1
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Ge X, Zhou H, Shen F, Yang G, Zhang Y, Zhang X, Li H. SARS-CoV-2 subgenomic RNA: formation process and rapid molecular diagnostic methods. Clin Chem Lab Med 2024; 62:1019-1028. [PMID: 38000044 DOI: 10.1515/cclm-2023-0846] [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: 08/04/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which caused coronavirus disease-2019 (COVID-19) is spreading worldwide and posing enormous losses to human health and socio-economic. Due to the limitations of medical and health conditions, it is still a huge challenge to develop appropriate discharge standards for patients with COVID-19 and to use medical resources in a timely and effective manner. Similar to other coronaviruses, SARS-CoV-2 has a very complex discontinuous transcription process to generate subgenomic RNA (sgRNA). Some studies support that sgRNA of SARS-CoV-2 can only exist when the virus is active and is an indicator of virus replication. The results of sgRNA detection in patients can be used to evaluate the condition of hospitalized patients, which is expected to save medical resources, especially personal protective equipment. There have been numerous investigations using different methods, especially molecular methods to detect sgRNA. Here, we introduce the process of SARS-CoV-2 sgRNA formation and the commonly used molecular diagnostic methods to bring a new idea for clinical detection in the future.
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Affiliation(s)
- Xiao Ge
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Huizi Zhou
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Fangyuan Shen
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Guimao Yang
- Department of Medical Laboratory, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P.R. China
| | - Yubo Zhang
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Xiaoyu Zhang
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Heng Li
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
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2
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Berry GJ, Jhaveri TA, Larkin PMK, Mostafa H, Babady NE. ADLM Guidance Document on Laboratory Diagnosis of Respiratory Viruses. J Appl Lab Med 2024; 9:599-628. [PMID: 38695489 DOI: 10.1093/jalm/jfae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 06/06/2024]
Abstract
Respiratory viral infections are among the most frequent infections experienced worldwide. The COVID-19 pandemic has highlighted the need for testing and currently several tests are available for the detection of a wide range of viruses. These tests vary widely in terms of the number of viral pathogens included, viral markers targeted, regulatory status, and turnaround time to results, as well as their analytical and clinical performance. Given these many variables, selection and interpretation of testing requires thoughtful consideration. The current guidance document is the authors' expert opinion based on the preponderance of available evidence to address key questions related to best practices for laboratory diagnosis of respiratory viral infections including who to test, when to test, and what tests to use. An algorithm is proposed to help laboratories decide on the most appropriate tests to use for the diagnosis of respiratory viral infections.
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Affiliation(s)
- Gregory J Berry
- Columbia University Vagelos College of Physicians and Surgeons, New York-Presbyterian-Columbia University Irving Medical Center, New York, NY, United States
| | - Tulip A Jhaveri
- Department of Internal Medicine, Division of Infectious Diseases, University of Mississippi Medical Center, Jackson, MS, United States
| | - Paige M K Larkin
- University of Chicago Pritzker School of Medicine, NorthShore University Health System, Chicago, IL, United States
| | - Heba Mostafa
- Johns Hopkins School of Medicine, Department of Pathology, Baltimore, MD, United States
| | - N Esther Babady
- Clinical Microbiology and Infectious Disease Services, Department of Pathology and Laboratory Medicine and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States
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3
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Bang LL, Tornby DR, Pham STD, Assing K, Möller S, Palarasah Y, Madsen LW, Thomsen KG, Johansen IS, Pedersen RM, Andersen TE. Culturing of SARS-CoV-2 from patient samples: Protocol for optimal virus recovery and assessment of infectious viral load. J Virol Methods 2024; 326:114912. [PMID: 38447645 DOI: 10.1016/j.jviromet.2024.114912] [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: 12/01/2023] [Revised: 01/16/2024] [Accepted: 03/02/2024] [Indexed: 03/08/2024]
Abstract
Optimal sampling, preservation, and culturing of SARS-CoV-2 from COVID-19 patients are critical for successful recovery of virus isolates and to accurately estimate contagiousness of the patient. In this study, we investigated the influence of the type of sampling media, storage time, freezing conditions, sterile filtration, and combinations of these to determine the optimal pre-analytic conditions for virus recovery and estimation of infectious viral load in COVID-19 patients. Further, we investigated the viral shedding kinetics and mucosal antibody response in 38 COVID-19 hospitalized patients. We found Universal Transport Medium (Copan) to be the most optimal medium for preservation of SARS-CoV-2 infectivity. Our data showed that the probability of a positive viral culture was strongly correlated to Ct values, however some samples did not follow the general trend. We found a significant correlation between plaque forming units and levels of mucosal antibodies and found that high levels of mucosal antibodies correlated with reduced chance of isolating the virus. Our data reveals essential parameters to consider from specimen collection over storage to culturing technique for optimal chance of isolating SARS-CoV-2 and accurately estimating patient contagiousness.
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Affiliation(s)
- Line L Bang
- Department of Clinical Microbiology, Odense University Hospital and Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Ditte R Tornby
- Department of Clinical Microbiology, Odense University Hospital and Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Stephanie T D Pham
- Department of Cancer and Inflammation Research, Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Kristian Assing
- Department of Clinical Immunology, Odense University Hospital and Research Unit for Clinical Immunology, University of Southern Denmark, Odense, Denmark
| | - Sören Möller
- Open Patient Data Explorative Network (OPEN), Department of Clinical Research, University of Southern Denmark and Odense University Hospital, Odense 5000, Denmark
| | - Yaseelan Palarasah
- Department of Cancer and Inflammation Research, Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Lone W Madsen
- Department of Infectious Diseases, Odense University Hospital and Research Unit for Infectious Diseases, University of Southern Denmark, Odense, Denmark; Department of Regional Health Research, University of Southern Denmark, Denmark; Unit for Infectious Diseases, Department of medicine, Sygehus Lillebælt, Kolding, Denmark
| | - Karina G Thomsen
- Department of Clinical Microbiology, Odense University Hospital and Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Isik S Johansen
- Department of Infectious Diseases, Odense University Hospital and Research Unit for Infectious Diseases, University of Southern Denmark, Odense, Denmark
| | - Rune M Pedersen
- Department of Clinical Microbiology, Odense University Hospital and Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Thomas E Andersen
- Department of Clinical Microbiology, Odense University Hospital and Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
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4
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Ellsworth CR, Wang C, Katz AR, Chen Z, Islamuddin M, Yang H, Scheuermann SE, Goff KA, Maness NJ, Blair RV, Kolls JK, Qin X. Natural Killer Cells Do Not Attenuate a Mouse-Adapted SARS-CoV-2-Induced Disease in Rag2-/- Mice. Viruses 2024; 16:611. [PMID: 38675952 PMCID: PMC11054502 DOI: 10.3390/v16040611] [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: 01/25/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
This study investigates the roles of T, B, and Natural Killer (NK) cells in the pathogenesis of severe COVID-19, utilizing mouse-adapted SARS-CoV-2-MA30 (MA30). To evaluate this MA30 mouse model, we characterized MA30-infected C57BL/6 mice (B6) and compared them with SARS-CoV-2-WA1 (an original SARS-CoV-2 strain) infected K18-human ACE2 (K18-hACE2) mice. We found that the infected B6 mice developed severe peribronchial inflammation and rapid severe pulmonary edema, but less lung interstitial inflammation than the infected K18-hACE2 mice. These pathological findings recapitulate some pathological changes seen in severe COVID-19 patients. Using this MA30-infected mouse model, we further demonstrate that T and/or B cells are essential in mounting an effective immune response against SARS-CoV-2. This was evident as Rag2-/- showed heightened vulnerability to infection and inhibited viral clearance. Conversely, the depletion of NK cells did not significantly alter the disease course in Rag2-/- mice, underscoring the minimal role of NK cells in the acute phase of MA30-induced disease. Together, our results indicate that T and/or B cells, but not NK cells, mitigate MA30-induced disease in mice and the infected mouse model can be used for dissecting the pathogenesis and immunology of severe COVID-19.
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Affiliation(s)
- Calder R Ellsworth
- Division of Comparative Pathology, Tulane National Primate Research Center, Health Sciences Campus, 18703 Three Rivers Road, Covington, LA 70433, USA; (C.R.E.); (C.W.); (Z.C.); (M.I.); (S.E.S.); (K.A.G.); (N.J.M.); (R.V.B.)
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Chenxiao Wang
- Division of Comparative Pathology, Tulane National Primate Research Center, Health Sciences Campus, 18703 Three Rivers Road, Covington, LA 70433, USA; (C.R.E.); (C.W.); (Z.C.); (M.I.); (S.E.S.); (K.A.G.); (N.J.M.); (R.V.B.)
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Alexis R Katz
- Departments of Medicine and Pediatrics, Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, LA 70112, USA; (A.R.K.); (H.Y.); (J.K.K.)
| | - Zheng Chen
- Division of Comparative Pathology, Tulane National Primate Research Center, Health Sciences Campus, 18703 Three Rivers Road, Covington, LA 70433, USA; (C.R.E.); (C.W.); (Z.C.); (M.I.); (S.E.S.); (K.A.G.); (N.J.M.); (R.V.B.)
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Mohammad Islamuddin
- Division of Comparative Pathology, Tulane National Primate Research Center, Health Sciences Campus, 18703 Three Rivers Road, Covington, LA 70433, USA; (C.R.E.); (C.W.); (Z.C.); (M.I.); (S.E.S.); (K.A.G.); (N.J.M.); (R.V.B.)
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Haoran Yang
- Departments of Medicine and Pediatrics, Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, LA 70112, USA; (A.R.K.); (H.Y.); (J.K.K.)
- Department of Pulmonary Critical Care and Environmental Medicine, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Sarah E Scheuermann
- Division of Comparative Pathology, Tulane National Primate Research Center, Health Sciences Campus, 18703 Three Rivers Road, Covington, LA 70433, USA; (C.R.E.); (C.W.); (Z.C.); (M.I.); (S.E.S.); (K.A.G.); (N.J.M.); (R.V.B.)
| | - Kelly A Goff
- Division of Comparative Pathology, Tulane National Primate Research Center, Health Sciences Campus, 18703 Three Rivers Road, Covington, LA 70433, USA; (C.R.E.); (C.W.); (Z.C.); (M.I.); (S.E.S.); (K.A.G.); (N.J.M.); (R.V.B.)
| | - Nicholas J Maness
- Division of Comparative Pathology, Tulane National Primate Research Center, Health Sciences Campus, 18703 Three Rivers Road, Covington, LA 70433, USA; (C.R.E.); (C.W.); (Z.C.); (M.I.); (S.E.S.); (K.A.G.); (N.J.M.); (R.V.B.)
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Robert V Blair
- Division of Comparative Pathology, Tulane National Primate Research Center, Health Sciences Campus, 18703 Three Rivers Road, Covington, LA 70433, USA; (C.R.E.); (C.W.); (Z.C.); (M.I.); (S.E.S.); (K.A.G.); (N.J.M.); (R.V.B.)
| | - Jay K Kolls
- Departments of Medicine and Pediatrics, Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, LA 70112, USA; (A.R.K.); (H.Y.); (J.K.K.)
- Department of Pulmonary Critical Care and Environmental Medicine, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Xuebin Qin
- Division of Comparative Pathology, Tulane National Primate Research Center, Health Sciences Campus, 18703 Three Rivers Road, Covington, LA 70433, USA; (C.R.E.); (C.W.); (Z.C.); (M.I.); (S.E.S.); (K.A.G.); (N.J.M.); (R.V.B.)
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
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5
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Popova G, Jakjovska T, Arnaudova-Danevska I, Boskovska K, Spasovska OS. Multiplex PCR in Diagnosing Respiratory Tract Infections in Hospitalized Children. Pril (Makedon Akad Nauk Umet Odd Med Nauki) 2024; 45:61-68. [PMID: 38575379 DOI: 10.2478/prilozi-2024-0007] [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] [Indexed: 04/06/2024]
Abstract
OBJECTIVES To elaborate the utility of multiplex quantitative polymerase chain reaction (multiplex qPCR) for the accurate diagnosis of severe respiratory tract infections (RTIs) in hospitalized children. METHODS In two separate periods during 2022, 76 respiratory specimens (combined throat/nasopharyngeal swabs) were submitted for multiplex qPCR regarding 26 respiratory pathogens. The specimens were obtained from children with severe RTIs hospitalized in the Institute for Respiratory Diseases in Children, Skopje. RESULTS Multiplex qPCR detected at least one respiratory pathogen in all examined specimens (76/76), with 83% (63/76) rate of co-infections. Considering that positive results are only the ones with Ct value below 28, the rates of detected pathogens and co-infections decrease to 75% and 22%, respectively. The most commonly detected pathogens during the spring period were Parainfluenza type 3 (PIV3) followed by Adenovirus (AdV) and Respiratory syncytial virus type B (RSVB) with frequency rate of 23%, 19% and 19%, respectively. During the autumn period, the most common were RSVB and Streptococcus pneumoniae with frequency rate of 31% and 17%, respectively. CONCLUSION Multiplex qPCR is a powerful tool for diagnosing RTIs. Semi-quantification of the viral load by reporting Ct values added higher level of evidence for accurate diagnosis. Seasonal detection of the examined viruses was notable with higher prevalence of PIV3 in spring and RSVB in autumn period.
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Affiliation(s)
- Gorica Popova
- Institute for Respiratory Diseases in Children-Kozle, Skopje, RN Macedonia
- Faculty of Medical Sciences, Goce Delcev University, Stip, RN Macedonia
| | - Tatjana Jakjovska
- Institute for Respiratory Diseases in Children-Kozle, Skopje, RN Macedonia
- Faculty of Medicine, Ss. Cyril and Methodius University in Skopje, RN Macedonia
| | - Ivana Arnaudova-Danevska
- Institute for Respiratory Diseases in Children-Kozle, Skopje, RN Macedonia
- Faculty of Medicine, Ss. Cyril and Methodius University in Skopje, RN Macedonia
| | - Katerina Boskovska
- Institute for Respiratory Diseases in Children-Kozle, Skopje, RN Macedonia
- Faculty of Medicine, Ss. Cyril and Methodius University in Skopje, RN Macedonia
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6
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Dimcheff DE, Blair CN, Zhu Y, Chappell JD, Gaglani M, McNeal T, Ghamande S, Steingrub JS, Shapiro NI, Duggal A, Busse LW, Frosch AEP, Peltan ID, Hager DN, Gong MN, Exline MC, Khan A, Wilson JG, Qadir N, Ginde AA, Douin DJ, Mohr NM, Mallow C, Martin ET, Johnson NJ, Casey JD, Stubblefield WB, Gibbs KW, Kwon JH, Talbot HK, Halasa N, Grijalva CG, Baughman A, Womack KN, Hart KW, Swan SA, Surie D, Thornburg NJ, McMorrow ML, Self WH, Lauring AS. Total and Subgenomic RNA Viral Load in Patients Infected With SARS-CoV-2 Alpha, Delta, and Omicron Variants. J Infect Dis 2023; 228:235-244. [PMID: 36883903 PMCID: PMC10420395 DOI: 10.1093/infdis/jiad061] [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: 02/20/2023] [Accepted: 03/06/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic and subgenomic RNA levels are frequently used as a correlate of infectiousness. The impact of host factors and SARS-CoV-2 lineage on RNA viral load is unclear. METHODS Total nucleocapsid (N) and subgenomic N (sgN) RNA levels were measured by quantitative reverse transcription polymerase chain reaction (RT-qPCR) in specimens from 3204 individuals hospitalized with coronavirus disease 2019 (COVID-19) at 21 hospitals. RT-qPCR cycle threshold (Ct) values were used to estimate RNA viral load. The impact of time of sampling, SARS-CoV-2 variant, age, comorbidities, vaccination, and immune status on N and sgN Ct values were evaluated using multiple linear regression. RESULTS Mean Ct values at presentation for N were 24.14 (SD 4.53) for non-variants of concern, 25.15 (SD 4.33) for Alpha, 25.31 (SD 4.50) for Delta, and 26.26 (SD 4.42) for Omicron. N and sgN RNA levels varied with time since symptom onset and infecting variant but not with age, comorbidity, immune status, or vaccination. When normalized to total N RNA, sgN levels were similar across all variants. CONCLUSIONS RNA viral loads were similar among hospitalized adults, irrespective of infecting variant and known risk factors for severe COVID-19. Total N and subgenomic RNA N viral loads were highly correlated, suggesting that subgenomic RNA measurements add little information for the purposes of estimating infectivity.
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Affiliation(s)
- Derek E Dimcheff
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Christopher N Blair
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Yuwei Zhu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - James D Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Manjusha Gaglani
- Baylor Scott and White Health, Texas A&M University College of Medicine, Temple, Texas, USA
| | - Tresa McNeal
- Baylor Scott and White Health, Texas A&M University College of Medicine, Temple, Texas, USA
| | - Shekhar Ghamande
- Baylor Scott and White Health, Texas A&M University College of Medicine, Temple, Texas, USA
| | - Jay S Steingrub
- Department of Medicine, Baystate Medical Center, Springfield, Massachusetts, USA
| | - Nathan I Shapiro
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Abhijit Duggal
- Department of Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | | | - Anne E P Frosch
- Department of Medicine, Hennepin County Medical Center, Minneapolis, Minnesota, USA
| | - Ithan D Peltan
- Department of Medicine, Intermountain Medical Center, Murray, Utah, USA
- Department of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - David N Hager
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michelle N Gong
- Department of Medicine, Montefiore Health System, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Matthew C Exline
- Department of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Akram Khan
- Department of Medicine, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Jennifer G Wilson
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Nida Qadir
- Department of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Adit A Ginde
- Department of Emergency Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - David J Douin
- Department of Anesthesiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Nicholas M Mohr
- Department of Emergency Medicine, University of Iowa, Iowa City, Iowa, USA
| | | | - Emily T Martin
- School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Nicholas J Johnson
- Department of Emergency Medicine and Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, Washington, USA
| | - Jonathan D Casey
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - William B Stubblefield
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kevin W Gibbs
- Department of Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jennie H Kwon
- Department of Medicine, Washington University, St Louis, Missouri, USA
| | - H Keipp Talbot
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Natasha Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Carlos G Grijalva
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Adrienne Baughman
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kelsey N Womack
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kimberly W Hart
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Sydney A Swan
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Diya Surie
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Natalie J Thornburg
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Meredith L McMorrow
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Wesley H Self
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Adam S Lauring
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
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7
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Laverack M, Tallmadge RL, Venugopalan R, Sheehan D, Ross S, Rustamov R, Frederici C, Potter KS, Elvinger F, Warnick LD, Koretzky GA, Lawlis R, Plocharczyk E, Diel DG. The Cornell COVID-19 Testing Laboratory: A Model to High-Capacity Testing Hubs for Infectious Disease Emergency Response and Preparedness. Viruses 2023; 15:1555. [PMID: 37515241 PMCID: PMC10385863 DOI: 10.3390/v15071555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
The unprecedented COVID-19 pandemic posed major challenges to local, regional, and global economies and health systems, and fast clinical diagnostic workflows were urgently needed to contain the spread of SARS-CoV-2. Here, we describe the platform and workflow established at the Cornell COVID-19 Testing Laboratory (CCTL) for the high-throughput testing of clinical samples from the university and the surrounding community. This workflow enabled efficient and rapid detection and the successful control of SARS-CoV-2 infection on campus and its surrounding communities. Our cost-effective and fully automated workflow enabled the testing of over 8000 pooled samples per day and provided results for over 2 million samples. The automation of time- and effort-intensive sample processing steps such as accessioning and pooling increased laboratory efficiency. Customized software applications were developed to track and store samples, deconvolute positive pools, track and report results, and for workflow integration from sample receipt to result reporting. Additionally, quality control dashboards and turnaround-time tracking applications were built to monitor assay and laboratory performance. As infectious disease outbreaks pose a constant threat to both human and animal health, the highly effective workflow implemented at CCTL could be modeled to establish regional high-capacity testing hubs for infectious disease preparedness and emergency response.
