype network showed the distribution of haplotypes in USA (10,174), Denmark (5,637), India (4,089), Germany (2,350), Netherlands (1,899), Sweden (1,791), Italy (1,720), France (1,293), Ireland (1,257), Belgium (1,207), Singapore (1,193), Portugal (1,184) and Spain (1,133). Our analysis shows the highest haplotype in Europe with 84% and the lowest in Australia with 0.00001%. A model of scatter plot was generated with a regression line which provided the estimated rate of mutation, including 24.048 substitutions yearly. Our study concluded that the high global prevalence of the delta variants is due to a high frequency of infectivity, supporting the paradigm shift of the viral variants.
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Affiliation(s)
- Chiranjib Chakraborty
- 1Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126, India
| | - Ashish Ranjan Sharma
- 2Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Gangwon-do, Korea
| | | | | | - Sang-Soo Lee
- 2Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Gangwon-do, Korea
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23
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Feng W, Xiang Y, Wu L, Chen Z, Li Q, Chen J, Guo Y, Xia D, Chen N, Zhang L, Zhu S, Zhao K. Nucleocapsid protein of SARS-CoV-2 is a potential target for developing new generation of vaccine. J Clin Lab Anal 2022; 36:e24479. [PMID: 35527696 PMCID: PMC9169192 DOI: 10.1002/jcla.24479] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 03/28/2022] [Accepted: 04/23/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND SARS-CoV-2 has spread worldwide causing more than 400 million people with virus infections since early 2020. Currently, the existing vaccines targeting the spike glycoprotein (S protein) of SARS-CoV-2 are facing great challenge from the infection of SARS-CoV-2 virus and its multiple S protein variants. Thus, we need to develop a new generation of vaccines to prevent infection of the SARS-CoV-2 variants. Compared with the S protein, the nucleocapsid protein (N protein) of SARS-CoV-2 is more conservative and less mutations, which also plays a vital role in viral infection. Therefore, the N protein may have the great potential for developing new vaccines. METHODS The N protein of SARS-CoV-2 was recombinantly expressed and purified in Escherichia coli. Western Blot and ELISA assays were used to demonstrate the immunoreactivity of the recombinant N protein with the serum of 22 COVID-19 patients. We investigated further the response of the specific serum antibodies and cytokine production in BALB/c mice immunized with recombinant N protein by Western Blot and ELISA. RESULTS The N protein had good immunoreactivity and the production of IgG antibody against N protein in COVID-19 patients was tightly correlated with disease severity. Furthermore, the N protein was used to immunize BALB/c mice to have elicited strong immune responses. Not only high levels of IgG antibody, but also cytokine-IFN-γ were produced in the N protein-immunized mice. Importantly, the N protein immunization induced a high level of IgM antibody produced in the mice. CONCLUSION SARS-CoV-2 N protein shows a great big bundle of potentiality for developing a new generation of vaccines in fighting infection of SARS-CoV-2 and its variants.
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Affiliation(s)
- Weixu Feng
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
| | - Yunru Xiang
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
| | - Lianpeng Wu
- Department of Laboratory MedicineThe Sixth People Hospital of WenzhouWenzhouChina
| | - Zhuo Chen
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
| | - Qingfeng Li
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
| | - Jun Chen
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
| | - Yanru Guo
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
| | - Dandan Xia
- Department of Laboratory MedicineThe Sixth People Hospital of WenzhouWenzhouChina
| | - Na Chen
- Department of Laboratory MedicineThe Sixth People Hospital of WenzhouWenzhouChina
| | - Lifang Zhang
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
| | - Shanli Zhu
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
| | - Kong‐Nan Zhao
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
- Department of Obstetrics and GynaecologyThe Second Affiliated Hospital and Yuyin Children Hospital of Wenzhou Medical UniversityWenzhouChina
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQueenslandAustralia
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24
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Plyusnin I, Truong Nguyen PT, Sironen T, Vapalahti O, Smura T, Kant R. ClusTRace, a bioinformatic pipeline for analyzing clusters in virus phylogenies. BMC Bioinformatics 2022; 23:196. [PMID: 35643449 PMCID: PMC9143711 DOI: 10.1186/s12859-022-04709-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/04/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND SARS-CoV-2 is the highly transmissible etiologic agent of coronavirus disease 2019 (COVID-19) and has become a global scientific and public health challenge since December 2019. Several new variants of SARS-CoV-2 have emerged globally raising concern about prevention and treatment of COVID-19. Early detection and in-depth analysis of the emerging variants allowing pre-emptive alert and mitigation efforts are thus of paramount importance. RESULTS Here we present ClusTRace, a novel bioinformatic pipeline for a fast and scalable analysis of sequence clusters or clades in large viral phylogenies. ClusTRace offers several high-level functionalities including lineage assignment, outlier filtering, aligning, phylogenetic tree reconstruction, cluster extraction, variant calling, visualization and reporting. ClusTRace was developed as an aid for COVID-19 transmission chain tracing in Finland with the main emphasis on fast screening of phylogenies for markers of super-spreading events and other features of concern, such as high rates of cluster growth and/or accumulation of novel mutations. CONCLUSIONS ClusTRace provides an effective interface that can significantly cut down learning and operating costs related to complex bioinformatic analysis of large viral sequence sets and phylogenies. All code is freely available from https://bitbucket.org/plyusnin/clustrace/.
