201
|
Schrom E, Kinzig A, Forrest S, Graham AL, Levin SA, Bergstrom CT, Castillo-Chavez C, Collins JP, de Boer RJ, Doupé A, Ensafi R, Feldman S, Grenfell BT, Halderman JA, Huijben S, Maley C, Moses M, Perelson AS, Perrings C, Plotkin J, Rexford J, Tiwari M. Challenges in cybersecurity: Lessons from biological defense systems. Math Biosci 2023:109024. [PMID: 37270102 DOI: 10.1016/j.mbs.2023.109024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/27/2023] [Accepted: 05/20/2023] [Indexed: 06/05/2023]
Abstract
Defending against novel, repeated, or unpredictable attacks, while avoiding attacks on the 'self', are the central problems of both mammalian immune systems and computer systems. Both systems have been studied in great detail, but with little exchange of information across the different disciplines. Here, we present a conceptual framework for structured comparisons across the fields of biological immunity and cybersecurity, by framing the context of defense, considering different (combinations of) defensive strategies, and evaluating defensive performance. Throughout this paper, we pose open questions for further exploration. We hope to spark the interdisciplinary discovery of general principles of optimal defense, which can be understood and applied in biological immunity, cybersecurity, and other defensive realms.
Collapse
Affiliation(s)
- Edward Schrom
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, United States of America
| | - Ann Kinzig
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, United States of America
| | - Stephanie Forrest
- Biodesign Center for Biocomputation, Security and Society, Arizona State University, Tempe, AZ 85287, United States of America; School of Computing and Augmented Intelligence, Arizona State University, Tempe, AZ 85287, United States of America; Santa Fe Institute, Santa Fe, NM 87501, United States of America
| | - Andrea L Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, United States of America; Santa Fe Institute, Santa Fe, NM 87501, United States of America
| | - Simon A Levin
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, United States of America.
| | - Carl T Bergstrom
- Department of Biology, University of Washington, Seattle, WA 98195, United States of America
| | - Carlos Castillo-Chavez
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287, United States of America
| | - James P Collins
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, United States of America
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Adam Doupé
- School of Computing and Augmented Intelligence, Arizona State University, Tempe, AZ 85287, United States of America; Center for Cybersecurity and Trusted Foundations, Global Security Initiative, Arizona State University, Tempe, AZ 85287, United States of America
| | - Roya Ensafi
- Department of Electrical Engineering and Computer Science, Computer Science and Engineering Division, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Stuart Feldman
- Schmidt Futures, New York, NY 10011, United States of America
| | - Bryan T Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, United States of America; Princeton School of Public and International Affairs, Princeton University, Princeton, NJ 08544, United States of America
| | - J Alex Halderman
- Department of Electrical Engineering and Computer Science, Computer Science and Engineering Division, University of Michigan, Ann Arbor, MI 48109, United States of America; Center for Computer Security and Society, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Silvie Huijben
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, United States of America
| | - Carlo Maley
- Arizona Cancer Evolution Center, Arizona State University, Tempe, AZ 85287, United States of America; Biodesign Center for Biocomputation, Security and Society, Arizona State University, Tempe, AZ 85287, United States of America
| | - Melanie Moses
- Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, United States of America; Department of Biology, University of New Mexico, Albuquerque, NM 87131, United States of America; Santa Fe Institute, Santa Fe, NM 87501, United States of America
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America; Santa Fe Institute, Santa Fe, NM 87501, United States of America
| | - Charles Perrings
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, United States of America
| | - Joshua Plotkin
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, United States of America
| | - Jennifer Rexford
- Department of Computer Science, Princeton University, Princeton, NJ 08540, United States of America
| | - Mohit Tiwari
- Department of Electrical and Computer Engineering, University of Texas, Austin, TX 78712, United States of America
| |
Collapse
|
202
|
Moya VSR, Águila LA, Camara NM, Cisse SD, Mamady D, Keïta S, Bakary KM, Pérez LD, Casañas ED. Interferon in the treatment of ill adults with Covid-19 in the Republic of Guinea. Afr Health Sci 2023; 23:43-55. [PMID: 38223582 PMCID: PMC10782291 DOI: 10.4314/ahs.v23i2.6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024] Open
Abstract
Background Effective and safe antiviral treatments are required to refrain the COVID-19. Objectives Investigate the efficacy and safety of interferon in the treatment of COVID-19. Methods The inclusion criteria were patients who gave their signed consent, with detection confirmed by RT-PCR of SARS-CoV-2, 18 years and older. Patients received therapy as per the Guinea COVID-19 protocol in the group B; the group A received the same treatment including administration of interferon. The outcome measures the time to negative conversion of SARS-CoV-2, mortality, patients transferred to ICU and safety, according to the reports of adverse events. Results 345 patients were included, 171 in the group A and 174 in the group B. After the treatments, the RT-PCR negative results were attained in the patients in the group A in 9.15±4.79 days and in those in the group B in 14.83±6.67 days. No patient in the group A had to be transferred to ICU, and they all survived; in the group B, 26 patients were transferred to ICU and six of them died. There were eight adverse events with causality relation with interferon administration. Conclusions The interferon resulted effective and safe in contributing to the viral replication conversion to negative results in shorter time and to survival.
Collapse
Affiliation(s)
| | - Ladys Alfonso Águila
- Communitarian Teaching Policlinic “Mario Muñoz Monroy”, Vertientes, Camagüey, Cuba
| | | | | | | | - Sakoba Keïta
- National Agency for Public Health Safety, Republic of Guinea
| | | | - Lianet Díaz Pérez
- National Center for Animal and Plant, San José de las Lajas, Mayabeque, Cuba
| | - Elaine Díaz Casañas
- National Center for Animal and Plant, San José de las Lajas, Mayabeque, Cuba
| |
Collapse
|
203
|
Poli De Frias F, Cardenas Castillo R, Perez Garcia MF, Al-Himyary A. The Role of Bronchoalveolar Lavage in the Diagnosis of COVID-19 Pneumonia: A Report of Three Cases. Cureus 2023; 15:e41145. [PMID: 37519543 PMCID: PMC10386879 DOI: 10.7759/cureus.41145] [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] [Accepted: 06/29/2023] [Indexed: 08/01/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) initially infects and replicates in epithelial cells of the nasopharynx where there are relatively high levels of angiotensin-converting enzyme 2 receptor, which correlates with the highest sensitivity time point of the nasopharyngeal swab (NPS) real-time polymerase chain reaction (RT-PCR) during the first week, with subsequent decline thereafter. As viral shedding progresses throughout the respiratory tract, the virus can be detectable for up to 30 days in bronchoalveolar fluids. This report presents three cases of acute respiratory distress in the setting of multifocal pneumonia, with multiple false-negative NPS SARS-CoV-2/RT-PCR but positive SARS-CoV-2/RT-PCR in bronchoalveolar lavage (BAL) samples. Molecular RT-PCR testing remains the gold standard in the diagnosis of SARS-CoV-2 infection. However, the diagnostic accuracy of NPS RT-PCR may be affected by several factors. SARS-CoV-2/RT-PCR in BAL samples increases the diagnostic yield for coronavirus disease 2019 pneumonia; however, it is not widely available in many institutions and can be clinically challenging to perform. A multimodal approach is required for prompt diagnosis, especially in patients with a progressive disease, where a delay in therapy can be clinically detrimental.
Collapse
Affiliation(s)
| | | | - Maria F Perez Garcia
- Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, USA
| | - Ali Al-Himyary
- Pulmonary, Critical Care and Sleep Medicine, CHI St. Luke's Health, Baylor St. Luke's Medical Center, Houston, USA
| |
Collapse
|
204
|
Avadhanula V, Creighton CJ, Ferlic-Stark L, Sucgang R, Zhang Y, Nagaraj D, Nicholson EG, Rajan A, Menon VK, Doddapaneni H, Muzny DM, Metcalf G, Cregeen SJJ, Hoffman KL, Gibbs RA, Petrosino J, Piedra PA. Longitudinal host transcriptional responses to SARS-CoV-2 infection in adults with extremely high viral load. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.24.542181. [PMID: 37292999 PMCID: PMC10245966 DOI: 10.1101/2023.05.24.542181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Current understanding of viral dynamics of SARS-CoV-2 and host responses driving the pathogenic mechanisms in COVID-19 is rapidly evolving. Here, we conducted a longitudinal study to investigate gene expression patterns during acute SARS-CoV-2 illness. Cases included SARS-CoV-2 infected individuals with extremely high viral loads early in their illness, individuals having low SARS-CoV-2 viral loads early in their infection, and individuals testing negative for SARS-CoV-2. We could identify widespread transcriptional host responses to SARS-CoV-2 infection that were initially most strongly manifested in patients with extremely high initial viral loads, then attenuating within the patient over time as viral loads decreased. Genes correlated with SARS-CoV-2 viral load over time were similarly differentially expressed across independent datasets of SARS-CoV-2 infected lung and upper airway cells, from both in vitro systems and patient samples. We also generated expression data on the human nose organoid model during SARS-CoV-2 infection. The human nose organoid-generated host transcriptional response captured many aspects of responses observed in the above patient samples, while suggesting the existence of distinct host responses to SARS-CoV-2 depending on the cellular context, involving both epithelial and cellular immune responses. Our findings provide a catalog of SARS-CoV-2 host response genes changing over time.
Collapse
Affiliation(s)
- Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chad J. Creighton
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Laura Ferlic-Stark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard Sucgang
- Center for Health Data Science and Analytics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Divya Nagaraj
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Erin G. Nicholson
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Vipin Kumar Menon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harshavardhan Doddapaneni
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna Marie Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ginger Metcalf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Kristi Louise Hoffman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| |
Collapse
|
205
|
Alotaibi BA, Aldali JA, Aldali HJ, Alasiri GA, Elsokkary EM, Al Mugairi A, Almuqrin AM. Risk Factors for Glucose 6-Phosphate Dehydrogenase and COVID-19 Disease-A Retrospective Study at a Major Saudi Tertiary Center. Viruses 2023; 15:1224. [PMID: 37376524 DOI: 10.3390/v15061224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/19/2023] [Accepted: 05/21/2023] [Indexed: 06/29/2023] Open
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) insufficiency is a common enzymatic defect worldwide; it affects over 400 million people and is associated with various disorders. Recent research suggests that G6PD-deficient cells are susceptible to infection by human coronaviruses, as the G6PD enzyme is involved in the metabolism of oxidative stress, which may enhance COVID-19 mortality. This retrospective study aimed to examine the effect of COVID-19 on patients with G6PD deficiency by comparing the laboratory parameters of patients with G6PD enzyme deficiency alone, COVID-19 alone, and those with both COVID-19 and G6PD enzyme deficiency treated at a major Saudi tertiary center. The results indicated significant differences in hematological and biochemical parameters between the three patient groups, indicating that COVID-19 may influence these parameters, and that they could be used to measure the severity of COVID-19 disease. Moreover, this study suggests that patients with G6PD enzyme deficiency may be at higher risk for severe COVID-19 outcomes. Although the study is limited by the lack of a random selection method for group membership, the Kruskal-Wallis H-test was used to statistical assess the data. The study's findings can enhance the understanding of the relation between COVID-19 infected and G6PD-deficiency patients and inform clinical decision making for an improved patient outcome.
