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Peri Ibáñez ES, Mazzeo A, Silva C, Juncos MJ, Costa Navarro GS, Pallarés HM, Wolos VJ, Fiszman GL, Mundo SL, Caramelo JJ, Yanovsky MJ, Fingermann M, Castello AA, Gamarnik AV, Peinetti AS, Capdevila DA. Overcoming Limited Access to Virus Infection Rapid Testing: Development of a Lateral Flow Test for SARS-CoV-2 with Locally Available Resources. BIOSENSORS 2024; 14:416. [PMID: 39329791 PMCID: PMC11431090 DOI: 10.3390/bios14090416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 08/19/2024] [Accepted: 08/20/2024] [Indexed: 09/28/2024]
Abstract
The COVID-19 pandemic highlighted testing inequities in developing countries. Lack of lateral flow test (LFT) manufacturing capacity was a major COVID-19 response bottleneck in low- and middle-income regions. Here we report the development of an open-access LFT for SARS-CoV-2 detection comparable to commercial tests that requires only locally available supplies. The main critical resource is a locally developed horse polyclonal antibody (pAb) whose sensitivity and selectivity are greatly enhanced by affinity purification. We demonstrate that these Abs can perform similarly to commercial monoclonal antibodies (mAbs), as well as mAbs and other pAbs developed against the same antigen. We report a workflow for test optimization using nasopharyngeal swabs collected for RT-qPCR, spiked with the inactivated virus to determine analytical performance characteristics as the limit of detection, among others. Our final prototype showed a performance similar to available tests (sensitivity of 83.3% compared to RT-qPCR, and 90.9% compared to commercial antigen tests). Finally, we discuss the possibility and the challenges of utilizing affinity-purified pAbs as an alternative for the local development of antigen tests in an outbreak context and as a tool to address inequalities in access to rapid tests.
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Affiliation(s)
- Estefanía S. Peri Ibáñez
- Laboratorio de Inmunología y Virología (LIV), Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, B1876BXD Buenos Aires, Argentina (A.A.C.)
- Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), CONICET, Fundación Instituto Leloir, C1405BWE Ciudad Autónoma de Buenos Aires, Argentina; (A.M.); (C.S.); (M.J.J.); (G.S.C.N.); (H.M.P.); (J.J.C.); (M.J.Y.); (A.V.G.)
| | - Agostina Mazzeo
- Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), CONICET, Fundación Instituto Leloir, C1405BWE Ciudad Autónoma de Buenos Aires, Argentina; (A.M.); (C.S.); (M.J.J.); (G.S.C.N.); (H.M.P.); (J.J.C.); (M.J.Y.); (A.V.G.)
| | - Carolina Silva
- Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), CONICET, Fundación Instituto Leloir, C1405BWE Ciudad Autónoma de Buenos Aires, Argentina; (A.M.); (C.S.); (M.J.J.); (G.S.C.N.); (H.M.P.); (J.J.C.); (M.J.Y.); (A.V.G.)
- INQUIMAE (CONICET), Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), C1428EGA Ciudad Autónoma de Buenos Aires, Argentina
| | - Maria Juliana Juncos
- Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), CONICET, Fundación Instituto Leloir, C1405BWE Ciudad Autónoma de Buenos Aires, Argentina; (A.M.); (C.S.); (M.J.J.); (G.S.C.N.); (H.M.P.); (J.J.C.); (M.J.Y.); (A.V.G.)
| | - Guadalupe S. Costa Navarro
- Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), CONICET, Fundación Instituto Leloir, C1405BWE Ciudad Autónoma de Buenos Aires, Argentina; (A.M.); (C.S.); (M.J.J.); (G.S.C.N.); (H.M.P.); (J.J.C.); (M.J.Y.); (A.V.G.)
| | - Horacio M. Pallarés
- Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), CONICET, Fundación Instituto Leloir, C1405BWE Ciudad Autónoma de Buenos Aires, Argentina; (A.M.); (C.S.); (M.J.J.); (G.S.C.N.); (H.M.P.); (J.J.C.); (M.J.Y.); (A.V.G.)
| | - Virginia J. Wolos
- Universidad de Buenos Aires (UBA), Instituto de Oncología Ángel H. Roffo, Área Investigación, C1417DTB Ciudad Autónoma de Buenos Aires, Argentina; (V.J.W.); (G.L.F.)
| | - Gabriel L. Fiszman
- Universidad de Buenos Aires (UBA), Instituto de Oncología Ángel H. Roffo, Área Investigación, C1417DTB Ciudad Autónoma de Buenos Aires, Argentina; (V.J.W.); (G.L.F.)
| | - Silvia L. Mundo
- Cátedra de Inmunología, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires (UBA), C1427CWN Ciudad Autónoma de Buenos Aires, Argentina;
| | - Julio J. Caramelo
- Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), CONICET, Fundación Instituto Leloir, C1405BWE Ciudad Autónoma de Buenos Aires, Argentina; (A.M.); (C.S.); (M.J.J.); (G.S.C.N.); (H.M.P.); (J.J.C.); (M.J.Y.); (A.V.G.)
| | - Marcelo J. Yanovsky
- Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), CONICET, Fundación Instituto Leloir, C1405BWE Ciudad Autónoma de Buenos Aires, Argentina; (A.M.); (C.S.); (M.J.J.); (G.S.C.N.); (H.M.P.); (J.J.C.); (M.J.Y.); (A.V.G.)
| | - Matías Fingermann
- Instituto Nacional de Producción de Biológicos (INPB), ANLIS “Dr. Carlos G. Malbrán”, C1282AFF Ciudad Autónoma de Buenos Aires, Argentina;
| | - Alejandro A. Castello
- Laboratorio de Inmunología y Virología (LIV), Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, B1876BXD Buenos Aires, Argentina (A.A.C.)
- Centro de Medicina Traslacional, Hospital El Cruce Néstor C., Kirchner, B1888 Buenos Aires, Argentina
- Instituto de Ciencias de la Salud, Universidad Nacional Arturo Jauretche, B1888 Buenos Aires, Argentina
| | - Andrea V. Gamarnik
- Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), CONICET, Fundación Instituto Leloir, C1405BWE Ciudad Autónoma de Buenos Aires, Argentina; (A.M.); (C.S.); (M.J.J.); (G.S.C.N.); (H.M.P.); (J.J.C.); (M.J.Y.); (A.V.G.)
| | - Ana S. Peinetti
- INQUIMAE (CONICET), Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), C1428EGA Ciudad Autónoma de Buenos Aires, Argentina
| | - Daiana A. Capdevila
- Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), CONICET, Fundación Instituto Leloir, C1405BWE Ciudad Autónoma de Buenos Aires, Argentina; (A.M.); (C.S.); (M.J.J.); (G.S.C.N.); (H.M.P.); (J.J.C.); (M.J.Y.); (A.V.G.)
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Park J, Cho SI, Kang SG, Kim JW, Jung S, Lee SH, Han KS, Hwang SS. Long-term trends in cycle threshold values: a comprehensive analysis of COVID-19 dynamics, viral load, and reproduction number in South Korea. Front Public Health 2024; 12:1394565. [PMID: 39188798 PMCID: PMC11345234 DOI: 10.3389/fpubh.2024.1394565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 07/25/2024] [Indexed: 08/28/2024] Open
Abstract
Background With the emergence of COVID-19 cases, governments quickly responded with aggressive testing, contact tracing, isolation and quarantine measures. South Korea's testing strategy primarily relied on real-time reverse-transcriptase polymerase chain reaction (real-time RT-PCR), focusing on cycle threshold (Ct) values, indicative of viral load, to determine COVID-19 positivity. This study examined the long-term time series distribution of Ct values measured in the same laboratory using a nationally standardized testing type and sampling method in South Korea. It aimed to link Ct values, new COVID-19 cases, and the reproduction number (Rt), setting the stage for using Ct values effectively. Methods This study analyzed nationally collected 296,347 samples Ct values from February 2020 to January 2022 and examined their associations with the number of new cases and Rt trends. The data were categorized into four COVID-19 periods for in-depth analysis. Statistical methods included time series trend analysis, local regression for smoothing, linear regression for association analysis, and calculation of correlation coefficients. Results The median Ct values across four COVID-19 periods decreased gradually from 31.71 in the initial period to 21.27 in the fourth period, indicating higher viral load. The comparison of trends between Ct values and the number of new cases revealed that the decline in Ct values preceded the surge in new cases, particularly evident during the initial stages when new cases did not undergo a significant increase. Also, during variant emergence and vaccination rollout, marked shifts in Ct values were observed. Results from linear regression analysis revealed a significant negative relationship between Ct values and new cases (β = -0.33, p < 0.001, R 2 = 0.67). This implies that as Ct values decrease, new case numbers increase. Conclusion This study demonstrates the potential of Ct values as early indicators for predicting confirmed COVID-19 cases during the initial stages of the epidemic and suggests their relevance in large-scale epidemic monitoring, even when case numbers are similar.
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Affiliation(s)
- Jungeun Park
- Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Sung-il Cho
- Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Sang-Gu Kang
- Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Jee-Woun Kim
- Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Sunkyung Jung
- Seegene Medical Foundation, Seoul, Republic of Korea
| | - Sun-Hwa Lee
- Seegene Medical Foundation, Seoul, Republic of Korea
| | - Kyou-Sup Han
- Seegene Medical Foundation, Seoul, Republic of Korea
| | - Seung-sik Hwang
- Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
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David SC, Schaub A, Terrettaz C, Motos G, Costa LJ, Nolan DS, Augugliaro M, Wynn HK, Glas I, Pohl MO, Klein LK, Luo B, Bluvshtein N, Violaki K, Hugentobler W, Krieger UK, Peter T, Stertz S, Nenes A, Kohn T. Stability of influenza A virus in droplets and aerosols is heightened by the presence of commensal respiratory bacteria. J Virol 2024; 98:e0040924. [PMID: 38869284 PMCID: PMC11264603 DOI: 10.1128/jvi.00409-24] [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: 03/01/2024] [Accepted: 05/08/2024] [Indexed: 06/14/2024] Open
Abstract
Aerosol transmission remains a major challenge for control of respiratory viruses, particularly those causing recurrent epidemics, like influenza A virus (IAV). These viruses are rarely expelled alone, but instead are embedded in a consortium of microorganisms that populate the respiratory tract. The impact of microbial communities and inter-pathogen interactions upon stability of transmitted viruses is well-characterized for enteric pathogens, but is under-studied in the respiratory niche. Here, we assessed whether the presence of five different species of commensal respiratory bacteria could influence the persistence of IAV within phosphate-buffered saline and artificial saliva droplets deposited on surfaces at typical indoor air humidity, and within airborne aerosol particles. In droplets, presence of individual species or a mixed bacterial community resulted in 10- to 100-fold more infectious IAV remaining after 1 h, due to bacterial-mediated flattening of drying droplets and early efflorescence. Even when no efflorescence occurred at high humidity or the bacteria-induced changes in droplet morphology were abolished by aerosolization instead of deposition on a well plate, the bacteria remained protective. Staphylococcus aureus and Streptococcus pneumoniae were the most stabilizing compared to other commensals at equivalent density, indicating the composition of an individual's respiratory microbiota is a previously unconsidered factor influencing expelled virus persistence.IMPORTANCEIt is known that respiratory infections such as coronavirus disease 2019 and influenza are transmitted by release of virus-containing aerosols and larger droplets by an infected host. The survival time of viruses expelled into the environment can vary depending on temperature, room air humidity, UV exposure, air composition, and suspending fluid. However, few studies consider the fact that respiratory viruses are not alone in the respiratory tract-we are constantly colonized by a plethora of bacteria in our noses, mouth, and lower respiratory system. In the gut, enteric viruses are known to be stabilized against inactivation and environmental decay by gut bacteria. Despite the presence of a similarly complex bacterial microbiota in the respiratory tract, few studies have investigated whether viral stabilization could occur in this niche. Here, we address this question by investigating influenza A virus stabilization by a range of commensal bacteria in systems representing respiratory aerosols and droplets.
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Affiliation(s)
- Shannon C. David
- Laboratory of Environmental Virology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Aline Schaub
- Laboratory of Environmental Virology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Céline Terrettaz
- Laboratory of Environmental Virology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Laboratory of Atmospheric Processes and their Impacts, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Ghislain Motos
- Laboratory of Atmospheric Processes and their Impacts, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Laura J. Costa
- Laboratory of Environmental Virology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Laboratory of Atmospheric Processes and their Impacts, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Daniel S. Nolan
- Laboratory of Environmental Virology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Marta Augugliaro
- Institute for Atmospheric and Climate Science, ETH Zürich, Zürich, Switzerland
| | - Htet Kyi Wynn
- Laboratory of Environmental Virology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Irina Glas
- Institute of Medical Virology, University of Zürich, Zürich, Switzerland
| | - Marie O. Pohl
- Institute of Medical Virology, University of Zürich, Zürich, Switzerland
| | - Liviana K. Klein
- Institute for Atmospheric and Climate Science, ETH Zürich, Zürich, Switzerland
| | - Beiping Luo
- Institute for Atmospheric and Climate Science, ETH Zürich, Zürich, Switzerland
| | - Nir Bluvshtein
- Institute for Atmospheric and Climate Science, ETH Zürich, Zürich, Switzerland
| | - Kalliopi Violaki
- Laboratory of Atmospheric Processes and their Impacts, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Walter Hugentobler
- Laboratory of Atmospheric Processes and their Impacts, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Ulrich K. Krieger
- Institute for Atmospheric and Climate Science, ETH Zürich, Zürich, Switzerland
| | - Thomas Peter
- Institute for Atmospheric and Climate Science, ETH Zürich, Zürich, Switzerland
| | - Silke Stertz
- Institute of Medical Virology, University of Zürich, Zürich, Switzerland
| | - Athanasios Nenes
- Laboratory of Atmospheric Processes and their Impacts, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Institute of Chemical Engineering Sciences, Foundation for Research and Technology Hellas, Patras, Greece
| | - Tamar Kohn
- Laboratory of Environmental Virology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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Aboagye FT, Annison L, Hackman HK, Acquah ME, Ashong Y, Owusu-Frimpong I, Egyam BC, Annison S, Osei-Adjei G, Antwi-Baffour S. Molecular Epidemiology of SARS-CoV-2 within Accra Metropolis Postlockdown. Adv Virol 2024; 2024:2993144. [PMID: 38584794 PMCID: PMC10997420 DOI: 10.1155/2024/2993144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/31/2024] [Accepted: 03/11/2024] [Indexed: 04/09/2024] Open
Abstract
Introduction Currently, sequencing has been the only tool for the identification of circulating severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants. However, it is known to be an expensive and laborious approach involving high technical expertise. Considering the reduced adherence to preventive measures postlockdown in Accra, this study presents an alternative method that leverages polymerase chain reaction (PCR) to identify circulating SARS-CoV-2 variants in the Accra Metropolis postlockdown. Methods This prospective cross-sectional study was conducted between July and December 2022. Nasopharyngeal samples were collected from 268 consenting participants. Samples were subjected to nucleic acid extraction and followed by real-time polymerase chain reaction for the detection and quantification of SARS-CoV-2 RNA. SARS-CoV-2 positive samples were subsequently subjected to variant identification using rapid PCR. Findings. The prevalence of SARS-CoV-2 within the Accra Metropolis was 30.2%. The majority of the SARS-CoV-2 infection was diagnosed in females, participants aged 41-50 years, and symptomatic participants. Participants aged ≤10 years and females recorded the highest viral load while participants aged 41-50 years recorded the highest number of infections. The SARS-CoV-2 variants detected were Alpha (64.2%), Delta (22.2%), and Omicron (13.6%). Predictors of SARS-CoV-2 infection identified were chills, cough, headache, body weakness, sore throat, and dyspnoea in order of decreasing association with SARS-CoV-2 infection. There was a strong association between symptom status, gender, age, and SARS-CoV-2 infection. Conclusion There was a high prevalence of SARS-CoV-2 within the Accra Metropolis postlockdown within the sampling period. The Alpha variant of SARS-CoV-2 is the predominant circulating variant, and persons presenting with symptoms are most likely to be diagnosed with COVID-19. Children aged ≤10 years serve as a reservoir for infection transmission.
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Affiliation(s)
- Frank T. Aboagye
- Department of Medical Laboratory Technology, Faculty of Applied Sciences, Accra Technical University, Accra, Ghana
- Biomedical and Public Health Research Unit, Council for Scientific and Industrial Research–Water Research Institute, Accra, Ghana
| | - Lawrence Annison
- Department of Medical Laboratory Technology, Faculty of Applied Sciences, Accra Technical University, Accra, Ghana
| | - Henry Kwadwo Hackman
- Department of Medical Laboratory Technology, Faculty of Applied Sciences, Accra Technical University, Accra, Ghana
| | - Maame E. Acquah
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Yvonne Ashong
- Department of Parasitology, Noguchi Memorial Institute of Medical Research, College of Medical Sciences, University of Ghana, Legon, Accra, Ghana
| | - Isaac Owusu-Frimpong
- Biomedical and Public Health Research Unit, Council for Scientific and Industrial Research–Water Research Institute, Accra, Ghana
| | - Bill C. Egyam
- Department of Molecular Biology, MDS Lancet Laboratories Ghana Limited, East Legon, Accra, Ghana
| | - Sharon Annison
- Department of Epidemiology and Disease Control, School of Public Health, University of Ghana, Legon, Accra, Ghana
| | - George Osei-Adjei
- Department of Medical Laboratory Technology, Faculty of Applied Sciences, Accra Technical University, Accra, Ghana
| | - Samuel Antwi-Baffour
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, Korle-Bu, Accra, Ghana
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Jafari M, Jabrodini A, Pirouzi A, Meshkin A, Mohsenzadeh M. Comparative analysis of asymptomatic infection prevalence in Beta, Delta, and Omicron surges of COVID-19. Braz J Infect Dis 2024; 28:103724. [PMID: 38365183 PMCID: PMC10897804 DOI: 10.1016/j.bjid.2024.103724] [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: 09/30/2023] [Revised: 12/23/2023] [Accepted: 01/24/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has had a devastating impact on the global population, with an estimated 650 million people infected and more than 6.6 million lives lost. Asymptomatic individuals have been shown to play a significant role in the transmission of the virus. Therefore, this study aims to investigate and compare the prevalence of asymptomatic individuals across three waves associated with the Beta, Delta, and Omicron variants of the virus. METHODS This retrospective study was conducted between December 2020 and March 2022. The study population consisted of passengers on international flights who were referred to the Gerash Clinical and Molecular Diagnosis Laboratory. Real-time PCR was employed for the diagnosis of SARS-CoV-2. RESULTS Out of a total of 8592 foreign travelers referred to our laboratory, 139 (1.16 %) tested positive for SARS-CoV-2 infection and were asymptomatic. During the Beta surge, 35 (1.49 %) out of 2335 passengers tested positive for SARS-CoV-2. In the Delta surge, 31 (0.6 %) out of 5127 passengers tested positive. However, during the Omicron surge, a significantly higher number of passengers, specifically 73 (6.46 %) out of 1130, had a positive result for the SARS-CoV-2 test. CONCLUSION Considering the significant role of asymptomatic transmission in the spread of COVID-19, it is imperative to reconsider health policies when dealing with future surges of the Omicron subvariants. Additionally, we strongly recommend that the World Health Organization prioritize the development and distribution of second-generation vaccines that target not only disease but also infection prevention.