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Affiliation(s)
- Ilya Plyusnin
- Department of Veterinary Bioscience, University of Helsinki, 00014, Helsinki, Finland.
- Department of Virology, University of Helsinki, 00014, Helsinki, Finland.
| | | | - Tarja Sironen
- Department of Veterinary Bioscience, University of Helsinki, 00014, Helsinki, Finland
- Department of Virology, University of Helsinki, 00014, Helsinki, Finland
| | - Olli Vapalahti
- Department of Veterinary Bioscience, University of Helsinki, 00014, Helsinki, Finland
- Department of Virology, University of Helsinki, 00014, Helsinki, Finland
- Department of Virology and Immunology, Helsinki University Hospital, Diagnostic Center, 00029, Helsinki, Finland
| | - Teemu Smura
- Department of Virology, University of Helsinki, 00014, Helsinki, Finland
- Department of Virology and Immunology, Helsinki University Hospital, Diagnostic Center, 00029, Helsinki, Finland
| | - Ravi Kant
- Department of Veterinary Bioscience, University of Helsinki, 00014, Helsinki, Finland
- Department of Virology, University of Helsinki, 00014, Helsinki, Finland
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25
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Nunes DR, Braconi CT, Ludwig-Begall LF, Arns CW, Durães-Carvalho R. Deep phylogenetic-based clustering analysis uncovers new and shared mutations in SARS-CoV-2 variants as a result of directional and convergent evolution. PLoS One 2022; 17:e0268389. [PMID: 35609034 PMCID: PMC9129020 DOI: 10.1371/journal.pone.0268389] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/28/2022] [Indexed: 02/06/2023] Open
Abstract
Nearly two decades after the last epidemic caused by a severe acute respiratory syndrome coronavirus (SARS-CoV), newly emerged SARS-CoV-2 quickly spread in 2020 and precipitated an ongoing global public health crisis. Both the continuous accumulation of point mutations, owed to the naturally imposed genomic plasticity of SARS-CoV-2 evolutionary processes, as well as viral spread over time, allow this RNA virus to gain new genetic identities, spawn novel variants and enhance its potential for immune evasion. Here, through an in-depth phylogenetic clustering analysis of upwards of 200,000 whole-genome sequences, we reveal the presence of previously unreported and hitherto unidentified mutations and recombination breakpoints in Variants of Concern (VOC) and Variants of Interest (VOI) from Brazil, India (Beta, Eta and Kappa) and the USA (Beta, Eta and Lambda). Additionally, we identify sites with shared mutations under directional evolution in the SARS-CoV-2 Spike-encoding protein of VOC and VOI, tracing a heretofore-undescribed correlation with viral spread in South America, India and the USA. Our evidence-based analysis provides well-supported evidence of similar pathways of evolution for such mutations in all SARS-CoV-2 variants and sub-lineages. This raises two pivotal points: (i) the co-circulation of variants and sub-lineages in close evolutionary environments, which sheds light onto their trajectories into convergent and directional evolution, and (ii) a linear perspective into the prospective vaccine efficacy against different SARS-CoV-2 strains.