Collapse
Affiliation(s)
- Badi A Alotaibi
- Department of Clinical Laboratory Sciences, Collage of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia
- King Abdullah International Medical Research Center, P.O. Box 3660, Riyadh 11481, Saudi Arabia
| | - Jehad A Aldali
- Department of Pathology, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13317, Saudi Arabia
| | - Hamzah J Aldali
- Cellular and Molecular Medicine, College of Biomedical Science, University of Bristol, Bristol BS8 1QU, UK
| | - Glowi A Alasiri
- Department of Biochemistry, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13317, Saudi Arabia
| | - Emadeldin M Elsokkary
- Psychology, Organisation, Imam Mohammed Ibn Saud Islamic University (IMSIU), Riyadh 13317, Saudi Arabia
| | - Areej Al Mugairi
- Hematopathology Division, Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
| | - Abdulaziz M Almuqrin
- Department of Clinical Laboratory Sciences, Collage of Applied Medical Sciences, King Saud University, Riyadh 11433, Saudi Arabia
| |
Collapse
|
206
|
Kuznetsova NA, Ogarkova DA, Gushchin VA, Antipyat NА, Bacalin VV, Burgasova OA, Vasilchenko LA, Samkov AA, Simakova YV, Divisenko EV, Siniavin AE, Tkachuk AP, Kolobukhina LV, Shidlovskaya EV, Tyurin IN, Kruzhkova IS, Zlobin VI, Nikiforova MA, Odnoralov MA, Gintsburg AL. [Evaluation of the dynamics of detection of viable SARS-CoV-2 (Coronaviridae: Betacoronavirus: Sarbecovirus) in biological samples obtained from patients with COVID-19 in a health care setting, as one of the indicators of the infectivity of the virus]. Vopr Virusol 2023; 68:105-116. [PMID: 37264845 DOI: 10.36233/0507-4088-160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Indexed: 06/03/2023]
Abstract
INTRODUCTION The study of the mechanisms of transmission of the SARS-CoV-2 virus is the basis for building a strategy for anti-epidemic measures in the context of the COVID-19 pandemic. Understanding in what time frame a patient can spread SARS-CoV-2 is just as important as knowing the transmission mechanisms themselves. This information is necessary to develop effective measures to prevent infection by breaking the chains of transmission of the virus. The aim of the work is to identify the infectious SARS-CoV-2 virus in patient samples in the course of the disease and to determine the duration of virus shedding in patients with varying severity of COVID-19. MATERIALS AND METHODS In patients included in the study, biomaterial (nasopharyngeal swabs) was subjected to analysis by quantitative RT-PCR and virological determination of infectivity of the virus. RESULTS We have determined the timeframe of maintaining the infectivity of the virus in patients hospitalized with severe and moderate COVID-19. Based on the results of the study, we made an analysis of the relationship between the amount of detected SARS-CoV-2 RNA and the infectivity of the virus in vitro in patients with COVID-19. The median time of the infectious virus shedding was 8 days. In addition, a comparative analysis of different protocols for the detection of the viral RNA in relation to the identification of the infectious virus was carried out. CONCLUSION The obtained data make it possible to assess the dynamics of SARS-CoV-2 detection and viral load in patients with COVID-19 and indicate the significance of these parameters for the subsequent spread of the virus and the organization of preventive measures.
Collapse
Affiliation(s)
- N A Kuznetsova
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - D A Ogarkova
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - V A Gushchin
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - N А Antipyat
- Infectious Clinical Hospital No. 1 of the Department of Health of the Moscow
| | | | | | - L A Vasilchenko
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - A A Samkov
- Infectious Clinical Hospital No. 1 of the Department of Health of the Moscow
| | - Y V Simakova
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - E V Divisenko
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - A E Siniavin
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - A P Tkachuk
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - L V Kolobukhina
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - E V Shidlovskaya
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - I N Tyurin
- Infectious Clinical Hospital No. 1 of the Department of Health of the Moscow
| | - I S Kruzhkova
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - V I Zlobin
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - M A Nikiforova
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - M A Odnoralov
- Infectious Clinical Hospital No. 1 of the Department of Health of the Moscow
| | - A L Gintsburg
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| |
Collapse
|
207
|
Corchis-Scott R, Geng Q, Al Riahi AM, Labak A, Podadera A, Ng KKS, Porter LA, Tong Y, Dixon JC, Menard SL, Seth R, McKay RM. Actionable wastewater surveillance: application to a university residence hall during the transition between Delta and Omicron resurgences of COVID-19. Front Public Health 2023; 11:1139423. [PMID: 37265515 PMCID: PMC10230041 DOI: 10.3389/fpubh.2023.1139423] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 04/28/2023] [Indexed: 06/03/2023] Open
Abstract
Wastewater surveillance has gained traction during the COVID-19 pandemic as an effective and non-biased means to track community infection. While most surveillance relies on samples collected at municipal wastewater treatment plants, surveillance is more actionable when samples are collected "upstream" where mitigation of transmission is tractable. This report describes the results of wastewater surveillance for SARS-CoV-2 at residence halls on a university campus aimed at preventing outbreak escalation by mitigating community spread. Another goal was to estimate fecal shedding rates of SARS-CoV-2 in a non-clinical setting. Passive sampling devices were deployed in sewer laterals originating from residence halls at a frequency of twice weekly during fall 2021 as the Delta variant of concern continued to circulate across North America. A positive detection as part of routine sampling in late November 2021 triggered daily monitoring and further isolated the signal to a single wing of one residence hall. Detection of SARS-CoV-2 within the wastewater over a period of 3 consecutive days led to a coordinated rapid antigen testing campaign targeting the residence hall occupants and the identification and isolation of infected individuals. With knowledge of the number of individuals testing positive for COVID-19, fecal shedding rates were estimated to range from 3.70 log10 gc ‧ g feces-1 to 5.94 log10 gc ‧ g feces-1. These results reinforce the efficacy of wastewater surveillance as an early indicator of infection in congregate living settings. Detections can trigger public health measures ranging from enhanced communications to targeted coordinated testing and quarantine.
Collapse
Affiliation(s)
- Ryland Corchis-Scott
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Qiudi Geng
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Abdul Monem Al Riahi
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Amr Labak
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Ana Podadera
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Kenneth K. S. Ng
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Lisa A. Porter
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
| | - Yufeng Tong
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Jess C. Dixon
- Department of Kinesiology, University of Windsor, Windsor, ON, Canada
| | | | - Rajesh Seth
- Civil and Environmental Engineering, University of Windsor, Windsor, ON, Canada
| | - R. Michael McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| |
Collapse
|
208
|
Flückiger M, Ludwig M. Spatial networks and the spread of COVID-19: results and policy implications from Germany. JAHRBUCH FUR REGIONALWISSENSCHAFTT = REVIEW OF REGIONAL RESEARCH 2023; 43:1-27. [PMID: 37520679 PMCID: PMC10183698 DOI: 10.1007/s10037-023-00185-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 03/22/2023] [Indexed: 08/01/2023]
Abstract
Spatial networks are known to be informative about the spatiotemporal transmission dynamics of COVID-19. Using district-level panel data from Germany that cover the first 22 weeks of 2020, we show that mobility, commuter and social networks all predict the spatiotemporal propagation of the epidemic. The main innovation of our approach is that it incorporates the whole network and updated information on case numbers across districts over time. We find that when disease incidence increases in network neighbouring regions, case numbers in the home district surge one week later. The magnitude of these network transmission effects is comparable to within-district transmission, illustrating the importance of networks as drivers of local disease dynamics. After the introduction of containment policies in mid-March, network transmission intensity drops substantially. Our analysis suggests that this reduction is primarily due to a change in quality-not quantity-of interregional movements. This implies that blanket mobility restrictions are not a prerequisite for containing the interregional spread of COVID-19.
Collapse
Affiliation(s)
| | - Markus Ludwig
- CESifo, Munich, Germany
- Technische Universität Braunschweig, Braunschweig, Germany
| |
Collapse
|
209
|
Schenk H, Heidinger P, Insam H, Kreuzinger N, Markt R, Nägele F, Oberacher H, Scheffknecht C, Steinlechner M, Vogl G, Wagner AO, Rauch W. Prediction of hospitalisations based on wastewater-based SARS-CoV-2 epidemiology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162149. [PMID: 36773921 PMCID: PMC9911153 DOI: 10.1016/j.scitotenv.2023.162149] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 05/03/2023]
Abstract
Wastewater-based epidemiology is widely applied in Austria since April 2020 to monitor the SARS-CoV-2 pandemic. With a steadily increasing number of monitored wastewater facilities, 123 plants covering roughly 70 % of the 9 million population were monitored as of August 2022. In this study, the SARS-CoV-2 viral concentrations in raw sewage were analysed to infer short-term hospitalisation occupancy. The temporal lead of wastewater-based epidemiological time series over hospitalisation occupancy levels facilitates the construction of forecast models. Data pre-processing techniques are presented, including the approach of comparing multiple decentralised wastewater signals with aggregated and centralised clinical data. Time‑lead quantification was performed using cross-correlation analysis and coefficient of determination optimisation approaches. Multivariate regression models were successfully applied to infer hospitalisation bed occupancy. The results show a predictive potential of viral loads in sewage towards Covid-19 hospitalisation occupancy, with an average lead time towards ICU and non-ICU bed occupancy between 14.8-17.7 days and 8.6-11.6 days, respectively. The presented procedure provides access to the trend and tipping point behaviour of pandemic dynamics and allows the prediction of short-term demand for public health services. The results showed an increase in forecast accuracy with an increase in the number of monitored wastewater treatment plants. Trained models are sensitive to changing variant types and require recalibration of model parameters, likely caused by immunity by vaccination and/or infection. The utilised approach displays a practical and rapidly implementable application of wastewater-based epidemiology to infer hospitalisation occupancy.