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Affiliation(s)
- Mohammad Jafari
- Cellular and Molecular Research Center, Gerash University of Medical Sciences, Gerash, Iran
| | - Ahmad Jabrodini
- Cellular and Molecular Research Center, Gerash University of Medical Sciences, Gerash, Iran
| | - Aliyar Pirouzi
- Cellular and Molecular Research Center, Gerash University of Medical Sciences, Gerash, Iran
| | - Ahmad Meshkin
- Education Development Center, Committee of Medical Education Development, Gerash University of Medical Sciences, Gerash, Iran
| | - Mehdi Mohsenzadeh
- Cellular and Molecular Research Center, Gerash University of Medical Sciences, Gerash, Iran.
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Scheim DE, Vottero P, Santin AD, Hirsh AG. Sialylated Glycan Bindings from SARS-CoV-2 Spike Protein to Blood and Endothelial Cells Govern the Severe Morbidities of COVID-19. Int J Mol Sci 2023; 24:17039. [PMID: 38069362 PMCID: PMC10871123 DOI: 10.3390/ijms242317039] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Consistent with well-established biochemical properties of coronaviruses, sialylated glycan attachments between SARS-CoV-2 spike protein (SP) and host cells are key to the virus's pathology. SARS-CoV-2 SP attaches to and aggregates red blood cells (RBCs), as shown in many pre-clinical and clinical studies, causing pulmonary and extrapulmonary microthrombi and hypoxia in severe COVID-19 patients. SARS-CoV-2 SP attachments to the heavily sialylated surfaces of platelets (which, like RBCs, have no ACE2) and endothelial cells (having minimal ACE2) compound this vascular damage. Notably, experimentally induced RBC aggregation in vivo causes the same key morbidities as for severe COVID-19, including microvascular occlusion, blood clots, hypoxia and myocarditis. Key risk factors for COVID-19 morbidity, including older age, diabetes and obesity, are all characterized by markedly increased propensity to RBC clumping. For mammalian species, the degree of clinical susceptibility to COVID-19 correlates to RBC aggregability with p = 0.033. Notably, of the five human betacoronaviruses, the two common cold strains express an enzyme that releases glycan attachments, while the deadly SARS, SARS-CoV-2 and MERS do not, although viral loads for COVID-19 and the two common cold infections are similar. These biochemical insights also explain the previously puzzling clinical efficacy of certain generics against COVID-19 and may support the development of future therapeutic strategies for COVID-19 and long COVID patients.
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Affiliation(s)
- David E Scheim
- US Public Health Service, Commissioned Corps, Inactive Reserve, Blacksburg, VA 24060, USA
| | - Paola Vottero
- Department of Biomedical Engineering, University of Alberta, Edmonton, AB T6G 1Z2, Canada
| | - Alessandro D Santin
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale School of Medicine, P.O. Box 208063, New Haven, CT 06520, USA
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Galperine T, Choi Y, Pagani JL, Kritikos A, Papadimitriou-Olivgeris M, Méan M, Scherz V, Opota O, Greub G, Guery B, Bertelli C. Temporal changes in fecal microbiota of patients infected with COVID-19: a longitudinal cohort. BMC Infect Dis 2023; 23:537. [PMID: 37596518 PMCID: PMC10436399 DOI: 10.1186/s12879-023-08511-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/04/2023] [Indexed: 08/20/2023] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a multifaceted disease potentially responsible for various clinical manifestations including gastro-intestinal symptoms. Several evidences suggest that the intestine is a critical site of immune cell development, gut microbiota could therefore play a key role in lung immune response. We designed a monocentric longitudinal observational study to describe the gut microbiota profile in COVID-19 patients and compare it to a pre-existing cohort of ventilated non-COVID-19 patients. METHODS From March to December 2020, we included patients admitted for COVID-19 in medicine (43 not ventilated) or intensive care unit (ICU) (14 ventilated) with a positive SARS-CoV-2 RT-PCR assay in a respiratory tract sample. 16S metagenomics was performed on rectal swabs from these 57 COVID-19 patients, 35 with one and 22 with multiple stool collections. Nineteen non-COVID-19 ICU controls were also enrolled, among which 14 developed ventilator-associated pneumonia (pneumonia group) and five remained without infection (control group). SARS-CoV-2 viral loads in fecal samples were measured by qPCR. RESULTS Although similar at inclusion, Shannon alpha diversity appeared significantly lower in COVID-19 and pneumonia groups than in the control group at day 7. Furthermore, the microbiota composition became distinct between COVID-19 and non-COVID-19 groups. The fecal microbiota of COVID-19 patients was characterized by increased Bacteroides and the pneumonia group by Prevotella. In a distance-based redundancy analysis, only COVID-19 presented significant effects on the microbiota composition. Moreover, patients in ICU harbored increased Campylobacter and decreased butyrate-producing bacteria, such as Lachnospiraceae, Roseburia and Faecalibacterium as compared to patients in medicine. Both the stay in ICU and patient were significant factors affecting the microbiota composition. SARS-CoV-2 viral loads were higher in ICU than in non-ICU patients. CONCLUSIONS Overall, we identified distinct characteristics of the gut microbiota in COVID-19 patients compared to control groups. COVID-19 patients were primarily characterized by increased Bacteroides and decreased Prevotella. Moreover, disease severity showed a negative correlation with butyrate-producing bacteria. These features could offer valuable insights into potential targets for modulating the host response through the microbiota and contribute to a better understanding of the disease's pathophysiology. TRIAL REGISTRATION CER-VD 2020-00755 (05.05.2020) & 2017-01820 (08.06.2018).
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Affiliation(s)
- Tatiana Galperine
- Service of Infectious Diseases, Lausanne University Hospital and University of Lausanne, Rue du Bugnon 46, BH10-553, 1011, Lausanne, Switzerland
| | - Yangji Choi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Jean-Luc Pagani
- Service of Intensive Care, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Antonios Kritikos
- Service of Infectious Diseases, Lausanne University Hospital and University of Lausanne, Rue du Bugnon 46, BH10-553, 1011, Lausanne, Switzerland
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Matthaios Papadimitriou-Olivgeris
- Service of Infectious Diseases, Lausanne University Hospital and University of Lausanne, Rue du Bugnon 46, BH10-553, 1011, Lausanne, Switzerland
| | - Marie Méan
- Division of Internal Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Valentin Scherz
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Onya Opota
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Benoit Guery
- Service of Infectious Diseases, Lausanne University Hospital and University of Lausanne, Rue du Bugnon 46, BH10-553, 1011, Lausanne, Switzerland.
| | - Claire Bertelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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8
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Guterres A. Viral load: We need a new look at an old problem? J Med Virol 2023; 95:e29061. [PMID: 37638475 DOI: 10.1002/jmv.29061] [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: 01/27/2023] [Revised: 07/22/2023] [Accepted: 08/17/2023] [Indexed: 08/29/2023]
Abstract
The concept of viral load was introduced in the 1980s to measure the amount of viral genetic material in a person's blood, primarily for human immunodeficiency virus (HIV). It has since become crucial for monitoring HIV infection progression and assessing the efficacy of antiretroviral therapy. However, during the coronavirus disease 2019 pandemic, the term "viral load" became widely popularized, not only for the scientific community but for the general population. Viral load plays a critical role in both clinical patient management and research, providing valuable insights for antiviral treatment strategies, vaccination efforts, and epidemiological control measures. As measuring viral load is so important, why don't researchers discuss the best way to do it? Is it simply acceptable to use raw Ct values? Relying solely on Ct values for viral load estimation can be problematic due to several reasons. First, Ct values can vary between different quantitative polymerase chain reaction assays, platforms, and laboratories, making it difficult to compare data across studies. Second, Ct values do not directly measure the quantity of viral particles in a sample and they can be influenced by various factors such as initial viral load, sample quality, and assay sensitivity. Moreover, variations in viral RNA extraction and reverse-transcription steps can further impact the accuracy of viral load estimation, emphasizing the need for careful interpretation of Ct values in viral load assessment. Interestingly, we did not observe scientific articles addressing different strategies to quantify viral load. The absence of standardized and validated methods impedes the implementation of viral load monitoring in clinical management. The variability in cell quantities within samples and the variation in viral particle numbers within infected cells further challenge accurate viral load measurement and interpretation. To advance the field and improve patient outcomes, there is an urgent need for the development and validation of tailored, standardized methods for precise viral load quantification.
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Affiliation(s)
- Alexandro Guterres
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
- Laboratório de Tecnologia Imunológica, Instituto de Tecnologia em Imunobiológicos, Vice-Diretoria de Desenvolvimento Tecnológico, Bio-Manguinhos, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
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9
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Heudobler M, Baurecht H, Schmied H, Heudobler D, Jochem C, Sedlmeier AM, Weber A, Bauernfeind S, Leitzmann M, Salzberger B, Lampl BMJ. Association of epidemiological and clinical features with PCR cycle threshold values of SARS-CoV-2 infection: a cross-sectional study. Pathog Glob Health 2023; 117:476-484. [PMID: 36519354 PMCID: PMC10262808 DOI: 10.1080/20477724.2022.2158003] [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: 12/23/2022] Open
Abstract
The cycle threshold (Ct) in quantitative real-time reverse-transcriptase polymerase chain reaction (qRT-PCR) is inversely correlated to the amount of viral nucleic acid or viral load and can be regarded as an indicator of infectivity. We examined the association of socio-demographic and clinical characteristics of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) polymerase chain reaction (PCR) positive cases with PCR cycle threshold (Ct) values at the time of diagnosis. SARS-CoV-2 cases reported between 12 October 2020 and 24 January 2021 in Regensburg were analyzed employing bivariate and multivariable methods. We included 3,029 SARS-CoV-2 cases (31% asymptomatic at diagnosis) and analyzed the association of case characteristics with Ct values in 2,606 cases. Among symptomatic patients, cough (38.0%), rhinitis (32.4%), headache (32.0), and fever/chills (29.9%) were the most frequent complaints. Ct values ≤20 were more frequent in symptomatic cases (20.9% vs. 11.3%), whereas Ct values >30 were more common in asymptomatic cases (32.6% vs. 18.0%). Ct values >20 and ≤30 were most common in symptomatic and asymptomatic cases (48.0% vs 40.7%). We observed lower median Ct values of E and N gene in symptomatic cases. In a random forest model, the total number of symptoms, respiratory symptoms, and age were most strongly associated with low Ct values. In conclusion, certain symptoms and age were associated with lower Ct values. Ct values can be used as a pragmatic approach in estimating infectivity at the first notification of a case and, thus, in guiding containment measures.
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Affiliation(s)
- Marlies Heudobler
- Regensburg Department of Public Health, Altmühlstraße 3, Regensburg, Germany
| | - Hansjörg Baurecht
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Helen Schmied
- Regensburg Department of Public Health, Altmühlstraße 3, Regensburg, Germany
| | - Daniel Heudobler
- Department of Internal Medicine 3, University Hospital Regensburg, Regensburg, Germany
| | - Carmen Jochem
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Anja M Sedlmeier
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Andrea Weber
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Stilla Bauernfeind
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - Michael Leitzmann
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Bernd Salzberger
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - Benedikt M J Lampl
- Regensburg Department of Public Health, Altmühlstraße 3, Regensburg, Germany
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
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10
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Vilcapoma J, Aliyeva A, Hayden A, Chandrasekaran AR, Zhou L, Punnoose JA, Yang D, Hansen C, Shiu SCC, Russell A, George KS, Wong WP, Halvorsen K. A non-enzymatic test for SARS-CoV-2 RNA using DNA nanoswitches. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.31.23290613. [PMID: 37398235 PMCID: PMC10312858 DOI: 10.1101/2023.05.31.23290613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The emergence of a highly contagious novel coronavirus in 2019 led to an unprecedented need for large scale diagnostic testing. The associated challenges including reagent shortages, cost, deployment delays, and turnaround time have all highlighted the need for an alternative suite of low-cost tests. Here, we demonstrate a diagnostic test for SARS-CoV-2 RNA that provides direct detection of viral RNA and eliminates the need for costly enzymes. We employ DNA nanoswitches that respond to segments of the viral RNA by a change in shape that is readable by gel electrophoresis. A new multi-targeting approach samples 120 different viral regions to improve the limit of detection and provide robust detection of viral variants. We apply our approach to a cohort of clinical samples, positively identifying a subset of samples with high viral loads. Since our method directly detects multiple regions of viral RNA without amplification, it eliminates the risk of amplicon contamination and renders the method less susceptible to false positives. This new tool can benefit the COVID-19 pandemic and future emerging outbreaks, providing a third option between amplification-based RNA detection and protein antigen detection. Ultimately, we believe this tool can be adapted both for low-resource onsite testing as well as for monitoring viral loads in recovering patients.
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Affiliation(s)
- Javier Vilcapoma
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
| | - Asmer Aliyeva
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
| | - Andrew Hayden
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
| | | | - Lifeng Zhou
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
| | | | - Darren Yang
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Clinton Hansen
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Simon Chi-Chin Shiu
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
| | - Alexis Russell
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208
| | - Kirsten St. George
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208
- Department of Biomedical Science, University at Albany, State University of New York, Albany, NY 12208
| | - Wesley P. Wong
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
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Ghimire R, Shrestha R, Amaradhi R, Patton T, Whitley C, Chanda D, Liu L, Ganesh T, More S, Channappanavar R. Toll-like receptor 7 (TLR7)-mediated antiviral response protects mice from lethal SARS-CoV-2 infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539929. [PMID: 37214943 PMCID: PMC10197544 DOI: 10.1101/2023.05.08.539929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
SARS-CoV-2-induced impaired antiviral and excessive inflammatory responses cause fatal pneumonia. However, the key pattern recognition receptors that elicit effective antiviral and lethal inflammatory responses in-vivo are not well defined. CoVs possess single-stranded RNA (ssRNA) genome that is abundantly produced during infection and stimulates both antiviral interferon (IFN) and inflammatory cytokine/ chemokine responses. Therefore, in this study, using wild-type control and TLR7 deficient BALB/c mice infected with a mouse-adapted SARS-COV-2 (MA-CoV-2), we evaluated the role of TLR7 signaling in MA-CoV-2-induced antiviral and inflammatory responses and disease outcome. We show that TLR7-deficient mice are more susceptible to MA-CoV-2 infection as compared to infected control mice. Further evaluation of MA-CoV-2 infected lungs showed significantly reduced mRNA levels of antiviral type I (IFNα/β) and type III (IFNλ) IFNs, IFN stimulated genes (ISGs, ISG15 and CXCL10), and several pro-inflammatory cytokines/chemokines in TLR7 deficient compared to control mice. Reduced lung IFN/ISG levels and increased morbidity/mortality in TLR7 deficient mice correlated with high lung viral titer. Detailed examination of total cells from MA-CoV-2 infected lungs showed high neutrophil count in TLR7 deficient mice compared to control mice. Additionally, blocking TLR7 activity post-MA-CoV-2 infection using a specific inhibitor also enhanced disease severity. In summary, our results conclusively establish that TLR7 signaling is protective during SARS-CoV-2 infection, and despite robust inflammatory response, TLR7-mediated IFN/ISG responses likely protect the host from lethal disease. Given similar outcomes in control and TLR7 deficient humans and mice, these results show that MA-CoV-2 infected mice serve as excellent model to study COVID-19.
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12
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Djorwé S, Bousfiha A, Nzoyikorera N, Nkurunziza V, Ait Mouss K, Kawthar B, Malki A. Epidemiology, clinical characteristics and risk factors of coronavirus disease 2019 (COVID-19) in Casablanca. Access Microbiol 2023; 5:acmi000400. [PMID: 37223059 PMCID: PMC10202397 DOI: 10.1099/acmi.0.000400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/20/2023] [Indexed: 05/25/2023] Open
Abstract
This is an analytical cross-sectional study of coronavirus disease 2019 (COVID-19) based on data collected between 1 November 2020 and 31 March 2021 in Casablanca focusing on the disease's epidemiological status and risk factors. A total of 4569 samples were collected and analysed by reverse-transcription polymerase chain reaction (RT-PCR); 967 patients were positive, representing a prevalence of 21.2 % for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The mean age was 47.5±18 years, and infection was more common in young adults (<60 years). However, all age groups were at risk of COVID-19, and in terms of disease severity, the elderly were at greater risk because of potential underlying health problems. Among the clinical signs reported in this study, loss of taste and/or smell, fever, cough and fatigue were highly significant predictors of a positive COVID-19 test result (P<0.001). An assessment of the reported symptoms revealed that 27 % of COVID-19-positive patients (n=261) experienced loss of taste and/or smell, whereas only 2 % (n=72) of COVID-19-negative patients did (P<0.001). This result was consistent between univariate (OR=18.125) and multivariate (adjusted OR=10.484) logistic regression analyses, indicating that loss of taste and/or smell is associated with a more than 10-fold higher multivariate adjusted probability of a positive COVID-19 test (adjusted OR=10.48; P<0.001). Binary logistic regression model analysis based on clinical signs revealed that loss of taste and/or smell had a performance index of 0.846 with a P<0.001, confirming the diagnostic utility of this symptom for the prediction of COVID-19-positive status. In conclusion, symptom evaluation and a RT-PCR [taking into account cycle threshold (C t) values of the PCR proxy] test remain the most useful screening tools for diagnosing COVID-19. However, loss of taste/smell, fatigue, fever and cough remain the strongest independent predictors of a positive COVID-19 result.