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Affiliation(s)
- Melissa Laverack
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center (AHDC), College of Veterinary Medicine, Cornell COVID-19 Testing Laboratory (CCTL), Cornell University, Ithaca, NY 14853, USA
| | - Rebecca L Tallmadge
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center (AHDC), College of Veterinary Medicine, Cornell COVID-19 Testing Laboratory (CCTL), Cornell University, Ithaca, NY 14853, USA
| | - Roopa Venugopalan
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center (AHDC), College of Veterinary Medicine, Cornell COVID-19 Testing Laboratory (CCTL), Cornell University, Ithaca, NY 14853, USA
| | - Daniel Sheehan
- Information Technology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Scott Ross
- Information Technology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Rahim Rustamov
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center (AHDC), College of Veterinary Medicine, Cornell COVID-19 Testing Laboratory (CCTL), Cornell University, Ithaca, NY 14853, USA
| | - Casey Frederici
- Cayuga Medical Center, Cayuga Health System, Ithaca, NY 14850, USA
| | - Kim S Potter
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center (AHDC), College of Veterinary Medicine, Cornell COVID-19 Testing Laboratory (CCTL), Cornell University, Ithaca, NY 14853, USA
| | - François Elvinger
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center (AHDC), College of Veterinary Medicine, Cornell COVID-19 Testing Laboratory (CCTL), Cornell University, Ithaca, NY 14853, USA
| | - Lorin D Warnick
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center (AHDC), College of Veterinary Medicine, Cornell COVID-19 Testing Laboratory (CCTL), Cornell University, Ithaca, NY 14853, USA
| | - Gary A Koretzky
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
- Department of Medicine, Weill Cornell Medicine, Cornell University, New York City, NY 10065, USA
| | - Robert Lawlis
- Cayuga Medical Center, Cayuga Health System, Ithaca, NY 14850, USA
| | | | - Diego G Diel
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center (AHDC), College of Veterinary Medicine, Cornell COVID-19 Testing Laboratory (CCTL), Cornell University, Ithaca, NY 14853, USA
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8
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Tang MHE, Ng KL, Edslev SM, Ellegaard K, Stegger M, Alexandersen S. Comparative subgenomic mRNA profiles of SARS-CoV-2 Alpha, Delta and Omicron BA.1, BA.2 and BA.5 sub-lineages using Danish COVID-19 genomic surveillance data. EBioMedicine 2023; 93:104669. [PMID: 37348163 PMCID: PMC10281627 DOI: 10.1016/j.ebiom.2023.104669] [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: 02/08/2023] [Revised: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has rapidly spread worldwide in the population since it was first detected in late 2019. The transcription and replication of coronaviruses, although not fully understood, is characterised by the production of genomic length RNA and shorter subgenomic RNAs to make viral proteins and ultimately progeny virions. Observed levels of subgenomic RNAs differ between sub-lineages and open reading frames but their biological significance is presently unclear. METHODS Using a large and diverse panel of virus sequencing data produced as part of the Danish COVID-19 routine surveillance together with information in electronic health registries, we assessed the association of subgenomic RNA levels with demographic and clinical variables of the infected individuals. FINDINGS Our findings suggest no significant statistical relationship between levels of subgenomic RNAs and host-related factors. INTERPRETATION Differences between lineages and subgenomic ORFs may be related to differences in target cell tropism, early virus replication/transcription kinetics or sequence features. FUNDING The author(s) received no specific funding for this work.
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Affiliation(s)
- Man-Hung Eric Tang
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Kim Lee Ng
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Sofie Marie Edslev
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Kirsten Ellegaard
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Soren Alexandersen
- Division of Diagnostic Preparedness, Statens Serum Institut, Copenhagen, Denmark.
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Roesmann F, Jakobsche I, Pallas C, Wilhelm A, Raffel J, Kohmer N, Toptan T, Berger A, Goetsch U, Ciesek S, Widera M. Comparison of the Ct-values for genomic and subgenomic SARS-CoV-2 RNA reveals limited predictive value for the presence of replication competent virus. J Clin Virol 2023; 165:105499. [PMID: 37327554 DOI: 10.1016/j.jcv.2023.105499] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/23/2023] [Accepted: 05/28/2023] [Indexed: 06/18/2023]
Abstract
SARS-CoV-2 is the causative agent of the acute respiratory disease COVID-19. In addition to the full length positive-sensed, single-stranded genomic RNA (gRNA), viral subgenomic RNAs (sgRNAs) that are required for expression of the 3' region of the genome are synthesized in virus-infected cells. However, whether these sgRNA-species might be used as a measure of active virus replication and to predict infectivity is still under debate. The commonly used methods to monitor and quantitate SARS-CoV-2 infections are based on RT-qPCR analysis and the detection of gRNA. The infectivity of a sample obtained from nasopharyngeal or throat swabs is associated with the viral load and inversely correlates with Ct-values, however, a cut-off value predicting the infectivity highly depends on the performance of the assay. Furthermore, gRNA derived Ct-values result from nucleic acid detection and do not necessarily correspond to active replicating virus. We established a multiplex RT-qPCR assay on the cobas 6800 omni utility channel concomitantly detecting SARS-CoV-2 gRNAOrf1a/b, sgRNAE,7a,N, and human RNaseP-mRNA used as human input control. We compared the target specific Ct-values with the viral culture frequency and performed ROC curve analysis to determine the assay sensitivity and specificity. We found no advantage in the prediction of viral culture when using sgRNA detection compared to gRNA only, since Ct-values for gRNA and sgRNA were highly correlated and gRNA offered a slightly more reliable predictive value. Single Ct-values alone only provide a very limited prediction for the presence of replication competent virus. Hence, careful consideration of the medical history including symptom onset has to be considered for risk stratification.
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Affiliation(s)
- Fabian Roesmann
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Sandhofstr. 2-4, House 75, Room 1.207, Frankfurt am Main 60528, Germany
| | - Irene Jakobsche
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Sandhofstr. 2-4, House 75, Room 1.207, Frankfurt am Main 60528, Germany
| | - Christiane Pallas
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Sandhofstr. 2-4, House 75, Room 1.207, Frankfurt am Main 60528, Germany
| | - Alexander Wilhelm
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Sandhofstr. 2-4, House 75, Room 1.207, Frankfurt am Main 60528, Germany
| | - Johanna Raffel
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Sandhofstr. 2-4, House 75, Room 1.207, Frankfurt am Main 60528, Germany
| | - Niko Kohmer
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Sandhofstr. 2-4, House 75, Room 1.207, Frankfurt am Main 60528, Germany
| | - Tuna Toptan
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Sandhofstr. 2-4, House 75, Room 1.207, Frankfurt am Main 60528, Germany
| | - Annemarie Berger
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Sandhofstr. 2-4, House 75, Room 1.207, Frankfurt am Main 60528, Germany
| | - Udo Goetsch
- Health Protection Authority, Frankfurt am Main, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Sandhofstr. 2-4, House 75, Room 1.207, Frankfurt am Main 60528, Germany; German Center for Infection Research, DZIF, Braunschweig, Germany; Branch Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Frankfurt am Main, Germany
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Sandhofstr. 2-4, House 75, Room 1.207, Frankfurt am Main 60528, Germany.
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10
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Osborn LJ, Chen PY, Flores-Vazquez J, Mestas J, Salas E, Glucoft M, Smit MA, Costales C, Dien Bard J. Clinical utility of SARS-CoV-2 subgenomic RT-PCR in a pediatric quaternary care setting. J Clin Virol 2023; 164:105494. [PMID: 37210881 DOI: 10.1016/j.jcv.2023.105494] [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: 03/21/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND During active transcription, SARS-CoV-2 generates subgenomic regions of viral RNA. While standard SARS-CoV-2 RT-PCR amplifies region(s) of genomic RNA, it cannot distinguish active infection from remnant viral genomic material. However, screening for subgenomic RNA (sgRNA) by RT-PCR may aid in the determination of actively transcribing virus. OBJECTIVES To evaluate the clinical utility of SARS-CoV-2 sgRNA RT-PCR testing in a pediatric population. STUDY DESIGN Retrospective analysis was performed on inpatients from February-September 2022 positive for SARS-CoV-2 by RT-PCR with a concomitant order for sgRNA RT-PCR. Chart abstractions were conducted to determine clinical outcomes, management, and infection prevention and control (IPC) practices. RESULTS Of 95 SARS-CoV-2 positive samples from 75 unique patients, 27 (28.4%) were positive by sgRNA RT-PCR. A negative sgRNA RT-PCR test allowed for de-isolation in 68 (71.6%) patient episodes. Regardless of age or sex, a positive sgRNA RT-PCR result significantly correlated with disease severity (P = 0.007), generalized COVID-19 symptoms (P = 0.012), hospitalization for COVID-19 (P = 0.019), and immune status (P = 0.024). Moreover, sgRNA RT-PCR results prompted changes in management in 28 patients (37.3%); specifically, therapeutic escalation in 13/27 (48.1%) positives and de-escalation in 15/68 (22.1%) negatives. CONCLUSIONS Taken together, these findings underscore the clinical utility of sgRNA RT-PCR testing in a pediatric population as we report significant associations between sgRNA RT-PCR results and clinical parameters related to COVID-19. These findings align with the proposed use of sgRNA RT-PCR testing to guide patient management and IPC practices in the hospital setting.
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Affiliation(s)
- Lucas J Osborn
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Pei Ying Chen
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Jessica Flores-Vazquez
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Javier Mestas
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Edahrline Salas
- Department of Infection Prevention and Control, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Marisa Glucoft
- Department of Infection Prevention and Control, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Michael A Smit
- Department of Infection Prevention and Control, Children's Hospital Los Angeles, Los Angeles, CA, United States; Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Cristina Costales
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.
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11
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Maya S, Kahn JG. COVID-19 testing protocols to guide duration of isolation: a cost-effectiveness analysis. BMC Public Health 2023; 23:864. [PMID: 37170225 PMCID: PMC10173903 DOI: 10.1186/s12889-023-15762-0] [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: 08/17/2022] [Accepted: 04/26/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND The Omicron variant of SARS-CoV-2 led to a steep rise in transmissions, and emerging variants continue to influence case rates across the US. As public tolerance for isolation abated, CDC guidance on duration of at-home isolation of COVID-19 cases was shortened to five days if no symptoms, with no laboratory test requirement, despite more cautious approaches advocated by other federal experts. METHODS We conducted a decision tree analysis of alternative protocols for ending COVID-19 isolation, estimating net costs (direct and productivity), secondary infections, and incremental cost-effectiveness ratios. Sensitivity analyses assessed the impact of input uncertainty. RESULTS Per 100 individuals, five-day isolation had 23 predicted secondary infections and a net cost of $33,000. Symptom check on day five (CDC guidance) yielded a 23% decrease in secondary infections (to 17.8), with a net cost of $45,000. Antigen testing on day six yielded 2.9 secondary infections and $63,000 in net costs. This protocol, compared to the next best protocol of antigen testing on day five of a maximum eight-day isolation, cost an additional $1,300 per secondary infection averted. Antigen or polymerase chain reaction testing on day five were dominated (more expensive and less effective) versus antigen testing on day six. Results were qualitatively robust to uncertainty in key inputs. CONCLUSIONS A six-day isolation with antigen testing to confirm the absence of contagious virus appears the most effective and cost-effective de-isolation protocol to shorten at-home isolation of individuals with COVID-19.
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Affiliation(s)
- Sigal Maya
- Philip R. Lee Institute for Health Policy Studies, University of California San Francisco, 490 Illinois St, Box 0936, 95158, San Francisco, CA, USA.
| | - James G Kahn
- Philip R. Lee Institute for Health Policy Studies, University of California San Francisco, 490 Illinois St, Box 0936, 95158, San Francisco, CA, USA
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12
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Ribeiro IP, Nascimento LGD, Tort LFL, Pereira EC, Menezes LSR, Malta FC, Oliveira BCEPDD, Rodrigues JP, Manso PPDA, Pelajo M, Bonaldo MC, Silva PCR, Siqueira MM, Brasil P, Fumian TM. Infectious SARS-CoV-2 Particles from Rectal Swab Samples from COVID-19 Patients in Brazil. Viruses 2023; 15:v15051152. [PMID: 37243238 DOI: 10.3390/v15051152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/02/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
The main objective of this study was to investigate the dynamic of SARS-CoV-2 viral excretion in rectal swab (RS), saliva, and nasopharyngeal swab (NS) samples from symptomatic patients and asymptomatic contacts. In addition, in order to evaluate the replication potential of SARS-CoV-2 in the gastrointestinal (GI) tract and the excretion of infectious SARS-CoV-2 from feces, we investigated the presence of subgenomic nucleoprotein gene (N) mRNA (sgN) in RS samples and cytopathic effects in Vero cell culture. A prospective cohort study was performed to collect samples from symptomatic patients and contacts in Rio de Janeiro, Brazil, from May to October 2020. One hundred and seventy-six patients had samples collected at home visits and/or during the follow up, resulting in a total of 1633 RS, saliva, or NS samples. SARS-CoV-2 RNA was detected in 130 (73.9%) patients who had at least one sample that tested positive for SARS-CoV-2. The presence of replicating SARS-CoV-2 in RS samples, measured by the detection of sgN mRNA, was successfully achieved in 19.4% (6/31) of samples, whilst infectious SARS-CoV-2, measured by the generation of cytopathic effects in cell culture, was identified in only one RS sample. Although rare, our results demonstrated the replication capacity of SARS-CoV-2 in the GI tract, and infectious viruses in one RS sample. There is still a gap in the knowledge regarding SARS-CoV-2 fecal-oral transmission. Additional studies are warranted to investigate fecal or wastewater exposure as a risk factor for transmission in human populations.
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Affiliation(s)
- Ieda Pereira Ribeiro
- Laboratório de Medicina Experimental e Saúde, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Lilian Gonçalves do Nascimento
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Luis Fernando Lopez Tort
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
- Laboratório de Virologia Molecular, Universidad de la República, Centro Universitario Regional Litoral Norte, Salto 50000, Uruguay
| | - Elisa Cavalcante Pereira
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Lidiane Souza Raphael Menezes
- Laboratório de Medicina Experimental e Saúde, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Fabio Correia Malta
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | | | - João Paulo Rodrigues
- Laboratório de Medicina Experimental e Saúde, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Pedro Paulo de Abreu Manso
- Laboratório de Medicina Experimental e Saúde, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Marcelo Pelajo
- Laboratório de Medicina Experimental e Saúde, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Myrna Cristina Bonaldo
- Laboratório de Medicina Experimental e Saúde, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Paola Cristina Resende Silva
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Marilda Mendonça Siqueira
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Patricia Brasil
- Laboratório de Doenças Febris Agudas, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Tulio Machado Fumian
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
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13
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Vreman S, van der Heijden EMDL, Ravesloot L, Ludwig IS, van den Brand JMA, Harders F, Kampfraath AA, Egberink HF, Gonzales JL, Oreshkova N, Broere F, van der Poel WHM, Gerhards NM. Immune Responses and Pathogenesis following Experimental SARS-CoV-2 Infection in Domestic Cats. Viruses 2023; 15:v15051052. [PMID: 37243138 DOI: 10.3390/v15051052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Several reports demonstrated the susceptibility of domestic cats to SARS-CoV-2 infection. Here, we describe a thorough investigation of the immune responses in cats after experimental SARS-CoV-2 inoculation, along with the characterization of infection kinetics and pathological lesions. Specific pathogen-free domestic cats (n = 12) were intranasally inoculated with SARS-CoV-2 and subsequently sacrificed on DPI (days post-inoculation) 2, 4, 7 and 14. None of the infected cats developed clinical signs. Only mild histopathologic lung changes associated with virus antigen expression were observed mainly on DPI 4 and 7. Viral RNA was present until DPI 7, predominantly in nasal and throat swabs. The infectious virus could be isolated from the nose, trachea and lungs until DPI 7. In the swab samples, no biologically relevant SARS-CoV-2 mutations were observed over time. From DPI 7 onwards, all cats developed a humoral immune response. The cellular immune responses were limited to DPI 7. Cats showed an increase in CD8+ cells, and the subsequent RNA sequence analysis of CD4+ and CD8+ subsets revealed a prominent upregulation of antiviral and inflammatory genes on DPI 2. In conclusion, infected domestic cats developed a strong antiviral response and cleared the virus within the first week after infection without overt clinical signs and relevant virus mutations.