Collapse
Affiliation(s)
- Hannes Schenk
- Unit of Environmental Engineering, University of Innsbruck, Technikerstraße 13, Innsbruck 6020, Austria.
| | - Petra Heidinger
- Austrian Centre of Industrial Biotechnology, Krenngasse 37, Graz 8010, Austria.
| | - Heribert Insam
- Department of Microbiology, University of Innsbruck, Technikerstraße 25d, Innsbruck 6020, Austria.
| | - Norbert Kreuzinger
- Institute of Water Quality and Resource Management at TU Wien, Karlsplatz 13, Vienna 1040, Austria.
| | - Rudolf Markt
- Department of Microbiology, University of Innsbruck, Technikerstraße 25d, Innsbruck 6020, Austria; Department of Health Sciences and Social Work, Carinthia University of Applied Sciences, St. Veiter Straße, 47, Klagenfurt 9020, Austria.
| | - Fabiana Nägele
- Department of Microbiology, University of Innsbruck, Technikerstraße 25d, Innsbruck 6020, Austria.
| | - Herbert Oberacher
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Müllerstraße, 44, Innsbruck 6020, Austria.
| | - Christoph Scheffknecht
- Institut für Umwelt und Lebensmittelsicherheit des Landes Vorarlberg, Montfortstraße 4, Bregenz 6900, Austria.
| | - Martin Steinlechner
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Müllerstraße, 44, Innsbruck 6020, Austria.
| | - Gunther Vogl
- Institut f¨ur Lebensmittelsicherheit, Veterinärmedizin und Umwelt, Kirchengasse 43, Klagenfurt 9020, Austria.
| | - Andreas Otto Wagner
- Department of Microbiology, University of Innsbruck, Technikerstraße 25d, Innsbruck 6020, Austria.
| | - Wolfgang Rauch
- Unit of Environmental Engineering, University of Innsbruck, Technikerstraße 13, Innsbruck 6020, Austria.
| |
Collapse
|
210
|
Maya S, Kahn JG. COVID-19 testing protocols to guide duration of isolation: a cost-effectiveness analysis. BMC Public Health 2023; 23:864. [PMID: 37170225 PMCID: PMC10173903 DOI: 10.1186/s12889-023-15762-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 04/26/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND The Omicron variant of SARS-CoV-2 led to a steep rise in transmissions, and emerging variants continue to influence case rates across the US. As public tolerance for isolation abated, CDC guidance on duration of at-home isolation of COVID-19 cases was shortened to five days if no symptoms, with no laboratory test requirement, despite more cautious approaches advocated by other federal experts. METHODS We conducted a decision tree analysis of alternative protocols for ending COVID-19 isolation, estimating net costs (direct and productivity), secondary infections, and incremental cost-effectiveness ratios. Sensitivity analyses assessed the impact of input uncertainty. RESULTS Per 100 individuals, five-day isolation had 23 predicted secondary infections and a net cost of $33,000. Symptom check on day five (CDC guidance) yielded a 23% decrease in secondary infections (to 17.8), with a net cost of $45,000. Antigen testing on day six yielded 2.9 secondary infections and $63,000 in net costs. This protocol, compared to the next best protocol of antigen testing on day five of a maximum eight-day isolation, cost an additional $1,300 per secondary infection averted. Antigen or polymerase chain reaction testing on day five were dominated (more expensive and less effective) versus antigen testing on day six. Results were qualitatively robust to uncertainty in key inputs. CONCLUSIONS A six-day isolation with antigen testing to confirm the absence of contagious virus appears the most effective and cost-effective de-isolation protocol to shorten at-home isolation of individuals with COVID-19.
Collapse
Affiliation(s)
- Sigal Maya
- Philip R. Lee Institute for Health Policy Studies, University of California San Francisco, 490 Illinois St, Box 0936, 95158, San Francisco, CA, USA.
| | - James G Kahn
- Philip R. Lee Institute for Health Policy Studies, University of California San Francisco, 490 Illinois St, Box 0936, 95158, San Francisco, CA, USA
| |
Collapse
|
211
|
Hirokawa K, Hirota J, Kawaguchi D, Masaki Y, Onita C. Investigating the epidemiological and economic effects of a third-party certification policy for restaurants with COVID-19 prevention measures. Sci Rep 2023; 13:7655. [PMID: 37169796 PMCID: PMC10173234 DOI: 10.1038/s41598-023-34498-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/03/2023] [Indexed: 05/13/2023] Open
Abstract
This study investigates the effects of a third-party certification policy for restaurants (including bars) that comply with indoor infection-prevention measures on COVID-19 cases and economic activities. We focus on the case of Yamanashi Prefecture in Japan, which introduced a third-party certification policy that accredits facilities, predominantly restaurants, that comply with the designated guidelines. We employ a difference-in-differences design for each of our epidemiological and economic analyses. The estimation results show that, from July 2020 to April 2021, the certification policy reduced the total number of new infection cases by approximately 45.3% (848 cases), while increasing total sales and the number of customers per restaurant by approximately 12.8% (3.21 million Japanese yen or $30,000) and 30.3% (2909 customers), respectively, compared to the non-intervention scenarios. The results suggest that a third-party certification policy can be an effective policy to mitigate the trade-off between economic activities and infection prevention during a pandemic, especially when effective vaccines are not widely available.
Collapse
Affiliation(s)
- Kazuya Hirokawa
- Graduate School of Public Policy, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Jumpei Hirota
- Graduate School of Public Policy, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Daiji Kawaguchi
- Graduate School of Public Policy, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
- RIETI, Tokyo, Japan.
- IZA, Bonn, Germany.
| | - Yusuke Masaki
- Graduate School of Public Policy, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Chiaki Onita
- Graduate School of Public Policy, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| |
Collapse
|
212
|
Sarker F, Chowdhury MH, Ratul IJ, Islam S, Mamun KA. An interactive national digital surveillance system to fight against COVID-19 in Bangladesh. Front Digit Health 2023; 5:1059446. [PMID: 37250527 PMCID: PMC10210141 DOI: 10.3389/fdgth.2023.1059446] [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: 10/01/2022] [Accepted: 03/06/2023] [Indexed: 05/31/2023] Open
Abstract
Background COVID-19 has affected many people globally, including in Bangladesh. Due to a lack of preparedness and resources, Bangladesh has experienced a catastrophic health crisis, and the devastation caused by this deadly virus has not yet been halted. Hence, precise and rapid diagnostics and infection tracing are essential for managing the condition and limiting its spread. The conventional screening procedure, such as reverse transcription polymerase chain reaction (RT-PCR), is not available in most rural areas and is time-consuming. Therefore, a data-driven intelligent surveillance system can be advantageous for rapid COVID-19 screening and risk estimation. Objectives This study describes the design, development, implementation, and characteristics of a nationwide web-based surveillance system for educating, screening, and tracking COVID-19 at the community level in Bangladesh. Methods The system consists of a mobile phone application and a cloud server. The data is collected by community health professionals via home visits or telephone calls and analyzed using rule-based artificial intelligence (AI). Depending on the results of the screening procedure, a further decision is made regarding the patient. This digital surveillance system in Bangladesh provides a platform to support government and non-government organizations, including health workers and healthcare facilities, in identifying patients at risk of COVID-19. It refers people to the nearest government healthcare facility, collecting and testing samples, tracking and tracing positive cases, following up with patients, and documenting patient outcomes. Results This study began in April 2020, and the results are provided in this paper till December 2022. The system has successfully completed 1,980,323 screenings. Our rule-based AI model categorized them into five separate risk groups based on the acquired patient information. According to the data, around 51% of the overall screened populations are safe, 35% are low risk, 9% are high risk, 4% are mid risk, and the remaining 1% is very high risk. The dashboard integrates all collected data from around the nation onto a single platform. Conclusion This screening can help the symptomatic patient take immediate action, such as isolation or hospitalization, depending on the severity. This surveillance system can also be utilized for risk mapping, planning, and allocating health resources to more vulnerable areas to reduce the virus's severity.
Collapse
Affiliation(s)
- Farhana Sarker
- CMED Health Ltd., Dhaka, Bangladesh
- Department of CSE, University of Liberal Arts, Dhaka, Bangladesh
| | | | - Ishrak Jahan Ratul
- Advanced Intelligent Multidisciplinary Systems Lab (AIMS Lab), United International University, Dhaka, Bangladesh
| | - Shariful Islam
- School of Exercise & Nutrition Sciences, Faculty of Health, Deakin University, Burwood, VIC, Australia
| | - Khondaker A. Mamun
- CMED Health Ltd., Dhaka, Bangladesh
- Advanced Intelligent Multidisciplinary Systems Lab (AIMS Lab), United International University, Dhaka, Bangladesh
- Department of CSE, United International University, Dhaka, Bangladesh
| |
Collapse
|
213
|
Frediani JK, Parsons R, McLendon KB, Westbrook AL, Lam W, Martin G, Pollock NR. The New Normal: Delayed Peak SARS-CoV-2 Viral Loads Relative to Symptom Onset and Implications for COVID-19 Testing Programs. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.09.23289735. [PMID: 37214887 PMCID: PMC10197800 DOI: 10.1101/2023.05.09.23289735] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Background Early in the COVID-19 pandemic, peak viral loads coincided with symptom onset. We hypothesized that in a highly immune population, symptom onset might occur earlier in infection, coinciding with lower viral loads. Methods We assessed SARS-CoV-2 and influenza A viral loads relative to symptom duration in recently-tested adults. Symptomatic participants ≥16y presenting to testing sites in Georgia (4/2022-4/2023; Omicron variant predominant) provided symptom duration. Nasal swab samples were tested by the Xpert Xpress SARS-CoV-2/Flu/RSV assay and Ct values recorded. Nucleoprotein concentrations in SARS-CoV-2 PCR-positive samples were measured by Single Molecule Array. To estimate hypothetical antigen rapid diagnostic test (Ag RDT) sensitivity on each day after symptom onset, percentages of individuals with Ct value ≤30 or ≤25 were calculated. Results Of 621 SARS-CoV-2 PCR-positive individuals (64.1% women, median 40.9y), 556/621 (89.5%) had a history of vaccination, natural infection, or both. By both Ct value and antigen concentration measurements, median viral loads rose from the day of symptom onset and peaked on the fourth day. Ag RDT sensitivity estimates were 35.7-71.4% on the first day, 63.9-78.7% on the third day, and 78.6-90.6% on the fourth day of symptoms.In 74 influenza A PCR-positive individuals (55.4% women; median 35.0y), median influenza viral loads peaked on the second day of symptoms. Conclusions In a highly immune adult population, median SARS-CoV-2 viral loads peaked on the fourth day of symptoms. Influenza A viral loads peaked soon after symptom onset. These findings have implications for ongoing use of Ag RDTs for COVID-19 and influenza. Key Points In a highly immune adult population, median SARS-CoV-2 viral loads by cycle threshold and antigen measurements peaked on the fourth day of symptoms, with implications for testing practice. In contrast, viral loads for influenza A peaked soon after symptom onset.