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Affiliation(s)
- Soulandi Djorwé
- Laboratory of Physiopathology and Molecular Genetics, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca (Morocco), Avenue Cdt Driss El Harti, PB 7955 Sidi Othman Casablanca, Morocco
- Bourgogne Laboratory of Medical and Scientific Analysis, 136, Residence Belhcen, Bd Bourgogne, Casablanca, Morocco
| | - Amale Bousfiha
- Laboratory of Physiopathology and Molecular Genetics, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca (Morocco), Avenue Cdt Driss El Harti, PB 7955 Sidi Othman Casablanca, Morocco
| | - Néhémie Nzoyikorera
- National Reference Laboratory, National Institute of Public Health, Bujumbura, Burundi
- Higher Institute of Biosciences and Biotechnology, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
- Laboratory of Microbial Biotechnology and Infectiology Research, Mohammed VI Center for Research & Innovation, Rabat, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
| | - Victor Nkurunziza
- Laboratory of Hematology, University Hospital Centre Ibn Rochd, 1, Rue des Hôpitaux, 20100, Casablanca, Morocco
| | - Khadija Ait Mouss
- Department of Microbiology, Faculty of Medicine and Pharmacy, Hassan II University of Casablanca, 19 rue Tarik Bnou Zyad, 20360, Casablanca, Morocco
| | - Bellamine Kawthar
- Bourgogne Laboratory of Medical and Scientific Analysis, 136, Residence Belhcen, Bd Bourgogne, Casablanca, Morocco
| | - Abderrahim Malki
- Laboratory of Physiopathology and Molecular Genetics, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca (Morocco), Avenue Cdt Driss El Harti, PB 7955 Sidi Othman Casablanca, Morocco
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13
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Clements N, Arvelo I, Arnold P, Heredia NJ, Hodges UW, Deresinski S, Cook PW, Hamilton KA. Informing Building Strategies to Reduce Infectious Aerosol Transmission Risk by Integrating DNA Aerosol Tracers with Quantitative Microbial Risk Assessment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:5771-5781. [PMID: 37000413 DOI: 10.1021/acs.est.2c08131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Using aerosol-based tracers to estimate risk of infectious aerosol transmission aids in the design of buildings with adequate protection against aerosol transmissible pathogens, such as SARS-CoV-2 and influenza. We propose a method for scaling a SARS-CoV-2 bulk aerosol quantitative microbial risk assessment (QMRA) model for impulse emissions, coughing or sneezing, with aerosolized synthetic DNA tracer concentration measurements. With point-of-emission ratios describing relationships between tracer and respiratory aerosol emission characteristics (i.e., volume and RNA or DNA concentrations) and accounting for aerosolized pathogen loss of infectivity over time, we scale the inhaled pathogen dose and risk of infection with time-integrated tracer concentrations measured with a filter sampler. This tracer-scaled QMRA model is evaluated through scenario testing, comparing the impact of ventilation, occupancy, masking, and layering interventions on infection risk. We apply the tracer-scaled QMRA model to measurement data from an ambulatory care room to estimate the risk reduction resulting from HEPA air cleaner operation. Using DNA tracer measurements to scale a bulk aerosol QMRA model is a relatively simple method of estimating risk in buildings and can be applied to understand the impact of risk mitigation efforts.
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Affiliation(s)
- Nicholas Clements
- Paul M. Rady Department of Mechanical Engineering, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Ilan Arvelo
- SafeTraces, Inc., Pleasanton, California 94588, United States
| | - Phil Arnold
- SafeTraces, Inc., Pleasanton, California 94588, United States
| | | | - Ulrike W Hodges
- SafeTraces, Inc., Pleasanton, California 94588, United States
| | - Stan Deresinski
- Stanford University School of Medicine, Stanford, California 94305, United States
| | - Peter W Cook
- Independent researcher, Atlanta, Georgia 30333, United States
| | - Kerry A Hamilton
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona 85281, United States
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, Arizona 85281, United States
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14
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Amado LA, Coelho WLDCNP, Alves ADR, Carneiro VCDS, Moreira ODC, de Paula VS, Lemos AS, Duarte LA, Gutman EG, Fontes-Dantas FL, Gonçalves JPDC, Ramos CHF, Ramos Filho CHF, Cavalcanti MG, Amaro MP, Kader RL, Medronho RDA, Sarmento DJDS, Alves-Leon SV. Clinical Profile and Risk Factors for Severe COVID-19 in Hospitalized Patients from Rio de Janeiro, Brazil: Comparison between the First and Second Pandemic Waves. J Clin Med 2023; 12:2568. [PMID: 37048652 PMCID: PMC10094970 DOI: 10.3390/jcm12072568] [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: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 03/30/2023] Open
Abstract
Since COVID-19 was declared a pandemic, Brazil has become one of the countries most affected by this disease. A year into the pandemic, a second wave of COVID-19 emerged, with a rapid spread of a new SARS-CoV-2 lineage of concern. Several vaccines have been granted emergency-use authorization, leading to a decrease in mortality and severe cases in many countries. However, the emergence of SARS-CoV-2 variants raises the alert for potential new waves of transmission and an increase in pathogenicity. We compared the demographic and clinical data of critically ill patients infected with COVID-19 hospitalized in Rio de Janeiro during the first and second waves between July 2020 and October 2021. In total, 106 participants were included in this study; among them, 88% had at least one comorbidity, and 37% developed severe disease. Disease severity was associated with older age, pre-existing neurological comorbidities, higher viral load, and dyspnea. Laboratory biomarkers related to white blood cells, coagulation, cellular injury, inflammation, renal, and liver injuries were significantly associated with severe COVID-19. During the second wave of the pandemic, the necessity of invasive respiratory support was higher, and more individuals with COVID-19 developed acute hepatitis, suggesting that the progression of the second wave resulted in an increase in severe cases. These results can contribute to understanding the behavior of the COVID-19 pandemic in Brazil and may be helpful in predicting disease severity, which is a pivotal for guiding clinical care, improving patient outcomes, and defining public policies.
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Affiliation(s)
- Luciane Almeida Amado
- Laboratory of Technological Development in Virology, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro 21040-900, Brazil
| | | | - Arthur Daniel Rocha Alves
- Laboratory of Technological Development in Virology, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Vanessa Cristine de Souza Carneiro
- Laboratory of Technological Development in Virology, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro 21040-900, Brazil
- Laboratory of Molecular Virology, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Otacilio da Cruz Moreira
- Laboratory of Molecular Virology, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro 21040-900, Brazil
- Real Time PCR Platform RPT09A, Laboratory of Molecular Biology and Endemic Diseases, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Vanessa Salete de Paula
- Laboratory of Molecular Virology, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Andreza Salvio Lemos
- Laboratory of Translacional Neurosciences, Biomedical Institute, Federal University of the State of Rio de Janeiro-UNIRIO, Rio de Janeiro 22290-240, Brazil
| | - Larissa Araujo Duarte
- Laboratory of Translacional Neurosciences, Biomedical Institute, Federal University of the State of Rio de Janeiro-UNIRIO, Rio de Janeiro 22290-240, Brazil
- School of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Elisa Gouvea Gutman
- Laboratory of Translacional Neurosciences, Biomedical Institute, Federal University of the State of Rio de Janeiro-UNIRIO, Rio de Janeiro 22290-240, Brazil
- School of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Fabricia Lima Fontes-Dantas
- Laboratory of Translacional Neurosciences, Biomedical Institute, Federal University of the State of Rio de Janeiro-UNIRIO, Rio de Janeiro 22290-240, Brazil
- Department of Pharmacology and Psychobiology, Roberto Alcântara Gomes Institute Biology (IBRAG), Rio de Janeiro State University (UERJ), Rio de Janeiro 20551-030, Brazil
| | - João Paulo da Costa Gonçalves
- Laboratory of Translacional Neurosciences, Biomedical Institute, Federal University of the State of Rio de Janeiro-UNIRIO, Rio de Janeiro 22290-240, Brazil
| | - Carlos Henrique Ferreira Ramos
- Unit of Intensive Treatment, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | | | - Marta Guimarães Cavalcanti
- Epidemiology and Evaluation Service, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Marisa Pimentel Amaro
- Post-Graduate Program in Infectious and Parasitic Diseases, School of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Rafael Lopes Kader
- Post-Graduate Program in Infectious and Parasitic Diseases, School of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | | | | | - Soniza Vieira Alves-Leon
- Laboratory of Translacional Neurosciences, Biomedical Institute, Federal University of the State of Rio de Janeiro-UNIRIO, Rio de Janeiro 22290-240, Brazil
- School of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
- Department of Neurology, Reference and Research Center for Multiple Sclerosis and Other Central Nervous System Idiopathic Demyelinating Inflammatory Diseases, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
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15
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Nairz M, Todorovic T, Gehrer CM, Grubwieser P, Burkert F, Zimmermann M, Trattnig K, Klotz W, Theurl I, Bellmann-Weiler R, Weiss G. Single-Center Experience in Detecting Influenza Virus, RSV and SARS-CoV-2 at the Emergency Department. Viruses 2023; 15:v15020470. [PMID: 36851685 PMCID: PMC9958692 DOI: 10.3390/v15020470] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/02/2023] [Accepted: 02/04/2023] [Indexed: 02/10/2023] Open
Abstract
Reverse transcription polymerase chain reaction (RT-PCR) on respiratory tract swabs has become the gold standard for sensitive and specific detection of influenza virus, respiratory syncytial virus (RSV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this retrospective analysis, we report on the successive implementation and routine use of multiplex RT-PCR testing for patients admitted to the Internal Medicine Emergency Department (ED) at a tertiary care center in Western Austria, one of the hotspots in the early coronavirus disease 2019 (COVID-19) pandemic in Europe. Our description focuses on the use of the Cepheid® Xpert® Xpress closed RT-PCR system in point-of-care testing (POCT). Our indications for RT-PCR testing changed during the observation period: From the cold season 2016/2017 until the cold season 2019/2020, we used RT-PCR to diagnose influenza or RSV infection in patients with fever and/or respiratory symptoms. Starting in March 2020, we used the RT-PCR for SARS-CoV-2 and a multiplex version for the combined detection of all these three respiratory viruses to also screen subjects who did not present with symptoms of infection but needed in-hospital medical treatment for other reasons. Expectedly, the switch to a more liberal RT-PCR test strategy resulted in a substantial increase in the number of tests. Nevertheless, we observed an immediate decline in influenza virus and RSV detections in early 2020 that coincided with public SARS-CoV-2 containment measures. In contrast, the extensive use of the combined RT-PCR test enabled us to monitor the re-emergence of influenza and RSV detections, including asymptomatic cases, at the end of 2022 when COVID-19 containment measures were no longer in place. Our analysis of PCR results for respiratory viruses from a real-life setting at an ED provides valuable information on the epidemiology of those infections over several years, their contribution to morbidity and need for hospital admission, the risk for nosocomial introduction of such infection into hospitals from asymptomatic carriers, and guidance as to how general precautions and prophylactic strategies affect the dynamics of those infections.
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16
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Sadasivan H, Wadden J, Goliya K, Ranjan P, Dickson RP, Blaauw D, Das R, Narayanasamy S. Rapid Real-time Squiggle Classification for Read until using RawMap. ARCHIVES OF CLINICAL AND BIOMEDICAL RESEARCH 2023; 7:45-57. [PMID: 36938368 PMCID: PMC10022530 DOI: 10.26502/acbr.50170318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
ReadUntil enables Oxford Nanopore Technology's (ONT) sequencers to selectively sequence reads of target species in real-time. This enables efficient microbial enrichment for applications such as microbial abundance estimation and is particularly beneficial for metagenomic samples with a very high fraction of non-target reads (> 99% can be human reads). However, read-until requires a fast and accurate software filter that analyzes a short prefix of a read and determines if it belongs to a microbe of interest (target) or not. The baseline Read Until pipeline uses a deep neural network-based basecaller called Guppy and is slow and inaccurate for this task (~60% of bases sequenced are unclassified). We present RawMap, an efficient CPU-only microbial species-agnostic Read Until classifier for filtering non-target human reads in the squiggle space. RawMap uses a Support Vector Machine (SVM), which is trained to distinguish human from microbe using non-linear and non-stationary characteristics of ONT's squiggle output (continuous electrical signals). Compared to the baseline Read Until pipeline, RawMap is a 1327X faster classifier and significantly improves the sequencing time and cost, and compute time savings. We show that RawMap augmented pipelines reduce sequencing time and cost by ~24% and computing cost by 22%. Additionally, since RawMap is agnostic to microbial species, it can also classify microbial species it is not trained on. We also discuss how RawMap may be used as an alternative to the RT-PCR test for viral load quantification of SARS-CoV-2.
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Affiliation(s)
- Harisankar Sadasivan
- Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, 48109, USA
| | - Jack Wadden
- Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, 48109, USA
| | - Kush Goliya
- Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, 48109, USA
| | - Piyush Ranjan
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, 48109, USA
| | - Robert P Dickson
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, 48109, USA
| | - David Blaauw
- Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, 48109, USA
| | - Reetuparna Das
- Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, 48109, USA
| | - Satish Narayanasamy
- Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, 48109, USA
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17
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Hughes DM, Cheyne CP, Ashton M, Coffey E, Crozier A, Semple MG, Buchan I, García-Fiñana M. Association of SARS-CoV-2 viral load distributions with individual demographics and suspected variant type: results from the Liverpool community testing pilot, England, 6 November 2020 to 8 September 2021. Euro Surveill 2023; 28:2200129. [PMID: 36700865 PMCID: PMC9881177 DOI: 10.2807/1560-7917.es.2023.28.4.2200129] [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: 02/01/2022] [Accepted: 11/04/2022] [Indexed: 01/27/2023] Open
Abstract
BackgroundThe PCR quantification cycle (Cq) is a proxy measure of the viral load of a SARS-CoV-2-infected individual.AimTo investigate if Cq values vary according to different population characteristics, in particular demographic ones, and within the COVID-19 pandemic context, notably the SARS-CoV-2 type/variant individuals get infected with.MethodsWe considered all positive PCR results from Cheshire and Merseyside, England, between 6 November 2020 and 8 September 2021. Cq distributions were inspected with Kernel density estimates. Multivariable quantile regression models assessed associations between people's features and Cq.ResultsWe report Cq values for 188,821 SARS-CoV-2 positive individuals. Median Cqs increased with decreasing age for suspected wild-type virus and Alpha variant infections, but less so, if not, for Delta. For example, compared to 30-39-year-olds (median age group), 5-11-year-olds exhibited 1.8 (95% CI: 1.5 to 2.1), 2.2 (95% CI: 1.8 to 2.6) and 0.8 (95% CI: 0.6 to 0.9) higher median Cqs for suspected wild-type, Alpha and Delta positives, respectively, in multivariable analysis. 12-18-year-olds also had higher Cqs for wild-type and Alpha positives, however, not for Delta. Overall, in univariable analysis, suspected Delta positives reported 2.8 lower median Cqs than wild-type positives (95% CI: 2.7 to 2.8; p < 0.001). Suspected Alpha positives had 1.5 (95% CI: 1.4 to 1.5; p < 0.001) lower median Cqs than wild type.ConclusionsWild-type- or Alpha-infected school-aged children (5-11-year-olds) might transmit less than adults (> 18 years old), but have greater mixing exposures. Smaller differences in viral loads with age occurred in suspected Delta infections. Suspected-Alpha- or Delta-infections involved higher viral loads than wild type, suggesting increased transmission risk. COVID-19 control strategies should consider age and dominant variant.