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Affiliation(s)
- Sandra Vreman
- Wageningen Bioveterinary Research, Wageningen University & Research, 8221 RA Lelystad, The Netherlands
| | - Elisabeth M D L van der Heijden
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
| | - Lars Ravesloot
- Wageningen Bioveterinary Research, Wageningen University & Research, 8221 RA Lelystad, The Netherlands
| | - Irene S Ludwig
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
| | - Judith M A van den Brand
- Division of Pathology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
| | - Frank Harders
- Wageningen Bioveterinary Research, Wageningen University & Research, 8221 RA Lelystad, The Netherlands
| | - Andries A Kampfraath
- Wageningen Bioveterinary Research, Wageningen University & Research, 8221 RA Lelystad, The Netherlands
| | - Herman F Egberink
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
| | - Jose L Gonzales
- Wageningen Bioveterinary Research, Wageningen University & Research, 8221 RA Lelystad, The Netherlands
| | - Nadia Oreshkova
- Wageningen Bioveterinary Research, Wageningen University & Research, 8221 RA Lelystad, The Netherlands
| | - Femke Broere
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
| | - Wim H M van der Poel
- Wageningen Bioveterinary Research, Wageningen University & Research, 8221 RA Lelystad, The Netherlands
| | - Nora M Gerhards
- Wageningen Bioveterinary Research, Wageningen University & Research, 8221 RA Lelystad, The Netherlands
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14
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Arya AK, Garg A, Pal S, Sinha R, Tejan N, Pandey A, Ghoshal U. Evaluation of Rapid Antigen Test as a Marker of SARS-CoV-2 Infectivity. Cureus 2023; 15:e36962. [PMID: 37131571 PMCID: PMC10149086 DOI: 10.7759/cureus.36962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2023] [Indexed: 04/03/2023] Open
Abstract
Background Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that emerged in late 2019 continues to spread globally. Reverse transcriptase polymerase chain reaction (RT-PCR), which is considered the gold standard for diagnosis, does not always indicate contagiousness. This study was planned to evaluate the performance of the rapid antigen test (RAT) with the duration of symptoms and the usefulness of these tests in determining the infectivity of patients by performing sub-genomic RT-PCR. Methodology This prospective, observational study was designed to compare the diagnostic value of the COVID-19 RAT (SD Biosensor, Korea) with COVID-19 RT-PCR (Thermo Fisher, USA) by serial testing of patients. To evaluate the infectivity of the virus, sub-genomic RT-PCR was performed on previous RAT and RT-PCR-positive samples. Results Of 200 patients, 102 were positive on both RT-PCR and RAT, with 87 patients serially followed and tested. The sensitivity and specificity of RAT were 92.73% and 93.33%, respectively, in symptomatic patients. The mean duration of RAT positivity was 9.1 days, and the mean duration of RT-PCR positivity was 12.6 days. Sub-genomic RT-PCR test was performed on samples that were reported to be positive by RAT, and 73/87 (83.9%) patients were found to be positive. RAT was positive in symptomatic patients whose duration of illness was less than 10 days or those with a cycle threshold value below 32. Conclusions Thus, RAT can be used as the marker of infectivity of SARS-CoV-2 in symptomatic patients, especially in healthcare workers.
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15
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Tandjaoui-Lambiotte Y, Lomont A, Moenne-Locoz P, Seytre D, Zahar JR. Spread of viruses, which measures are the most apt to control COVID-19? Infect Dis Now 2023; 53:104637. [PMID: 36526247 PMCID: PMC9746078 DOI: 10.1016/j.idnow.2022.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 11/22/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022]
Abstract
The persistent debate about the modes of transmission of SARS-CoV2 and preventive measures has illustrated the limits of our knowledge regarding the measures to be implemented in the face of viral risk. Past and present (pandemic-related) scientific data underline the complexity of the phenomenon and its variability over time. Several factors contribute to the risk of transmission, starting with incidence in the general population (i.e., colonization pressure) and herd immunity. Other major factors include intensity of symptoms, interactions with the reservoir (proximity and duration of contact), the specific characteristics of the virus(es) involved, and a number of unpredictable elements (humidity, temperature, ventilation…). In this review, we will emphasize the difficulty of "standardizing" the situations that might explain the discrepancies found in the literature. We will show that the airborne route remains the main mode of transmission. Regarding preventive measures of prevention, while vaccination remains the cornerstone of the fight against viral outbreaks, we will remind the reader that wearing a mask is the main barrier measure and that the choice of type of mask depends on the risk situations. Finally, we believe that the recent pandemic should induce us in the future to modify our recommendations by adapting our measures in hospitals, not to the pathogen concerned, which is currently the case, but rather to the type of at-risk situation.
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Affiliation(s)
- Y Tandjaoui-Lambiotte
- Service de Pneumologie-Infectiologie, CH Saint Denis, 2 rue Dr. Delafontaine, 93200, France
| | - A Lomont
- Unité de Prévention du Risque Infectieux, Service de microbiologie clinique, GHU Paris Seine Saint-Denis, Université Sorbonne Paris Nord, France
| | - P Moenne-Locoz
- Unité de Prévention du Risque Infectieux, Service de microbiologie clinique, GHU Paris Seine Saint-Denis, Université Sorbonne Paris Nord, France
| | - D Seytre
- Unité de Prévention du Risque Infectieux, Service de microbiologie clinique, GHU Paris Seine Saint-Denis, Université Sorbonne Paris Nord, France
| | - J R Zahar
- Unité de Prévention du Risque Infectieux, Service de microbiologie clinique, GHU Paris Seine Saint-Denis, Université Sorbonne Paris Nord, France.
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16
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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: 8] [Impact Index Per Article: 8.0] [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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17
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Abstract
SARS-CoV-2 viral load and detection of infectious virus in the respiratory tract are the two key parameters for estimating infectiousness. As shedding of infectious virus is required for onward transmission, understanding shedding characteristics is relevant for public health interventions. Viral shedding is influenced by biological characteristics of the virus, host factors and pre-existing immunity (previous infection or vaccination) of the infected individual. Although the process of human-to-human transmission is multifactorial, viral load substantially contributed to human-to-human transmission, with higher viral load posing a greater risk for onward transmission. Emerging SARS-CoV-2 variants of concern have further complicated the picture of virus shedding. As underlying immunity in the population through previous infection, vaccination or a combination of both has rapidly increased on a global scale after almost 3 years of the pandemic, viral shedding patterns have become more distinct from those of ancestral SARS-CoV-2. Understanding the factors and mechanisms that influence infectious virus shedding and the period during which individuals infected with SARS-CoV-2 are contagious is crucial to guide public health measures and limit transmission. Furthermore, diagnostic tools to demonstrate the presence of infectious virus from routine diagnostic specimens are needed.
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Affiliation(s)
- Olha Puhach
- Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Benjamin Meyer
- Centre for Vaccinology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Isabella Eckerle
- Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland.
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.
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18
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Wang D, Lu H, Li Y, Shen J, Jiang G, Xiang J, Qin H, Guan M. Application of ultrasensitive assay for SARS-CoV-2 antigen in nasopharynx in the management of COVID-19 patients with comorbidities during the peak of 2022 Shanghai epidemics in a tertiary hospital. Clin Chem Lab Med 2023; 61:510-520. [PMID: 36480433 DOI: 10.1515/cclm-2022-0661] [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: 07/08/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Various comorbidities associated with COVID-19 add up in severity of the disease and obviously prolonged the time for viral clearance. This study investigated a novel ultrasensitive MAGLUMI® SARS-CoV-2 Ag chemiluminescent immunoassay assay (MAG-CLIA) for diagnosis and monitoring the infectivity of COVID-19 patients with comorbid conditions during the pandemic of 2022 Shanghai. METHODS Analytical performances of the MAG-CLIA were evaluated, including precision, limit of quantitation, linearity and specificity. Nasopharyngeal specimens from 232 hospitalized patients who were SARS-CoV-2 RT-qPCR positive and from 477 healthy donors were included. The longitudinal studies were performed by monitoring antigen concentrations alongside with RT-qPCR results in 14 COVID-19 comorbid participants for up to 22 days. The critical antigen concentration in determining virus infectivity was evaluated at the reference cycle threshold (Ct) of 35. RESULTS COVID-19 patients were well-identified using an optimal threshold of 0.64 ng/L antigen concentration, with sensitivity and specificity of 95.7% (95% CI: 92.2-97.9%) and 98.3% (95% CI: 96.7-99.3%), respectively, while the Wondfo LFT exhibited those of 34.9% (95% CI: 28.8-41.4%) and 100% (95% CI: 99.23-100%), respectively. The sensitivity of MAG-CLIA remained 91.46% (95% CI: 83.14-95.8%) for the samples with Ct values between 35 and 40. Close dynamic consistence was observed between MAG-CLIA and viral load time series in the longitudinal studies. The critical value of 8.82 ng/L antigen showed adequate sensitivity and specificity in evaluating the infectivity of hospitalized convalescent patients with comorbidities. CONCLUSIONS The MAG-CLIA SARS-CoV-2 Ag detection is an effective and alternative approach for rapid diagnosis and enables us to evaluate the infectivity of hospitalized convalescent patients with comorbidities.
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Affiliation(s)
- Di Wang
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Hailong Lu
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Yaju Li
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Jiazhen Shen
- Research & Development Department, Shenzhen New Industries Biomedical Engineering Co., Ltd., Shenzhen, P.R. China
| | - Guangjie Jiang
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Jin Xiang
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Huanhuan Qin
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Ming Guan
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, P.R. China.,Shanghai Huashen Institute of Microbes and Infections, Shanghai, P.R. China
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19
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Waggoner JJ, Tyburski EA, Lam WA. SARS-CoV-2 Results in Self-collected Nasal Swabs vs Swabs Collected by Health Care Workers in Children and Adolescents-Reply. JAMA 2023; 329:425-426. [PMID: 36749337 DOI: 10.1001/jama.2022.21599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | | | - Wilbur A Lam
- Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia
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20
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Kang S, Kim JY, Park H, Lim SY, Kim J, Chang E, Bae S, Jung J, Kim MJ, Chong YP, Lee S, Choi S, Kim YS, Park M, Kim S. Comparison of secondary attack rate and viable virus shedding between patients with SARS-CoV-2 Delta and Omicron variants: A prospective cohort study. J Med Virol 2023; 95:e28369. [PMID: 36458559 PMCID: PMC9877691 DOI: 10.1002/jmv.28369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/12/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022]
Abstract
There are limited data comparing the transmission rates and kinetics of viable virus shedding of the Omicron variant to those of the Delta variant. We compared these rates in hospitalized patients infected with Delta and Omicron variants. We prospectively enrolled adult patients with COVID-19 admitted to a tertiary care hospital in South Korea between September 2021 and May 2022. Secondary attack rates were calculated by epidemiologic investigation, and daily saliva samples were collected to evaluate viral shedding kinetics. Genomic and subgenomic SARS-CoV-2 RNA was measured by PCR, and virus culture was performed from daily saliva samples. A total of 88 patients with COVID-19 who agreed to daily sampling and were interviewed, were included. Of the 88 patients, 48 (59%) were infected with Delta, and 34 (41%) with Omicron; a further 5 patients gave undetectable or inconclusive RNA PCR results and 1 was suspected of being coinfected with both variants. Omicron group had a higher secondary attack rate (31% [38/124] vs. 7% [34/456], p < 0.001). Survival analysis revealed that shorter viable virus shedding period was observed in Omicron variant compared with Delta variant (median 4, IQR [1-7], vs. 8.5 days, IQR [5-12 days], p < 0.001). Multivariable analysis revealed that moderate-to-critical disease severity (HR: 1.96), and immunocompromised status (HR: 2.17) were independent predictors of prolonged viral shedding, whereas completion of initial vaccine series or first booster-vaccinated status (HR: 0.49), and Omicron infection (HR: 0.44) were independently associated with shorter viable virus shedding. Patients with Omicron infections had higher transmission rates but shorter periods of transmissible virus shedding than those with Delta infections.
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Affiliation(s)
- Sung‐Woon Kang
- Department of Infectious Diseases, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Ji Yeun Kim
- Department of Infectious Diseases, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Heedo Park
- Department of Biomedical Sciences, BK21 Graduate ProgramKorea University College of MedicineSeoulRepublic of Korea
- Department of Microbiology, Institute for Viral Diseases, Vaccine Innovation Center, College of MedicineKorea UniversitySeoulSouth Korea
| | - So Yun Lim
- Department of Infectious Diseases, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Jeonghun Kim
- Department of Biomedical Sciences, BK21 Graduate ProgramKorea University College of MedicineSeoulRepublic of Korea
- Department of Microbiology, Institute for Viral Diseases, Vaccine Innovation Center, College of MedicineKorea UniversitySeoulSouth Korea
| | - Euijin Chang
- Department of Infectious Diseases, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Seongman Bae
- Department of Infectious Diseases, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Jiwon Jung
- Department of Infectious Diseases, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Min Jae Kim
- Department of Infectious Diseases, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Yong Pil Chong
- Department of Infectious Diseases, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Sang‐Oh Lee
- Department of Infectious Diseases, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Sang‐Ho Choi
- Department of Infectious Diseases, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Yang Soo Kim
- Department of Infectious Diseases, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Man‐Seong Park
- Department of Biomedical Sciences, BK21 Graduate ProgramKorea University College of MedicineSeoulRepublic of Korea
- Department of Microbiology, Institute for Viral Diseases, Vaccine Innovation Center, College of MedicineKorea UniversitySeoulSouth Korea
| | - Sung‐Han Kim
- Department of Infectious Diseases, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
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21
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Theaux C, Martin Y, Montoto Piazza L, Wenk G, Notaristefano G, Miño L, Sevilla ME, Aprea V, Claps A, Nabaes Jodar M, Acuña D, Salvatori M, Álvarez L, Langan ME, Turk G, Del Olmo R, Viegas M, Bruno M, Bokser V. Persistence of SARS-CoV-2 RNA shedding and infectivity in immunized population: Prospective study along different epidemiological periods in Argentina. PLoS One 2023; 18:e0285704. [PMID: 37196044 DOI: 10.1371/journal.pone.0285704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 04/30/2023] [Indexed: 05/19/2023] Open
Abstract
During the pandemic of COVID-19, numerous waves of infections affected the two hemispheres with different impacts on each country. Throughout these waves, and with the emergence of new variants, health systems and scientists have tried to provide real-time responses to the complex biology of SARS-CoV-2, dealing with different clinical presentations, biological characteristics, and clinical impact of these variants. In this context, knowing the extent period in which an infected individual releases infectious viral particles has important implications for public health. This work aimed to investigate viral RNA shedding and infectivity of SARS-CoV-2 beyond 10 days after symptom onset (SO). A prospective multicenter study was performed between July/2021 and February/2022 on 116 immunized strategic personnel with COVID-19 diagnosed by RT-qPCR, with asymptomatic (7%), mild (91%) or moderate disease (2%). At the time of diagnosis, 70% had 2 doses of vaccines, 26% had 2 plus a booster, and 4% had one dose. After day 10 from SO, sequential nasopharyngeal swabs were taken to perform RT-qPCR, viral isolation, and S gene sequencing when possible. Viral sequences were obtained in 98 samples: 43% were Delta, 16% Lambda, 15% Gamma, 25% Omicron (BA.1) and 1% Non-VOC/VOI, in accordance with the main circulating variants at each moment. SARS-CoV-2 RNA was detected 10 days post SO in 57% of the subjects. Omicron was significantly less persistent. Noteworthy, infective viruses could not be isolated in any of the samples. In conclusion, a 10-days isolation period was useful to prevent further infections, and proved valid for the variants studied. Recently, even shorter periods have been applied, as the Omicron variant is prevalent, and worldwide population is largely vaccinated. In the future, facing the possible emergence of new variants and considering immunological status, a return to 10 days may be necessary.