Collapse
Affiliation(s)
| | - Richard Parsons
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA USA
| | - Kaleb B. McLendon
- Emory/Children’s Laboratory for Innovative Assay Development, Department of Pathology, Emory University, Atlanta, GA USA
| | - Adrianna L. Westbrook
- Pediatric Biostatistics Core, Department of Pediatrics, Emory University, Atlanta, GA USA
| | - Wilbur Lam
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA USA
- Aflac Cancer and Blood Disorders Center of Children’s Healthcare of Atlanta, Atlanta, GA USA
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA USA
| | - Greg Martin
- Department of Medicine, Emory University School of Medicine, Atlanta, GA USA
| | - Nira R. Pollock
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, MA USA
| |
Collapse
|
214
|
Simon DS, Yew CW, Kumar VS. Multiplexed Reverse Transcription Loop-Mediated Isothermal Amplification Coupled with a Nucleic Acid-Based Lateral Flow Dipstick as a Rapid Diagnostic Method to Detect SARS-CoV-2. Microorganisms 2023; 11:1233. [PMID: 37317207 PMCID: PMC10223058 DOI: 10.3390/microorganisms11051233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 04/30/2023] [Accepted: 05/03/2023] [Indexed: 06/16/2023] Open
Abstract
Due to the high reproduction rate of COVID-19, it is important to identify and isolate infected patients at the early stages of infection. The limitations of current diagnostic methods are speed, cost, and accuracy. Furthermore, new viral variants have emerged with higher rates of infectivity and mortality, many with mutations at various primer binding sites, which may evade detection via conventional PCR kits. Therefore, a rapid method that is sensitive, specific, and cost-effective is needed for a point-of-care molecular test. Accordingly, we developed a rapid molecular SARS-CoV-2 detection kit with high specificity and sensitivity, RT-PCR, taking advantage of the loop-mediated isothermal amplification (LAMP) technique. Four sets of six primers were designed based on conserved regions of the SARS-CoV-2 genome: two outer, two inner and two loop primers. Using the optimized protocol, SARS-CoV-2 genes were detected as quickly as 10 min but were most sensitive at 30 min, detecting as little as 100 copies of template DNA. We then coupled the RT-LAMP with a lateral flow dipstick (LFD) for multiplex detection. The LFD could detect two genic amplifications on a single strip, making it suitable for multiplexed detection. The development of a multiplexed RT-LAMP-LFD reaction on crude VTM samples would be suitable for the point-of-care diagnosis of COVID-19 in diagnostic laboratories as well as in private homes.
Collapse
Affiliation(s)
| | | | - Vijay Subbiah Kumar
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Malaysia; (D.S.S.); (C.-W.Y.)
| |
Collapse
|
215
|
Alonso-Navarro R, Ramírez M, Masiá M, Paredes R, Montejano R, Povar-Echeverria M, Carratalà J, Salavert M, Bernal E, Dueñas C, Flores J, Fanjul F, Gutiérrez I, Rico V, Mateu L, Cadiñanos J, Berenguer J, Soriano A. Time from symptoms onset to remdesivir is associated with the risk of ICU admission: a multicentric analyses. BMC Infect Dis 2023; 23:286. [PMID: 37142994 PMCID: PMC10157565 DOI: 10.1186/s12879-023-08222-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/04/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Shorter duration of symptoms before remdesivir has been associated with better outcomes. Our goal was to evaluate variables associated with the need of ICU admission in a cohort of hospitalized patients for COVID-19 under remdesivir including the period from symptoms onset to remdesivir. METHODS We conducted a retrospective multicentric study analysing all patients admitted with COVID-19 in 9 Spanish hospitals who received treatment with remdesivir in October 2020. The main outcome was the need of ICU admission after 24 h of the first dose of remdesivir. RESULTS In our cohort of 497 patients, the median of days from symptom onset to remdesivir was 5 days, and 70 of them (14.1%) were later admitted into ICU. The clinical outcomes associated with ICU admission were days from symptoms onset (5 vs. 6; p = 0.023), clinical signs of severe disease (respiratory rate, neutrophil count, ferritin levels and very-high mortality rate in SEIMC-Score) and the use of corticosteroids and anti-inflammatory drugs before ICU. The only variable significatively associated with risk reduction in the Cox-regression analyses was ≤ 5 days from symptoms onset to RDV (HR: 0.54, CI95%: 0.31-0.92; p = 0.024). CONCLUSION For patients admitted to the hospital with COVID-19, the prescription of remdesivir within 5 days from symptoms onset diminishes the need of ICU admission.
Collapse
Affiliation(s)
| | | | - Mar Masiá
- Elche General University Hospital, Elche, Spain
- Carlos III Health Institute-CIBERINFEC, Madrid, Spain
| | - Roger Paredes
- Carlos III Health Institute-CIBERINFEC, Madrid, Spain
- German Trias i Pujol University Hospital, Barcelona, Spain
| | - Rocío Montejano
- Carlos III Health Institute-CIBERINFEC, Madrid, Spain
- La Paz University Hospital, Madrid, Spain
| | | | - Jordi Carratalà
- Carlos III Health Institute-CIBERINFEC, Madrid, Spain
- Bellvitge University Hospital-IDIBELL, University of Barcelona, Barcelona, Spain
| | - Miguel Salavert
- La Fe Universitary and Politechnic Hospital of Valencia-IIS-La Fe, Valencia, Spain
| | - Enrique Bernal
- Reina Sofía University Hospital of Murcia, Murcia, Spain
| | - Carlos Dueñas
- Clinic University Hospital of Valladolid, Valladolid, Spain
| | - Juan Flores
- Arnau de Vilanova University Hospital, Lleida, Spain
| | - Francisco Fanjul
- Son Espases University Hospital-IdISBa, Palma de Mallorca, Spain
| | - Isabel Gutiérrez
- Gregorio Marañón General University Hospital (IiSGM), Madrid, Spain
| | - Verónica Rico
- Department of Infectious Diseases, Clinic Hospital of Barcelona, Barcelona, Spain
| | - Lourdes Mateu
- German Trias i Pujol University Hospital, Barcelona, Spain
| | | | - Juan Berenguer
- Gregorio Marañón General University Hospital (IiSGM), Madrid, Spain
- Carlos III Health Institute-CIBERINFEC, Madrid, Spain
| | - Alex Soriano
- Department of Infectious Diseases, Clinic Hospital of Barcelona, Barcelona, Spain.
- Carlos III Health Institute-CIBERINFEC, Madrid, Spain.
| |
Collapse
|
216
|
Murphy C, Wong JY, Cowling BJ. Nonpharmaceutical interventions for managing SARS-CoV-2. Curr Opin Pulm Med 2023; 29:184-190. [PMID: 36856551 PMCID: PMC10090342 DOI: 10.1097/mcp.0000000000000949] [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: 03/02/2023]
Abstract
PURPOSE OF REVIEW Initial response strategies to the COVID-19 pandemic were heavily reliant on nonpharmaceutical interventions (NPIs), a set of measures implemented to slow or even stop the spread of infection. Here, we reviewed key measures used during the COVID-19 pandemic. RECENT FINDINGS Some NPIs were successful in reducing the transmission of SARS-CoV-2. Personal protective measures such as face masks were widely used, and likely had some effect on transmission. The development and production of rapid antigen tests allowed self-diagnosis in the community, informing isolation and quarantine measures. Community-wide measures such as school closures, workplace closures and complete stay-at-home orders were able to reduce contacts and prevent transmission. They were widely used in the pandemic and contributed to reduce transmission in the community; however, there were also negative unintended consequences in the society and economy. SUMMARY NPIs slowed the spread of SARS-CoV-2 and are essential for pandemic preparedness and response. Understanding which measures are more effective at reducing transmission with lower costs is imperative.
Collapse
Affiliation(s)
- Caitriona Murphy
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam
| | - Jessica Y. Wong
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam
| | - Benjamin J. Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam
- Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| |
Collapse
|
217
|
Vedelago C, Li J, Lowry K, Howard C, Wuethrich A, Trau M. A Multiplexed SERS Microassay for Accurate Detection of SARS-CoV-2 and Variants of Concern. ACS Sens 2023; 8:1648-1657. [PMID: 37026968 PMCID: PMC10081832 DOI: 10.1021/acssensors.2c02782] [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: 12/19/2022] [Accepted: 03/29/2023] [Indexed: 04/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 variants play an important role in predicting patient outcome during postinfection, and with growing fears of COVID-19 reservoirs in domestic and wild animals, it is necessary to adapt detection systems for variant detection. However, variant-specific detection remains challenging. Surface-enhanced Raman scattering is a sensitive and multiplexing technique that allows the simultaneous detection of multiple targets for accurate identification. Here we propose the development of a multiplex SERS microassay to detect both the spike and nucleocapsid structural proteins of SARS-CoV-2. The designed SERS microassay integrates gold-silver hollow nanobox barcodes and electrohydrodynamically induced nanomixing which in combination enables highly specific and sensitive detection of SARS-CoV-2 and the S-protein epitopes to delineate between ancestral prevariant strains with the newer variants of concern, Delta and Omicron. The microassay allows detection from as low as 20 virus/μL and 50 pg/mL RBD protein and can clearly identify the virus among infected versus healthy nasopharyngeal swabs, with the potential to identify between variants. The detection of both S- and N-proteins of SARS-CoV-2 and the differentiation of variants on the SERS microassay can aid the early detection of COVID-19 to reduce transmission rates and lead into adequate treatments for those severely affected by the virus.
Collapse
Affiliation(s)
- Courtney Vedelago
- Centre for Personalised Nanomedicine, Australian
Institute for Bioengineering and Nanotechnology (AIBN), The University of
Queensland, Brisbane, QLD 4072, Australia
| | - Junrong Li
- Centre for Personalised Nanomedicine, Australian
Institute for Bioengineering and Nanotechnology (AIBN), The University of
Queensland, Brisbane, QLD 4072, Australia
| | - Kym Lowry
- The Queensland Paediatric Infectious Diseases (QIPD)
Sakzewski Research Group, Queensland Children’s
Hospital, Brisbane, QLD 4101, Australia
- University of Queensland Centre for
Clinical Research (UQCCR), Royal Brisbane and Women’s Hospital,
Brisbane, QLD 4029, Australia
| | - Christopher Howard
- Centre for Personalised Nanomedicine, Australian
Institute for Bioengineering and Nanotechnology (AIBN), The University of
Queensland, Brisbane, QLD 4072, Australia
| | - Alain Wuethrich
- Centre for Personalised Nanomedicine, Australian
Institute for Bioengineering and Nanotechnology (AIBN), The University of
Queensland, Brisbane, QLD 4072, Australia
| | - Matt Trau
- Centre for Personalised Nanomedicine, Australian
Institute for Bioengineering and Nanotechnology (AIBN), The University of
Queensland, Brisbane, QLD 4072, Australia
- School of Chemistry and Molecular Biosciences,
The University of Queensland, Brisbane, QLD 4072,
Australia
| |
Collapse
|
218
|
Sun Z, Chai L, Ma R. Long-Term Care Research in the Context of COVID-19 Pandemic: A Bibliometric Analysis. Healthcare (Basel) 2023; 11:healthcare11091248. [PMID: 37174790 PMCID: PMC10178488 DOI: 10.3390/healthcare11091248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Despite the increasing awareness of long-term care (LTC) research after the outbreak of COVID-19 pandemic, little attention was given to quantitatively describe the evolution of the research field during this period. A total of 1024 articles retrieved from the Web of Science Core Collection database were systematically analyzed using CiteSpace visualization software. The overall characteristics analysis showed that, in the context of the pandemic, attention to LTC research increased significantly-over 800 articles were published in the past two years. The USA, Canada, Italy, and England formed the leading LTC research group, which was consistent with the conclusions of existing bibliometric studies on LTC research before the outbreak. A rigorous analysis based on a dual perspective of references and keywords was applied to reveal that, compared with previous studies, in the context of the pandemic, the focus shifted from the mental and physical health status of older adults in need of LTC to the impact of the pandemic on those of older adults in LTC facilities, from the prevention of general epidemics to the prevention and response of significant public health emergencies, from providing and paying for LTC to strategies for LTC facilities to improve the quality of LTC and well-being of their residents during the pandemic. These findings can provide help and reference for academics, civil folks, and LTC practitioners, as well as help with the sustainable development of LTC research in the context of COVID-19 pandemic.