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Affiliation(s)
- David M Hughes
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool, United Kingdom
| | - Christopher P Cheyne
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool, United Kingdom
| | - Matthew Ashton
- Department of Public Health, Liverpool City Council, Liverpool, United Kingdom
| | - Emer Coffey
- Department of Public Health, Liverpool City Council, Liverpool, United Kingdom
| | - Alex Crozier
- Division of biosciences, University College London, London, United Kingdom
| | - Malcolm G Semple
- Health Protection Research Unity in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Science, University of Liverpool, United Kingdom
| | - Iain Buchan
- Department of Public Health, Policy and Systems, Institute of Population Health, University of Liverpool, Liverpool, United Kingdom
| | - Marta García-Fiñana
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool, United Kingdom
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18
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Gachoud D, Bertelli C, Rufer N. Understanding the parameters guiding the best practice for treating B-cell-depleted patients with COVID-19 convalescent plasma therapy. Br J Haematol 2023; 200:e25-e27. [PMID: 36354067 PMCID: PMC9877798 DOI: 10.1111/bjh.18540] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022]
Affiliation(s)
- David Gachoud
- Department of Internal MedicineLausanne University Hospital and University of LausanneLausanneSwitzerland,Medical Education Unit, School of Medicine, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
| | - Claire Bertelli
- Institute of MicrobiologyLausanne University Hospital and University of LausanneLausanneSwitzerland
| | - Nathalie Rufer
- Interregional Blood Transfusion SRCEpalingesSwitzerland,Department of OncologyLausanne University Hospital and University of LausanneEpalingesSwitzerland
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19
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Schwob JM, Miauton A, Petrovic D, Perdrix J, Senn N, Gouveia A, Jaton K, Opota O, Maillard A, Minghelli G, Cornuz J, Greub G, Genton B, D’Acremont V. Antigen rapid tests, nasopharyngeal PCR and saliva PCR to detect SARS-CoV-2: A prospective comparative clinical trial. PLoS One 2023; 18:e0282150. [PMID: 36827328 PMCID: PMC9955963 DOI: 10.1371/journal.pone.0282150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 01/07/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Nasopharyngeal antigen Rapid Diagnostic Tests (RDTs), saliva RT-PCR and nasopharyngeal (NP) RT-PCR have shown different performance characteristics to detect patients infected by SARS-CoV-2, according to the viral load (VL)-and thus transmissibility. METHODS In October 2020, we conducted a prospective trial involving patients presenting at testing centres with symptoms of COVID-19. We compared detection rates and performance of RDT, saliva PCR and nasopharyngeal (NP) PCR, according to VL and symptoms duration. RESULTS Out of 949 patients enrolled, 928 patients had all three tests performed. Detection rates were 35.2% (95%CI 32.2-38.4%) by RDT, 39.8% (36.6-43.0%) by saliva PCR, 40.1% (36.9-43.3%) by NP PCR, and 41.5% (38.3-44.7%) by any test. For those with viral loads (VL) ≥106 copies/ml, detection rates were 30.3% (27.3-33.3), 31.4% (28.4-34.5), 31.5% (28.5-34.6), and 31.6% (28.6-34.7%) respectively. Sensitivity of RDT compared to NP PCR was 87.4% (83.6-90.6%) for all positive patients, 94.5% (91.5-96.7%) for those with VL≥105 and 96.5% (93.6-98.3%) for those with VL≥106. Sensitivity of STANDARD-Q®, Panbio™ and COVID-VIRO® Ag tests were 92.9% (86.4-96.9%), 86.1% (78.6-91.7%) and 84.1% (76.9-89.7%), respectively. For those with VL≥106, sensitivity was 96.6% (90.5-99.3%), 97.8% (92.1-99.7%) and 95.3% (89.4-98.5%) respectively. No patient with VL<104 was detected by RDT. Specificity of RDT was 100% (99.3-100%) compared to any PCR. RDT sensitivity was similar <4 days (87.8%, 83.5-91.3%) and ≥4 days (85.7%, 75.9-92.6%) after symptoms onset (p = 0.6). Sensitivity of saliva and NP PCR were 95.7% (93.1-97.5%) and 96.5% (94.1-98.1%), respectively, compared to the other PCR. CONCLUSIONS RDT results allow rapid identification of COVID cases with immediate isolation of most contagious individuals. RDT can thus be a game changer both in ambulatory care and community testing aimed at stopping transmission chains, and even more so in resource-constrained settings thanks to its very low price. When PCR is performed, saliva could replace NP swabbing. TRIAL REGISTRATION ClinicalTrial.gov Identifier: NCT04613310 (03/11/2020).
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Affiliation(s)
- Jean-Marc Schwob
- Department of Policlinics, Centre for Primary Care and Public Health (Unisanté), Lausanne, Switzerland
- * E-mail:
| | - Alix Miauton
- Department of Policlinics, Centre for Primary Care and Public Health (Unisanté), Lausanne, Switzerland
| | - Dusan Petrovic
- Department of Epidemiology and Health Systems, Centre for Primary Care and Public Health (Unisanté), Lausanne, Switzerland
| | - Jean Perdrix
- Department of Policlinics, Centre for Primary Care and Public Health (Unisanté), Lausanne, Switzerland
| | - Nicolas Senn
- Department of Policlinics, Centre for Primary Care and Public Health (Unisanté), Lausanne, Switzerland
- University of Lausanne, Lausanne, Switzerland
| | - Alexandre Gouveia
- Department of Policlinics, Centre for Primary Care and Public Health (Unisanté), Lausanne, Switzerland
| | - Katia Jaton
- University of Lausanne, Lausanne, Switzerland
- Institute of Microbiology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Onya Opota
- University of Lausanne, Lausanne, Switzerland
- Institute of Microbiology, University Hospital of Lausanne, Lausanne, Switzerland
| | | | | | - Jacques Cornuz
- Department of Policlinics, Centre for Primary Care and Public Health (Unisanté), Lausanne, Switzerland
- University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- University of Lausanne, Lausanne, Switzerland
- Institute of Microbiology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Blaise Genton
- Department of Policlinics, Centre for Primary Care and Public Health (Unisanté), Lausanne, Switzerland
- University of Lausanne, Lausanne, Switzerland
- Department of Training, Research and Innovation, Centre for Primary Care and Public Health (Unisanté), Lausanne, Switzerland
| | - Valérie D’Acremont
- Department of Policlinics, Centre for Primary Care and Public Health (Unisanté), Lausanne, Switzerland
- University of Lausanne, Lausanne, Switzerland
- Department of Training, Research and Innovation, Centre for Primary Care and Public Health (Unisanté), Lausanne, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
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20
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Bordoy AE, Saludes V, Panisello Yagüe D, Clarà G, Soler L, Paris de León A, Casañ C, Blanco-Suárez A, Guerrero-Murillo M, Rodríguez-Ponga B, Noguera-Julian M, Català-Moll F, Pey I, Armengol MP, Casadellà M, Parera M, Pluvinet R, Sumoy L, Clotet B, Giménez M, Martró E, Cardona PJ, Blanco I. Monitoring SARS-CoV-2 variant transitions using differences in diagnostic cycle threshold values of target genes. Sci Rep 2022; 12:21818. [PMID: 36528712 PMCID: PMC9758454 DOI: 10.1038/s41598-022-25719-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Monitoring the emergence of new SARS-CoV-2 variants is important to detect potential risks of increased transmission or disease severity. We investigated the identification of SARS-CoV-2 variants from real-time reverse transcriptase polymerase chain reaction (RT-PCR) routine diagnostics data. Cycle threshold (Ct) values of positive samples were collected from April 2021 to January 2022 in the Northern Metropolitan Area of Barcelona (n = 15,254). Viral lineage identification from whole genome sequencing (WGS) was available for 4618 (30.3%) of these samples. Pairwise differences in the Ct values between gene targets (ΔCt) were analyzed for variants of concern or interest circulating in our area. A specific delay in the Ct of the N-gene compared to the RdRp-gene (ΔCtNR) was observed for Alpha, Delta, Eta and Omicron. Temporal differences in ΔCtNR correlated with the dynamics of viral replacement of Alpha by Delta and of Delta by Omicron according to WGS results. Using ΔCtNR, prediction of new variants of concern at early stages of circulation was achieved with high sensitivity and specificity (91.1% and 97.8% for Delta; 98.5% and 90.8% for Omicron). Thus, tracking population-wide trends in ΔCt values obtained from routine diagnostics testing in combination with WGS could be useful for real-time management and response to local epidemics.
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Affiliation(s)
- Antoni E. Bordoy
- grid.411438.b0000 0004 1767 6330Northern Metropolitan Clinical Laboratory, Microbiology Department, Hospital Universitari Germans Trias i Pujol (HUGTiP), Badalona, Spain ,grid.429186.00000 0004 1756 6852Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Verónica Saludes
- grid.411438.b0000 0004 1767 6330Northern Metropolitan Clinical Laboratory, Microbiology Department, Hospital Universitari Germans Trias i Pujol (HUGTiP), Badalona, Spain ,grid.429186.00000 0004 1756 6852Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Spain ,grid.466571.70000 0004 1756 6246CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - David Panisello Yagüe
- grid.429186.00000 0004 1756 6852Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Gemma Clarà
- grid.411438.b0000 0004 1767 6330Northern Metropolitan Clinical Laboratory, Microbiology Department, Hospital Universitari Germans Trias i Pujol (HUGTiP), Badalona, Spain
| | - Laia Soler
- grid.411438.b0000 0004 1767 6330Northern Metropolitan Clinical Laboratory, Microbiology Department, Hospital Universitari Germans Trias i Pujol (HUGTiP), Badalona, Spain
| | - Alexia Paris de León
- grid.411438.b0000 0004 1767 6330Northern Metropolitan Clinical Laboratory, Microbiology Department, Hospital Universitari Germans Trias i Pujol (HUGTiP), Badalona, Spain
| | - Cristina Casañ
- grid.411438.b0000 0004 1767 6330Northern Metropolitan Clinical Laboratory, Microbiology Department, Hospital Universitari Germans Trias i Pujol (HUGTiP), Badalona, Spain
| | - Ana Blanco-Suárez
- grid.411438.b0000 0004 1767 6330Northern Metropolitan Clinical Laboratory, Microbiology Department, Hospital Universitari Germans Trias i Pujol (HUGTiP), Badalona, Spain
| | - Mercedes Guerrero-Murillo
- grid.411438.b0000 0004 1767 6330Clinical Genetics Department, Northern Metropolitan Clinical Laboratory, Hospital Universitari Germans Trias i Pujol (HUGTiP), Badalona, Spain
| | - Beatriz Rodríguez-Ponga
- grid.411438.b0000 0004 1767 6330Northern Metropolitan Clinical Laboratory, Microbiology Department, Hospital Universitari Germans Trias i Pujol (HUGTiP), Badalona, Spain ,grid.7080.f0000 0001 2296 0625Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Marc Noguera-Julian
- grid.411438.b0000 0004 1767 6330Institut de Recerca de la SIDA-IrsiCaixa, Hospital Universitari Germans Trias i Pujol (HUGTiP), Badalona, Spain ,grid.440820.aUniversity of Vic–Central University of Catalonia (UVic-UCC), Vic, Spain
| | - Francesc Català-Moll
- grid.411438.b0000 0004 1767 6330Institut de Recerca de la SIDA-IrsiCaixa, Hospital Universitari Germans Trias i Pujol (HUGTiP), Badalona, Spain
| | - Irina Pey
- grid.429186.00000 0004 1756 6852Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Maria Pilar Armengol
- grid.429186.00000 0004 1756 6852Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Maria Casadellà
- grid.411438.b0000 0004 1767 6330Institut de Recerca de la SIDA-IrsiCaixa, Hospital Universitari Germans Trias i Pujol (HUGTiP), Badalona, Spain
| | - Mariona Parera
- grid.411438.b0000 0004 1767 6330Institut de Recerca de la SIDA-IrsiCaixa, Hospital Universitari Germans Trias i Pujol (HUGTiP), Badalona, Spain
| | - Raquel Pluvinet
- grid.429186.00000 0004 1756 6852Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Lauro Sumoy
- grid.429186.00000 0004 1756 6852Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Bonaventura Clotet
- grid.411438.b0000 0004 1767 6330Institut de Recerca de la SIDA-IrsiCaixa, Hospital Universitari Germans Trias i Pujol (HUGTiP), Badalona, Spain
| | - Montserrat Giménez
- grid.411438.b0000 0004 1767 6330Northern Metropolitan Clinical Laboratory, Microbiology Department, Hospital Universitari Germans Trias i Pujol (HUGTiP), Badalona, Spain ,grid.512890.7CIBER in Respiratory Diseases (CIBERES), Madrid, Spain
| | - Elisa Martró
- grid.411438.b0000 0004 1767 6330Northern Metropolitan Clinical Laboratory, Microbiology Department, Hospital Universitari Germans Trias i Pujol (HUGTiP), Badalona, Spain ,grid.429186.00000 0004 1756 6852Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Spain ,grid.466571.70000 0004 1756 6246CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Pere-Joan Cardona
- grid.411438.b0000 0004 1767 6330Northern Metropolitan Clinical Laboratory, Microbiology Department, Hospital Universitari Germans Trias i Pujol (HUGTiP), Badalona, Spain ,grid.429186.00000 0004 1756 6852Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Spain ,grid.466571.70000 0004 1756 6246CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain ,grid.512890.7CIBER in Respiratory Diseases (CIBERES), Madrid, Spain ,grid.7080.f0000 0001 2296 0625Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Ignacio Blanco
- grid.411438.b0000 0004 1767 6330Northern Metropolitan Clinical Laboratory, Microbiology Department, Hospital Universitari Germans Trias i Pujol (HUGTiP), Badalona, Spain ,grid.411438.b0000 0004 1767 6330Clinical Genetics Department, Northern Metropolitan Clinical Laboratory, Hospital Universitari Germans Trias i Pujol (HUGTiP), Badalona, Spain
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21
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Li R, Zhao Y, Fan H, Chen M, Hu W, Zhang Q, Jin M, Liu GL, Huang L. Versatile nanorobot hand biosensor for specific capture and ultrasensitive quantification of viral nanoparticles. Mater Today Bio 2022; 16:100444. [PMID: 36204214 PMCID: PMC9531290 DOI: 10.1016/j.mtbio.2022.100444] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/24/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022]
Abstract
Accurate determination of the concentration and viability of the viral vaccine vectors is urgently needed for preventing the spread of the viral infections, but also supporting the development and assessment of recombinant virus-vectored vaccines. Herein, we describe a nanoplasmonic biosensor with nanoscale robot hand structure (Nano RHB) for the rapid, direct, and specific capture and quantification of adenovirus particles. The nanorobot allows simple operation in practical applications, such as real-time monitoring of vaccine quantity and quality, and evaluation of vaccine viability. Modification of the Nano RHB with branched gold nanostructures allow rapid and efficient assessment of human adenovirus viability, with ultrahigh detection sensitivity of only 100 copies/mL through one-step sandwich method. Nano RHB detection results were consistent with those from the gold standard median tissue culture infectious dose and real-time polymerase chain reaction assays. Additionally, the Nano RHB platform showed high detection specificity for different types of viral vectors and pseudoviruses. Altogether, these results demonstrate that the Nano RHB platform is a promising tool for efficient and ultrasensitive assessment of vaccines and gene delivery vectors.
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22
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Neukam K, Lucero A, Gutiérrez-Valencia A, Amaya L, Echegoyen N, Martelli A, Videla C, Di Lello FA, Martínez AP. Point-of-care detection of SARS-CoV-2 antigen among symptomatic vs. asymptomatic persons: Testing for COVID-19 vs. infectivity. Front Public Health 2022; 10:995249. [PMID: 36324442 PMCID: PMC9619045 DOI: 10.3389/fpubh.2022.995249] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/12/2022] [Indexed: 01/26/2023] Open
Abstract
Background Management of the coronavirus disease 2019 (COVID-19) pandemic caused by a novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) requires rapid and simple methods to detect COVID-19 patients and identify potential infectors. This study aimed to evaluate the utility of a point-of-care (PoC) rapid antigen diagnostic test (Ag-RDT) in these settings. Patients and methods Individuals who consecutively presented for SARS-CoV-2 testing at a tertiary care center in Buenos Aires, Argentina, underwent PoC Ag-RDT testing and real-time RT-PCR (qRT-PCR) on the same day during June 2021. Results Of 584 included subjects, 108 (18.5%) were symptomatic for COVID-19 while the remaining presented for miscellaneous reasons unrelated to possible or confirmed contact with a SARS-CoV-2-infected individual. A positive Ag-RDT result was obtained in 26 (24.1%) symptomatic and 7 (1.5%) asymptomatic persons (p < 0.001), which was concordant with qRT-PCR in 105/108 [97.2%, Cohen's kappa coefficient (κ) = 0.927] symptomatic and 467/476 (98.1% κ = 0.563) asymptomatic participants, with a positive percentage agreement (PPA; 95% confidence interval) of 89.7% (71.5-97.3%) and 42.9% (18.8-70.4%), respectively. None of the 11 false-negative diagnoses showed a Ct-value ≤20. Considering only failures with a Ct-value below 31 as hypothetical infectivity threshold of 105 SARS-CoV-2 RNA copies/mL, concordance was observed in 98.1% (κ = 0.746) in the asymptomatic population, accounting for a PPA of 66.7% (30.9-91%). Conclusions PoC Ag-RDT accurately detected active SARS-CoV-2 infection and showed acceptable diagnostic performance in asymptomatic persons potentially spreading infectious virus. Ag-RDT may therefore be useful to slow down or stop transmission by enabling adequate decisions on isolation at a public health level.
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Affiliation(s)
- Karin Neukam
- Unit of Infectious Diseases, Microbiology and Preventive Medicine, Virgen del Rocío University Hospital, Seville, Spain,Instituto de Biomedicina de Sevilla, University of Seville, Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain,*Correspondence: Karin Neukam
| | - Alicia Lucero
- Virology Section, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno “CEMIC”, Buenos Aires, Argentina
| | - Alicia Gutiérrez-Valencia
- Unit of Infectious Diseases, Microbiology and Preventive Medicine, Virgen del Rocío University Hospital, Seville, Spain,Instituto de Biomedicina de Sevilla, University of Seville, Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
| | - Lucas Amaya
- Virology Section, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno “CEMIC”, Buenos Aires, Argentina
| | - Natalia Echegoyen
- Virology Section, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno “CEMIC”, Buenos Aires, Argentina
| | - Antonella Martelli
- Virology Section, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno “CEMIC”, Buenos Aires, Argentina
| | - Cristina Videla
- Virology Section, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno “CEMIC”, Buenos Aires, Argentina
| | - Federico A. Di Lello
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina,Federico A. Di Lello
| | - Alfredo P. Martínez
- Virology Section, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno “CEMIC”, Buenos Aires, Argentina
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23
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Guardiani M, Frank P, Kostić A, Edenhofer G, Roth J, Uhlmann B, Enßlin T. Causal, Bayesian, & non-parametric modeling of the SARS-CoV-2 viral load distribution vs. patient's age. PLoS One 2022; 17:e0275011. [PMID: 36197849 PMCID: PMC9534394 DOI: 10.1371/journal.pone.0275011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/09/2022] [Indexed: 11/05/2022] Open
Abstract
The viral load of patients infected with SARS-CoV-2 varies on logarithmic scales and possibly with age. Controversial claims have been made in the literature regarding whether the viral load distribution actually depends on the age of the patients. Such a dependence would have implications for the COVID-19 spreading mechanism, the age-dependent immune system reaction, and thus for policymaking. We hereby develop a method to analyze viral-load distribution data as a function of the patients' age within a flexible, non-parametric, hierarchical, Bayesian, and causal model. The causal nature of the developed reconstruction additionally allows to test for bias in the data. This could be due to, e.g., bias in patient-testing and data collection or systematic errors in the measurement of the viral load. We perform these tests by calculating the Bayesian evidence for each implied possible causal direction. The possibility of testing for bias in data collection and identifying causal directions can be very useful in other contexts as well. For this reason we make our model freely available. When applied to publicly available age and SARS-CoV-2 viral load data, we find a statistically significant increase in the viral load with age, but only for one of the two analyzed datasets. If we consider this dataset, and based on the current understanding of viral load's impact on patients' infectivity, we expect a non-negligible difference in the infectivity of different age groups. This difference is nonetheless too small to justify considering any age group as noninfectious.
