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Moneshwaran S, Macrin D, Kanagathara N. An unprecedented global challenge, emerging trends and innovations in the fight against COVID-19: A comprehensive review. Int J Biol Macromol 2024; 267:131324. [PMID: 38574936 DOI: 10.1016/j.ijbiomac.2024.131324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 03/30/2024] [Accepted: 03/30/2024] [Indexed: 04/06/2024]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a highly contagious and dangerous virus that caused the global COVID-19 pandemic in early 2020. It primarily affects the respiratory system, leading to severe illness and high rates of mortality worldwide. The virus enters the body by binding to a receptor called ACE2, which is present in specific cells of the lungs known as type 2 alveolar epithelial cells. Numerous studies have investigated the consequences of SARS-CoV-2 infection, revealing various impacts on the body. This review provides an overview of SARS-CoV-2, including its structure and how it infects cells. It also examines the different variants of concern, such as Alpha, Beta, Gamma, Delta, and the more recent Omicron variant, discussing their characteristics and the level of damage they cause. The usage of drugs to treat COVID-19 is another aspect that has been covered and compares the effectiveness and use of antiviral drugs in the treatment and its potential benefits in COVID-19 treatment. Furthermore, this review explores the consequences and abnormalities associated with SARS-CoV-2 infection, including its impact on various organs and systems in the body. And also discussing the different COVID-19 vaccines available and their effectiveness in preventing infection and reducing the severity of illness. The current review ensures the recent update of the COVID research with expert's knowledge, collection of numerous data from reliable sources and methodologies as well as update of findings based on reviews. This review also provided clear contextual explanations to aid the interpretation and application of the results. The main motto and limitation of this manuscript are to address the computational methods of drug discovery against the rapidly evolving SARS-CoV-2 virus, which has been discussed. Additionally, current computational approaches which are cost effective and can able to predict the therapeutic agents for the treatment against the virus have also been discussed.
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Affiliation(s)
- S Moneshwaran
- Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Thandalam, Chennai 602 105, India
| | - D Macrin
- Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Thandalam, Chennai 602 105, India
| | - N Kanagathara
- Department of Physics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Thandalam, Chennai 602 105, India.
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Owens K, Esmaeili S, Schiffer JT. Heterogeneous SARS-CoV-2 kinetics due to variable timing and intensity of immune responses. JCI Insight 2024; 9:e176286. [PMID: 38573774 PMCID: PMC11141931 DOI: 10.1172/jci.insight.176286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 03/27/2024] [Indexed: 04/06/2024] Open
Abstract
The viral kinetics of documented SARS-CoV-2 infections exhibit a high degree of interindividual variability. We identified 6 distinct viral shedding patterns, which differed according to peak viral load, duration, expansion rate, and clearance rate, by clustering data from 768 infections in the National Basketball Association cohort. Omicron variant infections in previously vaccinated individuals generally led to lower cumulative shedding levels of SARS-CoV-2 than other scenarios. We then developed a mechanistic mathematical model that recapitulated 1,510 observed viral trajectories, including viral rebound and cases of reinfection. Lower peak viral loads were explained by a more rapid and sustained transition of susceptible cells to a refractory state during infection as well as by an earlier and more potent late, cytolytic immune response. Our results suggest that viral elimination occurs more rapidly during Omicron infection, following vaccination, and following reinfection due to enhanced innate and acquired immune responses. Because viral load has been linked with COVID-19 severity and transmission risk, our model provides a framework for understanding the wide range of observed SARS-CoV-2 infection outcomes.