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Affiliation(s)
- Clara Theaux
- División Laboratorio, Departamento de Diagnóstico y Tratamiento, Hospital General de Agudos Dr. Carlos G. Durand, Ciudad Autónoma de Buenos Aires, Argentina
| | - Yamila Martin
- Hospital Municipal de Rehabilitación Respiratoria María Ferrer, Ciudad Autónoma de Buenos Aires, Argentina
| | - Luciana Montoto Piazza
- Departamento de Diagnóstico y Tratamiento, Hospital General de Niños Pedro de Elizalde, Ciudad Autónoma de Buenos Aires, Argentina
| | - Gretel Wenk
- Departamento de Diagnóstico y Tratamiento, Hospital General de Niños Pedro de Elizalde, Ciudad Autónoma de Buenos Aires, Argentina
| | - Guillermo Notaristefano
- División Laboratorio, Departamento de Diagnóstico y Tratamiento, Hospital General de Agudos Dr. Carlos G. Durand, Ciudad Autónoma de Buenos Aires, Argentina
| | - Laura Miño
- División Promoción y Protección de la Salud, Hospital General de Niños Pedro de Elizalde, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Eugenia Sevilla
- División Promoción y Protección de la Salud, Hospital General de Niños Pedro de Elizalde, Ciudad Autónoma de Buenos Aires, Argentina
| | - Valeria Aprea
- División Promoción y Protección de la Salud, Hospital General de Niños Pedro de Elizalde, Ciudad Autónoma de Buenos Aires, Argentina
| | - Aldana Claps
- Departamento de Diagnóstico y Tratamiento, Hospital General de Niños Pedro de Elizalde, Ciudad Autónoma de Buenos Aires, Argentina
| | - Mercedes Nabaes Jodar
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, Ciudad Autónoma de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
- Consorcio Argentino de Genómica de SARS-CoV-2 (Proyecto PAIS), Ministerio de Ciencia, Tecnología e Innovación, Ciudad Autónoma de Buenos Aires, Argentina
| | - Dolores Acuña
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, Ciudad Autónoma de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
- Consorcio Argentino de Genómica de SARS-CoV-2 (Proyecto PAIS), Ministerio de Ciencia, Tecnología e Innovación, Ciudad Autónoma de Buenos Aires, Argentina
| | - Melina Salvatori
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), CONICET-Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Laura Álvarez
- División Promoción y Protección de la Salud, Hospital General de Agudos Dr. Carlos G. Durand, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Eugenia Langan
- División Promoción y Protección de la Salud, Hospital General de Agudos Dr. Carlos G. Durand, Ciudad Autónoma de Buenos Aires, Argentina
| | - Gabriela Turk
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), CONICET-Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Medicina, Departamento de Microbiología, Parasitología e Inmunología, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Ricardo Del Olmo
- Hospital Municipal de Rehabilitación Respiratoria María Ferrer, Ciudad Autónoma de Buenos Aires, Argentina
| | - Mariana Viegas
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, Ciudad Autónoma de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
- Consorcio Argentino de Genómica de SARS-CoV-2 (Proyecto PAIS), Ministerio de Ciencia, Tecnología e Innovación, Ciudad Autónoma de Buenos Aires, Argentina
| | - Miriam Bruno
- División Promoción y Protección de la Salud, Hospital General de Agudos Dr. Carlos G. Durand, Ciudad Autónoma de Buenos Aires, Argentina
| | - Vivian Bokser
- División Promoción y Protección de la Salud, Hospital General de Niños Pedro de Elizalde, Ciudad Autónoma de Buenos Aires, Argentina
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22
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Viloria Winnett A, Porter MK, Romano AE, Savela ES, Akana R, Shelby N, Reyes JA, Schlenker NW, Cooper MM, Carter AM, Ji J, Barlow JT, Tognazzini C, Feaster M, Goh YY, Ismagilov RF. Morning SARS-CoV-2 Testing Yields Better Detection of Infection Due to Higher Viral Loads in Saliva and Nasal Swabs upon Waking. Microbiol Spectr 2022; 10:e0387322. [PMID: 36287073 PMCID: PMC9769854 DOI: 10.1128/spectrum.03873-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/03/2022] [Indexed: 01/10/2023] Open
Abstract
Optimizing specimen collection methods to achieve the most reliable SARS-CoV-2 detection for a given diagnostic sensitivity would improve testing and minimize COVID-19 outbreaks. From September 2020 to April 2021, we performed a household-transmission study in which participants self-collected specimens every morning and evening throughout acute SARS-CoV-2 infection. Seventy mildly symptomatic participants collected saliva, and of those, 29 also collected nasal swab specimens. Viral load was quantified in 1,194 saliva and 661 nasal swab specimens using a high-analytical-sensitivity reverse transcription-quantitative PCR (RT-qPCR) assay. Viral loads in both saliva and nasal swab specimens were significantly higher in morning-collected specimens than in evening-collected specimens after symptom onset. This aspect of the biology of SARS-CoV-2 infection has implications for diagnostic testing. We infer that morning collection would have resulted in significantly improved detection and that this advantage would be most pronounced for tests with low to moderate analytical sensitivity. Collecting specimens for COVID-19 testing in the morning offers a simple and low-cost improvement to clinical diagnostic sensitivity of low- to moderate-analytical-sensitivity tests. IMPORTANCE Our findings suggest that collecting saliva and nasal swab specimens in the morning immediately after waking yields higher SARS-CoV-2 viral loads than collection later in the day. The higher viral loads from morning specimen collection are predicted to significantly improve detection of SARS-CoV-2 in symptomatic individuals, particularly when using moderate- to low-analytical-sensitivity COVID-19 diagnostic tests, such as rapid antigen tests.
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Affiliation(s)
| | | | - Anna E. Romano
- California Institute of Technology, Pasadena, California, USA
| | - Emily S. Savela
- California Institute of Technology, Pasadena, California, USA
| | - Reid Akana
- California Institute of Technology, Pasadena, California, USA
| | - Natasha Shelby
- California Institute of Technology, Pasadena, California, USA
| | | | | | | | | | - Jenny Ji
- California Institute of Technology, Pasadena, California, USA
| | - Jacob T. Barlow
- California Institute of Technology, Pasadena, California, USA
| | - Colten Tognazzini
- City of Pasadena Public Health Department, Pasadena, California, USA
| | - Matthew Feaster
- City of Pasadena Public Health Department, Pasadena, California, USA
| | - Ying-Ying Goh
- City of Pasadena Public Health Department, Pasadena, California, USA
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23
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A single-administration therapeutic interfering particle reduces SARS-CoV-2 viral shedding and pathogenesis in hamsters. Proc Natl Acad Sci U S A 2022; 119:e2204624119. [PMID: 36074824 PMCID: PMC9522362 DOI: 10.1073/pnas.2204624119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The high transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a primary driver of the COVID-19 pandemic. While existing interventions prevent severe disease, they exhibit mixed efficacy in preventing transmission, presumably due to their limited antiviral effects in the respiratory mucosa, whereas interventions targeting the sites of viral replication might more effectively limit respiratory virus transmission. Recently, intranasally administered RNA-based therapeutic interfering particles (TIPs) were reported to suppress SARS-CoV-2 replication, exhibit a high barrier to resistance, and prevent serious disease in hamsters. Since TIPs intrinsically target the tissues with the highest viral replication burden (i.e., respiratory tissues for SARS-CoV-2), we tested the potential of TIP intervention to reduce SARS-CoV-2 shedding. Here, we report that a single, postexposure TIP dose lowers SARS-CoV-2 nasal shedding, and at 5 days postinfection, infectious virus shed is below detection limits in 4 out of 5 infected animals. Furthermore, TIPs reduce shedding of Delta variant or WA-1 from infected to uninfected hamsters. Cohoused "contact" animals exposed to infected, TIP-treated animals exhibited significantly lower viral loads, reduced inflammatory cytokines, no severe lung pathology, and shortened shedding duration compared to animals cohoused with untreated infected animals. TIPs may represent an effective countermeasure to limit SARS-CoV-2 transmission.
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24
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Deming ME, Dong TQ, Agrawal V, Mills MG, Huang MLW, Greninger AL, Jerome KR, Wener MH, Paasche-Orlow MK, Kissinger P, Luk A, Hoffman RM, Stewart J, Kottkamp AC, Bershteyn A, Chu HY, Stankiewicz Karita HC, Johnston CM, Wald A, Barnabas R, Brown ER, Neuzil KM. Detection and Kinetics of Subgenomic Severe Acute Respiratory Syndrome Coronavirus 2 RNA Viral Load in Longitudinal Diagnostic RNA-Positive Samples. J Infect Dis 2022; 226:788-796. [PMID: 35150571 PMCID: PMC8903395 DOI: 10.1093/infdis/jiac048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/09/2022] [Indexed: 11/14/2022] Open
Abstract
While detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by diagnostic reverse-transcription polymerase chain reaction (RT-PCR) is highly sensitive for viral RNA, the nucleic acid amplification of subgenomic RNAs (sgRNAs) that are the product of viral replication may more accurately identify replication. We characterized the diagnostic RNA and sgRNA detection by RT-PCR from nasal swab samples collected daily by participants in postexposure prophylaxis or treatment studies for SARS-CoV-2. Among 1932 RT-PCR-positive swab samples with sgRNA tests, 40% (767) had detectable sgRNA. Above a diagnostic RNA viral load (VL) threshold of 5.1 log10 copies/mL, 96% of samples had detectable sgRNA with VLs that followed a linear trend. The trajectories of diagnostic RNA and sgRNA VLs differed, with 80% peaking on the same day but duration of sgRNA detection being shorter (8 vs 14 days). With a large sample of daily swab samples we provide comparative sgRNA kinetics and a diagnostic RNA threshold that correlates with replicating virus independent of symptoms or duration of illness.
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Affiliation(s)
- Meagan E Deming
- The Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Tracy Q Dong
- Vaccine and Infectious Disease Division, Fred Hutchinson, Cancer Research Center, Seattle, Washington, USA
| | - Vaidehi Agrawal
- The Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Margaret G Mills
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Meei Li W Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson, Cancer Research Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson, Cancer Research Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Mark H Wener
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Michael K Paasche-Orlow
- Section of General Internal Medicine, Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston, Massachusetts, USA
| | - Patricia Kissinger
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine
| | - Alfred Luk
- Section of Infectious Diseases, John W. Deming, Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Risa M Hoffman
- Division of Infectious Diseases, David Geffen School of Medicine at the University of California, Los Angeles, California, USA
| | - Jenell Stewart
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Division of Infectious Diseases & Immunology, Department of Medicine, New York University Grossman, School of Medicine, New York, New York, USA
| | - Angelica C Kottkamp
- Department of Population Health; New York University, Grossman School of Medicine, New York, New York, USA
| | - Anna Bershteyn
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Helen Y Chu
- Division of Infectious Diseases & Immunology, Department of Medicine, New York University Grossman, School of Medicine, New York, New York, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Christine M Johnston
- Vaccine and Infectious Disease Division, Fred Hutchinson, Cancer Research Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Division of Infectious Diseases & Immunology, Department of Medicine, New York University Grossman, School of Medicine, New York, New York, USA
| | - Anna Wald
- Vaccine and Infectious Disease Division, Fred Hutchinson, Cancer Research Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Division of Infectious Diseases & Immunology, Department of Medicine, New York University Grossman, School of Medicine, New York, New York, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Ruanne Barnabas
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Division of Infectious Diseases & Immunology, Department of Medicine, New York University Grossman, School of Medicine, New York, New York, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Elizabeth R Brown
- Vaccine and Infectious Disease Division, Fred Hutchinson, Cancer Research Center, Seattle, Washington, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Kathleen M Neuzil
- The Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
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25
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A Pilot Study Evaluating Subgenomic RNAs for Detection of Infectious SARS-CoV-2 in Nasopharyngeal Swabs. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2022. [DOI: 10.5812/archcid-128040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Background: The prolonged persistence of viral ribonucleic acid (RNA) in coronavirus disease 2019 (COVID-19) patients and the difficulty in differentiating between infectious virus and noninfectious viral RNA have impeded the use of current molecular diagnostic tests as a decision tool in quarantine termination. The performance of new methods to detect surrogate viability markers, such as subgenomic RNAs (sgRNAs), has been discussed, and numerous important questions are still needed to be addressed before broad implementation. Objectives: This study aimed to primarily evaluate the performance of SYBR green quantitative reverse transcription-polymerase chain reaction (RT-qPCR) targeting N and E sgRNAs as a surrogate of viability markers. Methods: This pilot study was carried out to detect genomic RNAs (gRNAs) and sgRNAs using RT-qPCR in cell culture infected with severe acute respiratory syndrome coronavirus 2 and nasopharyngeal swabbing samples from COVID-19 patients, and the results were compared to viral culture as a gold standard method for infectious virus detection. The diagnostic parameters and Cohen’s Kappa correlation index were then analyzed. Results: E subgenomic RNA detection was the most reliable predictor for actively replicating the virus as it showed the highest value of all diagnostic parameters with a good correlation with viral cultivation. The lowest cycle threshold value of gRNAs and sgN detection become undetectable by sgE within the range of 23 - 26. Conclusion: Using a suitable sgRNA type was important for test accuracy. The findings suggested E sgRNA detection as a promising surrogate approach to indicate a truly active viral infection, and when performed with a low-cost molecular test of SYBR green-based assay, it could support huge demands for routine analysis.
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Xie JW, He Y, Zheng YW, Wang M, Lin Y, Lin LR. Diagnostic accuracy of rapid antigen test for SARS-CoV-2: A systematic review and meta-analysis of 166,943 suspected COVID-19 patients. Microbiol Res 2022; 265:127185. [PMID: 36113309 PMCID: PMC9461282 DOI: 10.1016/j.micres.2022.127185] [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: 08/08/2022] [Revised: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 12/19/2022]
Abstract
To assess the diagnostic accuracy of the rapid antigen test (RAT) compared with RT-PCR (reference standard) for SARS-CoV-2, we searched MEDLINE/PubMed and Web of Science for relevant records. The QUADAS-2 tool was used to assess study quality, and quantitative synthesis was conducted using a bivariate random-effects model. The meta-analysis included 135 studies (166,943 samples). The pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio were 0.76 (95%CI: 0.73-0.79), 1.00 (95%CI: 1.00-1.00), 276.1 (95% CI, 184.1-414.1), 0.24 (95% CI, 0.21-0.27), and 1171 (95% CI, 782-1755), respectively. Compared to other sample types, nasal samples had the best RAT sensitivity [0.79 (95%CI: 0.71-0.85)]. The sensitivities of the different RAT kits ranged from 0.41 (95%CI: 0.23-0.61) to 0.90 (95%CI: 0.70-0.97). Sensitivity was markedly better in samples with lower Ct, and RAT achieved excellent pooled sensitivity at 1.00 (95%CI: 0.70-1.00) among samples with Ct < 20. Testing within 10 days of symptom onset resulted in a high sensitivity. For ≤ 3, ≤ 7, and ≤ 10 days, the sensitivities were 0.91 (95%CI: 0.83-0.96), 0.89 (95%CI: 0.84-0.93), and 0.88 (95%CI: 0.83-0.92), respectively. RAT kits show high sensitivity and specificity in early infection, especially when the viral load is high. Moreover, using nasal samples for antigen testing, which are moderately sensitive and patient-friendly, is a reliable alternative to nasopharyngeal sampling. RAT might be effective for fighting the COVID-19 pandemic; however, it must be complemented by the careful handling of negative test results.
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Affiliation(s)
- Jia-Wen Xie
- Center of Clinical Laboratory, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China; Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China
| | - Yun He
- Center of Clinical Laboratory, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China; Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China
| | - Ya-Wen Zheng
- Center of Clinical Laboratory, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China; Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China
| | - Mao Wang
- Center of Clinical Laboratory, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China; Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China
| | - Yong Lin
- Center of Clinical Laboratory, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China; Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China.
| | - Li-Rong Lin
- Center of Clinical Laboratory, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China; Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China.
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Dias VMDCH, Oliveira AF, Marinho AKBB, Santos Ferreira CED, Domingues CEF, Fortaleza CMCB, Vidal CFDL, Carrilho CMDDM, Pinheiro DOBP, de Assis DB, Medeiros EA, Morejón KML, Weissmann L, Michelin L, Carneiro M, Nogueira MDSDP, de Oliveira PRD, Buralli RJ, Stucchi RSB, Lins RS, Costa SF, Chebabo A. COVID-19 and isolation: Risks and implications in the scenario of new variants. Braz J Infect Dis 2022; 26:102703. [PMID: 36100081 PMCID: PMC9444891 DOI: 10.1016/j.bjid.2022.102703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/01/2022] [Accepted: 08/14/2022] [Indexed: 01/08/2023] Open
Abstract
With the emergence of new variants of SARS-CoV-2, questions about transmissibility, vaccine efficacy, and impact on mortality are important to support decision-making in public health measures. Modifications related to transmissibility combined with the fact that much of the population has already been partially exposed to infection and/or vaccination, have stimulated recommendations to reduce the isolation period for COVID-19. However, these new guidelines have raised questions about their effectiveness in reducing contamination and minimizing impact in work environments. Therefore, a collaborative task force was developed to review the subject in a non-systematic manner, answering questions about SARS-CoV-2 variants, COVID-19 vaccines, isolation/quarantine periods, testing to end the isolation period, and the use of masks as mitigation procedures. Overall, COVID-19 vaccines are effective in preventing severe illness and death but are less effective in preventing infection in the case of the Omicron variant. Any strategy that is adopted to reduce the isolation period should take into consideration the epidemiological situation of the geographical region, individual clinical characteristics, and mask for source control. The use of tests for isolation withdrawal should be evaluated with caution, due to results depending on various conditions and may not be reliable.
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Affiliation(s)
- Viviane Maria de Carvalho Hessel Dias
- Associação Brasileira dos Profissionais em Controle de Infecções e Epidemiologia Hospitalar, São Paulo, SP, Brazil; Sociedade Brasileira de Infectologia, São Paulo, SP, Brazil; Hospital Nossa Senhora das Graças, Curitiba, PR, Brazil; Hospital Marcelino Champagnat, Curitiba, PR, Brazil.
| | | | - Ana Karolina Barreto Berselli Marinho
- Associação Brasileira de Alergia e Imunologia, São Paulo, SP, Brazil; Serviço de Imunologia Clínica e Alergia, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Carlos Eduardo Dos Santos Ferreira
- Sociedade Brasileira de Patologia Clínica/Medicina Laboratorial, São Paulo, SP, Brazil; Laboratório Clínico ‒ Hospital Israelita Albert Einstein, São Paulo, SP, Brazil; Laboratório Central ‒ Hospital São Paulo, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | | | | | - Claudia Fernanda de Lacerda Vidal
- Associação Brasileira dos Profissionais em Controle de Infecções e Epidemiologia Hospitalar, São Paulo, SP, Brazil; Hospital das Clínicas da Universidade Federal de Pernambuco (HCUFPE), Recife, PE, Brazil
| | | | - Debora Otero Britto Passos Pinheiro
- Associação Brasileira dos Profissionais em Controle de Infecções e Epidemiologia Hospitalar, São Paulo, SP, Brazil; Hospital Universitário Pedro Ernesto, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, RJ, Brazil; Hospital Universitário Gaffrée e Guinle, Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Rio de Janeiro, RJ, Brazil
| | - Denise Brandão de Assis
- Divisão de Infecção Hospitalar/Centro de Vigilância Epidemiológica Prof. Alexandre Vranjac/Secretaria de Estado da Saúde de São Paulo, São Paulo, SP, Brazil
| | - Eduardo Alexandrino Medeiros
- Sociedade Brasileira de Infectologia, São Paulo, SP, Brazil; Disciplina de Infectologia, Escola Paulista de Medicina, Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Karen Mirna Loro Morejón
- Sociedade Brasileira de Infectologia, São Paulo, SP, Brazil; Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Leonardo Weissmann
- Sociedade Brasileira de Infectologia, São Paulo, SP, Brazil; Instituto de Infectologia Emilio Ribas, São Paulo, SP, Brazil; Faculdade de Medicina, Universidade de Ribeirão Preto (UNAERP), Guarujá, SP, Brazil
| | - Lessandra Michelin
- Sociedade Brasileira de Infectologia, São Paulo, SP, Brazil; Programa de Pós-Graduação em Ciências da Saúde, Universidade de Caxias do Sul (UCS), Rio Grande do Sul, RS, Brazil
| | - Marcelo Carneiro
- Associação Brasileira dos Profissionais em Controle de Infecções e Epidemiologia Hospitalar, São Paulo, SP, Brazil; Programa de Pós-Graduação Promoção da Saúde, Universidade de Santa Cruz do Sul (UNISC), Hospital Santa Cruz, Santa Cruz do Sul, RS, Brazil
| | | | - Priscila Rosalba Domingos de Oliveira
- Sociedade Brasileira de Infectologia, São Paulo, SP, Brazil; Instituto de Ortopedia e Traumatologia, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Rafael Junqueira Buralli
- Coordenação Geral de Saúde do Trabalhador, Departamento de Saúde Ambiental, do Trabalhador e Vigilância das Emergências em Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, DF, Brazil
| | - Raquel Silveira Bello Stucchi
- Sociedade Brasileira de Infectologia, São Paulo, SP, Brazil; Departamento de Clínica Médica, Área de Infectologia, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Rodrigo Schrage Lins
- Sociedade Brasileira de Infectologia, São Paulo, SP, Brazil; Hospital Naval Marcílio Dias, Rio de Janeiro, RJ, Brazil
| | - Silvia Figueiredo Costa
- Sociedade Brasileira de Infectologia, São Paulo, SP, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Alberto Chebabo
- Sociedade Brasileira de Infectologia, São Paulo, SP, Brazil; Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
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SARS-CoV-2 Virus Culture, Genomic and Subgenomic RNA Load, and Rapid Antigen Test in Experimentally Infected Syrian Hamsters. J Virol 2022; 96:e0103422. [PMID: 36040179 PMCID: PMC9517720 DOI: 10.1128/jvi.01034-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The duration of SARS-CoV-2 genomic RNA shedding is much longer than that of infectious SARS-CoV-2 in most COVID-19 patients. It is very important to determine the relationship between test results and infectivity for efficient isolation, contact tracing, and post-isolation. We characterized the duration of viable SARS-CoV-2, viral genomic and subgenomic RNA (gRNA and sgRNA), and rapid antigen test positivity in nasal washes, oropharyngeal swabs, and feces of experimentally infected Syrian hamsters. The duration of viral genomic RNA shedding is longer than that of viral subgenomic RNA, and far longer than those of rapid antigen test (RAgT) and viral culture positivity. The rapid antigen test results were strongly correlated with the viral culture results. The trend of subgenomic RNA is similar to that of genomic RNA, and furthermore, the subgenomic RNA load is highly correlated with the genomic RNA load. IMPORTANCE Our findings highlight the high correlation between rapid antigen test and virus culture results. The rapid antigen test would be an important supplement to real-time reverse transcription-RCR (RT-PCR) in early COVID-19 screening and in shortening the isolation period of COVID-19 patients. Because the subgenomic RNA load can be predicted from the genomic RNA load, measuring sgRNA does not add more benefit to determining infectivity than a threshold determined for gRNA based on viral culture.