Collapse
Affiliation(s)
- Zhaohui Sun
- Department of Law and Political Science, North China Electric Power University, Baoding 071003, China
| | - Lulu Chai
- Department of Law and Political Science, North China Electric Power University, Baoding 071003, China
| | - Ran Ma
- Department of Law and Political Science, North China Electric Power University, Baoding 071003, China
| |
Collapse
|
219
|
Xie R, Edwards KM, Adam DC, Leung KSM, Tsang TK, Gurung S, Xiong W, Wei X, Ng DYM, Liu GYZ, Krishnan P, Chang LDJ, Cheng SMS, Gu H, Siu GKH, Wu JT, Leung GM, Peiris M, Cowling BJ, Poon LLM, Dhanasekaran V. Resurgence of Omicron BA.2 in SARS-CoV-2 infection-naive Hong Kong. Nat Commun 2023; 14:2422. [PMID: 37105966 PMCID: PMC10134727 DOI: 10.1038/s41467-023-38201-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 04/20/2023] [Indexed: 04/29/2023] Open
Abstract
Hong Kong experienced a surge of Omicron BA.2 infections in early 2022, resulting in one of the highest per-capita death rates of COVID-19. The outbreak occurred in a dense population with low immunity towards natural SARS-CoV-2 infection, high vaccine hesitancy in vulnerable populations, comprehensive disease surveillance and the capacity for stringent public health and social measures (PHSMs). By analyzing genome sequences and epidemiological data, we reconstructed the epidemic trajectory of BA.2 wave and found that the initial BA.2 community transmission emerged from cross-infection within hotel quarantine. The rapid implementation of PHSMs suppressed early epidemic growth but the effective reproduction number (Re) increased again during the Spring festival in early February and remained around 1 until early April. Independent estimates of point prevalence and incidence using phylodynamics also showed extensive superspreading at this time, which likely contributed to the rapid expansion of the epidemic. Discordant inferences based on genomic and epidemiological data underscore the need for research to improve near real-time epidemic growth estimates by combining multiple disparate data sources to better inform outbreak response policy.
Collapse
Affiliation(s)
- Ruopeng Xie
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kimberly M Edwards
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Dillon C Adam
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kathy S M Leung
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Tim K Tsang
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Shreya Gurung
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Weijia Xiong
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Xiaoman Wei
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Daisy Y M Ng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Gigi Y Z Liu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Pavithra Krishnan
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Lydia D J Chang
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Samuel M S Cheng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Haogao Gu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Gilman K H Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Joseph T Wu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, New Territories, Hong Kong SAR, China
| | - Gabriel M Leung
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, New Territories, Hong Kong SAR, China
| | - Malik Peiris
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, New Territories, Hong Kong SAR, China
| | - Benjamin J Cowling
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, New Territories, Hong Kong SAR, China
| | - Leo L M Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, New Territories, Hong Kong SAR, China
| | - Vijaykrishna Dhanasekaran
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
| |
Collapse
|
220
|
Idris SN, Amelia TSM, Bhubalan K, Lazim AMM, Zakwan NAMA, Jamaluddin MI, Santhanam R, Amirul AAA, Vigneswari S, Ramakrishna S. The degradation of single-use plastics and commercially viable bioplastics in the environment: A review. ENVIRONMENTAL RESEARCH 2023; 231:115988. [PMID: 37105296 DOI: 10.1016/j.envres.2023.115988] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 04/17/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
Plastics have become an integral part of human life. Single-use plastics (SUPs) are disposable plastics designed to be used once then promptly discarded or recycled. This SUPs range from packaging and takeaway containers to disposable razors and hotel toiletries. Synthetic plastics, which are made of non-renewable petroleum and natural gas resources, require decades to perpetually disintegrate in nature thus contribute to plastic pollution worldwide, especially in marine environments. In response to these problems, bioplastics or bio-based and biodegradable polymers from renewable sources has been considered as an alternative. Understanding the mechanisms behind the degradation of conventional SUPs and biodegradability of their greener counterpart, bioplastics, is crucial for appropriate material selection in the future. This review aims to provide insights into the degradation or disintegration of conventional single-use plastics and the biodegradability of the different types of greener-counterparts, bioplastics, their mechanisms, and conditions. This review highlights on the biodegradation in the environments including composting systems. Here, the various types of alternative biodegradable polymers, such as bacterially biosynthesised bioplastics, natural fibre-reinforced plastics, starch-, cellulose-, lignin-, and soy-based polymers were explored. Review of past literature revealed that although bioplastics are relatively eco-friendly, their natural compositions and properties are inconsistent. Furthermore, the global plastic market for biodegradable plastics remains relatively small and require further research and commercialization efforts, especially considering the urgency of plastic and microplastic pollution as currently critical global issue. Biodegradable plastics have potential to replace conventional plastics as they show biodegradation ability under real environments, and thus intensive research on the various biodegradable plastics is needed to inform stakeholders and policy makers on the appropriate response to the gradually emerging biodegradable plastics.
Collapse
Affiliation(s)
- Siti Norliyana Idris
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Tan Suet May Amelia
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Kesaven Bhubalan
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia; Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Anim Maisara Mohd Lazim
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | | | - Muhammad Imran Jamaluddin
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Rameshkumar Santhanam
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Al-Ashraf Abdullah Amirul
- School of Biological Science, Universiti Sains Malaysia, Pulau Pinang, Malaysia; Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia; Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Penang, Malaysia.
| | - Sevakumaran Vigneswari
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia.
| | - Seeram Ramakrishna
- Center for Nanotechnology and Sustainability, national University of Singapore, 119260, Singapore.
| |
Collapse
|
221
|
de Graaf M, Langeveld J, Post J, Carrizosa C, Franz E, Izquierdo-Lara RW, Elsinga G, Heijnen L, Been F, van Beek J, Schilperoort R, Vriend R, Fanoy E, de Schepper EIT, Koopmans MPG, Medema G. Capturing the SARS-CoV-2 infection pyramid within the municipality of Rotterdam using longitudinal sewage surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 883:163599. [PMID: 37100150 PMCID: PMC10125208 DOI: 10.1016/j.scitotenv.2023.163599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/07/2023] [Accepted: 04/15/2023] [Indexed: 05/03/2023]
Abstract
Despite high vaccination rates in the Netherlands, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to circulate. Longitudinal sewage surveillance was implemented along with the notification of cases as two parts of the surveillance pyramid to validate the use of sewage for surveillance, as an early warning tool, and to measure the effect of interventions. Sewage samples were collected from nine neighborhoods between September 2020 and November 2021. Comparative analysis and modeling were performed to understand the correlation between wastewater and case trends. Using high resolution sampling, normalization of wastewater SARS-CoV-2 concentrations, and 'normalization' of reported positive tests for testing delay and intensity, the incidence of reported positive tests could be modeled based on sewage data, and trends in both surveillance systems coincided. The high collinearity implied that high levels of viral shedding around the onset of disease largely determined SARS-CoV-2 levels in wastewater, and that the observed relationship was independent of variants of concern and vaccination levels. Sewage surveillance alongside a large-scale testing effort where 58 % of a municipality was tested, indicated a five-fold difference in the number of SARS-CoV-2-positive individuals and reported cases through standard testing. Where trends in reported positive cases were biased due to testing delay and testing behavior, wastewater surveillance can objectively display SARS-CoV-2 dynamics for both small and large locations and is sensitive enough to measure small variations in the number of infected individuals within or between neighborhoods. With the transition to a post-acute phase of the pandemic, sewage surveillance can help to keep track of re-emergence, but continued validation studies are needed to assess the predictive value of sewage surveillance with new variants. Our findings and model aid in interpreting SARS-CoV-2 surveillance data for public health decision-making and show its potential as one of the pillars of future surveillance of (re)emerging viruses.
Collapse
Affiliation(s)
- Miranda de Graaf
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands; Pandemic and Disaster Preparedness Centre Rotterdam and Delft, the Netherlands.
| | - Jeroen Langeveld
- Partners4urbanwater, Nijmegen, the Netherlands; Delft University of Technology, Stevinweg 1, 2628 CN Delft, the Netherlands
| | - Johan Post
- Partners4urbanwater, Nijmegen, the Netherlands
| | - Christian Carrizosa
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands; Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Eelco Franz
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Ray W Izquierdo-Lara
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Goffe Elsinga
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Leo Heijnen
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Frederic Been
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Janko van Beek
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | - Rianne Vriend
- Regional Public Health Service Rotterdam-Rijnmond, Rotterdam, the Netherlands
| | - Ewout Fanoy
- Regional Public Health Service Rotterdam-Rijnmond, Rotterdam, the Netherlands
| | - Evelien I T de Schepper
- Department of General Practice, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands; Pandemic and Disaster Preparedness Centre Rotterdam and Delft, the Netherlands
| | - Gertjan Medema
- Pandemic and Disaster Preparedness Centre Rotterdam and Delft, the Netherlands; KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands; Delft University of Technology, Stevinweg 1, 2628 CN Delft, the Netherlands
| |
Collapse
|
222
|
Landis JT, Moorad R, Pluta LJ, Caro-Vegas C, McNamara RP, Eason AB, Bailey A, Villamor FCS, Juarez A, Wong JP, Yang B, Broussard GS, Damania B, Dittmer DP. Intra-Host Evolution Provides for the Continuous Emergence of SARS-CoV-2 Variants. mBio 2023; 14:e0344822. [PMID: 36786605 PMCID: PMC10127995 DOI: 10.1128/mbio.03448-22] [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: 12/20/2022] [Accepted: 01/13/2023] [Indexed: 02/15/2023] Open
Abstract
Variants of concern (VOC) in SARS-CoV-2 refer to viruses whose viral genomes differ from the ancestor virus by ≥3 single-nucleotide variants (SNVs) and that show the potential for higher transmissibility and/or worse clinical progression. VOC have the potential to disrupt ongoing public health measures and vaccine efforts. Still, too little is known regarding how frequently new viral variants emerge and under what circumstances. We report a study to determine the degree of SARS-CoV-2 sequence evolution in 94 patients and to estimate the frequency at which highly diverse variants emerge. Two cases accumulated ≥9 SNVs over a 2-week period and one case accumulated 23 SNVs over 3 weeks, including three nonsynonymous mutations in the spike protein (D138H, E554D, D614G). The remainder of the infected patients did not show signs of intra-host evolution. We estimate that in as much as 2% of hospitalized COVID-19 cases, variants with multiple mutations in the spike glycoprotein emerge in as little as 1 month of persistent intra-host virus replication. This suggests the continued local emergence of variants with multiple nonsynonymous SNVs, even in patients without overt immune deficiency. Surveillance by sequencing for (i) viremic COVID-19 patients, (ii) patients suspected of reinfection, and (iii) patients with diminished immune function may offer broad public health benefits. IMPORTANCE New SARS-CoV-2 variants can potentially disrupt ongoing public health measures and vaccine efforts. Still, little is known regarding how frequently new viral variants emerge and under what circumstances. Based on this study, we estimate that in hospitalized COVID-19 cases, variants with multiple mutations may emerge locally in as little as 1 month, even in patients without overt immune deficiency. Surveillance by sequencing for continuously shedding patients, patients suspected of reinfection, and patients with diminished immune function may offer broad public health benefits.