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Affiliation(s)
- Katherine Owens
- Fred Hutchinson Cancer Center, Vaccine and Infectious Diseases Division, Seattle, Washington, USA
| | - Shadisadat Esmaeili
- Fred Hutchinson Cancer Center, Vaccine and Infectious Diseases Division, Seattle, Washington, USA
| | - Joshua T. Schiffer
- Fred Hutchinson Cancer Center, Vaccine and Infectious Diseases Division, Seattle, Washington, USA
- University of Washington, Department of Medicine, Seattle, Washington, USA
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Port JR, Morris DH, Riopelle JC, Yinda CK, Avanzato VA, Holbrook MG, Bushmaker T, Schulz JE, Saturday TA, Barbian K, Russell CA, Perry-Gottschalk R, Shaia C, Martens C, Lloyd-Smith JO, Fischer RJ, Munster VJ. Host and viral determinants of airborne transmission of SARS-CoV-2 in the Syrian hamster. eLife 2024; 12:RP87094. [PMID: 38416804 PMCID: PMC10942639 DOI: 10.7554/elife.87094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2024] Open
Abstract
It remains poorly understood how SARS-CoV-2 infection influences the physiological host factors important for aerosol transmission. We assessed breathing pattern, exhaled droplets, and infectious virus after infection with Alpha and Delta variants of concern (VOC) in the Syrian hamster. Both VOCs displayed a confined window of detectable airborne virus (24-48 hr), shorter than compared to oropharyngeal swabs. The loss of airborne shedding was linked to airway constriction resulting in a decrease of fine aerosols (1-10 µm) produced, which are suspected to be the major driver of airborne transmission. Male sex was associated with increased viral replication and virus shedding in the air. Next, we compared the transmission efficiency of both variants and found no significant differences. Transmission efficiency varied mostly among donors, 0-100% (including a superspreading event), and aerosol transmission over multiple chain links was representative of natural heterogeneity of exposure dose and downstream viral kinetics. Co-infection with VOCs only occurred when both viruses were shed by the same donor during an increased exposure timeframe (24-48 hr). This highlights that assessment of host and virus factors resulting in a differential exhaled particle profile is critical for understanding airborne transmission.
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Affiliation(s)
- Julia R Port
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Dylan H Morris
- Department of Ecology and Evolutionary Biology, University of California, Los AngelesLos AngelesUnited States
| | - Jade C Riopelle
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Claude Kwe Yinda
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Victoria A Avanzato
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Myndi G Holbrook
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Trenton Bushmaker
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Jonathan E Schulz
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Taylor A Saturday
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Kent Barbian
- Rocky Mountain Research and Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Colin A Russell
- Department of Medical Microbiology | Amsterdam University Medical Center, University of AmsterdamAmsterdamNetherlands
| | - Rose Perry-Gottschalk
- Rocky Mountain Visual and Medical Arts Unit, Research Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Carl Shaia
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Craig Martens
- Rocky Mountain Research and Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - James O Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California, Los AngelesLos AngelesUnited States
| | - Robert J Fischer
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Vincent J Munster
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
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Owens K, Esmaeili-Wellman S, Schiffer JT. Heterogeneous SARS-CoV-2 kinetics due to variable timing and intensity of immune responses. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.08.20.23294350. [PMID: 37662228 PMCID: PMC10473815 DOI: 10.1101/2023.08.20.23294350] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The viral kinetics of documented SARS-CoV-2 infections exhibit a high degree of inter-individual variability. We identified six distinct viral shedding patterns, which differed according to peak viral load, duration, expansion rate and clearance rate, by clustering data from 768 infections in the National Basketball Association cohort. Omicron variant infections in previously vaccinated individuals generally led to lower cumulative shedding levels of SARS-CoV-2 than other scenarios. We then developed a mechanistic mathematical model that recapitulated 1510 observed viral trajectories, including viral rebound and cases of reinfection. Lower peak viral loads were explained by a more rapid and sustained transition of susceptible cells to a refractory state during infection, as well as an earlier and more potent late, cytolytic immune response. Our results suggest that viral elimination occurs more rapidly during omicron infection, following vaccination, and following re-infection due to enhanced innate and acquired immune responses. Because viral load has been linked with COVID-19 severity and transmission risk, our model provides a framework for understanding the wide range of observed SARS-CoV-2 infection outcomes.