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Affiliation(s)
- Danilo Rosa Nunes
- Department of Microbiology, Immunology and Parasitology, Paulista School of Medicine, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Carla Torres Braconi
- Department of Microbiology, Immunology and Parasitology, Paulista School of Medicine, Federal University of São Paulo, São Paulo, SP, Brazil
- * E-mail: (CTB); (RDC)
| | - Louisa F. Ludwig-Begall
- Department of Infectious and Parasitic Diseases, Veterinary Virology and Animal Viral Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Clarice Weis Arns
- Laboratory of Virology, University of Campinas, Campinas, SP, Brazil
| | - Ricardo Durães-Carvalho
- Department of Microbiology, Immunology and Parasitology, Paulista School of Medicine, Federal University of São Paulo, São Paulo, SP, Brazil
- * E-mail: (CTB); (RDC)
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26
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Sabitha S, Shobana N, Prakash P, Padmanaban S, Sathiyashree M, Saigeetha S, Chakravarthi S, Uthaman S, Park IK, Samrot AV. A Review of Different Vaccines and Strategies to Combat COVID-19. Vaccines (Basel) 2022; 10:vaccines10050737. [PMID: 35632493 PMCID: PMC9145217 DOI: 10.3390/vaccines10050737] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/05/2022] [Accepted: 05/05/2022] [Indexed: 01/09/2023] Open
Abstract
In December 2019, an unknown viral infection emerged and quickly spread worldwide, resulting in a global pandemic. This novel virus caused severe pneumonia and acute respiratory distress syndrome caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). It has caused 6.25 millions of deaths worldwide and remains a major concern for health, society, and the economy. As vaccination is one of the most efficient ways to combat this pandemic, different vaccines were developed in a short period. This review article discusses how coronavirus affected the top nations of the world and the vaccines being used for the prevention. Amongst the vaccines, some vaccines have already been approved, and some have been involved in clinical studies. The article also provides insight into different COVID-19 vaccine platforms, their preparation, working, efficacy, and side effects.
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Affiliation(s)
- Srinivasan Sabitha
- School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Sholinganallur, Rajiv Gandhi Salai, Chennai 600119, India; (S.S.); (N.S.); (P.P.); (M.S.)
| | - Nagarajan Shobana
- School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Sholinganallur, Rajiv Gandhi Salai, Chennai 600119, India; (S.S.); (N.S.); (P.P.); (M.S.)
| | - Pandurangan Prakash
- School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Sholinganallur, Rajiv Gandhi Salai, Chennai 600119, India; (S.S.); (N.S.); (P.P.); (M.S.)
| | - Sathiyamoorthy Padmanaban
- Department of Biomedical Sciences, Chonnam National University Medical School, Gwangju 58128, Korea;
- Biomedical Science Graduate Program (BMSGP), Chonnam National University, Gwangju 58128, Korea
| | - Mahendran Sathiyashree
- School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Sholinganallur, Rajiv Gandhi Salai, Chennai 600119, India; (S.S.); (N.S.); (P.P.); (M.S.)
| | - Subramanian Saigeetha
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore 632014, India;
| | - Srikumar Chakravarthi
- School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jalan SP2, Bandar Saujana Putra, Jenjarom 42610, Malaysia;
| | - Saji Uthaman
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA
- Correspondence: (S.U.); (I.-K.P.); (A.V.S.)
| | - In-Kyu Park
- Department of Biomedical Sciences, Chonnam National University Medical School, Gwangju 58128, Korea;
- Biomedical Science Graduate Program (BMSGP), Chonnam National University, Gwangju 58128, Korea
- Correspondence: (S.U.); (I.-K.P.); (A.V.S.)
| | - Antony V. Samrot
- School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jalan SP2, Bandar Saujana Putra, Jenjarom 42610, Malaysia;
- Centre for Materials Engineering and Regenerative Medicine, Bharath Institute of Higher Education and Research, Selaiyur 600073, India
- Correspondence: (S.U.); (I.-K.P.); (A.V.S.)
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Guo W, Fu Y, Jia R, Guo Z, Su C, Li J, Zhao X, Jin Y, Li P, Fan J, Zhang C, Qu P, Cui H, Gao S, Cheng H, Li J, Li X, Lu B, Xu X, Wang Z. Visualization of the infection risk assessment of SARS-CoV-2 through aerosol and surface transmission in a negative-pressure ward. ENVIRONMENT INTERNATIONAL 2022; 162:107153. [PMID: 35202929 PMCID: PMC8858715 DOI: 10.1016/j.envint.2022.107153] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/22/2022] [Accepted: 02/16/2022] [Indexed: 06/10/2023]
Abstract
Since December 2019, coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a great challenge to the world's public health system. Nosocomial infections have occurred frequently in medical institutions worldwide during this pandemic. Thus, there is an urgent need to construct an effective surveillance and early warning system for pathogen exposure and infection to prevent nosocomial infections in negative-pressure wards. In this study, visualization and construction of an infection risk assessment of SARS-CoV-2 through aerosol and surface transmission in a negative-pressure ward were performed to describe the distribution regularity and infection risk of SARS-CoV-2, the critical factors of infection, the air changes per hour (ACHs) and the viral variation that affect infection risk. The SARS-CoV-2 distribution data from this model were verified by field test data from the Wuhan Huoshenshan Hospital ICU ward. ACHs have a great impact on the infection risk from airborne exposure, while they have little effect on the infection risk from surface exposure. The variant strains demonstrated significantly increased viral loads and risks of infection. The level of protection for nurses and surgeons should be increased when treating patients infected with variant strains, and new disinfection methods, electrostatic adsorption and other air purification methods should be used in all human environments. The results of this study may provide a theoretical reference and technical support for reducing the occurrence of nosocomial infections.