Collapse
Affiliation(s)
- Justin T. Landis
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Razia Moorad
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Linda J. Pluta
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Carolina Caro-Vegas
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Ryan P. McNamara
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Anthony B. Eason
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Aubrey Bailey
- Kuopio Center for Gene and Cell Therapy, Kuopio, Finland
| | - Femi Cleola S. Villamor
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Angelica Juarez
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Jason P. Wong
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Brian Yang
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Grant S. Broussard
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Blossom Damania
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Dirk P. Dittmer
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| |
Collapse
|
223
|
Weber J, Bonn EL, Auer DL, Kirschneck C, Buchalla W, Scholz KJ, Cieplik F. Preprocedural mouthwashes for infection control in dentistry-an update. Clin Oral Investig 2023:10.1007/s00784-023-04953-z. [PMID: 37079156 PMCID: PMC10116478 DOI: 10.1007/s00784-023-04953-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/17/2023] [Indexed: 04/21/2023]
Abstract
OBJECTIVES Aerosols and splatter are routinely generated in dental practice and can be contaminated by potentially harmful bacteria or viruses such as SARS-CoV-2. Therefore, preprocedural mouthwashes containing antiseptic agents have been proposed as a potential measure for infection control in dental practice. This review article aims to summarize the clinical (and, if insufficient, preclinical) evidence on preprocedural mouthwashes containing antiseptic agents and to draw conclusions for dental practitioners. METHODS Literature on preprocedural mouthwashes for reduction of bacterial or viral load in dental aerosols was searched and summarized. RESULTS Preprocedural mouthwashes, particularly those containing chlorhexidine digluconate (CHX), cetylpyridinium chloride (CPC), or essential oils (EO), can significantly reduce the bacterial load in dental aerosols. With respect to viruses such as HSV-1, there are too little clinical data to draw any clear recommendations. On the other hand, clinical data is consolidating that CPC-containing mouthwashes can temporarily reduce the intraoral viral load and infectivity in SARS-CoV-2 positive individuals. Nevertheless, potential risks and side effects due to regular antiseptic use such as ecological effects or adaptation of bacteria need to be considered. CONCLUSIONS The use of preprocedural mouthwashes containing antiseptics can be recommended according to currently available data, but further studies are needed, particularly on the effects on other viruses besides SARS-CoV-2. When selecting a specific antiseptic, the biggest data basis currently exists for CHX, CPC, EO, or combinations thereof. CLINICAL RELEVANCE Preprocedural mouthwashes containing antiseptics can serve as part of a bundle of measures for protection of dental personnel despite some remaining ambiguities and in view of potential risks and side effects.
Collapse
Affiliation(s)
- Johanna Weber
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
- Department of Orthodontics, University Hospital Regensburg, Regensburg, Germany
| | - Eva L Bonn
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | - David L Auer
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | | | - Wolfgang Buchalla
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | - Konstantin J Scholz
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | - Fabian Cieplik
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany.
| |
Collapse
|
224
|
Ivanov A, Kryshen E, Semenova E. Nonlinear interdependence of the results of measuring anti-SARS-CoV-2 IgG levels using Abbott and Euroimmun test systems. J Clin Virol 2023; 164:105448. [PMID: 37146518 PMCID: PMC10116115 DOI: 10.1016/j.jcv.2023.105448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 05/07/2023]
Abstract
BACKGROUND There are significant number of tests used to determine the level of antibodies to SARS-CoV-2 which differ both in the methods underlying testing and in the antigenic targets used and classes of measured immunoglobulins. Comparison of the results obtained using various tests reveals their significant discrepancy when converted to the WHO recommended standard unit for measuring the level of specific immunoglobulins BAU/mL. The aim of this study is a comparison of anty-SARS-CoV-2 IgG levels, measured using test systems based on different methodological platforms - EuroImmun assay and Abbott assay. METHOD Abbott uses the immunochemiluminescence method CLIA, EuroImmun uses the enzyme immunoassay method ELISA. The dependences of the measurement error on the level of antibodies for the two test systems were approximated by power functions using the least squares method. The nonlinear relation of antibody levels values measured by Abbott assay and Euroimmun assay was approximated by an asymptotic function. RESULTS The study involved 112 people. Our results confirm the fallacy of using a single conversion coefficient in BAU/mL for anti-SARS-CoV-2 IgG levels measured by Abbott and EuroImmun. To describe the interdependence of anti-SARS-CoV-2 IgG Abbott and EuroImmun levels, we offer the function y = 18/π arctan(0.0009x) and a calculator that allows to easily recalculate the results obtained using these tests. CONCLUSION The non-linear nature of the interdependence of the measured anti-SARS-CoV-2 antibodies levels on the levels magnitude is one of the main reasons for the discrepancy between the tests results when converted to BAU/mL using a single conversion coefficient.
Collapse
Affiliation(s)
- Andrei Ivanov
- Saint-Petersburg State University Hospital, 154, Fontanka river embankment, Saint-Petersburg, 198103, Russian Federation; Almazov National Medical Research Centre, Saint-Petersburg, 2 Akkuratova str., 197341, Russian Federation; North-West Centre for Evidence-Based Medicine JSC, 28A Pulkovskoe shosse, Saint-Petersburg, 196247, Russian Federation.
| | - Evgeni Kryshen
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre «Kurchatov Institute», Gatchina, 188300, Russian Federation
| | - Elena Semenova
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre «Kurchatov Institute», Gatchina, 188300, Russian Federation
| |
Collapse
|
225
|
Rao R, Musante CJ, Allen R. A quantitative systems pharmacology model of the pathophysiology and treatment of COVID-19 predicts optimal timing of pharmacological interventions. NPJ Syst Biol Appl 2023; 9:13. [PMID: 37059734 PMCID: PMC10102696 DOI: 10.1038/s41540-023-00269-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 02/09/2023] [Indexed: 04/16/2023] Open
Abstract
A quantitative systems pharmacology (QSP) model of the pathogenesis and treatment of SARS-CoV-2 infection can streamline and accelerate the development of novel medicines to treat COVID-19. Simulation of clinical trials allows in silico exploration of the uncertainties of clinical trial design and can rapidly inform their protocols. We previously published a preliminary model of the immune response to SARS-CoV-2 infection. To further our understanding of COVID-19 and treatment, we significantly updated the model by matching a curated dataset spanning viral load and immune responses in plasma and lung. We identified a population of parameter sets to generate heterogeneity in pathophysiology and treatment and tested this model against published reports from interventional SARS-CoV-2 targeting mAb and antiviral trials. Upon generation and selection of a virtual population, we match both the placebo and treated responses in viral load in these trials. We extended the model to predict the rate of hospitalization or death within a population. Via comparison of the in silico predictions with clinical data, we hypothesize that the immune response to virus is log-linear over a wide range of viral load. To validate this approach, we show the model matches a published subgroup analysis, sorted by baseline viral load, of patients treated with neutralizing Abs. By simulating intervention at different time points post infection, the model predicts efficacy is not sensitive to interventions within five days of symptom onset, but efficacy is dramatically reduced if more than five days pass post symptom onset prior to treatment.
Collapse
Affiliation(s)
- Rohit Rao
- Early Clinical Development, Pfizer Worldwide Research, Development and Medical, Cambridge, MA, USA.
| | - Cynthia J Musante
- Early Clinical Development, Pfizer Worldwide Research, Development and Medical, Cambridge, MA, USA
| | - Richard Allen
- Early Clinical Development, Pfizer Worldwide Research, Development and Medical, Cambridge, MA, USA
| |
Collapse
|
226
|
Cortés-Sarabia K, Palomares-Monterrubio KH, Velázquez-Moreno JO, Luna-Pineda VM, Leyva-Vázquez MA, Vences-Velázquez A, Dircio-Maldonado R, Del Moral-Hernández O, Illades-Aguiar B. Seroprevalence of IgG and Subclasses against the Nucleocapsid of SARS-CoV-2 in Health Workers. Viruses 2023; 15:v15040955. [PMID: 37112935 PMCID: PMC10141201 DOI: 10.3390/v15040955] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/28/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Abstract
BACKGROUND The nucleocapsid protein of SARS-CoV-2 participates in viral replication, transcription, and assembly. Antibodies against this protein have been proposed for the epidemiological analysis of the seroprevalence of COVID-19 associated with natural infection by SARS-CoV-2. Health workers were one of the most exposed populations, and some had an asymptomatic form of the disease, so detecting IgG antibodies and subclasses against the N protein can help to reclassify their epidemiological status and obtain information about the effector mechanisms associated with viral elimination. METHODS In this study, we analyzed 253 serum samples collected in 2021 and derived from health workers, and evaluated the presence of total IgG and subclasses against the N protein of SARS-CoV-2 by indirect ELISA. RESULTS From the analyzed samples, 42.69% were positive to anti-N IgG antibodies. A correlation between COVID-19 asymptomatic infection and IgG antibodies was observed (p = 0.006). The detected subclasses were: IgG1 (82.4%), IgG2 (75.9%), IgG3 (42.6%), and IgG4 (72.6%). CONCLUSIONS This work provides evidence about the high seroprevalence of total IgG and subclasses of anti-N and their relations with the asymptomatic infection of SARS-CoV-2 and related symptoms.