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Affiliation(s)
- Matteo Guardiani
- Max Planck Institute for Astrophysics, Garching, Germany
- Fakultät für Physik, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Philipp Frank
- Max Planck Institute for Astrophysics, Garching, Germany
- Fakultät für Physik, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Andrija Kostić
- Max Planck Institute for Astrophysics, Garching, Germany
- Fakultät für Physik, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gordian Edenhofer
- Max Planck Institute for Astrophysics, Garching, Germany
- Fakultät für Physik, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jakob Roth
- Max Planck Institute for Astrophysics, Garching, Germany
- Fakultät für Physik, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Torsten Enßlin
- Max Planck Institute for Astrophysics, Garching, Germany
- Fakultät für Physik, Ludwig-Maximilians-Universität München, Munich, Germany
- Excellence Cluster ORIGINS, Garching, Germany
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24
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Daou M, Kannout H, Khalili M, Almarei M, Alhashami M, Alhalwachi Z, Alshamsi F, Tahseen Al Bataineh M, Azzam Kayasseh M, Al Khajeh A, Hasan SW, Tay GK, Feng SF, Ruta D, Yousef AF, Alsafar HS. Analysis of SARS-CoV-2 viral loads in stool samples and nasopharyngeal swabs from COVID-19 patients in the United Arab Emirates. PLoS One 2022; 17:e0274961. [PMID: 36137134 PMCID: PMC9499247 DOI: 10.1371/journal.pone.0274961] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 09/07/2022] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) was first identified in respiratory samples and was found to commonly cause cough and pneumonia. However, non-respiratory symptoms including gastrointestinal disorders are also present and a big proportion of patients test positive for the virus in stools for a prolonged period. In this cross-sectional study, we investigated viral load trends in stools and nasopharyngeal swabs and their correlation with multiple demographic and clinical factors. The study included 211 laboratory-confirmed cases suffering from a mild form of the disease and completing their isolation period at a non-hospital center in the United Arab Emirates. Demographic and clinical information was collected by standardized questionnaire and from the medical records of the patient. Of the 211 participants, 25% tested negative in both sample types at the time of this study and 53% of the remaining patients had detectable viral RNA in their stools. A positive fecal viral test was associated with male gender, diarrhea as a symptom, and hospitalization during infection. A positive correlation was also observed between a delayed onset of symptoms and a positive stool test. Viral load in stools positively correlated with, being overweight, exercising, taking antibiotics in the last 3 months and blood type O. The viral load in nasopharyngeal swabs, on the other hand, was higher for blood type A, and rhesus positive (Rh factor). Regression analysis showed no correlation between the viral loads measured in stool and nasopharyngeal samples in any given patient. The results of this work highlight the factors associated with a higher viral count in each sample. It also shows the importance of stool sample analysis for the follow-up and diagnosis of recovering COVID-19 patients.
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Affiliation(s)
- Mariane Daou
- Department of Biology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Hussein Kannout
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Mariam Khalili
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Mohamed Almarei
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Mohamed Alhashami
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Zainab Alhalwachi
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Fatima Alshamsi
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Mohammad Tahseen Al Bataineh
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Mohd Azzam Kayasseh
- Emirates Specialty Hospital, Dubai Healthcare City, Dubai, United Arab Emirates
| | - Abdulmajeed Al Khajeh
- Medical Education and Research Department, Dubai Health Authority, Dubai, United Arab Emirates
| | - Shadi W. Hasan
- Center for Membranes and Advanced Water Technology (CMAT), Department of Chemical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Guan K. Tay
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Division of Psychiatry, Faculty of Health and Medical Sciences, the University of Western Australia, Crawley, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Samuel F. Feng
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Mathematics, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Dymitr Ruta
- EBTIC, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Ahmed F. Yousef
- Department of Biology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center for Membranes and Advanced Water Technology (CMAT), Department of Chemical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Habiba S. Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Genetics and Molecular Biology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- * E-mail:
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25
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Gachoud D, Pillonel T, Tsilimidos G, Battolla D, Dumas D, Opota O, Fontana S, Vollenweider P, Manuel O, Greub G, Bertelli C, Rufer N. Antibody response and intra-host viral evolution after plasma therapy in COVID-19 patients pre-exposed or not to B-cell-depleting agents. Br J Haematol 2022; 199:549-559. [PMID: 36101920 PMCID: PMC9539045 DOI: 10.1111/bjh.18450] [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: 07/15/2022] [Revised: 08/19/2022] [Accepted: 08/28/2022] [Indexed: 12/16/2022]
Abstract
Administration of plasma therapy may contribute to viral control and survival of COVID-19 patients receiving B-cell-depleting agents that impair humoral immunity. However, little is known on the impact of anti-CD20 pre-exposition on the kinetics of SARS-CoV-2-specific antibodies. Here, we evaluated the relationship between anti-spike immunoglobulin G (IgG) kinetics and the clinical status or intra-host viral evolution after plasma therapy in 36 eligible hospitalized COVID-19 patients, pre-exposed or not to B-cell-depleting treatments. The majority of anti-CD20 pre-exposed patients (14/17) showed progressive declines of anti-spike IgG titres following plasma therapy, contrasting with the 4/19 patients who had not received B-cell-depleting agents (p = 0.0006). Patients with antibody decay also depicted prolonged clinical symptoms according to the World Health Organization (WHO) severity classification (p = 0.0267) and SARS-CoV-2 viral loads (p = 0.0032) before complete virus clearance. Moreover, they had higher mutation rates than patients able to mount an endogenous humoral response (p = 0.015), including three patients with one to four spike mutations, potentially associated with immune escape. No relevant differences were observed between patients treated with plasma from convalescent and/or mRNA-vaccinated donors. Our study emphasizes the need for an individualized clinical care and follow-up in the management of COVID-19 patients with B-cell lymphopenia.
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Affiliation(s)
- David Gachoud
- Department of Internal MedicineLausanne University Hospital and University of LausanneLausanneSwitzerland,Medical Education Unit, School of Medicine, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
| | - Trestan Pillonel
- Institute of MicrobiologyLausanne University Hospital and University of LausanneLausanneSwitzerland
| | - Gerasimos Tsilimidos
- Division of Hematology, Department of OncologyLausanne University Hospital and University of LausanneLausanneSwitzerland
| | - Dunia Battolla
- Department of Internal MedicineLausanne University Hospital and University of LausanneLausanneSwitzerland
| | - Dominique Dumas
- Department of Internal MedicineLausanne University Hospital and University of LausanneLausanneSwitzerland
| | - Onya Opota
- Institute of MicrobiologyLausanne University Hospital and University of LausanneLausanneSwitzerland
| | - Stefano Fontana
- Interregional Blood Transfusion SRCBernSwitzerland,Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
| | - Peter Vollenweider
- Department of Internal MedicineLausanne University Hospital and University of LausanneLausanneSwitzerland
| | - Oriol Manuel
- Infectious Diseases Service and Transplantation Center, Department of MedicineLausanne University Hospital and University of LausanneLausanneSwitzerland
| | - Gilbert Greub
- Institute of MicrobiologyLausanne University Hospital and University of LausanneLausanneSwitzerland,Infectious Diseases Service and Transplantation Center, Department of MedicineLausanne University Hospital and University of LausanneLausanneSwitzerland
| | - Claire Bertelli
- Institute of MicrobiologyLausanne University Hospital and University of LausanneLausanneSwitzerland
| | - Nathalie Rufer
- Interregional Blood Transfusion SRCEpalingesSwitzerland,Department of OncologyLausanne University Hospital and University of LausanneEpalingesSwitzerland
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26
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Yang D, Hansel DE, Curlin ME, Townes JM, Messer WB, Fan G, Qin X. Bimodal distribution pattern associated with the PCR cycle threshold (Ct) and implications in COVID-19 infections. Sci Rep 2022; 12:14544. [PMID: 36008543 PMCID: PMC9406279 DOI: 10.1038/s41598-022-18735-2] [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] [Received: 02/08/2022] [Accepted: 08/18/2022] [Indexed: 11/21/2022] Open
Abstract
SARS-CoV-2 is notable for its extremely high level of viral replication in respiratory epithelial cells, relative to other cell types. This may partially explain the high transmissibility and rapid global dissemination observed during the COVID-19 pandemic. Polymerase chain reaction (PCR) cycle threshold (Ct) number has been widely used as a proxy for viral load based on the inverse relationship between Ct number and amplifiable genome copies present in a sample. We examined two PCR platforms (Centers for Disease Control and Prevention 2019-nCoV Real-time RT-PCR, Integrated DNA Technologies; and TaqPath COVID-19 multi-plex combination kit, ThermoFisher Scientific) for their performance characteristics and Ct distribution patterns based on results generated from 208,947 clinical samples obtained between October 2020 and September 2021. From 14,231 positive tests, Ct values ranged from 8 to 39 and displayed a pronounced bimodal distribution. The bimodal distribution persisted when stratified by gender, age, and time period of sample collection during which different viral variants circulated. This finding may be a result of heterogeneity in disease progression or host response to infection irrespective of age, gender, or viral variants. Quantification of respiratory mucosal viral load may provide additional insight into transmission and clinical indicators helpful for infection control.
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Affiliation(s)
- Doris Yang
- Department of Pathology and Laboratory Medicine, Oregon Health & Science University School of Medicine, 3181 SW Sam Jackson Park Road, L-113, Portland, OR, 97239, USA
| | - Donna E Hansel
- Department of Pathology and Laboratory Medicine, Oregon Health & Science University School of Medicine, 3181 SW Sam Jackson Park Road, L-113, Portland, OR, 97239, USA
| | - Marcel E Curlin
- Department of Medicine, Division of Infectious Diseases, Oregon Health & Science University School of Medicine, Portland, OR, 97239, USA
| | - John M Townes
- Department of Medicine, Division of Infectious Diseases, Oregon Health & Science University School of Medicine, Portland, OR, 97239, USA
| | - William B Messer
- Department of Medicine, Division of Infectious Diseases, Oregon Health & Science University School of Medicine, Portland, OR, 97239, USA.,Department Molecular Microbiology and Immunology, Oregon Health & Science University School of Medicine, Portland, OR, 97239, USA
| | - Guang Fan
- Department of Pathology and Laboratory Medicine, Oregon Health & Science University School of Medicine, 3181 SW Sam Jackson Park Road, L-113, Portland, OR, 97239, USA
| | - Xuan Qin
- Department of Pathology and Laboratory Medicine, Oregon Health & Science University School of Medicine, 3181 SW Sam Jackson Park Road, L-113, Portland, OR, 97239, USA.
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27
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Xu J, Kerr L, Jiang Y, Suo W, Zhang L, Lao T, Chen Y, Zhang Y. Rapid Antigen Diagnostics as Frontline Testing in the COVID-19 Pandemic. SMALL SCIENCE 2022; 2:2200009. [PMID: 35942171 PMCID: PMC9349911 DOI: 10.1002/smsc.202200009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/25/2022] [Indexed: 11/09/2022] Open
Abstract
The ongoing global COVID-19 pandemic, caused by the SARS-CoV-2 virus, has resulted in significant loss of life since December 2019. Timely and precise virus detection has been proven as an effective solution to reduce the spread of the virus and to track the epidemic. Rapid antigen diagnostics has played a significant role in the frontline of COVID-19 testing because of its convenience, low cost, and high accuracy. Herein, different types of recently innovated in-lab and commercial antigen diagnostic technologies with emphasis on the strengths and limitations of these technologies including the limit of detection, sensitivity, specificity, affordability, and usability are systematically reviewed. The perspectives of assay development are looked into.
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Affiliation(s)
- Jiang Xu
- Department of Systems BiologyBlavatnik InstituteHarvard Medical SchoolBostonMA02115USA
- Department of Molecular VirologyVirogin Biotech Ltd.3800 Wesbrook MallVancouverBCV6S 2L9Canada
| | - Liam Kerr
- Department of Mechanical EngineeringCenter for Intelligent MachinesMcGill UniversityMontrealQCH3A0C3Canada
| | - Yue Jiang
- China-Australia Institute for Advanced Materials and ManufacturingJiaxing UniversityJiaxing314001China
| | - Wenhao Suo
- Dana-Farber Cancer InstituteHarvard Medical SchoolBostonMA02215USA
- Department of PathologyThe First Affiliated Hospital of Xiamen University55 Zhenhai RoadXiamen361003China
| | - Lei Zhang
- Department of Chemical EngineeringWaterloo Institute for NanotechnologyUniversity of Waterloo200 University Avenue WestWaterlooONN2L3G1Canada
| | - Taotao Lao
- Department of Molecular DiagnosticsBoston Molecules Inc.564 Main StreetWalthamMA02452USA
- Center for Immunology and Inflammatory DiseasesMassachusetts General HospitalHarvard Medical SchoolCharlestownMA02114USA
| | - Yuxin Chen
- Department of Laboratory MedicineNanjing Drum Tower HospitalNanjing University Medical SchoolNanjingJiangsu210008China
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery and High-EfficiencyCollaborative Innovation Center of Chemical Science and EngineeringSchool of Pharmaceutical Science and TechnologyTianjin UniversityTianjin300072China
- Frontiers Science Center for Synthetic Biology (Ministry of Education)Tianjin UniversityTianjin300072China
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28
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Jacot D, von Rotz U, Blondet F, Aebischer O, Matthieu P, De Rham M, Pantaleo G, Marchetti O, Greub G. SARS-CoV-2 seroprevalence in hospital healthcare workers in Western Switzerland at the end of the second pandemic wave. J Med Microbiol 2022; 71. [PMID: 35921229 DOI: 10.1099/jmm.0.001558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. In early January 2020, the pandemic of COVID-19 (coronavirus disease 2019) rapidly spread from China and caused a worldwide pandemic.Hypothesis. Healthcare workers represent a high-risk group for acquiring COVID-19 and for nosocomial transmission of severe acute respiratory coronavirus 2 (SARS-CoV-2).Aim. We aimed to investigate over a 1 year period, across two pandemic waves, the SARS-CoV-2 seroprevalence in employees at a Western Switzerland public hospital.Methodology. A prospective observational SARS-CoV-2 seroprevalence study was proposed to all hospital employees who enrolled on a voluntary basis.Results. Out of 594 participants recruited on a voluntary basis, 269 volunteers (45.3 %) had anti-SARS-CoV-2 antibodies: this seroprevalence was twice higher than that reported in the local community. Healthcare workers with prolonged exposure to patients with COVID-19 showed a significantly higher odds ratio (OR) of having a positive SARS-CoV-2 serology [OR 3.19, 95 % confidence interval (CI) 2.16-4.74]. Symptoms showing the highest association with a positive serology were anosmia (OR 11.9, 95 % CI 5.58-30.9) and ageusia (OR 10.3, 95 % CI 4.8-26.3). A total of 17.1 % (95 % CI 12.2-21.1 %) of SARS-CoV-2 seropositive volunteers did not report a suspicion of COVID-19 in their personal history.Conclusion. Overall, we observed that the impact of the second SARS-CoV-2 pandemic wave was considerable and significantly affected healthcare workers with prolonged exposure to patients with COVID-19.
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Affiliation(s)
- Damien Jacot
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 21 Rue du Bugnon, Lausanne CH-1011, Switzerland
| | - Urs von Rotz
- Healthcare Workers Medical Service, Ensemble Hospitalier de la Côte, Morges, Switzerland
| | - Fanny Blondet
- Department of Medicine, Ensemble Hospitalier de la Côte, 2 Chemin du Crêt, Morges CH-1110, Switzerland
| | - Oriane Aebischer
- Department of Medicine, Ensemble Hospitalier de la Côte, 2 Chemin du Crêt, Morges CH-1110, Switzerland
| | - Perreau Matthieu
- Institute of Immunology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Mikael De Rham
- Patients' Safety Program, General Direction, Ensemble Hospitalier de la Côte, Morges, Switzerland
| | - Giuseppe Pantaleo
- Institute of Immunology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Oscar Marchetti
- Department of Medicine, Ensemble Hospitalier de la Côte, 2 Chemin du Crêt, Morges CH-1110, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 21 Rue du Bugnon, Lausanne CH-1011, Switzerland.,Infectious Diseases Service, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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29
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Feng C, Hong S, Fan R, Shi X, Ma Z, Li C, Liu C, He C, Fan M, Wang R. Age and Sex Differences Among Mildly Symptomatic and Asymptomatic Patients with Omicron Infection in 2022 in Shanghai, China. J Multidiscip Healthc 2022; 15:1909-1919. [PMID: 36072277 PMCID: PMC9441582 DOI: 10.2147/jmdh.s375724] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 08/24/2022] [Indexed: 11/23/2022] Open
Abstract
Background An epidemic of the Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began in March 2022, and over 600,000 cases were confirmed until early May 2022 in Shanghai, China. Data on Omicron infections are available in other countries, but the clinical features of patients in the Chinese population, especially in Shanghai, are still lacking. We collected data from a subset of asymptomatic and mildly ill patients to learn about the age and sex disparity of Omicron infection based on changes in cycle threshold values. Methods The basic information of 325 patients who were consecutively admitted to the Shanghai Geriatrics Center was collected through medical records, and patients were tested for viral nucleic acid carriage using nasal swab samples during hospitalization. SAS 9.4 was used for data analysis, and a p value < 0.05% was considered statistically significant. Results Among the 325 included patients, 58.8% were males, with a mean age of 47.2 years and 13.6 days of hospitalization on average. The average number of nucleic acid tests among female patients was 4.7, which was higher than that among male patients (4.1). The median value of the slope for cycle threshold (Ct) changes in the nucleic acid detection (NAD) test was 1.4. Logistic regression indicated that the proportion of slope for Ct changes >1.5 was slightly higher among male patients than among female patients (odds ratio (OR) = 1.06, 95% confidence interval (CI): 0.68–1.66), and patients aged <45 years and 45–59 years had a higher proportion of slope for Ct changes >1.5 than patients aged ≥60 years. Ct values were more variable in the early stages of infection and stabilized in the later stages of infection. Conclusion Among patients with mild illness or asymptomatic infection, the Ct value is a good, timely, and cost-effective method to reflect the recovery progress of patients. The slope of Ct changes was steeper among younger patients and male patients, which indicates faster disease recovery.