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Fernandes da Silva D, Santos JV, Santos Martins F. Number Needed to Quarantine and Proportion of Prevented Infectious Days by Quarantine: Evaluating the Effectiveness of COVID-19 Contact Tracing. Public Health Rep 2022; 137:1178-1186. [PMID: 35989593 PMCID: PMC9548448 DOI: 10.1177/00333549221114343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Objectives: Information on the effectiveness of COVID-19 contact tracing is lacking. We proposed 2 measures for evaluating the effectiveness of contact tracing and applied them in a public health unit in northern Portugal. Methods: This retrospective cohort study included the contacts of people with COVID-19 diagnosed July 1–September 15, 2020. We examined 2 measures: (1) number needed to quarantine (NNQ), as the number of quarantine person-days needed to prevent 1 potential infectious person-day; and (2) proportion of prevented infectious days by quarantine (PPID), as the number of potential infectious days prevented by quarantine divided by all infectious days. We assessed these measures by sociodemographic characteristics, types of contacts, and intervention timings (ie, time between diagnosis or symptom onset and intervention). We considered 3 scenarios for infectiousness periods: 10 days before to 10 days after symptom onset, 3 days before to 3 days after symptom onset, and 2 days before to 10 days after symptom onset. Results: We found an NNQ of 19.8-41.8 person-days and a PPID of 19.7%-38.2%, depending on the infectiousness period scenario. Effectiveness was higher among cohabitants and symptomatic contacts than among social or asymptomatic contacts. NNQ and PPID changed by intervention timings: the effectiveness of contact tracing decreased with time from diagnosis to quarantine of contacts and with time from symptom onset of the index case to contacts’ quarantine. Conclusions: These proposed measures of contact tracing effectiveness of communicable diseases can be important for decision making and prioritizing contact tracing when resources are scarce. They are also useful measures for communication with the general population, policy makers, and clinicians because they are easy to understand and use to assess the impact of health interventions.
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Affiliation(s)
- Diogo Fernandes da Silva
- Public Health Unit, Agrupamento de Centros de Saúde Grande Porto VIII–Espinho/Gaia, ARS Norte, Porto, Portugal
| | - João Vasco Santos
- Public Health Unit, Agrupamento de Centros de Saúde Grande Porto VIII–Espinho/Gaia, ARS Norte, Porto, Portugal
- Department of Community Medicine, Information and Health Decision Sciences (MEDCIDS), Faculty of Medicine, University of Porto, Porto, Portugal
- Centre for Health Technology and Services Research (CINTESIS), Porto, Portugal
| | - Filipa Santos Martins
- Public Health Unit, Agrupamento de Centros de Saúde Grande Porto VIII–Espinho/Gaia, ARS Norte, Porto, Portugal
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A single-administration therapeutic interfering particle reduces SARS-CoV-2 viral shedding and pathogenesis in hamsters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022. [PMID: 35982679 DOI: 10.1101/2022.08.10.503534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The high transmissibility of SARS-CoV-2 is a primary driver of the COVID-19 pandemic. While existing interventions prevent severe disease, they exhibit mixed efficacy in preventing transmission, presumably due to their limited antiviral effects in the respiratory mucosa, whereas interventions targeting the sites of viral replication might more effectively limit respiratory virus transmission. Recently, intranasally administered RNA-based therapeutic interfering particles (TIPs) were reported to suppress SARS-CoV-2 replication, exhibit a high barrier to resistance, and prevent serious disease in hamsters. Since TIPs intrinsically target the tissues with the highest viral replication burden (i.e., respiratory tissues for SARS-CoV-2), we tested the potential of TIP intervention to reduce SARS-CoV-2 shedding. Here, we report that a single, post-exposure TIP dose lowers SARS-CoV-2 nasal shedding and at 5 days post-infection infectious virus shed is below detection limits in 4 out of 5 infected animals. Furthermore, TIPs reduce shedding of Delta variant or WA-1 from infected to uninfected hamsters. Co-housed 'contact' animals exposed to infected, TIP-treated, animals exhibited significantly lower viral loads, reduced inflammatory cytokines, no severe lung pathology, and shortened shedding duration compared to animals co-housed with untreated infected animals. TIPs may represent an effective countermeasure to limit SARS-CoV-2 transmission. Significance COVID-19 vaccines are exceptionally effective in preventing severe disease and death, but they have mixed efficacy in preventing virus transmission, consistent with established literature that parenteral vaccines for other viruses fail to prevent mucosal virus shedding or transmission. Likewise, small-molecule antivirals, while effective in reducing viral-disease pathogenesis, also appear to have inconsistent efficacy in preventing respiratory virus transmission including for SARS-CoV-2. Recently, we reported the discovery of a single-administration antiviral Therapeutic Interfering Particle (TIP) against SARS-CoV-2 that prevents severe disease in hamsters and exhibits a high genetic barrier to the evolution of resistance. Here, we report that TIP intervention also reduces SARS-CoV-2 transmission between hamsters.
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Molecular detection of SARS-COV-2 in exhaled breath at the point-of-need. Biosens Bioelectron 2022; 217:114663. [PMID: 36150327 PMCID: PMC9424122 DOI: 10.1016/j.bios.2022.114663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/17/2022] [Accepted: 08/24/2022] [Indexed: 12/19/2022]
Abstract
The SARS-CoV-2 pandemic has highlighted the need for improved technologies to help control the spread of contagious pathogens. While rapid point-of-need testing plays a key role in strategies to rapidly identify and isolate infectious patients, current test approaches have significant shortcomings related to assay limitations and sample type. Direct quantification of viral shedding in exhaled particles may offer a better rapid testing approach, since SARS-CoV-2 is believed to spread mainly by aerosols. It assesses contagiousness directly, the sample is easy and comfortable to obtain, sampling can be standardized, and the limited sample volume lends itself to a fast and sensitive analysis. In view of these benefits, we developed and tested an approach where exhaled particles are efficiently sampled using inertial impaction in a micromachined silicon chip, followed by an RT-qPCR molecular assay to detect SARS-CoV-2 shedding. Our portable, silicon impactor allowed for the efficient capture (>85%) of respiratory particles down to 300 nm without the need for additional equipment. We demonstrate using both conventional off-chip and in-situ PCR directly on the silicon chip that sampling subjects’ breath in less than a minute yields sufficient viral RNA to detect infections as early as standard sampling methods. A longitudinal study revealed clear differences in the temporal dynamics of viral load for nasopharyngeal swab, saliva, breath, and antigen tests. Overall, after an infection, the breath-based test remains positive during the first week but is the first to consistently report a negative result, putatively signalling the end of contagiousness and further emphasizing the potential of this tool to help manage the spread of airborne respiratory infections.
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Li H, Zhao X, Li J, Zheng H, Zhao Y, Yang J, Zhou J, Yang F, Chen Y, Zuo Y, Lai Q, Long H, Li Y, Jin W, Shi H, Liu L. Nasal Mucosa Exploited by SARS-CoV-2 for Replicating and Shedding during Reinfection. Viruses 2022; 14:v14081608. [PMID: 35893674 PMCID: PMC9394478 DOI: 10.3390/v14081608] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 02/01/2023] Open
Abstract
Reinfection risk is a great concern with regard to the COVID-19 pandemic because a large proportion of the population has recovered from an initial infection, and previous reports found that primary exposure to SARS-CoV-2 protects against reinfection in rhesus macaques without viral presence and pathological injury; however, a high possibility for reinfection at the current stage of the pandemic has been proven. We found the reinfection of SARS-CoV-2 in Syrian hamsters with continuous viral shedding in the upper respiratory tracts and few injuries in the lung, and nasal mucosa was exploited by SARS-CoV-2 for replication and shedding during reinfection; meanwhile, no viral replication or enhanced damage was observed in the lower respiratory tracts. Consistent with the mild phenotype in the reinfection, increases in mRNA levels in cytokines and chemokines in the nasal mucosa but only slight increases in the lung were found. Notably, the high levels of neutralizing antibodies in serum could not prevent reinfection in hamsters but may play roles in benefitting the lung recovery and symptom relief of COVID-19. In summary, Syrian hamsters could be reinfected by SARS-CoV-2 with mild symptoms but with obvious viral shedding and replication, and both convalescent and vaccinated patients should be wary of the transmission and reinfection of SARS-CoV-2.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Longding Liu
- Correspondence: ; Tel.: +86-871-6833-5905; Fax: +86-871-6833-4483
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Heimdal I, Lysvand H, Krokstad S, Christensen A, Døllner H, Nordbø SA. Detection of subgenomic mRNA from endemic human coronavirus OC43 and NL63 compared to viral genomic loads, single virus detection and clinical manifestations in children with respiratory tract infections. J Clin Virol 2022; 154:105247. [PMID: 35907394 PMCID: PMC9306218 DOI: 10.1016/j.jcv.2022.105247] [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: 04/29/2022] [Revised: 07/17/2022] [Accepted: 07/21/2022] [Indexed: 11/30/2022]
Abstract
Background The importance of endemic human coronavirus (HCoV) in children has been insufficiently elucidated upon. Our aims were to develop subgenomic (sg) mRNA tests for HCoV species OC43 and NL63, and to evaluate the relationships to HCoV genomic loads, single HCoV detections and clinical manifestations. Methods We have used an 11-yearlong cohort study of children admitted with respiratory tract infection (RTI) and hospital controls. Nasopharyngeal aspirates were analyzed for HCoV subtypes OC43 and NL63 with in-house diagnostic PCR. Positive samples were tested with newly developed real-time PCRs targeting sg mRNA coding for the nucleocapsid protein. Results OC43 sg mRNA was detected in 86% (105/122) of available OC43-positive samples in the RTI group, and in 63% (12/19) of control samples. NL63 sg mRNA was detected in 72% (71/98) and 71% (12/17) of available NL63-positive patient and control samples, respectively. In RTI samples, sg mRNA detection was strongly associated with a Ct value <32 in both diagnostic PCR tests (OC43: OR = 54, 95% CI [6.8–428]; NL63: OR = 42, 95% CI [9.0–198]) and single NL63 detections (OR = 6.9, 95% CI [1.5–32]). Comparing RTI and controls, only OC43 was associated with RTI when adjusted for age (aOR = 3.2, 95% CI [1.1–9.4]). Conclusion We found strong associations between OC43 and NL63 sg mRNA and high viral genomic loads. sg mRNA for OC43 was associated with RTI. The association between sg mRNA and clinical manifestations needs further evaluation.
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Affiliation(s)
- Inger Heimdal
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
| | - Hilde Lysvand
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Sidsel Krokstad
- Department of Medical Microbiology, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
| | - Andreas Christensen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; Department of Medical Microbiology, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
| | - Henrik Døllner
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; Children's Clinic, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
| | - Svein Arne Nordbø
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; Department of Medical Microbiology, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
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Tallmadge RL, Laverack M, Cronk B, Venugopalan R, Martins M, Zhang X, Elvinger F, Plocharczyk E, Diel DG. Viral RNA Load and Infectivity of SARS-CoV-2 in Paired Respiratory and Oral Specimens from Symptomatic, Asymptomatic, or Postsymptomatic Individuals. Microbiol Spectr 2022; 10:e0226421. [PMID: 35575498 PMCID: PMC9241670 DOI: 10.1128/spectrum.02264-21] [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: 11/13/2021] [Accepted: 04/17/2022] [Indexed: 11/30/2022] Open
Abstract
In the present study, we assessed the diagnostic sensitivity and determined the viral RNA load and infectivity of SARS-CoV-2 in paired respiratory (nasopharyngeal and anterior nares) and oral samples (saliva and sublingual swab). Samples were collected from 77 individuals of which 75 were diagnosed with COVID-19 and classified as symptomatic (n = 29), asymptomatic (n = 31), or postsymptomatic (n = 15). Specimens were collected at one time point from each individual, between day 1 and 23 after the initial COVID-19 diagnosis, and included self-collected saliva (S), or sublingual (SL) swab, and bilateral anterior nares (AN) swab, followed by health care provider collected nasopharyngeal (NP) swab. Sixty-three specimen sets were tested using five assay/platforms. The diagnostic sensitivity of each assay/platform and specimen type was determined. Of the 63 specimen sets, SARS-CoV-2 was detected in 62 NP specimens, 52 AN specimens, 59 saliva specimens, and 31 SL specimens by at least one platform. Infectious SARS-CoV-2 was isolated from 21 NP, 13 AN, 12 saliva, and one SL specimen out of 50 specimen sets. SARS-CoV-2 isolation was most successful up to 5 days after initial COVID-19 diagnosis using NP specimens from symptomatic patients (16 of 24 positives, 66.67%), followed by specimens from asymptomatic patients (5 of 17 positives, 29.41%), while it was not very successful with specimens from postsymptomatic patients. Benefits of self-collected saliva and AN specimens balance the loss of sensitivity relative to NP specimens. Therefore, saliva and AN specimens are acceptable alternatives for symptomatic SARS-CoV-2 diagnostic testing or surveillance with increased sampling frequency of asymptomatic individuals. IMPORTANCE The dynamics of infection with SARS-CoV-2 have a significant impact on virus infectivity and in the diagnostic sensitivity of molecular and classic virus detection tests. In the present study we determined the diagnostic sensitivity of paired respiratory (nasopharyngeal and anterior nares swabs) and oral secretions (saliva and sublingual swab) and assessed infectious virus shedding patterns by symptomatic, asymptomatic, or postsymptomatic individuals. Understanding the diagnostic performance of these specimens and the patterns of infectious virus shedding in these bodily secretions provides critical information to control COVID-19, and may help to refine guidelines on isolation and quarantine of positive individuals and their close contacts identified through epidemiological investigations.
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Affiliation(s)
- Rebecca L. Tallmadge
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, Cornell COVID-19 Testing Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Melissa Laverack
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, Cornell COVID-19 Testing Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Brittany Cronk
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, Cornell COVID-19 Testing Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Roopa Venugopalan
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, Cornell COVID-19 Testing Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Mathias Martins
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - XiuLin Zhang
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, Cornell COVID-19 Testing Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - François Elvinger
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, Cornell COVID-19 Testing Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | | | - Diego G. Diel
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, Cornell COVID-19 Testing Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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Phuphuakrat A, Pasomsub E, Srichatrapimuk S, Kirdlarp S, Suksatu A, Srisaowakarn C, Manopwisedjaroen S, Ludowyke N, Purwono PB, Priengprom T, Wongsa A, Thakkinstian A, Hongeng S, Malathum K, Thitithanyanont A, Tassaneetrithep B. Detectable Duration of Viable SARS-CoV-2, Total and Subgenomic SARS-CoV-2 RNA in Noncritically Ill COVID-19 Patients: a Prospective Cohort Study. Microbiol Spectr 2022; 10:e0050322. [PMID: 35604133 PMCID: PMC9241878 DOI: 10.1128/spectrum.00503-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/28/2022] [Indexed: 01/01/2023] Open
Abstract
Determination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectivity is important in guiding the infection control and differentiating between reinfection and persistent viral RNA. Although viral culture is the gold standard to determine viral infectivity, the method is not practical. We studied the kinetics of SARS-CoV-2 total RNAs and subgenomic RNAs (sgRNAs) and their potential role as surrogate markers of viral infectivity. The kinetics of SARS-CoV-2 sgRNAs compared to those of the culture and total RNA shedding in a prospective cohort of patients diagnosed with coronavirus disease 2019 (COVID-19) were investigated. A total of 260 nasopharyngeal swabs from 36 patients were collected every other day after entering the study until the day of viral total RNA clearance, as measured by reverse transcription PCR (RT-PCR). Time to cessation of viral shedding was in order from shortest to longest: by viral culture, sgRNA RT-PCR, and total RNA RT-PCR. The median time (interquartile range) to negativity of viral culture, subgenomic N transcript, and N gene were 7 (5 to 9), 11 (9 to 16), and 18 (13 to 21) days, respectively (P < 0.001). Further analysis identified the receipt of steroid as the factors associated with longer duration of viral infectivity (hazard ratio, 3.28; 95% confidence interval, 1.02 to 10.61; P = 0.047). We propose the potential role of the detection of SARS-CoV-2 subgenomic RNA as the surrogate marker of viral infectivity. Patients with negative subgenomic N RNA RT-PCR could be considered for ending isolation. IMPORTANCE Our study, combined with existing evidence, suggests the feasibility of the use of subgenomic RNA RT-PCR as a surrogate marker for SARS-CoV-2 infectivity. The kinetics of SARS-CoV-2 subgenomic RNA should be further investigated in immunocompromised patients.