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Affiliation(s)
- Katherine Owens
- Fred Hutchinson Cancer Center, Vaccine and Infectious Diseases Division
| | | | - Joshua T Schiffer
- Fred Hutchinson Cancer Center, Vaccine and Infectious Diseases Division
- University of Washington, Department of Medicine
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5
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Park HS, Yin A, Barranta C, Lee JS, Caputo CA, Sachithanandham J, Li M, Yoon S, Sitaras I, Jedlicka A, Eby Y, Ram M, Fernandez RE, Baker OR, Shenoy AG, Mosnaim GS, Fukuta Y, Patel B, Heath SL, Levine AC, Meisenberg BR, Spivak ES, Anjan S, Huaman MA, Blair JE, Currier JS, Paxton JH, Gerber JM, Petrini JR, Broderick PB, Rausch W, Cordisco ME, Hammel J, Greenblatt B, Cluzet VC, Cruser D, Oei K, Abinante M, Hammitt LL, Sutcliffe CG, Forthal DN, Zand MS, Cachay ER, Raval JS, Kassaye SG, Marshall CE, Yarava A, Lane K, McBee NA, Gawad AL, Karlen N, Singh A, Ford DE, Jabs DA, Appel LJ, Shade DM, Lau B, Ehrhardt S, Baksh SN, Shapiro JR, Ou J, Na YB, Knoll MD, Ornelas-Gatdula E, Arroyo-Curras N, Gniadek TJ, Caturegli P, Wu J, Ndahiro N, Betenbaugh MJ, Ziman A, Hanley DF, Casadevall A, Shoham S, Bloch EM, Gebo KA, Tobian AAR, Laeyendecker O, Pekosz A, Klein SL, Sullivan DJ. Outpatient COVID-19 convalescent plasma recipient antibody thresholds correlated to reduced hospitalizations within a randomized trial. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.13.23288353. [PMID: 37131659 PMCID: PMC10153328 DOI: 10.1101/2023.04.13.23288353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
BACKGROUND The COVID-19 convalescent plasma (CCP) viral specific antibody levels that translate into recipient post-transfusion antibody levels sufficient to prevent disease progression is not defined. METHODS This secondary analysis correlated donor and recipient antibody levels to hospitalization risk among unvaccinated, seronegative CCP recipients within the outpatient, double blind, randomized clinical trial that compared CCP to control plasma. The majority of COVID-19 CCP arm hospitalizations (15/17, 88%) occurred in this unvaccinated, seronegative subgroup. A functional cutoff to delineate recipient high versus low post-transfusion antibody levels was established by two methods: 1) analyzing virus neutralization-equivalent anti-S-RBD IgG responses in donors or 2) receiver operating characteristic (ROC) analysis. RESULTS SARS-CoV-2 anti-S-RBD IgG antibody was diluted by a factor of 21.3 into post-transfusion seronegative recipients from matched donor units. Viral specific antibody delivered approximated 1.2 mg. The high antibody recipients transfused early (symptom onset within 5 days) had no hospitalizations. A CCP recipient analysis for antibody thresholds correlated to reduced hospitalizations found a significant association with Fisher's exact test between early and high antibodies versus all other CCP recipients (or control plasma) with antibody cutoffs established by both methods-donor virus neutralization-based cutoff: (0/85; 0% versus 15/276; 5.6%) p=0.03 or ROC based cutoff: (0/94; 0% versus 15/267; 5.4%) p=0.01. CONCLUSION In unvaccinated, seronegative CCP recipients, early transfusion of plasma units corresponding to the upper 30% of all study donors reduced outpatient hospitalizations. These high antibody level plasma units, given early, should be reserved for therapeutic use.Trial registration: NCT04373460. FUNDING Defense Health Agency and others.