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Affiliation(s)
- Weiqi Guo
- Academy of Military Sciences, Beijing, China
| | - Yingying Fu
- Academy of Military Sciences, Beijing, China
| | - Rui Jia
- China Biotechnology Co. LTD, Beijing, China
| | | | - Chen Su
- Academy of Military Sciences, Beijing, China
| | - Jiaming Li
- Academy of Military Sciences, Beijing, China
| | - Xiuguo Zhao
- Academy of Military Sciences, Beijing, China
| | - Yifei Jin
- Academy of Military Sciences, Beijing, China
| | - Penghui Li
- Academy of Military Sciences, Beijing, China
| | - Jinbo Fan
- Academy of Military Sciences, Beijing, China
| | - Cheng Zhang
- Academy of Military Sciences, Beijing, China
| | - Pengtao Qu
- Academy of Military Sciences, Beijing, China
| | - Huan Cui
- Academy of Military Sciences, Beijing, China
| | - Sheng Gao
- Academy of Military Sciences, Beijing, China
| | | | - Jingjing Li
- Academy of Military Sciences, Beijing, China
| | - Xiang Li
- Academy of Military Sciences, Beijing, China
| | - Bing Lu
- Academy of Military Sciences, Beijing, China.
| | - Xinxi Xu
- Academy of Military Sciences, Beijing, China.
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Samieefar N, Rashedi R, Akhlaghdoust M, Mashhadi M, Darzi P, Rezaei N. Delta Variant: The New Challenge of COVID-19 Pandemic, an Overview of Epidemiological, Clinical, and Immune Characteristics. ACTA BIO-MEDICA : ATENEI PARMENSIS 2022; 93:e2022179. [PMID: 35315394 PMCID: PMC8972886 DOI: 10.23750/abm.v93i1.12210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 09/07/2021] [Indexed: 11/23/2022]
Abstract
The SARS-CoV-2 genome has undergone several mutations since the beginning of the pandemic in December 2019. A number of these mutants were associated with higher transmissibility, higher mortality, or hospitalization rates, which were named the variants of concern. B.1.617.2 or the Delta variant has made a lot of concern as it has been responsible for the most recent COVID-19 outbreaks throughout the world. Higher transmissibility, a 60 percent increase in hospitalization rates compared to the wild type, higher viral loads, and reduced response to available vaccines are among the key factors why this variant has become a variant of concern. 148 countries are currently fighting with this variant, hoping to better understand the epidemiological, immunological, and clinical characteristics of this disease in order to find the best way to overcome these new outbreaks. Although reduced efficiency of vaccines on this variant and its higher pre-symptomatic transmissibility have made it complicated to control the disease, higher vaccination coverage and following sanitation rules can help control the outbreaks.
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Affiliation(s)
| | | | | | | | | | - Nima Rezaei
- University of Medical Sciences, Tehran, Iran.
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29
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Hirabara SM, Serdan TDA, Gorjao R, Masi LN, Pithon-Curi TC, Covas DT, Curi R, Durigon EL. SARS-COV-2 Variants: Differences and Potential of Immune Evasion. Front Cell Infect Microbiol 2022; 11:781429. [PMID: 35118007 PMCID: PMC8805732 DOI: 10.3389/fcimb.2021.781429] [Citation(s) in RCA: 105] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/20/2021] [Indexed: 12/16/2022] Open
Abstract
The structural spike (S) glycoprotein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) plays an essential role in infection and is an important target for neutralizing antibody recognition. Mutations in the S gene can generate variants of concern (VOCs), which improve “viral fitness” through selective or survival advantages, such as increased ACE-2 receptor affinity, infectivity, viral replication, higher transmissibility, resistance to neutralizing antibodies and immune escape, increasing disease severity and reinfection risk. Five VOCs have been recognized and include B.1.1.7 (U.K.), B.1.351 (South Africa), P.1 (Brazil), B.1.617.2 (India), and B.1.1.529 (multiple countries). In this review, we addressed the following critical points concerning VOCs: a) characteristics of the SARS-CoV-2 VOCs with mutations in the S gene; b) possible evasion of variants from neutralizing antibodies generated through vaccination, previous infection, or immune therapies; c) potential risk of new pandemic waves induced by the variants worldwide; and d) perspectives for further studies and actions aimed at preventing or reducing the impact of new variants during the current COVID-19 pandemic.