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Affiliation(s)
- Angsana Phuphuakrat
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Ekawat Pasomsub
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sirawat Srichatrapimuk
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Samut Prakan, Thailand
| | - Suppachok Kirdlarp
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Samut Prakan, Thailand
| | - Ampa Suksatu
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Chanya Srisaowakarn
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Natali Ludowyke
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Priyo Budi Purwono
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Thongkoon Priengprom
- Center of Research Excellence in Immunoregulation, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Artit Wongsa
- Center of Research Excellence in Immunoregulation, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Ammarin Thakkinstian
- Department of Clinical Epidemiology and Biostatistics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Suradej Hongeng
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Kumthorn Malathum
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | | | - Boonrat Tassaneetrithep
- Center of Research Excellence in Immunoregulation, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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36
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Kung YA, Lee KM, Chiang HJ, Huang SY, Wu CJ, Shih SR. Molecular Virology of SARS-CoV-2 and Related Coronaviruses. Microbiol Mol Biol Rev 2022; 86:e0002621. [PMID: 35343760 PMCID: PMC9199417 DOI: 10.1128/mmbr.00026-21] [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] [Indexed: 02/07/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The global COVID-19 pandemic continues to threaten the lives of hundreds of millions of people, with a severe negative impact on the global economy. Although several COVID-19 vaccines are currently being administered, none of them is 100% effective. Moreover, SARS-CoV-2 variants remain an important worldwide public health issue. Hence, the accelerated development of efficacious antiviral agents is urgently needed. Coronavirus depends on various host cell factors for replication. An ongoing research objective is the identification of host factors that could be exploited as targets for drugs and compounds effective against SARS-CoV-2. In the present review, we discuss the molecular mechanisms of SARS-CoV-2 and related coronaviruses, focusing on the host factors or pathways involved in SARS-CoV-2 replication that have been identified by genome-wide CRISPR screening.
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Affiliation(s)
- Yu-An Kung
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kuo-Ming Lee
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Division of Infectious Diseases, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Huan-Jung Chiang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Sheng-Yu Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chung-Jung Wu
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Research Center for Food and Cosmetic Safety, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
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37
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Cuypers L, Bode J, Beuselinck K, Laenen L, Dewaele K, Janssen R, Capron A, Lafort Y, Paridaens H, Bearzatto B, Cauchie M, Huwart A, Degosserie J, Fagnart O, Overmeire Y, Rouffiange A, Vandecandelaere I, Deffontaine M, Pilate T, Yin N, Micalessi I, Roisin S, Moons V, Reynders M, Steyaert S, Henin C, Lazarova E, Obbels D, Dufrasne FE, Pirenne H, Schepers R, Collin A, Verhasselt B, Gillet L, Jonckheere S, Van Lint P, Van den Poel B, Van der Beken Y, Stojkovic V, Garrino MG, Segers H, Vos K, Godefroid M, Pede V, Nollet F, Claes V, Verschraegen I, Bogaerts P, Van Gysel M, Leurs J, Saegeman V, Soetens O, Vanhee M, Schiettekatte G, Huyghe E, Martens S, Lemmens A, Nailis H, Laffineur K, Steensels D, Vanlaere E, Gras J, Roussel G, Gijbels K, Boudewijns M, Sion C, Achtergael W, Maurissen W, Iliano L, Chantrenne M, Vanheule G, Flies R, Hougardy N, Berth M, Verbeke V, Morent R, Vankeerberghen A, Bontems S, Kehoe K, Schallier A, Ho G, Bafort K, Raymaekers M, Pypen Y, Heinrichs A, Schuermans W, Cuigniez D, Lali SE, Drieghe S, Ory D, Le Mercier M, Van Laethem K, Thoelen I, Vandamme S, Mansoor I, Vael C, De Sloovere M, Declerck K, Dequeker E, Desmet S, Maes P, Lagrou K, André E. Nationwide Harmonization Effort for Semi-Quantitative Reporting of SARS-CoV-2 PCR Test Results in Belgium. Viruses 2022; 14:1294. [PMID: 35746765 PMCID: PMC9230955 DOI: 10.3390/v14061294] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 02/05/2023] Open
Abstract
From early 2020, a high demand for SARS-CoV-2 tests was driven by several testing indications, including asymptomatic cases, resulting in the massive roll-out of PCR assays to combat the pandemic. Considering the dynamic of viral shedding during the course of infection, the demand to report cycle threshold (Ct) values rapidly emerged. As Ct values can be affected by a number of factors, we considered that harmonization of semi-quantitative PCR results across laboratories would avoid potential divergent interpretations, particularly in the absence of clinical or serological information. A proposal to harmonize reporting of test results was drafted by the National Reference Centre (NRC) UZ/KU Leuven, distinguishing four categories of positivity based on RNA copies/mL. Pre-quantified control material was shipped to 124 laboratories with instructions to setup a standard curve to define thresholds per assay. For each assay, the mean Ct value and corresponding standard deviation was calculated per target gene, for the three concentrations (107, 105 and 103 copies/mL) that determine the classification. The results of 17 assays are summarized. This harmonization effort allowed to ensure that all Belgian laboratories would report positive PCR results in the same semi-quantitative manner to clinicians and to the national database which feeds contact tracing interventions.
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Affiliation(s)
- Lize Cuypers
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium; (J.B.); (K.B.); (L.L.); (K.D.); (R.J.); (E.D.); (S.D.); (K.L.); (E.A.)
| | - Jannes Bode
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium; (J.B.); (K.B.); (L.L.); (K.D.); (R.J.); (E.D.); (S.D.); (K.L.); (E.A.)
| | - Kurt Beuselinck
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium; (J.B.); (K.B.); (L.L.); (K.D.); (R.J.); (E.D.); (S.D.); (K.L.); (E.A.)
| | - Lies Laenen
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium; (J.B.); (K.B.); (L.L.); (K.D.); (R.J.); (E.D.); (S.D.); (K.L.); (E.A.)
| | - Klaas Dewaele
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium; (J.B.); (K.B.); (L.L.); (K.D.); (R.J.); (E.D.); (S.D.); (K.L.); (E.A.)
| | - Reile Janssen
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium; (J.B.); (K.B.); (L.L.); (K.D.); (R.J.); (E.D.); (S.D.); (K.L.); (E.A.)
| | - Arnaud Capron
- Epidemiology of Infectious Diseases and Quality Service Unit, Scientific Directorate of Epidemiology and Public Health, Sciensano, 1000 Brussels, Belgium; (A.C.); (Y.L.)
| | - Yves Lafort
- Epidemiology of Infectious Diseases and Quality Service Unit, Scientific Directorate of Epidemiology and Public Health, Sciensano, 1000 Brussels, Belgium; (A.C.); (Y.L.)
| | - Henry Paridaens
- Clinical Laboratory, Centre Hospitalier Régional de la Citadelle, 4000 Liège, Belgium;
| | - Bertrand Bearzatto
- Federal Testing Platform COVID-19, Centre des Technologies Moléculaires Appliquées (CTMA), Institute of Experimental and Clinical Research (IREC), Cliniques Universitaires Saint-Luc and Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium;
| | | | | | - Jonathan Degosserie
- Federal Testing Platform COVID-19, Department of Laboratory Medicine, CHU UCL Namur, 5530 Yvoir, Belgium;
| | - Olivier Fagnart
- Saint-Jean Hospital Laboratory, Cebiodi, 1000 Brussels, Belgium;
| | - Yarah Overmeire
- Microbiology, Labo Nuytinck, Anacura, 9940 Evergem, Belgium;
| | | | | | - Marine Deffontaine
- Laboratory of Clinical Biology, Centre Hopsitalier de Mouscron, 7700 Mouscron, Belgium;
| | - Thomas Pilate
- Clinical Laboratory, Laboratory Medicine, AZ Diest, 3290 Diest, Belgium;
| | - Nicolas Yin
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles—Universitair Laboratorium Brussel (LHUB-ULB), Université de Bruxelles (ULB), 1000 Brussels, Belgium;
| | - Isabel Micalessi
- Clinical Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium;
| | - Sandrine Roisin
- Microbiology, Centre Hospitalier Universitaire de Tivoli, 7100 La Louvière, Belgium;
| | - Veronique Moons
- Microbiology, LKO-LMC Medical Laboratory, 3800 Sint-Truiden, Belgium;
| | - Marijke Reynders
- Laboratory Medicine, AZ Sint-Jan Brugge-Oostende AV, 8000 Brugge, Belgium;
| | - Sophia Steyaert
- Clinical Laboratory, AZ Maria Middelares, 9000 Gent, Belgium;
| | - Coralie Henin
- Federal Testing Platform COVID-19, Université Libre de Bruxelles, 1070 Brussels, Belgium;
| | - Elena Lazarova
- Centre Hospitalier Régional de la Haute Senne, Department of Clinical Biology, 7060 Soignies, Belgium;
| | - Dagmar Obbels
- Imelda, Clinical Laboratory, 2820 Bonheiden, Belgium;
| | | | - Hendri Pirenne
- Synlab Belgium, Synlab Laboratory Collard, 4020 Liège, Belgium;
| | - Raf Schepers
- Synlab Belgium, Synlab Laboratory Heppignies, 6220 Heppignies, Belgium;
| | | | - Bruno Verhasselt
- Federal Testing Platform COVID-19, Department of Laboratory Medicine, Ghent University and Ghent University Hospital, 9000 Gent, Belgium;
| | - Laurent Gillet
- Federal Testing Platform COVID-19, University of Liège, 4000 Liège, Belgium;
| | - Stijn Jonckheere
- Jan Yperman Hospital, Laboratory of Clinical Biology, 8900 Ieper, Belgium;
| | | | - Bea Van den Poel
- Clinical Laboratory, General Hospital Jan Portaels, 1800 Vilvoorde, Belgium;
| | - Yolien Van der Beken
- Military Medicine Lab Capacity, Military Hospital Queen Astrid, 1120 Brussels, Belgium;
| | - Violeta Stojkovic
- Centre Hospitalier Bois de l’Abbaye, Laboratory Service, 4100 Seraing, Belgium;
| | | | | | - Kevin Vos
- RZ Heilig Hart Tienen, Clinical Biology, 3300 Tienen, Belgium;
| | | | - Valerie Pede
- AZ Sint-Elisabeth Zottegem, Laboratory of Clinical Biology, 9600 Zottegem, Belgium;
| | - Friedel Nollet
- Biogazelle NV, Diagnostic Testing, 9052 Zwijnaarde, Belgium;
| | - Vincent Claes
- Institute of Clinical Biology ULB-IBC, 1170 Brussels, Belgium;
| | | | - Pierre Bogaerts
- CHU UCL Namur, Department of Laboratory Medicine, Molecular Diagnostics Center, 5530 Yvoir, Belgium;
| | | | | | | | - Oriane Soetens
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, 1090 Brussels, Belgium;
| | - Merijn Vanhee
- Clinical Laboratory, Laboratory Medicine, AZ Delta, 8800 Roeselare, Belgium;
| | | | - Evelyne Huyghe
- ZNA Middelheim, Clinical Laboratory, 2020 Antwerp, Belgium;
| | | | - Ann Lemmens
- AZ Sint-Maarten, Laboratory of Clinical Biology, 2800 Mechelen, Belgium;
| | | | | | - Deborah Steensels
- Clinical Laboratory, Campus Sint-Jan, Hospital Oost-Limburg, 3600 Genk, Belgium;
| | - Elke Vanlaere
- Clinical Laboratory, AZ Sint-Lucas Hospital, 9000 Gent, Belgium;
| | - Jérémie Gras
- Institute of Pathology and Genetics, 6041 Gosselies, Belgium;
| | - Gatien Roussel
- Clinique Saint Pierre, Laboratory, 1340 Ottignies, Belgium;
| | | | - Michael Boudewijns
- Clinical Laboratory, Campus Kennedylaan, AZ Groeninge, 8500 Kortrijk, Belgium;
| | - Catherine Sion
- Grand Hôpital de Charleroi, Clinical Biology and Microbiology, 6060 Gilly, Belgium;
| | - Wim Achtergael
- Clinical Laboratory, Algemeen Stedelijk Ziekenhuis Aalst, 9300 Aalst, Belgium;
| | | | - Luc Iliano
- Laboratory for Medical Biology Iliano, 9070 Destelbergen, Belgium;
| | | | | | | | - Nicolas Hougardy
- Clinical Biology Unit, Vivalia Clinique du Sud-Luxembourg, 6700 Arlon, Belgium;
| | - Mario Berth
- Clinical Laboratory, AZ Alma, 9900 Eeklo, Belgium;
| | | | - Robin Morent
- Department of Laboratory Medicine, Campus Henri Serruys, AZ Sint-Jan Brugge, 8400 Oostende, Belgium;
| | - Anne Vankeerberghen
- Laboratory of Molecular Biology, Campus Aalst-Asse-Ninove, Onze-Lieve-Vrouwziekenhuis, 9300 Aalst, Belgium;
| | - Sébastien Bontems
- Clinical Laboratory, Unit of Clinical Microbiology, CHU Liège, 4000 Liège, Belgium;
| | - Kaat Kehoe
- Microbiology, Algemeen Medisch Laboratorium, 2020 Antwerp, Belgium;
| | | | - Giang Ho
- Laboratory, Clinique du MontLégia, Groupe Santé CHC, 4000 Liège, Belgium;
| | - Kristof Bafort
- Clinical Laboratory, Mariaziekenhuis Noorderhart, 3900 Pelt, Belgium;
| | - Marijke Raymaekers
- Laboratory for Molecular Diagnostics, Jessa Hospital, 3500 Hasselt, Belgium;
| | - Yolande Pypen
- Microbiology, Laboratory Somedi, 2220 Heist-op-den-Berg, Belgium;
| | - Amelie Heinrichs
- Laboratory of Clinical Biology, Hospital Arlon—Vivalia, 6700 Arlon, Belgium;
| | - Wim Schuermans
- Clinical Laboratory, Ziekenhuis Geel, 2440 Geel, Belgium;
| | | | | | - Stefanie Drieghe
- Microbiology, Algemeen Medisch Laboratorium West, 8850 Ardooie, Belgium;
| | - Dieter Ory
- Clinical Laboratory, Heilig Hart Ziekenhuis Mol, 2400 Mol, Belgium;
| | - Marie Le Mercier
- Federal Testing Platform COVID-19, University Hospitals Antwerp, 2650 Edegem, Belgium;
| | - Kristel Van Laethem
- Federal Testing Platform COVID-19, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium;
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Rega Institute for Medical Research, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium;
| | - Inge Thoelen
- Clinical Laboratory, AZ Vesalius Tongeren, 3700 Tongeren, Belgium;
| | - Sarah Vandamme
- Microbiology Laboratory, University Hospitals Antwerp, 2650 Edegem, Belgium;
| | - Iqbal Mansoor
- Clinical Laboratory, Hospital Hornu Epicura, 7301 Boussu, Belgium;
| | - Carl Vael
- Clinical Laboratory, AZ Klina, 2930 Brasschaat, Belgium;
| | | | | | - Elisabeth Dequeker
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium; (J.B.); (K.B.); (L.L.); (K.D.); (R.J.); (E.D.); (S.D.); (K.L.); (E.A.)
| | - Stefanie Desmet
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium; (J.B.); (K.B.); (L.L.); (K.D.); (R.J.); (E.D.); (S.D.); (K.L.); (E.A.)
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Piet Maes
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Rega Institute for Medical Research, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium;
| | - Katrien Lagrou
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium; (J.B.); (K.B.); (L.L.); (K.D.); (R.J.); (E.D.); (S.D.); (K.L.); (E.A.)
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Emmanuel André
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium; (J.B.); (K.B.); (L.L.); (K.D.); (R.J.); (E.D.); (S.D.); (K.L.); (E.A.)
- Federal Testing Platform COVID-19, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium;
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
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Considerations regarding Interpretation of Positive SARS-CoV-2 Molecular Results with Late Cycle Threshold Values. J Clin Microbiol 2022; 60:e0050122. [PMID: 35658526 PMCID: PMC9491168 DOI: 10.1128/jcm.00501-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
COVID-19 disease lies on a spectrum, ranging from completely asymptomatic to mild disease to severe and critical disease. Studies have shown that prolonged shedding or sporadic detection of SARS-CoV-2 RNA can occur long after symptom resolution. Adding to these clinical complexities is the demand for testing for SARS-CoV-2 at all stages of diseases, frequently driven by screening of asymptomatic persons, something that traditionally has not been performed for other viral respiratory diseases. This can lead to positive results from nucleic acid amplification tests (NAATs), such as RT-PCR, with late cycle threshold (CT) values near the test’s limit of detection. In this commentary, we review unique attributes of COVID-19 and causes of NAAT late CT values. We provide interpretation considerations as well as strategies to aid in test interpretation.