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Affiliation(s)
- Can Feng
- Department of Cardiology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, People’s Republic of China
| | - Shihui Hong
- Department of Cardiology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, People’s Republic of China
| | - Rong Fan
- Department of Cardiology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, People’s Republic of China
| | - Xinjie Shi
- Department of Neurology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, People’s Republic of China
| | - Zhao Ma
- Department of Acupuncture and Moxibustion, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, People’s Republic of China
| | - Changgui Li
- Department of Hematology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, People’s Republic of China
| | - Chenghao Liu
- Department of Endocrinology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, People’s Republic of China
| | - Cong He
- Department of Gastroenterology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, People’s Republic of China
| | - Min Fan
- Department of Cardiology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, People’s Republic of China
- Correspondence: Min Fan; Ruiping Wang, Email ;
| | - Ruiping Wang
- Clinical Research Center, Shanghai Skin Diseases Hospital, Tongji University, Shanghai, People’s Republic of China
- School of Public Health, Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
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30
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Grewal S, Syed Gurcoo M, Sudhan Sharma S. Comparative analysis of specificity and sensitivity between Cobas 6800 system and SARS-CoV-2 rRT-PCR to detect COVID-19 infection in clinical samples. Arch Microbiol 2022; 204:502. [PMID: 35852637 PMCID: PMC9295087 DOI: 10.1007/s00203-022-03118-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 11/25/2022]
Abstract
Fast and reliable testing for the COVID 19 infection is the need of the hour for the development of effective and reliable tools and assays. However, it is difficult to find the performance relativity among all these tests which are poorly understood. In this study, we aimed to evaluate the two different platforms where we determine the difference of sensitivity and specificity between the fully automated analyzer (Roche Diagnostics Cobas 6800 SARS-CoV-2 test) under FDA Emergency Use Authorization (EUA) and the laboratory designed test (SARS-CoV-2 rRT-PCR) based on the protocol developed by ICMR (Indian Council for Medical Research). The study was conducted for individual samples. We performed our study with two different approaches, first with validation method consisting of 188 samples (2 batches) on cobas 6800 instrument (Roche Molecular Systems, Branchburg, NJ) soon after we received US FDA EUA on 1 June 2021, all these samples were tested earlier with laboratory designed tests on 25th and 26th May 2021. Over all agreement between the two tests is of 88% and the coefficient of agreement between the two testing platform Cohen’sκ coefficient was found to be 0.76 (95% CI, 2.5897–13.4103) suggesting the substantial agreement between the two platforms. However, in some of the cases, both tests have shown a little disagreement. An overall discordance rate between two systems was found 11.1%. The difference may be due to the limit of detection, variation in the sequences of the primer design or may be due to other factors depicting the importance of comparing the two platforms used in the testing for SARS-CoV-2. Second approach includes head to head evaluation which comprises 1631 samples showed overall agreement of 99% and kappa value of 0.98. These results showed that cobas is effective and reliable assay for the detection of SARS-CoV-2 infection.
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Affiliation(s)
- Simmi Grewal
- Department of Microbiology, Government Medical College, Jammu, 180001, Jammu and Kashmir, India
| | - Mehreen Syed Gurcoo
- Department of Microbiology, Government Medical College, Jammu, 180001, Jammu and Kashmir, India
| | - Shashi Sudhan Sharma
- Department of Microbiology, Government Medical College, Jammu, 180001, Jammu and Kashmir, India.
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31
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Channappanavar R, Selvaraj M, More S, Perlman S. Alveolar macrophages protect mice from MERS-CoV-induced pneumonia and severe disease. Vet Pathol 2022; 59:627-638. [PMID: 35499307 DOI: 10.1177/03009858221095270] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Emerging and re-emerging human coronaviruses (hCoVs) cause severe respiratory illness in humans, but the basis for lethal pneumonia in these diseases is not well understood. Alveolar macrophages (AMs) are key orchestrators of host antiviral defense and tissue tolerance during a variety of respiratory infections, and AM dysfunction is associated with severe COVID-19. In this study, using a mouse model of Middle East respiratory syndrome coronavirus (MERS-CoV) infection, we examined the role of AMs in MERS pathogenesis. Our results show that depletion of AMs using clodronate (CL) liposomes significantly increased morbidity and mortality in human dipeptidyl peptidase 4 knock-in (hDPP4-KI) mice. Detailed examination of control and AM-depleted lungs at different days postinfection revealed increased neutrophil activity but a significantly reduced MERS-CoV-specific CD4 T-cell response in AM-deficient lungs during later stages of infection. Furthermore, enhanced MERS severity in AM-depleted mice correlated with lung inflammation and lesions. Collectively, these data demonstrate that AMs are critical for the development of an optimal virus-specific T-cell response and controlling excessive inflammation during MERS-CoV infection.
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Affiliation(s)
| | | | - Sunil More
- Oklahoma State University, Stillwater, OK
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Rovito R, Augello M, Ben-Haim A, Bono V, d'Arminio Monforte A, Marchetti G. Hallmarks of Severe COVID-19 Pathogenesis: A Pas de Deux Between Viral and Host Factors. Front Immunol 2022; 13:912336. [PMID: 35757770 PMCID: PMC9231592 DOI: 10.3389/fimmu.2022.912336] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/02/2022] [Indexed: 12/15/2022] Open
Abstract
Two years into Coronavirus Disease 2019 (COVID-19) pandemic, a comprehensive characterization of the pathogenesis of severe and critical forms of COVID-19 is still missing. While a deep dysregulation of both the magnitude and functionality of innate and adaptive immune responses have been described in severe COVID-19, the mechanisms underlying such dysregulations are still a matter of scientific debate, in turn hampering the identification of new therapies and of subgroups of patients that would most benefit from individual clinical interventions. Here we review the current understanding of viral and host factors that contribute to immune dysregulation associated with COVID-19 severity in the attempt to unfold and broaden the comprehension of COVID-19 pathogenesis and to define correlates of protection to further inform strategies of targeted therapeutic interventions.
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Affiliation(s)
- Roberta Rovito
- Clinic of Infectious Diseases and Tropical Medicine, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Matteo Augello
- Clinic of Infectious Diseases and Tropical Medicine, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Assaf Ben-Haim
- Clinic of Infectious Diseases and Tropical Medicine, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Valeria Bono
- Clinic of Infectious Diseases and Tropical Medicine, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Antonella d'Arminio Monforte
- Clinic of Infectious Diseases and Tropical Medicine, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Giulia Marchetti
- Clinic of Infectious Diseases and Tropical Medicine, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
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Pu Y, Weng Y, Wu Y, Gao F, Zheng X, Xiong X, Lv H, Kong Q. Antibody Response to SARS-CoV-2 in the First Batch of COVID-19 Patients in China by a Self-Developed Rapid IgM-IgG Test. Front Cell Infect Microbiol 2022; 12:915751. [PMID: 35719335 PMCID: PMC9204641 DOI: 10.3389/fcimb.2022.915751] [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: 04/08/2022] [Accepted: 04/28/2022] [Indexed: 12/02/2022] Open
Abstract
It has been over two years since the COVID-19 pandemic began and it is still an unprecedented global challenge. Here, we aim to characterize the antibody profile from a large batch of early COVID-19 cases in China, from January – March 2020. More than 1,000 serum samples from participants in Hubei and Zhejiang province were collected. A series of serum samples were also collected along the disease course from 70 patients in Shanghai and Chongqing for longitudinal analysis. The serologic assay (ALLtest) we developed was confirmed to have high sensitivity (92.58% - 97.55%) and high specificity (92.14% - 96.28%) for the detection of SARS-CoV-2 nucleocapsid-specific antibodies. Confirmed cases found in the Hubei Provincial Center for Disease Control and Prevention (HBCDC), showed a significantly (p = 0.0018) higher positive rate from the ALLtest than RNA test. Then, we further identified the disease course, age, sex, and symptoms that were correlating factors with our ALLtest results. In summary, we confirmed the high reliability of our ALLtest and its important role in COVID-19 diagnosis. The correlating factors we identified will require special attention during future clinical application.
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Affiliation(s)
- Yiyi Pu
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
| | - Youhong Weng
- Institute of Parasitic Diseases, Hangzhou Medical College, Hangzhou, China
| | - Yahan Wu
- Institute of Parasitic Diseases, Hangzhou Medical College, Hangzhou, China
| | - Fei Gao
- Department of Research and Development, Hangzhou AllTest Biotech Co., Ltd, Hangzhou, China
| | - Xiaojun Zheng
- Department of Research and Development, Hangzhou AllTest Biotech Co., Ltd, Hangzhou, China
| | - Xianqin Xiong
- Department of Research and Development, Hangzhou AllTest Biotech Co., Ltd, Hangzhou, China
| | - Hangjun Lv
- Institute of Parasitic Diseases, Hangzhou Medical College, Hangzhou, China
| | - Qingming Kong
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China.,Institute of Parasitic Diseases, Hangzhou Medical College, Hangzhou, China
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Prentiss M, Chu A, Berggren KK. Finding the infectious dose for COVID-19 by applying an airborne-transmission model to superspreader events. PLoS One 2022; 17:e0265816. [PMID: 35679278 PMCID: PMC9182663 DOI: 10.1371/journal.pone.0265816] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 03/08/2022] [Indexed: 12/19/2022] Open
Abstract
We probed the transmission of COVID-19 by applying an airborne transmission model to five well-documented case studies-a Washington state church choir, a Korean call center, a Korean exercise class, and two different Chinese bus trips. For all events the likely index patients were pre-symptomatic or mildly symptomatic, which is when infective patients are most likely to interact with large groups of people. Applying the model to those events yields results that suggest the following: (1) transmission was airborne; (2) superspreading events do not require an index patient with an unusually high viral load; (3) the viral loads for all of the index patients were of the same order of magnitude and consistent with experimentally measured values for patients at the onset of symptoms, even though viral loads across the population vary by a factor of >108. In particular we used a Wells-Riley exposure model to calculate q, the total average number of infectious quanta inhaled by a person at the event. Given the q value for each event, the simple airborne transmission model was used to determined Sq, the rate at which the index patient exhaled infectious quanta and N0, the characteristic number of COVID-19 virions needed to induce infection. Despite the uncertainties in the values of some parameters of the superspreading events, all five events yielded (N0∼300-2,000 virions), which is similar to published values for influenza. Finally, this work describes the conditions under which similar methods can provide actionable information on the transmission of other viruses.
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Affiliation(s)
- Mara Prentiss
- Department of Physics, Harvard University, Cambridge, MA, United States of America
| | - Arthur Chu
- QVT Family Office, New York, NY, United States of America
| | - Karl K. Berggren
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, United States of America
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Villers J, Henriques A, Calarco S, Rognlien M, Mounet N, Devine J, Azzopardi G, Elson P, Andreini M, Tarocco N, Vassella C, Keiser O. SARS-CoV-2 aerosol transmission in schools: the effectiveness of different interventions. Swiss Med Wkly 2022; 152:w30178. [PMID: 35704941 DOI: 10.4414/smw.2022.w30178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Indoor aerosol transmission of SARS-CoV-2 has been widely recognised, especially in schools where children remain in closed indoor spaces and largely unvaccinated. Measures such as strategic natural ventilation and high efficiency particulate air (HEPA) filtration remain poorly implemented and mask mandates are often progressively lifted as vaccination rollout is enhanced. METHODS We adapted a previously developed aerosol transmission model to study the effect of interventions (natural ventilation, face masks, HEPA filtration and their combinations) on the concentration of virus particles in a classroom of 160 m3 containing one infectious individual. The cumulative dose of viruses absorbed by exposed occupants was calculated. RESULTS In the absence of interventions, the cumulative dose absorbed was 1.5 times higher in winter than in spring/summer, increasing chances of indoor airborne transmission in winter. However, natural ventilation was more effective in winter, leading to up to a 20-fold decrease in cumulative dose when six windows were fully open at all times. In winter, partly opening two windows all day or fully opening six windows at the end of each class was effective as well (2.7- to 3-fold decrease). In summer, good ventilation levels could be achieved through the opening of windows all day long (2- to 7-fold decrease depending on the number of windows open). Opening windows only during yard and lunch breaks had minimal effect (≤1.5-fold decrease). One HEPA filter was as effective as two windows partly open all day in winter (3-fold decrease) whereas two filters were more effective (5-fold decrease). Surgical face masks were very effective independently of the season (8-fold decrease). Combined interventions (i.e., natural ventilation, masks, and HEPA filtration) were the most effective (≥25-fold decrease) and remained highly effective in the presence of a super-spreader. INTERPRETATION Natural ventilation, face masks, and HEPA filtration are effective interventions to reduce SARS-CoV-2 aerosol transmission. These measures should be combined and complemented by additional interventions (e.g., physical distancing, hygiene, testing, contact tracing and vaccination) to maximise benefit.
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Affiliation(s)
| | - Andre Henriques
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
| | - Serafina Calarco
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Markus Rognlien
- Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Nicolas Mounet
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
| | - James Devine
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
| | | | - Philip Elson
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
| | - Marco Andreini
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
| | - Nicola Tarocco
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
| | - Claudia Vassella
- Federal Office of Public Health, Consumer Protection Directorate, Indoor Pollutants Unit, Berne, Switzerland
| | - Olivia Keiser
- Institute of Global Health, University of Geneva, Switzerland
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Shinoda H, Iida T, Makino A, Yoshimura M, Ishikawa J, Ando J, Murai K, Sugiyama K, Muramoto Y, Nakano M, Kiga K, Cui L, Nureki O, Takeuchi H, Noda T, Nishimasu H, Watanabe R. Automated amplification-free digital RNA detection platform for rapid and sensitive SARS-CoV-2 diagnosis. Commun Biol 2022; 5:473. [PMID: 35614128 PMCID: PMC9132978 DOI: 10.1038/s42003-022-03433-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/29/2022] [Indexed: 12/12/2022] Open
Abstract
In the ongoing COVID-19 pandemic, rapid and sensitive diagnosis of viral infection is a critical deterrent to the spread of SARS-CoV-2. To this end, we developed an automated amplification-free digital RNA detection platform using CRISPR-Cas13a and microchamber device (opn-SATORI), which automatically completes a detection process from sample mixing to RNA quantification in clinical specimens within ~9 min. Using the optimal Cas13a enzyme and magnetic beads technology, opn-SATORI detected SARS-CoV-2 genomic RNA with a LoD of < 6.5 aM (3.9 copies μL−1), comparable to RT-qPCR. Additionally, opn-SATORI discriminated between SARS-CoV-2 variants of concern, including alpha, delta, and omicron, with 98% accuracy. Thus, opn-SATORI can serve as a rapid and convenient diagnostic platform for identifying several types of viral infections. An automated amplification-free digital RNA detection platform using CRISPR-Cas13a and magnetic bead technology implemented in a microchamber device demonstrates sensitive SARS-CoV-2 genomic RNA detection and variant discrimination.
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Affiliation(s)
- Hajime Shinoda
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan.,CREST, Japan Science and Technology Agency, Saitama, Japan
| | - Tatsuya Iida
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan.,CREST, Japan Science and Technology Agency, Saitama, Japan
| | - Asami Makino
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan.,CREST, Japan Science and Technology Agency, Saitama, Japan
| | - Mami Yoshimura
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan.,CREST, Japan Science and Technology Agency, Saitama, Japan
| | - Junichiro Ishikawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Jun Ando
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan.,CREST, Japan Science and Technology Agency, Saitama, Japan
| | - Kazue Murai
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan
| | | | - Yukiko Muramoto
- CREST, Japan Science and Technology Agency, Saitama, Japan.,Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Masahiro Nakano
- CREST, Japan Science and Technology Agency, Saitama, Japan.,Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kotaro Kiga
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan.,Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Longzhu Cui
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Takeuchi
- Department of Molecular Virology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takeshi Noda
- CREST, Japan Science and Technology Agency, Saitama, Japan.,Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Hiroshi Nishimasu
- CREST, Japan Science and Technology Agency, Saitama, Japan. .,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan. .,Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan. .,Research Center for Advanced Science and Technology, Structural Biology Division, The University of Tokyo, Tokyo, Japan. .,Inamori Research Institute for Science, Kyoto, Japan.
| | - Rikiya Watanabe
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan. .,CREST, Japan Science and Technology Agency, Saitama, Japan.
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Henriques A, Mounet N, Aleixo L, Elson P, Devine J, Azzopardi G, Andreini M, Rognlien M, Tarocco N, Tang J. Modelling airborne transmission of SARS-CoV-2 using CARA: risk assessment for enclosed spaces. Interface Focus 2022; 12:20210076. [PMID: 35261732 PMCID: PMC8831086 DOI: 10.1098/rsfs.2021.0076] [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: 10/12/2021] [Accepted: 12/19/2021] [Indexed: 12/18/2022] Open
Abstract
The COVID-19 pandemic has highlighted the need for a proper risk assessment of respiratory pathogens in indoor settings. This paper documents the COVID Airborne Risk Assessment methodology, to assess the potential exposure of airborne SARS-CoV-2 viruses, with an emphasis on virological and immunological factors in the quantification of the risk. The model results from a multidisciplinary approach linking physical, mechanical and biological domains, enabling decision makers or facility managers to assess their indoor setting. The model was benchmarked against clinical data, as well as two real-life outbreaks, showing good agreement. A probability of infection is computed in several everyday-life settings and with various mitigation measures. The importance of super-emitters in airborne transmission is confirmed: 20% of infected hosts can emit approximately two orders of magnitude more viral-containing particles. The use of masks provides a fivefold reduction in viral emissions. Natural ventilation strategies are very effective to decrease the concentration of virions, although periodic venting strategies are not ideal in certain settings. Although vaccination is an effective measure against hospitalization, their effectiveness against transmission is not optimal, hence non-pharmaceutical interventions (ventilation, masks) should be actively supported. We also propose a critical threshold to define an acceptable risk level.