Collapse
Affiliation(s)
- Karen Cortés-Sarabia
- Laboratorio de Inmunobiología y Diagnóstico Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, Mexico
| | - Kenet Hisraim Palomares-Monterrubio
- Laboratorio de Inmunobiología y Diagnóstico Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, Mexico
| | - Jesús Omar Velázquez-Moreno
- Laboratorio de Inmunobiología y Diagnóstico Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, Mexico
| | - Víctor Manuel Luna-Pineda
- Unidad de Investigación en Inmunología y Proteómica, Laboratorio de Investigación en COVID-19, Hospital Infantil de México "Federico Gómez", Mexico City 06720, Mexico
| | - Marco Antonio Leyva-Vázquez
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, Mexico
| | - Amalia Vences-Velázquez
- Laboratorio de Inmunobiología y Diagnóstico Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, Mexico
| | - Roberto Dircio-Maldonado
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, Mexico
| | - Oscar Del Moral-Hernández
- Laboratorio de Virología, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, Mexico
| | - Berenice Illades-Aguiar
- Unidad de Investigación en Inmunología y Proteómica, Laboratorio de Investigación en COVID-19, Hospital Infantil de México "Federico Gómez", Mexico City 06720, Mexico
| |
Collapse
|
227
|
Lewek P, Banaś I, Witkowski K, Lewek J, Kardas P. The prevalence of symptoms and its correlation with sex in polish COVID-19 adult patients: Cross-sectional online open survey. Front Med (Lausanne) 2023; 10:1121558. [PMID: 37089602 PMCID: PMC10113468 DOI: 10.3389/fmed.2023.1121558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 02/23/2023] [Indexed: 04/08/2023] Open
Abstract
BackgroundThe understanding and treatment of COVID-19 has improved rapidly since December 2019 when SARS-CoV-2 was sequenced. However most papers on its symptomatology focus on hospitalized patients and address only a limited number of major presentations. Although differences depending on sex of COVID-19 patients have been previously confirmed (higher ICU admission and higher death rate for men), no publication has focused on sex-related differences in COVID-19 symptomatology.ObjectiveThe aim of the study was to present a reliable list of COVID-19 symptoms and identify any differences in symptom prevalence depending on sex.MethodsA sample of Polish patients suffering from COVID-19 were surveyed using a cross-sectional anonymous online survey in Polish available on a web-based surveying platform (Survey Monkey). The survey included 20 questions asking about COVID-19 symptoms, days of occurrence (from day 1 until day 14 and “15 days or more”) and patient characteristics including sex, age, height, weight, place of residence and type of therapy received during COVID-19. The survey was made available during the third COVID-19 wave in Poland. The link to the survey was distributed across social networks. Participation was open to anyone willing, without any incentives. The data was analyzed statistically.ResultsSurvey responses were collected from 2,408 participants (56.9% women) aged 18–90 (42 ± 12), 84.7% living in cities, who took part in the study between December 2020 and February 2021. Out of 54 predefined symptoms, the three most prevalent were fatigue (reported by 87.61% respondents), anosmia (73.74%) and headache (69.89%). Women were found to be more symptomatic than men, 31 symptoms occurred more often in women (including anosmia, headache and myalgias, p < 0.05). Subfebrility, fever and hemoptysis were more prevalent in men. Twelve symptoms (incl. hypothermia, sneezing and nausea) lasted longer in women than men (p < 0.05). Fatigue, cough, nasal dryness, xerostomia and polydipsia were the longest lasting symptoms of COVID-19 (lasted over 14 days).ConclusionOur study presents a wide range of symptoms, which may enable better recognition of COVID-19, especially in an outpatient setting. Understanding these differences in the symptomatology of community and hospitalized patients may help diagnose and treat patients faster and more accurately. Our findings also confirmed differences in symptomatology of COVID-19 between men and women, which may lay the foundation for a better understanding of the different courses of this disease in the sexes. Further studies are necessary to understand whether a different presentation correlates with a different outcome.
Collapse
Affiliation(s)
- Pawel Lewek
- Department of Family Medicine, Medical University of Lodz, Łódź, Poland
- *Correspondence: Pawel Lewek,
| | - Izabela Banaś
- Department of Family Medicine, Medical University of Lodz, Łódź, Poland
| | - Konrad Witkowski
- Department of Family Medicine, Medical University of Lodz, Łódź, Poland
| | - Joanna Lewek
- Department of Preventive Cardiology and Lipidology, Chair of Nephrology and Hypertension, Medical University of Lodz, Łódź, Poland
- Department of Cardiology and Adult Congenital Heart Diseases, Polish Mother's Memorial Hospital Research Institute (PMMHRI), Łódź, Poland
| | - Przemyslaw Kardas
- Department of Family Medicine, Medical University of Lodz, Łódź, Poland
| |
Collapse
|
228
|
Odagaki T. New compartment model for COVID-19. Sci Rep 2023; 13:5409. [PMID: 37012332 PMCID: PMC10068699 DOI: 10.1038/s41598-023-32159-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/23/2023] [Indexed: 04/05/2023] Open
Abstract
The SIR or susceptible-infected-recovered model is the standard compartment model for understanding epidemics and has been used all over the world for COVID-19. While the SIR model assumes that infected patients are identical to symptomatic and infectious patients, it is now known that in COVID-19 pre-symptomatic patients are infectious and there are significant number of asymptomatic patients who are infectious. In this paper, population is separated into five compartments for COVID-19; susceptible individuals (S), pre-symptomatic patients (P), asymptomatic patients (A), quarantined patients (Q) and recovered and/or dead patients (R). The time evolution of population in each compartment is described by a set of ordinary differential equations. Numerical solution to the set of differential equations shows that quarantining pre-symptomatic and asymptomatic patients is effective in controlling the pandemic.
Collapse
Affiliation(s)
- Takashi Odagaki
- Kyushu University, Fukuoka, 819-0395, Japan.
- Research Institute for Science Education, Inc., Kyoto, 603-8346, Japan.
| |
Collapse
|
229
|
Nahar K, Begum MN, Tony SR, Jubair M, Hossain MA, Karim Y, Faisal AA, Hossain ME, Rahman MZ, Rahman M. Nasal swab as an alternative specimen for the detection of severe acute respiratory syndrome coronavirus 2. Health Sci Rep 2023; 6:e1213. [PMID: 37077182 PMCID: PMC10106929 DOI: 10.1002/hsr2.1213] [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: 12/05/2022] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 04/21/2023] Open
Abstract
Background and Aims The coronavirus disease 2019 (COVID-19) has brought serious threats to public health worldwide. Nasopharyngeal, nasal swabs, and saliva specimens are used to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, limited data are available on the performance of less invasive nasal swab for testing COVID-19. This study aimed to compare the diagnostic performance of nasal swabs with nasopharyngeal swabs using real-time reverse transcription polymerase chain reaction (RT-PCR) considering viral load, onset of symptoms, and disease severity. Methods A total of 449 suspected COVIDCOVID-19 individuals were recruited. Both nasopharyngeal and nasal swabs were collected from the same individual. Viral RNA was extracted and tested by real-time RT-PCR. Metadata were collected using structured questionnaire and analyzed by SPSS and MedCalc software. Results The overall sensitivity of the nasopharyngeal swab was 96.6%, and the nasal swab was 83.4%. The sensitivity of nasal swabs was more than 97.7% for low and moderate C t values. Moreover, the performance of nasal swab was very high (>87%) for hospitalized patients and at the later stage >7 days of onset of symptoms. Conclusion Less invasive nasal swab sampling with adequate sensitivity can be used as an alternative to nasopharyngeal swabs for the detection of SARS-CoV-2 by real-time RT-PCR.
Collapse
Affiliation(s)
- Kamrun Nahar
- Virology LaboratoryInfectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, BangladeshMohakhaliDhaka1212Bangladesh
| | - Mst. Noorjahan Begum
- Virology LaboratoryInfectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, BangladeshMohakhaliDhaka1212Bangladesh
| | - Selim R. Tony
- Virology LaboratoryInfectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, BangladeshMohakhaliDhaka1212Bangladesh
| | - Mohammad Jubair
- Virology LaboratoryInfectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, BangladeshMohakhaliDhaka1212Bangladesh
| | - Md. Abir Hossain
- Virology LaboratoryInfectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, BangladeshMohakhaliDhaka1212Bangladesh
| | - Yeasir Karim
- Virology LaboratoryInfectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, BangladeshMohakhaliDhaka1212Bangladesh
| | - Abdullah Al. Faisal
- Virology LaboratoryInfectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, BangladeshMohakhaliDhaka1212Bangladesh
| | - Mohammad Enayet Hossain
- Virology LaboratoryInfectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, BangladeshMohakhaliDhaka1212Bangladesh
| | - Mohammed Ziaur Rahman
- Virology LaboratoryInfectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, BangladeshMohakhaliDhaka1212Bangladesh
| | - Mustafizur Rahman
- Virology LaboratoryInfectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, BangladeshMohakhaliDhaka1212Bangladesh
| |
Collapse
|
230
|
Nestor B, Hunter J, Kainkaryam R, Drysdale E, Inglis JB, Shapiro A, Nagaraj S, Ghassemi M, Foschini L, Goldenberg A. Machine learning COVID-19 detection from wearables. Lancet Digit Health 2023; 5:e182-e184. [PMID: 36963907 PMCID: PMC10032660 DOI: 10.1016/s2589-7500(23)00045-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/24/2022] [Accepted: 02/21/2023] [Indexed: 03/24/2023]
Affiliation(s)
- Bret Nestor
- Department of Computer Science, University of Toronto, Toronto, ON M5S 3H5, Canada; Vector Institute, Toronto, ON, Canada; Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jaryd Hunter
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Erik Drysdale
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jeffrey B Inglis
- Interdepartmental Graduate Program in Dynamical Neuroscience, University of California, Santa Barbara, Santa Barbara, CA, USA
| | | | - Sujay Nagaraj
- Department of Computer Science, University of Toronto, Toronto, ON M5S 3H5, Canada; Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Marzyeh Ghassemi
- Department of Computer Science, University of Toronto, Toronto, ON M5S 3H5, Canada; Vector Institute, Toronto, ON, Canada; Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Luca Foschini
- Evidation Health, San Mateo, CA, USA; Sage Bionetworks, Seattle, WA, USA
| | - Anna Goldenberg
- Department of Computer Science, University of Toronto, Toronto, ON M5S 3H5, Canada; Vector Institute, Toronto, ON, Canada; Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; CIFAR, Toronto, ON, Canada.
| |
Collapse
|
231
|
Chavda VP, Bezbaruah R, Dolia S, Shah N, Verma S, Savale S, Ray S. Convalescent plasma (hyperimmune immunoglobulin) for COVID-19 management: An update. Process Biochem 2023; 127:66-81. [PMID: 36741339 PMCID: PMC9886570 DOI: 10.1016/j.procbio.2023.01.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 01/21/2023] [Accepted: 01/25/2023] [Indexed: 02/01/2023]
Abstract
The pandemic COVID-19 has spread widely throughout the globe and has been responsible for millions of deaths worldwide. Recently, it has been identified that there is no specific and 100% effective treatment available to manage the infection especially for the severe cases. A significant amount of research efforts and clinical trials have been undertaken globally and many more are underway to find the potential treatment option. Earlier, convalescent plasma or hyperimmune immunoglobulin was effectively used in the treatment of many endemic or epidemic viral infections as a part of passive immunization. In this article, we have touched upon the immunopathology of COVID-19 infection, a basic understanding of convalescent plasma, it's manufacturing as well as evaluation, and have reviewed the scientific developments focussing on the potential of convalescent plasma vis-à-vis other modalities for the management of COVID-19. The article also covers various research approaches, clinical trials conducted globally, and the clinical trials which are at various stages for exploring the efficacy and safety of the convalescent plasma therapy (CPT) to predict its future perspective to manage COVID-19.