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39
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Junqueira C, Crespo Â, Ranjbar S, de Lacerda LB, Lewandrowski M, Ingber J, Parry B, Ravid S, Clark S, Schrimpf MR, Ho F, Beakes C, Margolin J, Russell N, Kays K, Boucau J, Das Adhikari U, Vora SM, Leger V, Gehrke L, Henderson LA, Janssen E, Kwon D, Sander C, Abraham J, Goldberg MB, Wu H, Mehta G, Bell S, Goldfeld AE, Filbin MR, Lieberman J. FcγR-mediated SARS-CoV-2 infection of monocytes activates inflammation. Nature 2022; 606:576-584. [PMID: 35385861 PMCID: PMC10071495 DOI: 10.1038/s41586-022-04702-4] [Citation(s) in RCA: 256] [Impact Index Per Article: 128.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/29/2022] [Indexed: 12/26/2022]
Abstract
SARS-CoV-2 can cause acute respiratory distress and death in some patients1. Although severe COVID-19 is linked to substantial inflammation, how SARS-CoV-2 triggers inflammation is not clear2. Monocytes and macrophages are sentinel cells that sense invasive infection to form inflammasomes that activate caspase-1 and gasdermin D, leading to inflammatory death (pyroptosis) and the release of potent inflammatory mediators3. Here we show that about 6% of blood monocytes of patients with COVID-19 are infected with SARS-CoV-2. Monocyte infection depends on the uptake of antibody-opsonized virus by Fcγ receptors. The plasma of vaccine recipients does not promote antibody-dependent monocyte infection. SARS-CoV-2 begins to replicate in monocytes, but infection is aborted, and infectious virus is not detected in the supernatants of cultures of infected monocytes. Instead, infected cells undergo pyroptosis mediated by activation of NLRP3 and AIM2 inflammasomes, caspase-1 and gasdermin D. Moreover, tissue-resident macrophages, but not infected epithelial and endothelial cells, from lung autopsies from patients with COVID-19 have activated inflammasomes. Taken together, these findings suggest that antibody-mediated SARS-CoV-2 uptake by monocytes and macrophages triggers inflammatory cell death that aborts the production of infectious virus but causes systemic inflammation that contributes to COVID-19 pathogenesis.
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Affiliation(s)
- Caroline Junqueira
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil.
| | - Ângela Crespo
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Shahin Ranjbar
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Luna B de Lacerda
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Mercedes Lewandrowski
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Jacob Ingber
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Blair Parry
- Emergency Medicine, Institute for Patient Care, Massachusetts General Hospital, Boston, MA, USA
| | - Sagi Ravid
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Sarah Clark
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Marie Rose Schrimpf
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Felicia Ho
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Caroline Beakes
- Emergency Medicine, Institute for Patient Care, Massachusetts General Hospital, Boston, MA, USA
| | - Justin Margolin
- Emergency Medicine, Institute for Patient Care, Massachusetts General Hospital, Boston, MA, USA
| | - Nicole Russell
- Emergency Medicine, Institute for Patient Care, Massachusetts General Hospital, Boston, MA, USA
| | - Kyle Kays
- Emergency Medicine, Institute for Patient Care, Massachusetts General Hospital, Boston, MA, USA
| | - Julie Boucau
- Ragon Institute, Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard Medical School, Cambridge, MA, USA
| | - Upasana Das Adhikari
- Ragon Institute, Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard Medical School, Cambridge, MA, USA
| | - Setu M Vora
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Valerie Leger
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lee Gehrke
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lauren A Henderson
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA
| | - Erin Janssen
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA
| | - Douglas Kwon
- Ragon Institute, Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard Medical School, Cambridge, MA, USA
| | - Chris Sander
- cBio Center, Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Jonathan Abraham
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Marcia B Goldberg
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Center for Bacterial Pathogenesis, Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Hao Wu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gautam Mehta
- Institute for Liver and Digestive Health, University College London, London, UK
- Institute of Hepatology, Foundation for Liver Research, London, UK
| | - Steven Bell
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Anne E Goldfeld
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Michael R Filbin
- Emergency Medicine, Institute for Patient Care, Massachusetts General Hospital, Boston, MA, USA.
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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SARS-CoV-2 Antigen Test Results to Infer Active or Non-Active Virus Replication Status in COVID-19 Patients. Diagnostics (Basel) 2022; 12:diagnostics12061338. [PMID: 35741149 PMCID: PMC9222063 DOI: 10.3390/diagnostics12061338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 12/12/2022] Open
Abstract
We used nasopharyngeal swab samples of patients with a symptomatic (n = 82) or asymptomatic (n = 20) coronavirus disease 2019 (COVID-19) diagnosis to assess the ability of antigen detection tests to infer active (potentially transmissible) or inactive (potentially non-transmissible) infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Using the subgenomic RNA (sgRNA) as an active replication marker of SARS-CoV-2, 48 (76.2%), 56 (88.9%), and 63 (100%) of 63 samples with sgRNA positive results tested positive with the SD BIOSENSOR STANDARD Q COVID-19 Ag (Standard Q), the SD BIOSENSOR STANDARD F COVID-19 Ag FIA (Standard F), or the Fujirebio LUMIPULSE G SARS-CoV-2 Ag (Lumipulse) assay, respectively. Conversely, 37 (94.9%), 29 (74.4%), and 7 (17.9%) of 39 samples with sgRNA negative results tested negative with Standard Q, Standard F, or Lumipulse, respectively. Stratifying results by the number of days of symptoms before testing revealed that most antigen positive/sgRNA positive results were among samples tested at 2–7 days regardless of the assay used. Conversely, most antigen negative/sgRNA negative results were among samples tested at 16–30 days only when Standard Q or Standard F were used. In conclusion, based on our findings, a negative antigen test, especially with the Lumipulse assay, or a positive antigen test, especially with the Standard F assay, may suggest, respectively, the absence or presence of replication-competent SARS-CoV-2.
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Hakre S, Lakhal-Naouar I, King DB, Burns JL, Jackson KN, Krauss SW, Chandrasekaran P, McCauley MD, Ober Shepherd BL, McHenry S, Bianchi EJ, Ouellette J, Darden JM, Sanborn AD, Daye SP, Kwon PO, Stubbs J, Brigantti CL, Hall TL, Beagle MH, Pieri JA, Frambes TR, O’Connell RJ, Modjarrad K, Murray CK, Jagodzinski LL, Scott PT, Peel SA. Virological and Serological Assessment of US Army Trainees Isolated for Coronavirus Disease 2019. J Infect Dis 2022; 226:1743-1752. [PMID: 35543272 PMCID: PMC9129211 DOI: 10.1093/infdis/jiac198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 05/09/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Laboratory screening for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a key mitigation measure to avoid the spread of infection among recruits starting basic combat training in a congregate setting. Because viral nucleic acid can be detected persistently after recovery, we evaluated other laboratory markers to distinguish recruits who could proceed with training from those who were infected. METHODS Recruits isolated for coronavirus disease 2019 (COVID-19) were serially tested for SARS-CoV-2 subgenomic ribonucleic acid (sgRNA), and viral load (VL) by reverse-transcriptase polymerase chain reaction (RT-PCR), and for anti- SARS-CoV-2. Cluster and quadratic discriminant analyses of results were performed. RESULTS Among 229 recruits isolated for COVID-19, those with a RT-PCR cycle threshold >30.49 (sensitivity 95%, specificity 96%) or having sgRNA log10 RNA copies/mL <3.09 (sensitivity and specificity 96%) at entry into isolation were likely SARS-CoV-2 uninfected. Viral load >4.58 log10 RNA copies/mL or anti-SARS-CoV-2 signal-to-cutoff ratio <1.38 (VL: sensitivity and specificity 93%; anti-SARS-CoV-2: sensitivity 83%, specificity 79%) had comparatively lower sensitivity and specificity when used alone for discrimination of infected from uninfected. CONCLUSIONS Orthogonal laboratory assays used in combination with RT-PCR may have utility in determining SARS-CoV-2 infection status for decisions regarding isolation.
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Affiliation(s)
- Shilpa Hakre
- Correspondence: Shilpa Hakre, DrPH MPH, Emerging Infectious Diseases Branch, Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720-A Rockledge Drive, Suite 400, Bethesda, MD 20817 ()
| | - Ines Lakhal-Naouar
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MarylandUSA,Walter Reed Army Institute of Research, Diagnostics and Countermeasures Branch, Silver Spring, Maryland, USA
| | - David B King
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MarylandUSA
| | - Jennifer L Burns
- Walter Reed Army Institute of Research, Pilot Bioproduction Facility, Silver Spring, Maryland, USA
| | - Kenya N Jackson
- Walter Reed Army Institute of Research, Experimental Therapeutics, Silver Spring, Maryland, USA
| | - Stephen W Krauss
- Walter Reed Army Institute of Research, Center for Military Psychiatry and Neuroscience, Silver Spring, Maryland, USA
| | - Prabha Chandrasekaran
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MarylandUSA,Walter Reed Army Institute of Research, Diagnostics and Countermeasures Branch, Silver Spring, Maryland, USA
| | - Melanie D McCauley
- Walter Reed Army Institute of Research, Emerging Infectious Diseases Branch, Silver Spring, Maryland, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MarylandUSA
| | - Brittany L Ober Shepherd
- Walter Reed Army Institute of Research, Emerging Infectious Diseases Branch, Silver Spring, Maryland, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MarylandUSA
| | - Samantha McHenry
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MarylandUSA
| | - Elizabeth J Bianchi
- Walter Reed Army Institute of Research, Emerging Infectious Diseases Branch, Silver Spring, Maryland, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MarylandUSA
| | - Jason Ouellette
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MarylandUSA,Walter Reed Army Institute of Research, Diagnostics and Countermeasures Branch, Silver Spring, Maryland, USA
| | - Janice M Darden
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MarylandUSA,Walter Reed Army Institute of Research, Diagnostics and Countermeasures Branch, Silver Spring, Maryland, USA
| | - Aaron D Sanborn
- Walter Reed Army Institute of Research, Clinical Trials Center, Silver Spring, Maryland, USA
| | - Sharon P Daye
- Walter Reed Army Institute of Research, One Health Branch, Silver Spring, Maryland, USA
| | - Paul O Kwon
- Program Executive Office for Simulation, Training and Instrumentation, Orlando, Florida, USA
| | | | - Crystal L Brigantti
- DiLorenzo Pentagon Health Clinic, Optometry, Washington, District of Columbia, USA
| | - Tara L Hall
- Moncrief Army Health Clinic, Fort Jackson, South Carolina, USA
| | | | - Jason A Pieri
- United States Army Training Center, Fort Jackson, South Carolina, USA
| | - Timothy R Frambes
- United States Army Training Center, Fort Jackson, South Carolina, USA
| | | | - Kayvon Modjarrad
- Walter Reed Army Institute of Research, Emerging Infectious Diseases Branch, Silver Spring, Maryland, USA
| | | | - Linda L Jagodzinski
- Walter Reed Army Institute of Research, Diagnostics and Countermeasures Branch, Silver Spring, Maryland, USA
| | - Paul T Scott
- Walter Reed Army Institute of Research, Emerging Infectious Diseases Branch, Silver Spring, Maryland, USA
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Yadav PD, Mohandas S, Shete AM, Nyayanit DA, Gupta N, Patil DY, Sapkal GN, Potdar V, Kadam M, Kumar A, Kumar S, Suryavanshi D, Mote CS, Abraham P, Panda S, Bhargava B. SARS-CoV-2 Kappa Variant Shows Pathogenicity in a Syrian Hamster Model. Vector Borne Zoonotic Dis 2022; 22:289-296. [PMID: 35580212 DOI: 10.1089/vbz.2021.0080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Objectives: The emergence of SARS-CoV-2 lineage B.1.617 variants in India has been associated with a surge in the number of daily infections. We investigated the pathogenic potential of Kappa (B.1.617.1) variant in Syrian golden hamsters. Methods: Two groups of Syrian golden hamsters (18 each) were inoculated intranasally with SARS-CoV-2 isolates, B.1 (D614G) and Kappa variant, respectively. The animals were monitored daily for the clinical signs and body weight. Throat swab, nasal wash, and organ samples (lungs, nasal turbinate, trachea) were collected and screened using SARS-CoV-2-specific RT-qPCR. Histopathologic evaluation of the lung samples was performed. Results: The hamsters infected with the Kappa variant demonstrated increased body weight loss compared to the B.1 lineage isolate. The highest viral RNA load was observed in the nasal turbinate and lung specimens of animals infected with both variants. A significantly higher sgRNA load was observed in the nasal swabs (7 DPI), trachea (3 DPI), and lungs (3 DPI) of hamsters infected with the Kappa variant. Neutralizing antibody response generated in the B.1 lineage-infected hamster sera were comparable against both B.1 and Kappa variant in contrast to Kappa variant-infected hamsters, which showed lower titers against B.1 lineage isolate. Gross and microscopic evaluation of the lung specimens showed severe lung lesions in hamsters infected with Kappa variant compared to B.1. Conclusions: The study demonstrates pathogenicity of Kappa variant in hamsters evident with reduced body weight, high viral RNA load in lungs, and pronounced lung lesions. Both Kappa variant- and B.1-infected hamsters produced neutralizing antibodies against both variants studied.
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Affiliation(s)
- Pragya D Yadav
- Maximum Containment Facility, Indian Council of Medical Research, National Institute of Virology, Pune, India
| | - Sreelekshmy Mohandas
- Maximum Containment Facility, Indian Council of Medical Research, National Institute of Virology, Pune, India
| | - Anita M Shete
- Maximum Containment Facility, Indian Council of Medical Research, National Institute of Virology, Pune, India
| | - Dimpal A Nyayanit
- Maximum Containment Facility, Indian Council of Medical Research, National Institute of Virology, Pune, India
| | - Nivedita Gupta
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, New Delhi, India
| | - Deepak Y Patil
- Maximum Containment Facility, Indian Council of Medical Research, National Institute of Virology, Pune, India
| | - Gajanan N Sapkal
- Maximum Containment Facility, Indian Council of Medical Research, National Institute of Virology, Pune, India
| | - Varsha Potdar
- Maximum Containment Facility, Indian Council of Medical Research, National Institute of Virology, Pune, India
| | - Manoj Kadam
- Maximum Containment Facility, Indian Council of Medical Research, National Institute of Virology, Pune, India
| | - Abhimanyu Kumar
- Maximum Containment Facility, Indian Council of Medical Research, National Institute of Virology, Pune, India
| | - Sanjay Kumar
- Department of Neurosurgery, Command Hospital (Southern Command), Armed Forces Medical College (AFMC), Pune, India
| | - Deepak Suryavanshi
- Maximum Containment Facility, Indian Council of Medical Research, National Institute of Virology, Pune, India
| | - Chandrashekhar S Mote
- Department of Veterinary Pathology, Krantisinh Nana Patil College of Veterinary Science, Shirwal, India
| | - Priya Abraham
- Maximum Containment Facility, Indian Council of Medical Research, National Institute of Virology, Pune, India
| | - Samiran Panda
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, New Delhi, India
| | - Balram Bhargava
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, New Delhi, India
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Mohandas S, Yadav PD, Sapkal G, Shete AM, Deshpande G, Nyayanit DA, Patil D, Kadam M, Kumar A, Mote C, Jain R. Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. EBioMedicine 2022; 79:103997. [PMID: 35405385 PMCID: PMC8993158 DOI: 10.1016/j.ebiom.2022.103997] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 12/11/2022] Open
Abstract
Background SARS-CoV-2 Omicron variant is rampantly spreading across the globe. We assessed the pathogenicity and immune response generated by BA.1.1 sub-lineage of SARS-CoV-2 [Omicron (R346K) variant] in 5 to 6-week old Syrian hamsters and compared the observations with that of Delta variant infection. Methods Virus shedding, organ viral load, lung disease and immune response generated in hamsters were sequentially assessed. Findings The disease characteristics of the Omicron (R346K) variant were found to be similar to that of the Delta variant infection in hamsters like viral replication in the respiratory tract and interstitial pneumonia. The Omicron (R346K) infected hamsters demonstrated lesser body weight reduction and viral RNA load in the throat swab and nasal wash samples in comparison to the Delta variant infection. The viral load in the lungs and nasal turbinate samples and the lung disease severity of the Omicron (R346K) infected hamsters were found comparable with that of the Delta variant infected hamsters. Neutralizing antibody response against Omicron (R346K) variant was detected from day 5 and the cross-neutralization titre of the sera against other variants showed severe reduction ie., 7 fold reduction against Alpha and no titers against B.1, Beta and Delta. Interpretation This preliminary data shows that Omicron (R346K) variant infection can produce moderate to severe lung disease similar to that of the Delta variant and the neutralizing antibodies produced in response to Omicron (R346K) variant infection shows poor neutralizing ability against other co-circulating SARS-CoV-2 variants like Delta which necessitates caution as it may lead to increased cases of reinfection. Funding This study was supported by 10.13039/501100001411Indian Council of Medical Research as an intramural grant (COVID-19) to ICMR-National Institute of Virology, Pune.
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Affiliation(s)
- Sreelekshmy Mohandas
- Maximum Containment Laboratory, Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra 411021, India
| | - Pragya D Yadav
- Maximum Containment Laboratory, Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra 411021, India.
| | - Gajanan Sapkal
- Maximum Containment Laboratory, Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra 411021, India
| | - Anita M Shete
- Maximum Containment Laboratory, Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra 411021, India
| | - Gururaj Deshpande
- Maximum Containment Laboratory, Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra 411021, India
| | - Dimpal A Nyayanit
- Maximum Containment Laboratory, Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra 411021, India
| | - Deepak Patil
- Maximum Containment Laboratory, Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra 411021, India
| | - Manoj Kadam
- Maximum Containment Laboratory, Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra 411021, India; Krantisinh Nana Patil College of Veterinary Science, Shirwal, Maharashtra 412801, India
| | - Abhimanyu Kumar
- Maximum Containment Laboratory, Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra 411021, India; Krantisinh Nana Patil College of Veterinary Science, Shirwal, Maharashtra 412801, India
| | - Chandrashekhar Mote
- Krantisinh Nana Patil College of Veterinary Science, Shirwal, Maharashtra 412801, India
| | - Rajlaxmi Jain
- Maximum Containment Laboratory, Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, Maharashtra 411021, India
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Chen Z, Ng RWY, Lui G, Ling L, Chow C, Yeung ACM, Boon SS, Wang MH, Chan KCC, Chan RWY, Hui DSC, Chan PKS. Profiling of SARS-CoV-2 Subgenomic RNAs in Clinical Specimens. Microbiol Spectr 2022; 10:e0018222. [PMID: 35311586 PMCID: PMC9045320 DOI: 10.1128/spectrum.00182-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 02/24/2022] [Indexed: 12/19/2022] Open
Abstract
SARS-CoV-2 transcribes a set of subgenomic RNAs (sgRNAs) essential for the translation of structural and accessory proteins to sustain its life cycle. We applied RNA-seq on 375 respiratory samples from individual COVID-19 patients and revealed that the majority of the sgRNAs were canonical transcripts with N being the most abundant (36.2%), followed by S (11.6%), open reading frame 7a (ORF7a; 10.3%), M (8.4%), ORF3a (7.9%), ORF8 (6.0%), E (4.6%), ORF6 (2.5%), and ORF7b (0.3%); but ORF10 was not detected. The profile of most sgRNAs, except N, showed an independent association with viral load, time of specimen collection after onset, age of the patient, and S-614D/G variant with ORF7b and then ORF6 being the most sensitive to changes in these characteristics. Monitoring of 124 serial samples from 10 patients using sgRNA-specific real-time RT-PCR revealed a potential of adopting sgRNA as a marker of viral activity. Respiratory samples harboring a full set of canonical sgRNAs were mainly collected early within 1 to 2 weeks from onset, and most of the stool samples (90%) were negative for sgRNAs despite testing positive by diagnostic PCR targeting genomic RNA. ORF7b was the first to become undetectable and again being the most sensitive surrogate marker for a full set of canonical sgRNAs in clinical samples. The potential of using sgRNA to monitor viral activity and progression of SARS-CoV-2 infection, and hence as one of the objective indicators to triage patients for isolation and treatment should be considered. IMPORTANCE Attempts to use subgenomic RNAs (sgRNAs) of SARS-CoV-2 to identify active infection of COVID-19 have produced diverse results. In this work, we applied next-generation sequencing and RT-PCR to profile the full spectrum of SARS-CoV-2 sgRNAs in a large cohort of respiratory and stool samples collected throughout infection. Numerous known and novel discontinuous transcription events potentially encoding full-length, deleted and frameshift proteins were observed. In particular, the expression profile of canonical sgRNAs was associated with genomic RNA level and clinical characteristics. Our study found sgRNAs as potential biomarkers for monitoring infectivity and progression of SARS-CoV-2 infection, which provides an alternative target for the management and treatment of COVID-19 patients.