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Affiliation(s)
- Han-Sol Park
- W. Harry Feinstone Department of Molecular Microbiology and Immunology; Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Anna Yin
- W. Harry Feinstone Department of Molecular Microbiology and Immunology; Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Caelan Barranta
- W. Harry Feinstone Department of Molecular Microbiology and Immunology; Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - John S Lee
- W. Harry Feinstone Department of Molecular Microbiology and Immunology; Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Christopher A Caputo
- W. Harry Feinstone Department of Molecular Microbiology and Immunology; Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jaiprasath Sachithanandham
- W. Harry Feinstone Department of Molecular Microbiology and Immunology; Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Maggie Li
- W. Harry Feinstone Department of Molecular Microbiology and Immunology; Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Steve Yoon
- W. Harry Feinstone Department of Molecular Microbiology and Immunology; Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ioannis Sitaras
- W. Harry Feinstone Department of Molecular Microbiology and Immunology; Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Anne Jedlicka
- W. Harry Feinstone Department of Molecular Microbiology and Immunology; Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Yolanda Eby
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Malathi Ram
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Reinaldo E Fernandez
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Owen R Baker
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aarthi G Shenoy
- Department of Medicine, Division of Hematology and Oncology, MedStar Washington Hospital Center, Washington DC, USA
| | - Giselle S Mosnaim
- Division of Allergy and Immunology, Department of Medicine, NorthShore University Health System, Evanston, IL, USA
| | - Yuriko Fukuta
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, Houston, TX, USA
| | - Bela Patel
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Texas Health Science Center, Houston, TX, USA
| | - Sonya L Heath
- Department of Medicine, Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Adam C Levine
- Department of Emergency Medicine, Rhode Island Hospital, Brown University, Providence, RI, USA
| | | | - Emily S Spivak
- Department of Medicine, Division of Infectious Diseases, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Shweta Anjan
- Department of Medicine, Division of Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Moises A Huaman
- Department of Medicine, Division of Infectious Diseases, University of Cincinnati, Cincinnati, OH, USA
| | - Janis E Blair
- Department of Medicine, Division of Infectious Diseases, Mayo Clinic Hospital, Phoenix, AZ, USA
| | - Judith S Currier
- Department of Medicine, Division of Infectious Diseases, University of California, Los Angeles, CA, USA
| | - James H Paxton
- Department of Emergency Medicine, Wayne State University School of Medicine, Detroit, MI, USA
| | - Jonathan M Gerber
- Department of Medicine, Division of Hematology and Oncology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | | | | | | | - Jean Hammel
- Nuvance Health Norwalk Hospital, Norwalk, CT, USA
| | | | - Valerie C Cluzet
- Nuvance Health Vassar Brothers Medical Center, Poughkeepsie, NY, USA
| | - Daniel Cruser
- Nuvance Health Vassar Brothers Medical Center, Poughkeepsie, NY, USA
| | | | | | - Laura L Hammitt
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Catherine G Sutcliffe
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Donald N Forthal
- Department of Medicine, Division of Infectious Diseases, University of California, Irvine, CA, USA
| | - Martin S Zand
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Edward R Cachay
- Department of Medicine, Division of Infectious Diseases, University of California, San Diego, CA, USA
| | - Jay S Raval
- Department of Pathology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Seble G Kassaye
- Department of Medicine, Division of Infectious Diseases, Georgetown University Medical Center Washington DC, USA
| | - Christi E Marshall
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anusha Yarava
- Department of Neurology, Brain Injury Outcomes, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Karen Lane
- Department of Neurology, Brain Injury Outcomes, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nichol A McBee
- Department of Neurology, Brain Injury Outcomes, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Amy L Gawad
- Department of Neurology, Brain Injury Outcomes, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicky Karlen
- Department of Neurology, Brain Injury Outcomes, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Atika Singh
- Department of Neurology, Brain Injury Outcomes, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel E Ford
- Institute for Clinical and Translational Research Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Douglas A Jabs
- Department of Ophthalmology Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Lawrence J Appel
- Welch Center for Prevention, Epidemiology and Clinical Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David M Shade
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Bryan Lau
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Stephan Ehrhardt
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Sheriza N Baksh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Janna R Shapiro
- W. Harry Feinstone Department of Molecular Microbiology and Immunology; Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jiangda Ou
- Department of Neurology, Brain Injury Outcomes, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yu Bin Na
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Maria D Knoll
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Elysse Ornelas-Gatdula
- Chemistry-Biology Interface Program, Zanvyl Krieger School of Arts & Sciences, Johns Hopkins University, Baltimore MD, USA
| | - Netzahualcoyotl Arroyo-Curras
- Chemistry-Biology Interface Program, Zanvyl Krieger School of Arts & Sciences, Johns Hopkins University, Baltimore MD, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas J Gniadek