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Affiliation(s)
- Sandro M. Hirabara
- Interdisciplinary Program of Health Sciences, Cruzeiro do Sul University, São Paulo, Brazil
- *Correspondence: Sandro M. Hirabara,
| | - Tamires D. A. Serdan
- Department of Molecular Pathobiology, New York University, New York, NY, United States
| | - Renata Gorjao
- Interdisciplinary Program of Health Sciences, Cruzeiro do Sul University, São Paulo, Brazil
| | - Laureane N. Masi
- Interdisciplinary Program of Health Sciences, Cruzeiro do Sul University, São Paulo, Brazil
| | - Tania C. Pithon-Curi
- Interdisciplinary Program of Health Sciences, Cruzeiro do Sul University, São Paulo, Brazil
| | - Dimas T. Covas
- Butantan Institute, São Paulo, Brazil
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Rui Curi
- Interdisciplinary Program of Health Sciences, Cruzeiro do Sul University, São Paulo, Brazil
- Immunobiological Production Section, Bioindustrial Center, Butantan Institute, São Paulo, Brazil
| | - Edison L. Durigon
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Scientific Platform Pasteur University of São Paulo, São Paulo, Brazil
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30
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In Silico Screening of Potential Phytocompounds from Several Herbs against SARS-CoV-2 Indian Delta Variant B.1.617.2 to Inhibit the Spike Glycoprotein Trimer. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12020665] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In October 2020, the SARS-CoV-2 B.1.617 lineage was discovered in India. It has since become a prominent variant in several Indian regions and 156 countries, including the United States of America. The lineage B.1.617.2 is termed the delta variant, harboring diverse spike mutations in the N-terminal domain (NTD) and the receptor-binding domain (RBD), which may heighten its immune evasion potentiality and cause it to be more transmissible than other variants. As a result, it has sparked substantial scientific investigation into the development of effective vaccinations and anti-viral drugs. Several efforts have been made to examine ancient medicinal herbs known for their health benefits and immune-boosting action against SARS-CoV-2, including repurposing existing FDA-approved anti-viral drugs. No efficient anti-viral drugs are available against the SARS-CoV-2 Indian delta variant B.1.617.2. In this study, efforts were made to shed light on the potential of 603 phytocompounds from 22 plant species to inhibit the Indian delta variant B.1.617.2. We also compared these compounds with the standard drug ceftriaxone, which was already suggested as a beneficial drug in COVID-19 treatment; these compounds were compared with other FDA-approved drugs: remdesivir, chloroquine, hydroxy-chloroquine, lopinavir, and ritonavir. From the analysis, the identified phytocompounds acteoside (−7.3 kcal/mol) and verbascoside (−7.1 kcal/mol), from the plants Clerodendrum serratum and Houttuynia cordata, evidenced a strong inhibitory effect against the mutated NTD (MT-NTD). In addition, the phytocompounds kanzonol V (−6.8 kcal/mol), progeldanamycin (−6.4 kcal/mol), and rhodoxanthin (−7.5 kcal/mol), from the plant Houttuynia cordata, manifested significant prohibition against RBD. Nevertheless, the standard drug, ceftriaxone, signals less inhibitory effect against MT-NTD and RBD with binding affinities of −6.3 kcal/mol and −6.5 kcal/mol, respectively. In this study, we also emphasized the pharmacological properties of the plants, which contain the screened phytocompounds. Our research could be used as a lead for future drug design to develop anti-viral drugs, as well as for preening the Siddha formulation to control the Indian delta variant B.1.617.2 and other future SARS-CoV-2 variants.