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Affiliation(s)
- Zigui Chen
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Rita Way Yin Ng
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Grace Lui
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Chit Chow
- Department of Anatomical and Cellular Pathology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Apple Chung Man Yeung
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Siaw Shi Boon
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Maggie Haitian Wang
- Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kate Ching Ching Chan
- Department of Paediatrics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Renee Wan Yi Chan
- Department of Paediatrics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - David Shu Cheong Hui
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Paul Kay Sheung Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
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Rahmani A, Dini G, Leso V, Montecucco A, Kusznir Vitturi B, Iavicoli I, Durando P. Duration of SARS-CoV-2 shedding and infectivity in the working age population: a systematic review and meta-analysis. LA MEDICINA DEL LAVORO 2022; 113:e2022014. [PMID: 35481581 PMCID: PMC9073762 DOI: 10.23749/mdl.v113i2.12724] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/22/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND During the COVID-19 pandemic, working age individuals have been implicated in sustaining the resurgence of SARS-CoV-2 infections, and multiple outbreaks have been observed in several occupational settings. In this regard, Occupational Physicians play a crucial role in the management of infected workers, particularly in the safe return-to-work of subjects after clinical resolution. To this end, knowledge of the duration of the infective phase in the working age population is essential, taking into account previous evidence suggesting that PCR positivity does not coincide with virus viability. METHODS A systematic review and meta-analysis, searching major scientific databases, including PubMed/MEDLINE, Scopus and Web of Science, were performed in order to synthesize the available evidence regarding the mean and maximal duration of infectivity compared to the mean and maximal duration of viral RNA shedding. A subgroup analysis of the studies was performed according to the immunocompetent or immunocompromised immune status of the majority of the enrolled individuals. RESULTS Twenty studies were included in the final qualitative and quantitative analysis (866 individuals). Overall, a mean duration of RT-PCR positivity after symptom onset was found equal to 27.9 days (95%CI 23.3-32.5), while the mean duration of replicant competent virus isolation was 7.3 days (95%CI 5.7-8.8). The mean duration of SARS-CoV-2 shedding resulted equal to 26.5 days (95%CI 21.4-31.6) and 36.3 days (95%CI 21.9-50.6), and the mean duration of SARS-CoV-2 infectivity was 6.3 days (95%CI 4.9-7.8) and 29.5 days (95%CI 12.5-46.5), respectively considering immunocompetent and immunocompromised individuals. The maximum duration of infectivity among immunocompetent subjects was reported after 18 days from symptom onset, while in immunocompromised individuals it lasted up to 112 days. CONCLUSIONS These findings suggest that the test-based strategy before return-to-work might not be warranted after 21 days among immunocompetent working age individuals, and could keep many workers out of occupation, reducing their livelihood and productivity.
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Affiliation(s)
- Alborz Rahmani
- Department of Health Sciences, University of Genoa; Occupational Medicine Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.
| | - Guglielmo Dini
- Department of Health Sciences, University of Genoa; Occupational Medicine Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.
| | - Veruscka Leso
- Section of Occupational Medicine, Department of Public Health, University of Naples Federico II, Naples, Italy.
| | - Alfredo Montecucco
- Department of Health Sciences, University of Genoa; Occupational Medicine Unit, IRCCS Ospedale Policlinico San Martino.
| | | | - Ivo Iavicoli
- Section of Occupational Medicine, Department of Public Health, University of Naples Federico II, Naples, Italy.
| | - Paolo Durando
- Department of Health Sciences, University of Genoa; Occupational Medicine Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.
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Seok H, Lim S, Kim JY, Park CH, Kim JH, Woo ML, Won H, Kang YM, Oh HS, Song KH, Jung YJ, Kim T, Jo S, Choi WS. Infectivity of Coronavirus Disease 2019: A Prospective Cohort Study in the Korean Metropolitan Area. J Korean Med Sci 2022; 37:e106. [PMID: 35411726 PMCID: PMC9001183 DOI: 10.3346/jkms.2022.37.e106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/17/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Although several characteristics of coronavirus disease 2019 (COVID-19), an ongoing pandemic disease, have been identified, data on the infectivity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are limited. METHODS This prospective cohort study was conducted to analyze the infectivity of SARS-CoV-2 based on data of all patients diagnosed with COVID-19 confirmed using real-time polymerase chain reaction test from January to April 2020 in Gyeonggi-do, the largest province in Korea. RESULTS Of the 502 patients, 298 consisting of 106 clusters with 5,909 contacts were included. Of these, 277 (93.0%) were symptomatic, and the most common symptoms were cough, fever, sputum, sore throat, and headache. A total of 94 patients (31.5%) had pneumonia, while 8 (2.7%) died during the follow-up period. The secondary attack rate (SAR) in the study population was 3.5% (204/5,909). In exposure settings, the SAR was higher in religious gathering (13.5% [95% confidence interval, 10.7-16.8%]), workplaces (8.49% [95% CI, 6.08-11.74%]), and schools (6.38% [95% CI, 3.39-11.69%]) than in health care facilities (1.92% [95% CI, 1.45-2.55%]). Sore throat at any period, dyspnea at diagnosis or any period, lower cycle threshold value in the lower respiratory tract samples, leukocytosis, and higher bilirubin levels were associated with higher infectivity of COVID-19. The presence of symptoms was not related to the infectivity. CONCLUSION In establishing the infection control strategies for COVID-19, the variables associated with high infectivity may be considered.
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Affiliation(s)
- Hyeri Seok
- Division of Infectious Diseases, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Ansan, Korea
| | - Seungkwan Lim
- Department of Internal Medicine, Gyeonggi Provincial Medical Center, Ansung Hospital, Anseong, Korea
| | - Ji-Yeon Kim
- Division of Infectious Disease, Department of Medicine, Seongnam Citizens Medical Center, Seongnam, Korea
| | - Chul Hee Park
- Department of Internal Medicine, Gyeonggi Provincial Medical Center, Icheon Hospital, Icheon, Korea
| | - Joon Ho Kim
- Department of Surgery, Gyeonggi Provincial Medical Center, Uijeongbu Hospital, Uijeongbu, Korea
| | - Myoung Lyeol Woo
- Department of Internal Medicine, Gyeonggi Provincial Medical Center, Uijeongbu Hospital, Uijeongbu, Korea
| | - Hyejin Won
- Department of Internal Medicine, Gyeonggi Provincial Medical Center, Pocheon Hospital, Pocheon, Korea
| | - Yu Min Kang
- Division of Infectious Disease, Department of Internal Medicine, Myongji Hospital, Goyang, Korea
| | - Hong Sang Oh
- Department of Internal Medicine, Armed Forces Capital Hospital, Seongnam, Korea
| | - Kyoung-Ho Song
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Yun Jung Jung
- Department of Pulmonary and Critical Care Medicine, Ajou University School of Medicine, Suwon, Korea
| | - Tark Kim
- Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
| | - Soonam Jo
- Infectious Disease Control Center, Gyeonggi Provincial Government, Suwon, Korea
| | - Won Suk Choi
- Division of Infectious Diseases, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Ansan, Korea.
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Fomenko A, Weibel S, Moezi H, Menger K, Schmucker C, Metzendorf MI, Motschall E, Falcone V, Huzly D, Panning M, Rücker G, Hengel H. Assessing severe acute respiratory syndrome coronavirus 2 infectivity by reverse-transcription polymerase chain reaction: A systematic review and meta-analysis. Rev Med Virol 2022; 32:e2342. [PMID: 35366033 PMCID: PMC9111068 DOI: 10.1002/rmv.2342] [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: 12/21/2021] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 12/19/2022]
Abstract
The cornerstone of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) detection is reverse‐transcription polymerase chain reaction (RT‐PCR) of viral RNA. As a surrogate assay SARS‐CoV‐2 RNA detection does not necessarily imply infectivity. Only virus isolation in permissive cell culture systems can indicate infectivity. Here, we review the evidence on RT‐PCR performance in detecting infectious SARS‐CoV‐2. We searched for any studies that used RT‐PCR and cell culture to determine infectious SARS‐CoV‐2 in respiratory samples. We assessed (i) diagnostic accuracy of RT‐PCR compared to cell culture as reference test, (ii) performed meta‐analysis of positive predictive values (PPV) and (iii) determined the virus isolation probabilities depending on cycle threshold (Ct) or log10 genome copies/ml using logistic regression. We included 55 studies. There is substantial statistical and clinical heterogeneity. Seven studies were included for diagnostic accuracy. Sensitivity ranged from 90% to 99% and specificity from 29% to 92%. In meta‐analysis, the PPVs varied across subgroups with different sampling times after symptom onset, with 1% (95% confidence interval [CI], 0%–7%) in sampling beyond 10 days and 27% (CI, 19%–36%) to 46% (CI, 33%–60%) in subgroups that also included earlier samples. Estimates of virus isolation probability varied between 6% (CI, 0%–100%) and 50% (CI, 0%–100%) at a Ct value of 30 and between 0% (CI, 0%–22%) and 63% (CI, 0%–100%) at 5 log10 genome copies/ml. Evidence on RT‐PCR performance in detecting infectious SARS‐CoV‐2 in respiratory samples was limited. Major limitations were heterogeneity and poor reporting. RT‐PCR and cell culture protocols need further standardisation.
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Affiliation(s)
- Alexey Fomenko
- Institute of Virology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Stephanie Weibel
- Department of Anaesthesiology, Intensive Care, Emergency and Pain Medicine, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Helia Moezi
- Department of Anaesthesiology, Intensive Care, Emergency and Pain Medicine, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Kristina Menger
- Department of Anaesthesiology, Intensive Care, Emergency and Pain Medicine, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Christine Schmucker
- Institute for Evidence in Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Maria-Inti Metzendorf
- Cochrane Metabolic and Endocrine Disorders Group, Institute of General Practice, Medical Faculty, Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Edith Motschall
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Valeria Falcone
- Institute of Virology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Daniela Huzly
- Institute of Virology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Marcus Panning
- Institute of Virology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Gerta Rücker
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Hartmut Hengel
- Institute of Virology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
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Jeewandara C, Guruge D, Pushpakumara PD, Madhusanka D, Jayadas TT, Chaturanga IP, Aberathna IS, Danasekara S, Pathmanathan T, Jayathilaka D, Somathilaka G, Kuruppu H, Gomes L, Gunasekara V, Wijayamuni R, Ogg GS, Malavige GN. Sensitivity and specificity of two WHO approved SARS-CoV2 antigen assays in detecting patients with SARS-CoV2 infection. BMC Infect Dis 2022; 22:276. [PMID: 35317731 PMCID: PMC8938642 DOI: 10.1186/s12879-022-07240-6] [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: 06/07/2021] [Accepted: 03/03/2022] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND SARS-CoV-2 rapid antigen (Ag) detection kits are widely used in addition to quantitative reverse transcription PCR PCR (RT-qPCR), as they are cheaper with a rapid turnaround time. As there are many concerns regarding their sensitivity and specificity, in different settings, we evaluated two WHO approved rapid Ag kits in a large cohort of Sri Lankan individuals. METHODS Paired nasopharangeal swabs were obtained from 4786 participants for validation of the SD-Biosensor rapid Ag assay and 3325 for the Abbott rapid Ag assay, in comparison to RT-qPCR. A short questionnaire was used to record symptoms at the time of testing, and blood samples were obtained from 2721 of them for detection of SARS-CoV-2 specific antibodies. RESULTS The overall sensitivity of the SD-Biosensor Ag kit was 36.5% and the Abbott Ag test was 50.76%. The Abbott Ag test showed specificity of 99.4% and the SD-Biosensor Ag test 97.5%. At Ct values < 25, the sensitivity was 71.3% to 76.6% for the SD-Biosensor Ag test and 77.3% to 88.9% for the Abbott Ag test. The Ct values for all genes (RdRP, S, E and N) tested with all RT-qPCR kits were significantly lower for the positive results of the Abbott Ag test compared to the SD-Biosensor test. 209 (48.04%) individuals who had antibodies gave a positive RT-qPCR result, and antibody positivity rates were higher at Ct values > 30 (46.1 to 82.9%). 32.1% of those who gave a positive result with the SD-Biosensor Ag test and 26.3% of those who gave positive results with the Abbott Ag test had SARS-CoV-2 antibodies at the time of detection. CONCLUSIONS Both rapid Ag tests appeared to be highly sensitive in detecting individuals at lower Ct values, in a community setting in Sri Lanka, but it will be important to further establish the relationship to infectivity.
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Affiliation(s)
- Chandima Jeewandara
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | | | - Pradeep Darshana Pushpakumara
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Deshan Madhusanka
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Tibutius Thanesh Jayadas
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | | | - Inoka Sepali Aberathna
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Saubhagya Danasekara
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Thilagaraj Pathmanathan
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Deshni Jayathilaka
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Gayasha Somathilaka
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Heshan Kuruppu
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Laksiri Gomes
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | | | | | - Graham S Ogg
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka.,MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Gathsaurie Neelika Malavige
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka. .,MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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49
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Maya S, Kahn JG. Cost-effectiveness of antigen testing for ending COVID-19 isolation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.03.21.22272687. [PMID: 35350204 PMCID: PMC8963687 DOI: 10.1101/2022.03.21.22272687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Background The Omicron variant of SARS-CoV-2 led to a steep rise in transmissions. Recently, as public tolerance for isolation abated, CDC guidance on duration of at-home isolation of COVID-19 cases was shortened to five days if no symptoms, with no lab test requirement, despite more cautious approaches advocated by other federal experts. Methods We conducted a decision tree analysis of alternative protocols for ending COVID-19 isolation, estimating net costs (direct and productivity), secondary infections, and incremental cost-effectiveness ratios. Sensitivity analyses assessed the impact of input uncertainty. Results Per 100 individuals, five-day isolation had 23 predicted secondary infections and a net cost of $33,000. Symptom check on day five (CDC guidance) yielded a 23% decrease in secondary infections (to 17.8), with a net cost of $45,000. Antigen testing on day six yielded 2.9 secondary infections and $63,000 in net costs. This protocol, compared to the next best protocol of antigen testing on day five of a maximum eight-day isolation, cost an additional $1,300 per secondary infection averted. Antigen or polymerase chain reaction testing on day five were dominated (more expensive and less effective) versus antigen testing on day six. Results were qualitatively robust to uncertainty in key inputs. Conclusions A six-day isolation with antigen testing to confirm the absence of contagious virus appears the most effective and cost-effective de-isolation protocol to shorten at-home isolation of individuals with COVID-19.
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Affiliation(s)
- Sigal Maya
- Philip R. Lee Institute for Health Policy Studies, University of California San Francisco, San Francisco, CA, USA
| | - James G. Kahn
- Philip R. Lee Institute for Health Policy Studies, University of California San Francisco, San Francisco, CA, USA
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50
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Direct comparison of Xpert Xpress, FilmArray Respiratory Panel, Lumipulse antigen test, and RT-qPCR in 165 nasopharyngeal swabs. BMC Infect Dis 2022; 22:221. [PMID: 35246055 PMCID: PMC8894560 DOI: 10.1186/s12879-022-07185-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/19/2022] [Indexed: 12/22/2022] Open
Abstract
Background The nucleic acid amplification test (NAAT) and antigen test are approved diagnostic tests for COVID-19. In this study, we aimed to investigate the assay performance of two NAATs (Xpert Xpress SARS-CoV-2 and FilmArray Respiratory Panel) and a quantitative antigen test (Lumipulse). Methods One hundred and sixty-five nasopharyngeal swabs were subjected to Xpert, FilmArray, Lumipulse, and RT-qPCR assays. Results Of 165 samples, RT-qPCR showed 100 positives and 65 negatives. The Xpert had an overall agreement of 99.4% (95% confidence interval [CI]: 96.7–99.4%), sensitivity of 99% (95% CI: 96.8–99%), and specificity of 100% (95% CI: 96.6–100%). FilmArray had an overall agreement of 98.8% (95% CI: 95.9–98.8%), sensitivity of 98% (95% CI: 95.6–98%), and specificity of 100% (95% CI: 96.3–100%). Lumipulse had an overall agreement of 95.5% (95% CI: 91.8–95.5%), sensitivity of 92.3% (95% CI: 89.2–92.3%), and specificity of 100% (95% CI: 95.5–100%). The κ coefficient showed excellent agreement between each test and RT-qPCR. There was a high correlation between Xpert Ct values, RT-qPCR Ct values, viral loads and antigen level. Conclusions Xpert Xpress and FilmArray Respiratory Panel exhibited an equivalent performance. The Lumipulse antigen test was slightly less sensitive than the NAATs, but showed high assay performance except for samples with low viral load. The Xpert Xpress, FilmArray Respiratory Panel and Lumipulse antigen tests offer rapid sample-to-answer data, allowing random access detection on automated devices.
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