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Affiliation(s)
- Andre Henriques
- CERN (European Organization for Nuclear Research), Geneva, Switzerland
| | - Nicolas Mounet
- CERN (European Organization for Nuclear Research), Geneva, Switzerland
| | - Luis Aleixo
- CERN (European Organization for Nuclear Research), Geneva, Switzerland
| | - Philip Elson
- CERN (European Organization for Nuclear Research), Geneva, Switzerland
| | - James Devine
- CERN (European Organization for Nuclear Research), Geneva, Switzerland
| | | | - Marco Andreini
- CERN (European Organization for Nuclear Research), Geneva, Switzerland
| | - Markus Rognlien
- NTNU (Norwegian University of Science and Technology), Torgarden, Norway
| | - Nicola Tarocco
- CERN (European Organization for Nuclear Research), Geneva, Switzerland
| | - Julian Tang
- Respiratory Sciences, University of Leicester, Leicester, UK
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Puchinger K, Castelletti N, Rubio-Acero R, Geldmacher C, Eser TM, Deák F, Paunovic I, Bakuli A, Saathoff E, von Meyer A, Markgraf A, Falk P, Reich J, Riess F, Girl P, Müller K, Radon K, Guggenbuehl Noller JM, Wölfel R, Hoelscher M, Kroidl I, Wieser A, Olbrich L. The interplay of viral loads, clinical presentation, and serological responses in SARS-CoV-2 - Results from a prospective cohort of outpatient COVID-19 cases. Virology 2022; 569:37-43. [PMID: 35245784 PMCID: PMC8855229 DOI: 10.1016/j.virol.2022.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/15/2022] [Accepted: 02/15/2022] [Indexed: 11/24/2022]
Abstract
Risk factors for disease progression and severity of SARS-CoV-2 infections require an understanding of acute and long-term virological and immunological dynamics. Fifty-one RT-PCR positive COVID-19 outpatients were recruited between May and December 2020 in Munich, Germany, and followed up at multiple defined timepoints for up to one year. RT-PCR and viral culture were performed and seroresponses measured. Participants were classified applying the WHO clinical progression scale. Short symptom to test time (median 5.0 days; p = 0.0016) and high viral loads (VL; median maximum VL: 3∙108 copies/mL; p = 0.0015) were indicative for viral culture positivity. Participants with WHO grade 3 at baseline had significantly higher VLs compared to those with WHO 1 and 2 (p = 0.01). VLs dropped fast within 1 week of symptom onset. Maximum VLs were positively correlated with the magnitude of Ro-N-Ig seroresponse (p = 0.022). Our results describe the dynamics of VLs and antibodies to SARS-CoV-2 in mild to moderate cases that can support public health measures during the ongoing global pandemic.
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Affiliation(s)
- Kerstin Puchinger
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany
| | - Noemi Castelletti
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany; Institute of Radiation Medicine, Helmholtz Zentrum München, 85764, Neuherberg, Germany.
| | - Raquel Rubio-Acero
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Germany
| | - Tabea M Eser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Germany
| | - Flora Deák
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Germany
| | - Ivana Paunovic
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany
| | - Abhishek Bakuli
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany
| | - Elmar Saathoff
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Germany
| | - Alexander von Meyer
- Institute for Laboratory Medicine, Medical Microbiology and Technical Hygienics, Munich Municipal Hospital Group, 81675, Munich, Germany
| | - Alisa Markgraf
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany
| | - Philine Falk
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany
| | - Jakob Reich
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany
| | - Friedrich Riess
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Germany
| | - Philipp Girl
- German Center for Infection Research (DZIF), Partner Site Munich, Germany; Bundeswehr Institute of Microbiology, 80937, Munich, Germany
| | - Katharina Müller
- German Center for Infection Research (DZIF), Partner Site Munich, Germany; Bundeswehr Institute of Microbiology, 80937, Munich, Germany
| | - Katja Radon
- Center for International Health, Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, University Hospital Munich (LMU), Ziemssenstr. 1, 80336, Munich, Germany
| | | | - Roman Wölfel
- German Center for Infection Research (DZIF), Partner Site Munich, Germany; Bundeswehr Institute of Microbiology, 80937, Munich, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Germany
| | - Inge Kroidl
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Germany
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Germany
| | - Laura Olbrich
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Germany; Oxford Vaccine Group, Department of Paediatrics, And the NIHR Oxford Biomedical Research Centre, University of Oxford, OX1 2JD, Oxford, UK
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Mishra B, Ranjan J, Purushotham P, Kar P, Payal P, Saha S, Deshmukh V, Das S. Comparison of Cycle Threshold and Clinical Status Among Different Age Groups of COVID-19 Cases. Cureus 2022; 14:e24194. [PMID: 35592201 PMCID: PMC9110806 DOI: 10.7759/cureus.24194] [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] [Accepted: 04/16/2022] [Indexed: 12/02/2022] Open
Abstract
Introduction The COVID-19 pandemic has shaken the entire world ever since its emergence in March 2020. The disease manifestation of COVID-19 has been more severe, with a high degree of mortality in the elderly than in the young population. The cycle threshold (Ct ) value obtained in the real-time polymerase chain reaction (RT-PCR) has been used as the surrogate marker of viral load. Therefore, assessing Ct value and clinical status among different age groups with SARS-CoV-2 infection is required to understand the viral kinetics and to assess the transmission potential of that particular age group. Purpose The aim of this study was to compare the viral load and clinical status among different age groups with COVID-19 infection. Methods and materials A retrospective cross-sectional study was carried out to analyze the Ct values of SARS-CoV-2 positive samples reported from April 2020 till May 2021. The results of 13,820 RT-PCR (reverse transcriptase-polymerase chain reaction) positive samples were included for analysis of Ct values. Ct values of confirmatory genes were taken into consideration, and Ct values below 25, >25 to 30, and >30 were categorized as high, moderate, and low viral load, respectively. Age group was stratified into ≤18 years (young), 18-60 years (adult), and >60 years (elderly). The data were analyzed using SPSS Windows Version 25.0. Results The mean Ct values were 27.9, 26, and 26.2 in the young, adult, and elderly age groups, respectively. The mean Ct values of young patients were significantly higher as compared to adult and elderly patients (p<0.05). The percentage of high viral load (Ct<25) was found to be significantly higher in adults and elderly (44.6% & 43.7%) as compared to young (32.2%) (p<0.001). Majority of the COVID-19 positive cases younger than 18 years (75.9%) were asymptomatic as compared to 64.5% and 59.7% in the adult and elderly age groups, respectively. Conclusion This study observed a significantly high proportion of viral load in the adult and elderly population, which plays a substantial contribution to SARS-CoV-2 transmission, whereas the majority of the young population being asymptomatic plays a major role as silent transmitters. The study reemphasizes the need for strict adherence to COVID-appropriate behaviors.
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Affiliation(s)
- Baijayantimala Mishra
- Department of Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Bhubaneswar, IND
| | - Jai Ranjan
- Department of Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Bhubaneswar, IND
| | - Prashanth Purushotham
- Department of Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Bhubaneswar, IND
| | - Punyatoya Kar
- Department of Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Bhubaneswar, IND
| | - Poesy Payal
- Department of Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Bhubaneswar, IND
| | - Swarnatrisha Saha
- Department of Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Bhubaneswar, IND
| | - Vaishnavi Deshmukh
- Department of Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Bhubaneswar, IND
| | - Sivasankar Das
- Department of Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Bhubaneswar, IND
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Jayakody H, Rowland D, Pereira C, Blackwell R, Lasota T, Laverick M, Tisi L, Leese HS, Walsham ADS. Development of a high sensitivity RT-PCR assay for detection of SARS-CoV-2 in individual and pooled nasopharyngeal samples. Sci Rep 2022; 12:5369. [PMID: 35354857 PMCID: PMC8965539 DOI: 10.1038/s41598-022-09254-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/21/2022] [Indexed: 12/23/2022] Open
Abstract
The COVID-19 pandemic requires sensitive detection of the SARS-CoV-2 virus from samples to ensure accurate detection of infected patients, an essential component of effective national track and trace programs. Due to the scaling challenges of large sample numbers, sample pooling is an attractive solution to reduce both extraction and amplification reagent costs, if high sensitivity can be maintained. We demonstrate that the Erba Molecular ErbaMDx SARS-CoV-2 RT-PCR Kit (EM kit) delivers high sensitivity, achieving analytical detection of 5 copies/reaction SARS-CoV-2 genomic RNA, and 200 copies/mL SARS-CoV-2 inactivated virus spiked into nasopharyngeal swab (NP) samples and extracted through workflow. Furthermore, the EM Kit demonstrates high sensitivity in both pooled (1 in 5) and non-pooled NP samples when compared to an FDA Emergency Use Authorization approved assay, following published FDA guidelines. These findings demonstrate that the EM Kit is suitable for sample pooling, with minimal impact on assay performance. As the COVID-19 pandemic progresses, high sensitivity assays such as the EM Kit will have an important role in ensuring high throughput and sensitive testing using pooled samples can be maintained, delivering the most cost-effective sample extraction and amplification option for national test and trace programs.
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Affiliation(s)
- Harindi Jayakody
- Erba Molecular, Ely, Cambridgeshire, UK
- Materials for Health Lab, Department of Chemical Engineering, University of Bath, Bath, UK
| | | | | | | | | | | | | | - Hannah S Leese
- Materials for Health Lab, Department of Chemical Engineering, University of Bath, Bath, UK
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Dadras O, Afsahi AM, Pashaei Z, Mojdeganlou H, Karimi A, Habibi P, Barzegary A, Fakhfouri A, Mirzapour P, Janfaza N, Dehghani S, Afroughi F, Dashti M, Khodaei S, Mehraeen E, Voltarelli F, Sabatier J, SeyedAlinaghi S. The relationship between COVID-19 viral load and disease severity: A systematic review. Immun Inflamm Dis 2022; 10:e580. [PMID: 34904379 PMCID: PMC8926507 DOI: 10.1002/iid3.580] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/14/2021] [Accepted: 11/22/2021] [Indexed: 02/05/2023] Open
Abstract
INTRODUCTION Patients with COVID-19 may present different viral loads levels. However, the relationship between viral load and disease severity in COVID-19 is still unknown. Therefore, this study aimed to systematically review the association between SARS-CoV-2 viral load and COVID-19 severity. METHODS The relevant studies using the keywords of "COVID-19" and "viral load" were searched in the databases of PubMed, Scopus, Google Scholar, and Web of Science. A two-step title/abstract screening process was carried out and the eligible studies were included in the study. RESULTS Thirty-four studies were included from the initial 1015 records. The vast majority of studies have utilized real-time reverse transcription-polymerase chain reaction of the nasopharyngeal/respiratory swabs to report viral load. Viral loads were commonly reported either as cycle threshold (Ct ) or log10 RNA copies/ml. CONCLUSION The results were inconclusive about the relationship between COVID-19 severity and viral load, as a similar number of studies either approved or opposed this hypothesis. However, the studies denote the direct relationship between older age and higher SARS-CoV-2 viral load, which is a known risk factor for COVID-19 mortality. The higher viral load in older patients may serve as a mechanism for any possible relationships between COVID-19 viral load and disease severity. There was a positive correlation between SARS-CoV-2 viral load and its transmissibility. Nonetheless, further studies are recommended to precisely characterize this matter.
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Affiliation(s)
- Omid Dadras
- The Excellent Center for Dengue and Community Public Health (EC for DACH), School of Public HealthWalailak UniversityNakhon Si ThammaratThailand
| | - Amir M. Afsahi
- Department of Radiology, School of MedicineUniversity of California, San Diego (UCSD)La JollaCaliforniaUSA
| | - Zahra Pashaei
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High‐Risk BehaviorsTehran University of Medical SciencesTehranIran
| | | | - Amirali Karimi
- School of MedicineTehran University of Medical SciencesTehranIran
| | - Pedram Habibi
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High‐Risk BehaviorsTehran University of Medical SciencesTehranIran
| | | | | | - Pegah Mirzapour
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High‐Risk BehaviorsTehran University of Medical SciencesTehranIran
| | - Nazanin Janfaza
- Internal Medicine Department, Imam Khomeini Hospital Complex, School of MedicineTehran University of Medical SciencesTehranIran
| | - Soheil Dehghani
- School of MedicineTehran University of Medical SciencesTehranIran
| | - Fatemeh Afroughi
- School of MedicineIslamic Azad UniversityTehranIran
- Pars HospitalIran University of Medical SciencesTehranIran
| | - Mohsen Dashti
- Department of RadiologyTabriz University of Medical SciencesTabrizIran
| | - Sepideh Khodaei
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High‐Risk BehaviorsTehran University of Medical SciencesTehranIran
| | - Esmaeil Mehraeen
- Department of Health Information TechnologyKhalkhal University of Medical SciencesKhalkhalIran
| | - Fabricio Voltarelli
- Graduation Program of Health Sciences, Faculty of MedicineFederal University of Mato GrossoCuiabáBrazil
| | - Jean‐Marc Sabatier
- Université Aix‐MarseilleInstitut deNeuro‐physiopathologie (INP)UMR 7051, Faculté de PharmacieMarseilleFrance
| | - SeyedAhmad SeyedAlinaghi
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High‐Risk BehaviorsTehran University of Medical SciencesTehranIran
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42
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Acer Ö, Bahçe YG, Özüdoğru O. Association of viral load with age, gender, disease severity and death in SARS-CoV-2 variants. J Med Virol 2022; 94:3063-3069. [PMID: 35212012 DOI: 10.1002/jmv.27677] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/02/2022] [Accepted: 02/21/2022] [Indexed: 11/12/2022]
Abstract
In the current study, the relationship between viral load, demographic characteristics, and disease information in 1007(48.5%) patients with Delta variant (B.1.617.2), and 1070 (51.5%) patients with Alpha variant (B1.1.7) mutations was investigated. We found that there was a significant difference in viral load between patients who died from the Alpha variant and those who were discharged (p<0.05). Nevertheless, no significant difference was observed in patients with Delta variant. The viral load in patients who died from the Alpha variant was significantly higher than those who were discharged (p<0.05). The viral load was found to be higher in females in patients with Delta variant, whereas it was very close in males and females in patients with Alpha variant (p>0.05). No significant difference was detected between the cycle threshold values (Ct) and disease severity. In terms of the mean Ct values, statistical differences were observed in patients with Delta and Alpha variant. The Alpha variant was found to have a higher viral load than the Delta variant. Furthermore, Delta variant was found to be higher in the 40-year-old and under-age group than in the Alpha variant, whereas the Alpha variant was higher in the 40-year-old and older group. While the rate of moderate and severe patients in Alpha variant was found to be higher, the rate of mild survivors was found to be higher in Delta variant. In conclusion, The increase in vaccination prior to the appearance of the Delta variant in our region may have influenced the viral load and clinical status of the patients. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ömer Acer
- Siirt University, Medical Faculty, Department of Medical Microbiology, 56100, Siirt, Turkey
| | - Yasemin Genç Bahçe
- Siirt Training and Research Hospital, Microbiology Laboratory, 56100, Siirt, Turkey
| | - Osman Özüdoğru
- Siirt University, Medical Faculty, Department of Internal Medicine, 56100, Siirt, Turkey
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43
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Fierce L, Robey AJ, Hamilton C. High efficacy of layered controls for reducing exposure to airborne pathogens. INDOOR AIR 2022; 32:e12989. [PMID: 35225391 DOI: 10.1111/ina.12989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 12/19/2021] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
To optimize strategies for curbing the transmission of airborne pathogens, the efficacy of three key controls-face masks, ventilation, and physical distancing-must be well understood. In this study, we used the Quadrature-based model of Respiratory Aerosol and Droplets to quantify the reduction in exposure to airborne pathogens from various combinations of controls. For each combination of controls, we simulated thousands of scenarios that represent the tremendous variability in factors governing airborne transmission and the efficacy of mitigation strategies. While the efficacy of any individual control was highly variable among scenarios, combining universal mask-wearing with distancing of 1 m or more reduced the median exposure by more than 99% relative to a close, unmasked conversation, with further reductions if ventilation is also enhanced. The large reductions in exposure to airborne pathogens translated to large reductions in the risk of initial infection in a new host. These findings suggest that layering controls is highly effective for reducing transmission of airborne pathogens and will be critical for curbing outbreaks of novel viruses in the future.
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Affiliation(s)
- Laura Fierce
- Atmospheric Sciences and Global Change Division, Pacific Northwest National Laboratory, Richland, Washington, USA
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, New York, USA
| | - Alison J Robey
- Center for Environmental Studies, Williams College, Williamstown, Massachusetts, USA
| | - Cathrine Hamilton
- Department of Chemistry, Indiana University of Pennsylvania, Indiana, Pennsylvania, USA
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Euser S, Aronson S, Manders I, van Lelyveld S, Herpers B, Sinnige J, Kalpoe J, van Gemeren C, Snijders D, Jansen R, Schuurmans Stekhoven S, van Houten M, Lede I, Cohen Stuart J, Slijkerman Megelink F, Kapteijns E, den Boer J, Sanders E, Wagemakers A, Souverein D. SARS-CoV-2 viral-load distribution reveals that viral loads increase with age: a retrospective cross-sectional cohort study. Int J Epidemiol 2022; 50:1795-1803. [PMID: 34999848 PMCID: PMC8499942 DOI: 10.1093/ije/dyab145] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/28/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Describing the SARS-CoV-2 viral-load distribution in different patient groups and age categories. METHODS All results from first nasopharyngeal (NP) and oropharyngeal (OP) swabs from unique patients tested via SARS-CoV-2 reverse transcriptase polymerase chain reaction (RT-PCR) collected between 1 January and 1 December 2020 predominantly in the Public Health Services regions Kennemerland and Hollands Noorden, province of North Holland, the Netherlands, were included in this study. SARS-CoV-2 PCR crossing-point (Cp)-values were used to estimate viral loads. RESULTS In total, 278 455 unique patients were tested, of whom 9.1% (n = 25.374) were SARS-CoV-2-positive. PCRs performed by Public Health Services (n = 211 914), in which sampling and inclusion were uniform, revealed a clear relation between age and SARS-CoV-2 viral load, with especially children aged <12 years showing lower viral loads than adults (β: -0.03, 95% confidence interval: -0.03 to -0.02, p < 0.001), independently of sex and/or symptom duration. Interestingly, the median Cp-values between the >79- and <12-year-old populations differed by more than four PCR cycles, suggesting an ∼16-fold difference in viral load. In addition, the proportion of children aged <12 years with a low load (Cp-value >30) was higher compared with other patients (31.1% vs 17.2%, p-value < 0.001). CONCLUSIONS In patients tested by Public Health Services, SARS-CoV-2 viral load increases with age. Further studies should elucidate whether the lower viral load in children is indeed related to their suggested limited role in SARS-CoV-2 transmission. Moreover, as rapid antigen tests are less sensitive than PCR, these results suggest that SARS-CoV-2 antigen tests have lower sensitivity in children than in adults.