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Tanra A, Tusholehah M. Lessons learned from COVID-19 pandemic: Indonesia's perspective. TAIWANESE JOURNAL OF PSYCHIATRY 2022. [DOI: 10.4103/tpsy.tpsy_10_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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32
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An outlook on potential protein targets of COVID-19 as a druggable site. Mol Biol Rep 2022; 49:10729-10748. [PMID: 35790657 PMCID: PMC9256362 DOI: 10.1007/s11033-022-07724-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/17/2022] [Indexed: 12/22/2022]
Abstract
BACKGROUND SARS-CoV-2 which causes COVID-19 disease has started a pandemic episode all over the world infecting millions of people and has created medical and economic crisis. From December 2019, cases originated from Wuhan city and started spreading at an alarming rate and has claimed millions of lives till now. Scientific studies suggested that this virus showed genomic similarity of about 90% with SARS-CoV and is found to be more contagious as compared to SARS-CoV and MERS-CoV. Since the pandemic, virus has undergone constant mutation and few strains have raised public concern like Delta and Omicron variants of SARS-CoV-2. OBJECTIVE This review focuses on the structural features of SARS-CoV-2 proteins and host proteins as well as their mechanism of action. We have also elucidated the repurposed drugs that have shown potency to inhibit these protein targets in combating COVID-19. Moreover, the article discusses the vaccines approved so far and those under clinical trials for their efficacy against COVID-19. CONCLUSION Using cryo-electron microscopy or X-ray diffraction, hundreds of crystallographic data of SARS-CoV-2 proteins have been published including structural and non-structural proteins. These proteins have a significant role at different aspects in the viral machinery and presented themselves as potential target for drug designing and therapeutic interventions. Also, there are few host cell proteins which helps in SARS-CoV-2 entry and proteolytic cleavage required for viral infection.
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33
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Li G, Zhang L, Xue P. Codon usage divergence in Delta variants (B.1.617.2) of SARS-CoV-2. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 97:105175. [PMID: 34871776 PMCID: PMC8641433 DOI: 10.1016/j.meegid.2021.105175] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/27/2021] [Accepted: 12/01/2021] [Indexed: 01/17/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spreads all over the world and brings great harm to humans in many countries. Many new SARS-CoV-2 variants appeared during its transmission. In the present study, the Delta variants (B.1.617.2) of SARS-CoV-2, which have appeared in many countries, were considered for analysis. In order to evaluate the evolutionary divergence of the Delta variants(B.1.617.2), the codon usage divergence in Delta variants (B.1.617.2) of SARS-CoV-2 was compared to that of the SARS-CoV-2 genomes emerged before June 2020. All Delta variants (B.1.617.2) and 350 early genomes of SARS-CoV-2 in the NCBI database were downloaded. Codon usage pattern including the basic composition, the GC ratio of the third position (GC3) and the first two positions (GC12) in codons, overall GC contents, the effective number of codons (ENC), the codon bias index (CBI), the relative synonymous codon usage (RSCU) values, etc., of all concerned important gene sequences were all calculated. Codon usage divergence of them was calculated via summing their standard deviations. The results suggested that base compositions in both Delta variants (B.1.617.2) of SARS-CoV-2 and the early SARS-CoV-2 genomes were similar to each other. However, the internal codon usage divergence for most genes in Delta variants (B.1.617.2) was significantly wider than that of SARS-CoV-2. The RSCU values were further used to explore the synonymous and non-synonymous mutations in the sequences of the Delta variants (B.1.617.2), and the results showed the synonymous mutations are more obvious than the non-synonymous in the concerned sequences. The related codon usage divergence analysis is helpful for further study on the adaptability and disease prognosis of the SARS-CoV-2 variants.
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Affiliation(s)
- Gun Li
- Laboratory for Biodiversity Science, Department of Biomedical Engineering, School of Electronic Information Engineering, Xi'An Technological University, Xi'An, China.
| | - Liang Zhang
- Laboratory for Biodiversity Science, Department of Biomedical Engineering, School of Electronic Information Engineering, Xi'An Technological University, Xi'An, China
| | - Pei Xue
- Laboratory for Biodiversity Science, Department of Biomedical Engineering, School of Electronic Information Engineering, Xi'An Technological University, Xi'An, China
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Xie C, Ding H, Ding J, Xue Y, Lu S, Lv H. Preparation of highly specific monoclonal antibodies against SARS-CoV-2 nucleocapsid protein and the preliminary development of antigen detection test strips. J Med Virol 2021; 94:1633-1640. [PMID: 34904253 PMCID: PMC9303534 DOI: 10.1002/jmv.27520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/22/2021] [Accepted: 12/10/2021] [Indexed: 12/15/2022]
Abstract
The coronavirus disease 2019 (COVID‐19) is outbreaking all over the world. To help fight this disease, it is necessary to establish an effective and rapid detection method. The nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is involved in viral replication, assembly, and immune regulation and plays an important role in the viral life cycle. Moreover, the N protein also could be a diagnostic factor and potential drug target. Therefore, by synthesizing the N gene sequence of SARS‐CoV‐2, constructing the pET‐28a (+)‐N recombinant plasmid, we expressed the N protein in Escherichia coli and obtained 15 monoclonal antibody (mAbs) against SARS‐CoV‐2‐N protein by the hybridomas and ascites, then an immunochromatographic test strip method detecting N antigen was established. In this study, we obtained 14 high‐titer and high‐specificity monoclonal antibodies, and the test strips exclusively react with the SARS‐CoV‐2‐N protein and no cross‐reactivity with other coronavirus and also recognize the recombinant N protein of Delta (B.1.617.2) variant. These mAbs can be used for the early and rapid diagnosis of SARS‐CoV‐2 infection through serological antigen.