- Department of Pathology and Laboratory Medicine, Northshore University Health System, Evanston, IL
| | - Patrizio Caturegli
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jinke Wu
- Advanced Mammalian Biomanufacturing Innovation Center, Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Nelson Ndahiro
- Advanced Mammalian Biomanufacturing Innovation Center, Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Michael J Betenbaugh
- Advanced Mammalian Biomanufacturing Innovation Center, Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Alyssa Ziman
- Department of Pathology and Laboratory Medicine, Wing-Kwai and Alice Lee-Tsing Chung Transfusion Service, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Daniel F Hanley
- Department of Neurology, Brain Injury Outcomes, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Arturo Casadevall
- W. Harry Feinstone Department of Molecular Microbiology and Immunology; Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Shmuel Shoham
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Evan M Bloch
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kelly A Gebo
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aaron A R Tobian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Oliver Laeyendecker
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Baltimore, MD, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology; Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Sabra L Klein
- W. Harry Feinstone Department of Molecular Microbiology and Immunology; Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - David J Sullivan
- W. Harry Feinstone Department of Molecular Microbiology and Immunology; Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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Aravind Kumar N, Aradhana S, Harleen, Vishnuraj MR. SARS-CoV-2 in digital era: Diagnostic techniques and importance of nucleic acid quantification with digital PCRs. Rev Med Virol 2023; 33:e2471. [PMID: 37529971 DOI: 10.1002/rmv.2471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/04/2023] [Accepted: 07/12/2023] [Indexed: 08/03/2023]
Abstract
Studies related to clinical diagnosis and research of SARS-CoV-2 are important in the current pandemic era. Although molecular biology has emphasised the importance of qualitative analysis, quantitative analysis with nucleic acids in relation to SARS-CoV-2 needs to be clearly emphasised, which can provide perspective for viral dynamic studies of SARS-CoV-2. In this regard, the requirement and utilization of digital PCR in COVID-19 research has substantially increased during the pandemic, necessitating the aggregation of its cardinal applications and future scopes. Hence, this meta-review comprehensively addresses and emphasises the importance of nucleic acid quantification of SARS-CoV-2 RNA with digital PCR (dPCR). Various quantitative techniques of clinical significance like immunological, proteomic and nucleic acid-based diagnosis and quantification, have been comparatively discussed. Furthermore, the core part of the article focusses on the working principle and advantages of digital PCR, along with its applications in COVID-19 research. Several important applications like viral load quantitation, environmental surveillance and assay validation have been extensively investigated and discussed. Certain key future scopes of clinical importance, like mortality prediction, viral/variant-symbiosis, and antiviral studies were also identified, suggesting several possible digital PCR applications in COVID-19 research.
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Affiliation(s)
- N Aravind Kumar
- Meat Species Identification Laboratory, ICAR - National Meat Research Institute, Hyderabad, Telangana, India
| | - S Aradhana
- Department of Biotechnology, School of Bio Sciences & Technology (SBST), Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Harleen
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - M R Vishnuraj
- Meat Species Identification Laboratory, ICAR - National Meat Research Institute, Hyderabad, Telangana, India
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7
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Viloria Winnett A, Akana R, Shelby N, Davich H, Caldera S, Yamada T, Reyna JRB, Romano AE, Carter AM, Kim MK, Thomson M, Tognazzini C, Feaster M, Goh YY, Chew YC, Ismagilov RF. Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods. PNAS NEXUS 2023; 2:pgad033. [PMID: 36926220 PMCID: PMC10013338 DOI: 10.1093/pnasnexus/pgad033] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/18/2023] [Accepted: 01/24/2023] [Indexed: 03/16/2023]
Abstract
SARS-CoV-2 viral-load measurements from a single-specimen type are used to establish diagnostic strategies, interpret clinical-trial results for vaccines and therapeutics, model viral transmission, and understand virus-host interactions. However, measurements from a single-specimen type are implicitly assumed to be representative of other specimen types. We quantified viral-load timecourses from individuals who began daily self-sampling of saliva, anterior-nares (nasal), and oropharyngeal (throat) swabs before or at the incidence of infection with the Omicron variant. Viral loads in different specimen types from the same person at the same timepoint exhibited extreme differences, up to 109 copies/mL. These differences were not due to variation in sample self-collection, which was consistent. For most individuals, longitudinal viral-load timecourses in different specimen types did not correlate. Throat-swab and saliva viral loads began to rise as many as 7 days earlier than nasal-swab viral loads in most individuals, leading to very low clinical sensitivity of nasal swabs during the first days of infection. Individuals frequently exhibited presumably infectious viral loads in one specimen type while viral loads were low or undetectable in other specimen types. Therefore, defining an individual as infectious based on assessment of a single-specimen type underestimates the infectious period, and overestimates the ability of that specimen type to detect infectious individuals. For diagnostic COVID-19 testing, these three single-specimen types have low clinical sensitivity, whereas a combined throat-nasal swab, and assays with high analytical sensitivity, was inferred to have significantly better clinical sensitivity to detect presumed pre-infectious and infectious individuals.