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Affiliation(s)
- Sjoerd Euser
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Sem Aronson
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
- Department of Internal Medicine, Spaarne Gasthuis, Hoofddorp/Haarlem, The Netherlands
| | - Irene Manders
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
- Department of Infectious Diseases, Public Health Service Kennemerland, Haarlem, The Netherlands
| | - Steven van Lelyveld
- Department of Internal Medicine, Spaarne Gasthuis, Hoofddorp/Haarlem, The Netherlands
| | - Bjorn Herpers
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Jan Sinnige
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Jayant Kalpoe
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | | | - Dominic Snijders
- Department of Pulmonary Disease, Spaarne Gasthuis, Hoofddorp/Haarlem, the Netherlands
| | - Ruud Jansen
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | | | - Marlies van Houten
- Department of Pediatrics, Spaarne Gasthuis, Hoofddorp/Haarlem, the Netherlands
| | - Ivar Lede
- Department of Medical Microbiology, Comicro BV Medical Microbiology, Hoorn, The Netherlands
| | - James Cohen Stuart
- Department of Medical Microbiology, Noordwest Ziekenhuisgroep, Alkmaar, The Netherlands
| | - Fred Slijkerman Megelink
- Department of Infectious Diseases, Public Health Service Hollands Noorden, Alkmaar, The Netherlands
| | - Erik Kapteijns
- Department of Pulmonary Disease, Rode Kruis Ziekenhuis, Beverwijk, The Netherlands
| | - Jeroen den Boer
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Elisabeth Sanders
- Department of Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Alex Wagemakers
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Dennis Souverein
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
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45
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Carrouel F, Gadea E, Esparcieux A, Dimet J, Langlois ME, Perrier H, Dussart C, Bourgeois D. Saliva Quantification of SARS-CoV-2 in Real-Time PCR From Asymptomatic or Mild COVID-19 Adults. Front Microbiol 2022; 12:786042. [PMID: 35046915 PMCID: PMC8761670 DOI: 10.3389/fmicb.2021.786042] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/09/2021] [Indexed: 12/14/2022] Open
Abstract
The fast spread of COVID-19 is related to the highly infectious nature of SARS-CoV-2. The disease is suggested to be transmitted through saliva droplets and nasal discharge. The saliva quantification of SARS-CoV-2 in real-time PCR from asymptomatic or mild COVID-19 adults has not been fully documented. This study analyzed the relationship between salivary viral load on demographics and clinical characteristics including symptoms, co-morbidities in 160 adults diagnosed as COVID-19 positive patients recruited between September and December 2020 in four French centers. Median initial viral load was 4.12 log10 copies/mL (IQR 2.95-5.16; range 0-10.19 log10 copies/mL). 68.6% of adults had no viral load detected. A median load reduction of 23% was observed between 0-2 days and 3-5 days, and of 11% between 3-5 days and 6-9 days for the delay from onset of symptoms to saliva sampling. No significant median difference between no-symptoms vs. symptoms patients was observed. Charge was consistently similar for the majority of the clinical symptoms excepted for headache with a median load value of 3.78 log10 copies/mL [1.95-4.58] (P < 0.003). SARS-CoV-2 RNA viral load was associated with headache and gastro-intestinal symptoms. The study found no statistically significant difference in viral loads between age groups, sex, or presence de co-morbidity. Our data suggest that oral cavity is an important site for SARS-CoV-2 infection and implicate saliva as a potential route of SARS-CoV-2 transmission.
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Affiliation(s)
- Florence Carrouel
- Health, Systemic, Process, UR4129 Research Unit, University Claude Bernard Lyon 1, University of Lyon, Lyon, France
| | - Emilie Gadea
- Equipe SNA-EPIS, EA4607, University Jean Monnet, Saint-Etienne, France
- Clinical Research Unit, Emile Roux Hospital Center, Le Puy-en-Velay, France
| | - Aurélie Esparcieux
- Department of Internal Medicine and Infectious Diseases, Protestant Infirmary, Caluire-et-Cuire, France
| | - Jérome Dimet
- Clinical Research Center, Intercommunal Hospital Center of Mont de Marsan et du Pays des Sources, Mont de Marsan, France
| | - Marie Elodie Langlois
- Department of Internal Medicine and Infectious Diseases, Saint Joseph Saint Luc Hospital, Lyon, France
| | - Hervé Perrier
- Clinical Research Unit, Protestant Infirmary, Lyon, France
| | - Claude Dussart
- Health, Systemic, Process, UR4129 Research Unit, University Claude Bernard Lyon 1, University of Lyon, Lyon, France
| | - Denis Bourgeois
- Health, Systemic, Process, UR4129 Research Unit, University Claude Bernard Lyon 1, University of Lyon, Lyon, France
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46
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Xu C, Liu W, Luo X, Huang X, Nielsen PV. Prediction and control of aerosol transmission of SARS-CoV-2 in ventilated context: from source to receptor. SUSTAINABLE CITIES AND SOCIETY 2022; 76:103416. [PMID: 34611508 PMCID: PMC8484231 DOI: 10.1016/j.scs.2021.103416] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 05/24/2023]
Abstract
Global spread of COVID-19 has seriously threatened human life and health. The aerosol transmission route of SARS-CoV-2 is observed often associated with infection clusters under poorly ventilated environment. In the context of COVID-19 pandemic, significant transformation and optimization of traditional ventilation systems are needed. This paper is aimed to offer better understanding and insights into effective ventilation design to maximize its ability in airborne risk control, for particularly the COVID-19. Comprehensive reviews of each phase of aerosol transmission of SARS-CoV-2 from source to receptor are conducted, so as to provide a theoretical basis for risk prediction and control. Infection risk models and their key parameters for risk assessment of SARS-CoV-2 are analyzed. Special focus is given on the efficacy of different ventilation strategies in mitigating airborne transmission. Ventilation interventions are found mainly impacting on the dispersion and inhalation phases of aerosol transmission. The airflow patterns become a key factor in controlling the aerosol diffusion and distribution. Novel and personalized ventilation design, effective integration with other environmental control techniques and resilient HVAC system design to adapt both common and epidemic conditions are still remaining challenging, which need to be solved with the aid of multidisciplinary research and intelligent technologies.
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Affiliation(s)
- Chunwen Xu
- College of Pipeline and Civil Engineering, China University of Petroleum, Qingdao 266580, China
| | - Wenbing Liu
- College of Pipeline and Civil Engineering, China University of Petroleum, Qingdao 266580, China
| | - Xilian Luo
- School of Human Settlements and Civil Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xingyu Huang
- School of Human Settlements and Civil Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Peter V Nielsen
- Division of Sustainability, Energy and Indoor Environment, Aalborg University, Aalborg 9000, Denmark
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47
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Sensitivity of airborne transmission of enveloped viruses to seasonal variation in indoor relative humidity. INTERNATIONAL COMMUNICATIONS IN HEAT AND MASS TRANSFER 2022. [PMCID: PMC8659254 DOI: 10.1016/j.icheatmasstransfer.2021.105747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In temperate climates, the peak in infection rates of enveloped viruses during the winter is likely heightened by seasonal variation in relative humidity within indoor spaces. While these seasonal trends are established in influenza and human coronaviruses, the mechanisms driving this seasonality remain poorly understood. Relative humidity impacts the evaporation rate and equilibrium size of airborne particles, which in turn may impact particle removal rates and virion viability. However, the relative importance of these two processes is not known. Here we use the Quadrature-based model of Respiratory Aerosol and Droplets to explore whether the seasonal variation in enveloped viruses is driven by differences in particle removal rates or by differences in virion inactivation rates. Through a large ensemble of simulations, we found that dry indoor conditions typical of winter lead to slower virion inactivation than humid indoor conditions typical of summer; in poorly ventilated spaces, this reduction in inactivation rates increases the airborne concentration of active virions, but this effect was important to virion exposure only when the susceptible person was farther than 2 m downwind of the infectious person. On the other hand, the impact of relative humidity on particle settling velocity did not significantly affect the removal or travel distance of virus-laden particles, suggesting that relative humidity is more likely to affect seasonal transmission via inactivation rates than via particle removal.
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48
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Bueno de Mesquita PJ, Delp WW, Chan WR, Bahnfleth WP, Singer BC. Control of airborne infectious disease in buildings: Evidence and research priorities. INDOOR AIR 2022; 32:e12965. [PMID: 34816493 DOI: 10.1111/ina.12965] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/07/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
The evolution of SARS-CoV-2 virus has resulted in variants likely to be more readily transmitted through respiratory aerosols, underscoring the increased potential for indoor environmental controls to mitigate risk. Use of tight-fitting face masks to trap infectious aerosol in exhaled breath and reduce inhalation exposure to contaminated air is of critical importance for disease control. Administrative controls including the regulation of occupancy and interpersonal spacing are also important, while presenting social and economic challenges. Indoor engineering controls including ventilation, exhaust, air flow control, filtration, and disinfection by germicidal ultraviolet irradiation can reduce reliance on stringent occupancy restrictions. However, the effects of controls-individually and in combination-on reducing infectious aerosol transfer indoors remain to be clearly characterized to the extent needed to support widespread implementation by building operators. We review aerobiologic and epidemiologic evidence of indoor environmental controls against transmission and present a quantitative aerosol transfer scenario illustrating relative differences in exposure at close-interactive, room, and building scales. We identify an overarching need for investment to implement building controls and evaluate their effectiveness on infection in well-characterized and real-world settings, supported by specific, methodological advances. Improved understanding of engineering control effectiveness guides implementation at scale while considering occupant comfort, operational challenges, and energy costs.
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Affiliation(s)
| | - William W Delp
- Indoor Environment Group, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Wanyu R Chan
- Indoor Environment Group, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - William P Bahnfleth
- Department of Architectural Engineering, Pennsylvania State University, State College, Pennsylvania, USA
| | - Brett C Singer
- Indoor Environment Group, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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49
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Maury E, Boldi MO, Greub G, Chavez V, Jaton K, Opota O. An Automated Dashboard to Improve Laboratory COVID-19 Diagnostics Management. Front Digit Health 2021; 3:773986. [PMID: 34939067 PMCID: PMC8685224 DOI: 10.3389/fdgth.2021.773986] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/12/2021] [Indexed: 11/13/2022] Open
Abstract
Background: In response to the COVID-19 pandemic, our microbial diagnostic laboratory located in a university hospital has implemented several distinct SARS-CoV-2 RT-PCR systems in a very short time. More than 148,000 tests have been performed over 12 months, which represents about 405 tests per day, with peaks to more than 1,500 tests per days during the second wave. This was only possible thanks to automation and digitalization, to allow high throughput, acceptable time to results and to maintain test reliability. An automated dashboard was developed to give access to Key Performance Indicators (KPIs) to improve laboratory operational management. Methods: RT-PCR data extraction of four respiratory viruses—SARS-CoV-2, influenza A and B and RSV—from our laboratory information system (LIS), was automated. This included age, gender, test result, RT-PCR instrument, sample type, reception time, requester, and hospitalization status etc. Important KPIs were identified and the visualization was achieved using an in-house dashboard based on the open-source language R (Shiny). Results: The dashboard is organized into three main parts. The “Filter” page presents all the KPIs, divided into five sections: (i) general and gender-related indicators, (ii) number of tests and positivity rate, (iii) cycle threshold and viral load, (iv) test durations, and (v) not valid results. Filtering allows to select a given period, a dedicated instrument, a given specimen, an age range or a requester. The “Comparison” page allows a custom charting of all the available variables, which represents more than 182 combination. The “Data” page, gives the user an access to the raw data in tables format, with possibility of filtering, allowing for a deeper analysis and data download. Informations are updated every 4 h. Conclusions: By giving a rapid access to a huge number of up-to-date information, represented using the most relevant visualization types, without the burden of timely data extraction and analysis, the dashboard represents a reliable and user-friendly tool for operational laboratory management. The dashboard represents a reliable and user-friendly tool improving the decision-making process, resource planning and quality management.
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Affiliation(s)
- Emma Maury
- Faculty of Business and Economics, University of Lausanne, Lausanne, Switzerland
| | - Marc-Olivier Boldi
- Faculty of Business and Economics, University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University and University Hospital of Lausanne, Lausanne, Switzerland.,Infectious Diseases Service, Lausanne University and University Hospital of Lausanne, Lausanne, Switzerland
| | - Valérie Chavez
- Faculty of Business and Economics, University of Lausanne, Lausanne, Switzerland
| | - Katia Jaton
- Institute of Microbiology, Lausanne University and University Hospital of Lausanne, Lausanne, Switzerland
| | - Onya Opota
- Institute of Microbiology, Lausanne University and University Hospital of Lausanne, Lausanne, Switzerland
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50
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Greub G, Caruana G, Schweitzer M, Imperiali M, Muigg V, Risch M, Croxatto A, Opota O, Heller S, Albertos Torres D, Tritten ML, Leuzinger K, Hirsch HH, Lienhard R, Egli A. Multicenter Technical Validation of 30 Rapid Antigen Tests for the Detection of SARS-CoV-2 (VALIDATE). Microorganisms 2021; 9:2589. [PMID: 34946190 PMCID: PMC8704317 DOI: 10.3390/microorganisms9122589] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/02/2021] [Accepted: 12/04/2021] [Indexed: 01/25/2023] Open
Abstract
During COVID19 pandemic, SARS-CoV-2 rapid antigen tests (RATs) were marketed with minimal or no performance data. We aimed at closing this gap by determining technical sensitivities and specificities of 30 RATs prior to market release. We developed a standardized technical validation protocol and assessed 30 RATs across four diagnostic laboratories. RATs were tested in parallel using the Standard Q® (SD Biosensor/Roche) assay as internal reference. We used left-over universal transport/optimum media from nasopharyngeal swabs of 200 SARS-CoV-2 PCR-negative and 100 PCR-positive tested patients. Transport media was mixed with assay buffer and applied to RATs according to manufacturer instructions. Sensitivities were determined according to viral loads. Specificity of at least 99% and sensitivity of 95%, 90%, and 80% had to be reached for 107, 106, 105 virus copies/mL, respectively. Sensitivities ranged from 43.5% to 98.6%, 62.3% to 100%, and 66.7% to 100% at 105, 106, 107 copies/mL, respectively. Automated assay readers such as ExDia or LumiraDx showed higher performances. Specificities ranged from 88.8% to 100%. Only 15 of 30 (50%) RATs passed our technical validation. Due to the high failure rate of 50%, mainly caused by lack of sensitivity, we recommend a thorough validation of RATs prior to market release.
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Affiliation(s)
- Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland; (G.C.); (A.C.); (O.O.)
- Infectious Diseases Service, Department of Internal Medicine, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
- Coordination Commission of Clinical Microbiology, Swiss Society of Microbiology, 1033 Cheseaux, Switzerland; (M.R.); (R.L.); (A.E.)
| | - Giorgia Caruana
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland; (G.C.); (A.C.); (O.O.)
| | - Michael Schweitzer
- Clinical Bacteriology and Mycology, University Hospital Basel, 4031 Basel, Switzerland; (M.S.); (V.M.); (S.H.); (D.A.T.)
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Mauro Imperiali
- Centro Medicina di Laboratorio Dr Risch, Via Arbostra 2, 6963 Pregassona, Switzerland;
| | - Veronika Muigg
- Clinical Bacteriology and Mycology, University Hospital Basel, 4031 Basel, Switzerland; (M.S.); (V.M.); (S.H.); (D.A.T.)
| | - Martin Risch
- Coordination Commission of Clinical Microbiology, Swiss Society of Microbiology, 1033 Cheseaux, Switzerland; (M.R.); (R.L.); (A.E.)
- Centro Medicina di Laboratorio Dr Risch, Via Arbostra 2, 6963 Pregassona, Switzerland;
| | - Antony Croxatto
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland; (G.C.); (A.C.); (O.O.)
- ADMed Microbiologie Laboratory, 2300 La Chaux-de-Fonds, Switzerland;
| | - Onya Opota
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland; (G.C.); (A.C.); (O.O.)
| | - Stefanie Heller
- Clinical Bacteriology and Mycology, University Hospital Basel, 4031 Basel, Switzerland; (M.S.); (V.M.); (S.H.); (D.A.T.)
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Diana Albertos Torres
- Clinical Bacteriology and Mycology, University Hospital Basel, 4031 Basel, Switzerland; (M.S.); (V.M.); (S.H.); (D.A.T.)
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
| | | | - Karoline Leuzinger
- Clinical Virology, University Hospital Basel, 4031 Basel, Switzerland; (K.L.); (H.H.H.)
- Transplantation & Clinical Virology, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Hans H. Hirsch
- Clinical Virology, University Hospital Basel, 4031 Basel, Switzerland; (K.L.); (H.H.H.)
- Transplantation & Clinical Virology, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, 4031 Basel, Switzerland
| | - Reto Lienhard
- Coordination Commission of Clinical Microbiology, Swiss Society of Microbiology, 1033 Cheseaux, Switzerland; (M.R.); (R.L.); (A.E.)
- ADMed Microbiologie Laboratory, 2300 La Chaux-de-Fonds, Switzerland;
| | - Adrian Egli
- Coordination Commission of Clinical Microbiology, Swiss Society of Microbiology, 1033 Cheseaux, Switzerland; (M.R.); (R.L.); (A.E.)
- Clinical Bacteriology and Mycology, University Hospital Basel, 4031 Basel, Switzerland; (M.S.); (V.M.); (S.H.); (D.A.T.)
- Clinical Virology, University Hospital Basel, 4031 Basel, Switzerland; (K.L.); (H.H.H.)
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