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Affiliation(s)
- Chengzuo Xie
- Institute of Parasitic Disease, Hangzhou Medical College, Hangzhou, China
| | - Haojie Ding
- Institute of Parasitic Disease, Hangzhou Medical College, Hangzhou, China
| | - Jianzu Ding
- Institute of Parasitic Disease, Hangzhou Medical College, Hangzhou, China
| | - Yangji Xue
- The Key Laboratory of Blood Safety Research, Blood Center of Zhejiang Province, Hangzhou, China
| | - Shaohong Lu
- Institute of Parasitic Disease, Hangzhou Medical College, Hangzhou, China
| | - Hangjun Lv
- Institute of Parasitic Disease, Hangzhou Medical College, Hangzhou, China
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35
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Warner BM, Santry LA, Leacy A, Chan M, Pham PH, Vendramelli R, Pei Y, Tailor N, Valcourt E, Leung A, He S, Griffin BD, Audet J, Willman M, Tierney K, Albietz A, Frost KL, Yates JG, Mould RC, Chan L, Mehrani Y, Knapp JP, Minott JA, Banadyga L, Safronetz D, Wood H, Booth S, Major PP, Bridle BW, Susta L, Kobasa D, Wootton SK. Intranasal vaccination with a Newcastle disease virus-vectored vaccine protects hamsters from SARS-CoV-2 infection and disease. iScience 2021; 24:103219. [PMID: 34632328 PMCID: PMC8492382 DOI: 10.1016/j.isci.2021.103219] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/24/2021] [Accepted: 09/30/2021] [Indexed: 02/08/2023] Open
Abstract
The pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of coronavirus disease 2019 (COVID-19). Worldwide efforts are being made to develop vaccines to mitigate this pandemic. We engineered two recombinant Newcastle disease virus (NDV) vectors expressing either the full-length SARS-CoV-2 spike protein (NDV-FLS) or a version with a 19 amino acid deletion at the carboxy terminus (NDV-Δ19S). Hamsters receiving two doses (prime-boost) of NDV-FLS developed a robust SARS-CoV-2-neutralizing antibody response, with elimination of infectious virus in the lungs and minimal lung pathology at five days post-challenge. Single-dose vaccination with NDV-FLS significantly reduced SARS-CoV-2 replication in the lungs but only mildly decreased lung inflammation. NDV-Δ19S-treated hamsters had a moderate decrease in SARS-CoV-2 titers in lungs and presented with severe microscopic lesions, suggesting that truncation of the spike protein was a less effective strategy. In summary, NDV-vectored vaccines represent a viable option for protection against COVID-19.