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Affiliation(s)
| | - Reid Akana
- California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Natasha Shelby
- California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Hannah Davich
- California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Saharai Caldera
- California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Taikun Yamada
- Pangea Laboratory LLC, 14762 Bentley Cir, Tustin, CA 92780, USA.,Zymo Research Corp., 17062 Murphy Ave, Irvine, CA 92614, USA
| | | | - Anna E Romano
- California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Alyssa M Carter
- California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Mi Kyung Kim
- California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Matt Thomson
- California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Colten Tognazzini
- Pasadena Public Health Department, 1845 N. Fair Oaks Ave, Pasadena, CA 91103, USA
| | - Matthew Feaster
- Pasadena Public Health Department, 1845 N. Fair Oaks Ave, Pasadena, CA 91103, USA
| | - Ying-Ying Goh
- Pasadena Public Health Department, 1845 N. Fair Oaks Ave, Pasadena, CA 91103, USA
| | - Yap Ching Chew
- Pangea Laboratory LLC, 14762 Bentley Cir, Tustin, CA 92780, USA.,Zymo Research Corp., 17062 Murphy Ave, Irvine, CA 92614, USA
| | - Rustem F Ismagilov
- California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
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8
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Eales O, Page AJ, Tang SN, Walters CE, Wang H, Haw D, Trotter AJ, Le Viet T, Foster-Nyarko E, Prosolek S, Atchison C, Ashby D, Cooke G, Barclay W, Donnelly CA, O’Grady J, Volz E, Darzi A, Ward H, Elliott P, Riley S. The use of representative community samples to assess SARS-CoV-2 lineage competition: Alpha outcompetes Beta and wild-type in England from January to March 2021. Microb Genom 2023; 9:mgen000887. [PMID: 36745545 PMCID: PMC9997751 DOI: 10.1099/mgen.0.000887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Genomic surveillance for SARS-CoV-2 lineages informs our understanding of possible future changes in transmissibility and vaccine efficacy and will be a high priority for public health for the foreseeable future. However, small changes in the frequency of one lineage over another are often difficult to interpret because surveillance samples are obtained using a variety of methods all of which are known to contain biases. As a case study, using an approach which is largely free of biases, we here describe lineage dynamics and phylogenetic relationships of the Alpha and Beta variant in England during the first 3 months of 2021 using sequences obtained from a random community sample who provided a throat and nose swab for rt-PCR as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. Overall, diversity decreased during the first quarter of 2021, with the Alpha variant (first identified in Kent) becoming predominant, driven by a reproduction number 0.3 higher than for the prior wild-type. During January, positive samples were more likely to be Alpha in those aged 18 to 54 years old. Although individuals infected with the Alpha variant were no more likely to report one or more classic COVID-19 symptoms compared to those infected with wild-type, they were more likely to be antibody-positive 6 weeks after infection. Further, viral load was higher in those infected with the Alpha variant as measured by cycle threshold (Ct) values. The presence of infections with non-imported Beta variant (first identified in South Africa) during January, but not during February or March, suggests initial establishment in the community followed by fade-out. However, this occurred during a period of stringent social distancing. These results highlight how sequence data from representative community surveys such as REACT-1 can augment routine genomic surveillance during periods of lineage diversity.