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Affiliation(s)
- Bryce M. Warner
- Zoonotic Diseases and Special Pathogens, Public Health Agency of Canada, Winnipeg, Canada
| | - Lisa A. Santry
- Department of Pathobiology, University of Guelph, Guelph, Canada
| | - Alexander Leacy
- Department of Pathobiology, University of Guelph, Guelph, Canada
| | - Mable Chan
- Zoonotic Diseases and Special Pathogens, Public Health Agency of Canada, Winnipeg, Canada
| | - Phuc H. Pham
- Department of Pathobiology, University of Guelph, Guelph, Canada
| | - Robert Vendramelli
- Zoonotic Diseases and Special Pathogens, Public Health Agency of Canada, Winnipeg, Canada
| | - Yanlong Pei
- Department of Pathobiology, University of Guelph, Guelph, Canada
| | - Nikesh Tailor
- Zoonotic Diseases and Special Pathogens, Public Health Agency of Canada, Winnipeg, Canada
| | - Emelissa Valcourt
- Zoonotic Diseases and Special Pathogens, Public Health Agency of Canada, Winnipeg, Canada
| | - Anders Leung
- Zoonotic Diseases and Special Pathogens, Public Health Agency of Canada, Winnipeg, Canada
| | - Shihua He
- Zoonotic Diseases and Special Pathogens, Public Health Agency of Canada, Winnipeg, Canada
| | - Bryan D. Griffin
- Zoonotic Diseases and Special Pathogens, Public Health Agency of Canada, Winnipeg, Canada
| | - Jonathan Audet
- Zoonotic Diseases and Special Pathogens, Public Health Agency of Canada, Winnipeg, Canada
| | - Marnie Willman
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Kevin Tierney
- Zoonotic Diseases and Special Pathogens, Public Health Agency of Canada, Winnipeg, Canada
| | - Alixandra Albietz
- Zoonotic Diseases and Special Pathogens, Public Health Agency of Canada, Winnipeg, Canada
| | - Kathy L. Frost
- Zoonotic Diseases and Special Pathogens, Public Health Agency of Canada, Winnipeg, Canada
| | - Jacob G.E. Yates
- Department of Pathobiology, University of Guelph, Guelph, Canada
| | - Robert C. Mould
- Department of Pathobiology, University of Guelph, Guelph, Canada
| | - Lily Chan
- Department of Pathobiology, University of Guelph, Guelph, Canada
| | - Yeganeh Mehrani
- Department of Pathobiology, University of Guelph, Guelph, Canada
| | - Jason P. Knapp
- Department of Pathobiology, University of Guelph, Guelph, Canada
| | | | - Logan Banadyga
- Zoonotic Diseases and Special Pathogens, Public Health Agency of Canada, Winnipeg, Canada
| | - David Safronetz
- Zoonotic Diseases and Special Pathogens, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Heidi Wood
- Zoonotic Diseases and Special Pathogens, Public Health Agency of Canada, Winnipeg, Canada
| | - Stephanie Booth
- Zoonotic Diseases and Special Pathogens, Public Health Agency of Canada, Winnipeg, Canada
| | - Pierre P. Major
- Juravinski Cancer Centre, 699 Concession Street, Hamilton, ON L8V 5C2, Canada
| | - Byram W. Bridle
- Department of Pathobiology, University of Guelph, Guelph, Canada
| | - Leonardo Susta
- Department of Pathobiology, University of Guelph, Guelph, Canada
| | - Darwyn Kobasa
- Zoonotic Diseases and Special Pathogens, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Sarah K. Wootton
- Department of Pathobiology, University of Guelph, Guelph, Canada
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36
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Narasimhan M, Mahimainathan L, Noh J, Muthukumar A. Silent SARS-CoV-2 Infections, Waning Immunity, Serology Testing, and COVID-19 Vaccination: A Perspective. Front Immunol 2021; 12:730404. [PMID: 34621274 PMCID: PMC8490796 DOI: 10.3389/fimmu.2021.730404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/31/2021] [Indexed: 12/14/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus causes a spectrum of clinical manifestations, ranging from asymptomatic to mild, moderate, or severe illness with multi-organ failure and death. Using a new machine learning algorithm developed by us, we have reported a significantly higher number of predicted COVID-19 cases than the documented counts across the world. The sole reliance on confirmed symptomatic cases overlooking the symptomless COVID-19 infections and the dynamics of waning immunity may not provide 'true' spectrum of infection proportion, a key element for an effective planning and implementation of protection and prevention strategies. We and others have previously shown that strategic orthogonal testing and leveraging systematic data-driven modeling approach to account for asymptomatics and waning cases may situationally have a compelling role in informing efficient vaccination strategies beyond prevalence reporting. However, currently Centers for Disease Control and Prevention (CDC) does not recommend serological testing either before or after vaccination to assess immune status. Given the 27% occurrence of breakthrough infections in fully vaccinated (FV) group with many being asymptomatics and still a larger fraction of the general mass remaining unvaccinated, the relaxed mask mandate and distancing by CDC can drive resurgence. Thus, we believe it is a key time to focus on asymptomatics (no symptoms) and oligosymptomatics (so mild that the symptoms remain unrecognized) as they can be silent reservoirs to propagate the infection. This perspective thus highlights the need for proactive efforts to reevaluate the current variables/strategies in accounting for symptomless and waning fractions.
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Affiliation(s)
- Madhusudhanan Narasimhan
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Lenin Mahimainathan
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Jungsik Noh
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Alagarraju Muthukumar
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, United States
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