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Affiliation(s)
- Oliver Eales
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- *Correspondence: Oliver Eales,
| | | | - Sonja N. Tang
- School of Public Health, Imperial College London, London, UK
| | - Caroline E. Walters
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Haowei Wang
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - David Haw
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | | | | | | | | | | | - Deborah Ashby
- School of Public Health, Imperial College London, London, UK
| | - Graham Cooke
- Department of Infectious Disease, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
| | - Wendy Barclay
- Department of Infectious Disease, Imperial College London, London, UK
| | - Christl A. Donnelly
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | | | - Erik Volz
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | | | - Ara Darzi
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
- Institute of Global Health Innovation at Imperial College London, London, UK
| | - Helen Ward
- School of Public Health, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
| | - Paul Elliott
- School of Public Health, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Health Data Research (HDR) UK London at Imperial College, London, UK
- UK Dementia Research Institute at Imperial College, London, UK
- *Correspondence: Paul Elliott,
| | - Steven Riley
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- *Correspondence: Steven Riley,
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9
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Ding C, Ni S, Zhang X, Xie J, Sun Y, He J, Mei Q, Huang L, He H, Liu Z, Gao Y. Evaluation of humoral immune responses induced by different SARS-CoV-2 spike trimers from wild-type and emerging variants with individual, sequential, and combinational delivered strategies. J Med Virol 2022; 94:5841-5849. [PMID: 35986565 PMCID: PMC9538904 DOI: 10.1002/jmv.28081] [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: 07/10/2022] [Revised: 08/17/2022] [Accepted: 08/17/2022] [Indexed: 01/06/2023]
Abstract
The spike trimer of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an effective target for inducing neutralizing antibodies by coronavirus disease 2019 (COVID-19) vaccines. However, the diversity of spike protein from emerging SASR-CoV-2 variants has become the major challenge for development of a universal vaccine. To investigate the immunogenicity of spike proteins from various circulating strains including wild type, Delta, and Omicron variants, we produced various natural spike trimers and designed three vaccination strategies, that is, individual, sequential, and bivalent regimens to assess autologous and heterogenous antibody responses in a mouse model. The results indicated that monovalent vaccine strategy with individual spike trimer could only induce binding and neutralizing antibodies against homologous viruses. However, sequential and bivalent immunization with Delta and Omicron spike trimers could induce significantly broader neutralizing antibody responses against heterogenous SARS-CoV-2. Interestingly, the spike trimer from Omicron variant showed superior immunogenicity in inducing antibody response against recently emerging XE variant. Taken together, our data supported the development of novel vaccination strategies or multivalent vaccine against emerging variants.
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Affiliation(s)
- Chengchao Ding
- The First Affiliated Hospital of USTC, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiChina
| | - Shuangshuang Ni
- The First Affiliated Hospital of USTC, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiChina
| | - Xiangyu Zhang
- The First Affiliated Hospital of USTC, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiChina
| | - Jiajia Xie
- The First Affiliated Hospital of USTC, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiChina
| | - Yong Sun
- Department of MicrobiologyAnhui Provincial Center for Disease Control and PreventionHefeiAnhuiChina
| | - Jun He
- Department of MicrobiologyAnhui Provincial Center for Disease Control and PreventionHefeiAnhuiChina
| | - Qingmin Mei
- The First Affiliated Hospital of USTC, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiChina
| | - Lina Huang
- The First Affiliated Hospital of USTC, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiChina
| | - Hongliang He
- The First Affiliated Hospital of USTC, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiChina
| | - Zhirong Liu
- Department of MicrobiologyAnhui Provincial Center for Disease Control and PreventionHefeiAnhuiChina
| | - Yong Gao
- The First Affiliated Hospital of USTC, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiChina
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