Collapse
Affiliation(s)
- Vivek P Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L M College of Pharmacy, Ahmedabad 380009, Gujarat, India
| | - Rajashri Bezbaruah
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Sheetal Dolia
- Intas Pharmaceuticals Ltd. (Plasma Fractionation Unit), Ahmedabad 382213, Gujarat, India
| | - Nirav Shah
- Department of Pharmaceutics, SAL Institute of Pharmacy, Sola, Ahmedabad 380060, India
| | - Sachin Verma
- Intas Pharmaceuticals Ltd. (Plasma Fractionation Unit), Ahmedabad 382213, Gujarat, India
| | - Shrinivas Savale
- AIC-LMCP Foundation, L M College of Pharmacy, Ahmedabad 380009, Gujarat, India
| | - Suma Ray
- Intas Pharmaceuticals Ltd. (Plasma Fractionation Unit), Ahmedabad 382213, Gujarat, India
| |
Collapse
|
232
|
Drain PK, Dalmat RR, Hao L, Bemer MJ, Budiawan E, Morton JF, Ireton RC, Hsiang TY, Marfatia Z, Prabhu R, Woosley C, Gichamo A, Rechkina E, Hamilton D, Montaño M, Cantera JL, Ball AS, Golez I, Smith E, Greninger AL, McElrath MJ, Thompson M, Grant BD, Meisner A, Gottlieb GS, Gale M. Duration of viral infectiousness and correlation with symptoms and diagnostic testing in non-hospitalized adults during acute SARS-CoV-2 infection: A longitudinal cohort study. J Clin Virol 2023; 161:105420. [PMID: 36913789 PMCID: PMC9981266 DOI: 10.1016/j.jcv.2023.105420] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/07/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023]
Abstract
BACKGROUND Guidelines for SARS-CoV-2 have relied on limited data on duration of viral infectiousness and correlation with COVID-19 symptoms and diagnostic testing. METHODS We enrolled ambulatory adults with acute SARS-CoV-2 infection and performed serial measurements of COVID-19 symptoms, nasal swab viral RNA, nucleocapsid (N) and spike (S) antigens, and replication-competent SARS-CoV-2 by viral growth in culture. We determined average time from symptom onset to a first negative test result and estimated risk of infectiousness, as defined by positive viral growth in culture. RESULTS Among 95 adults, median [interquartile range] time from symptom onset to first negative test result was 9 [5] days, 13 [6] days, 11 [4] days, and >19 days for S antigen, N antigen, culture growth, and viral RNA by RT-PCR, respectively. Beyond two weeks, virus growth and N antigen titers were rarely positive, while viral RNA remained detectable among half (26/51) of participants tested 21-30 days after symptom onset. Between 6-10 days from symptom onset, N antigen was strongly associated with culture positivity (relative risk=7.61, 95% CI: 3.01-19.22), whereas neither viral RNA nor symptoms were associated with culture positivity. During the 14 days following symptom onset, the presence of N antigen remained strongly associated (adjusted relative risk=7.66, 95% CI: 3.96-14.82) with culture positivity, regardless of COVID-19 symptoms. CONCLUSIONS Most adults have replication-competent SARS-CoV-2 for 10-14 after symptom onset. N antigen testing is a strong predictor of viral infectiousness and may be a more suitable biomarker, rather than absence of symptoms or viral RNA, to discontinue isolation within two weeks from symptom onset.
Collapse
Affiliation(s)
- Paul K Drain
- International Clinical Research Center, Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, WA, United States; Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, United States; Division of Allergy and Infectious Diseases, Department of Medicine, School of Medicine, University of Washington, Seattle, WA, United States.
| | - Ronit R Dalmat
- International Clinical Research Center, Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, WA, United States; Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, United States
| | - Linhui Hao
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, United States; Center for Emerging & Re-emerging Infectious Diseases, University of Washington, Seattle, WA, United States
| | - Meagan J Bemer
- International Clinical Research Center, Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, WA, United States
| | - Elvira Budiawan
- International Clinical Research Center, Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, WA, United States
| | - Jennifer F Morton
- International Clinical Research Center, Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, WA, United States
| | - Renee C Ireton
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, United States; Center for Emerging & Re-emerging Infectious Diseases, University of Washington, Seattle, WA, United States
| | - Tien-Ying Hsiang
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, United States; Center for Emerging & Re-emerging Infectious Diseases, University of Washington, Seattle, WA, United States
| | - Zarna Marfatia
- International Clinical Research Center, Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, WA, United States
| | - Roshni Prabhu
- International Clinical Research Center, Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, WA, United States
| | - Claire Woosley
- International Clinical Research Center, Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, WA, United States
| | - Adanech Gichamo
- International Clinical Research Center, Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, WA, United States
| | - Elena Rechkina
- International Clinical Research Center, Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, WA, United States
| | - Daphne Hamilton
- International Clinical Research Center, Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, WA, United States
| | - Michalina Montaño
- International Clinical Research Center, Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, WA, United States
| | | | | | - Inah Golez
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, United States; Center for Emerging & Re-emerging Infectious Diseases, University of Washington, Seattle, WA, United States
| | - Elise Smith
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, United States; Center for Emerging & Re-emerging Infectious Diseases, University of Washington, Seattle, WA, United States
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - M Juliana McElrath
- Division of Allergy and Infectious Diseases, Department of Medicine, School of Medicine, University of Washington, Seattle, WA, United States; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Matthew Thompson
- Department of Family Medicine, School of Medicine, University of Washington, Seattle, WA, United States
| | | | - Allison Meisner
- International Clinical Research Center, Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, WA, United States; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Geoffrey S Gottlieb
- Division of Allergy and Infectious Diseases, Department of Medicine, School of Medicine, University of Washington, Seattle, WA, United States; Center for Emerging & Re-emerging Infectious Diseases, University of Washington, Seattle, WA, United States; Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, WA, United States; Environmental Health & Safety Department, University of Washington, Seattle, WA, United States
| | - Michael Gale
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, United States; Center for Emerging & Re-emerging Infectious Diseases, University of Washington, Seattle, WA, United States
| |
Collapse
|
233
|
Park SW, Dushoff J, Grenfell BT, Weitz JS. Intermediate levels of asymptomatic transmission can lead to the highest epidemic fatalities. PNAS NEXUS 2023; 2:pgad106. [PMID: 37091542 PMCID: PMC10118396 DOI: 10.1093/pnasnexus/pgad106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/02/2022] [Accepted: 03/13/2023] [Indexed: 04/25/2023]
Abstract
Asymptomatic infections have hampered the ability to characterize and prevent the transmission of SARS-CoV-2 throughout the pandemic. Although asymptomatic infections reduce severity at the individual level, they can make population-level outcomes worse if asymptomatic individuals-unaware they are infected-transmit more than symptomatic individuals. Using an epidemic model, we show that intermediate levels of asymptomatic infection lead to the highest levels of epidemic fatalities when the decrease in symptomatic transmission, due either to individual behavior or mitigation efforts, is strong. We generalize this result to include presymptomatic transmission, showing that intermediate levels of nonsymptomatic transmission lead to the highest levels of fatalities. Finally, we extend our framework to illustrate how the intersection of asymptomatic spread and immunity profiles determine epidemic trajectories, including population-level severity, of future variants. In particular, when immunity provides protection against symptoms, but not against infections or deaths, epidemic trajectories can have faster growth rates and higher peaks, leading to more total deaths. Conversely, even modest levels of protection against infection can mitigate the population-level effects of asymptomatic spread.
Collapse
Affiliation(s)
- Sang Woo Park
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Jonathan Dushoff
- Department of Biology, McMaster University, Hamilton, ON, Canada
- Department of Mathematics and Statistics, McMaster University, Hamilton, ON, Canada
- M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Bryan T Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Princeton School of Public and International Affairs, Princeton University, Princeton, NJ, USA
| | | |
Collapse
|
234
|
KhudaBukhsh WR, Khalsa SK, Kenah E, Rempała GA, Tien JH. COVID-19 dynamics in an Ohio prison. Front Public Health 2023; 11:1087698. [PMID: 37064663 PMCID: PMC10098107 DOI: 10.3389/fpubh.2023.1087698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/20/2023] [Indexed: 03/31/2023] Open
Abstract
Incarcerated individuals are a highly vulnerable population for infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Understanding the transmission of respiratory infections within prisons and between prisons and surrounding communities is a crucial component of pandemic preparedness and response. Here, we use mathematical and statistical models to analyze publicly available data on the spread of SARS-CoV-2 reported by the Ohio Department of Rehabilitation and Corrections (ODRC). Results from mass testing conducted on April 16, 2020 were analyzed together with time of first reported SARS-CoV-2 infection among Marion Correctional Institution (MCI) inmates. Extremely rapid, widespread infection of MCI inmates was reported, with nearly 80% of inmates infected within 3 weeks of the first reported inmate case. The dynamical survival analysis (DSA) framework that we use allows the derivation of explicit likelihoods based on mathematical models of transmission. We find that these data are consistent with three non-exclusive possibilities: (i) a basic reproduction number >14 with a single initially infected inmate, (ii) an initial superspreading event resulting in several hundred initially infected inmates with a reproduction number of approximately three, or (iii) earlier undetected circulation of virus among inmates prior to April. All three scenarios attest to the vulnerabilities of prisoners to COVID-19, and the inability to distinguish among these possibilities highlights the need for improved infection surveillance and reporting in prisons.
Collapse
Affiliation(s)
- Wasiur R. KhudaBukhsh
- School of Mathematical Sciences, The University of Nottingham, Nottingham, United Kingdom
| | - Sat Kartar Khalsa
- Wexner Medical Center, The Ohio State University, Columbus, OH, United States
| | - Eben Kenah
- Division of Biostatistics, The Ohio State University, Columbus, OH, United States
| | - Gregorz A. Rempała
- Division of Biostatistics, Department of Mathematics, The Ohio State University, Columbus, OH, United States
| | - Joseph H. Tien
- Division of Epidemiology, Department of Mathematics, The Ohio State University, Columbus, OH, United States
- *Correspondence: Joseph H. Tien
| |
Collapse
|
235
|
Della Marca R, Loy N, Tosin A. An SIR model with viral load-dependent transmission. J Math Biol 2023; 86:61. [PMID: 36973464 PMCID: PMC10042434 DOI: 10.1007/s00285-023-01901-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 02/01/2023] [Accepted: 03/11/2023] [Indexed: 03/29/2023]
Abstract
The viral load is known to be a chief predictor of the risk of transmission of infectious diseases. In this work, we investigate the role of the individuals' viral load in the disease transmission by proposing a new susceptible-infectious-recovered epidemic model for the densities and mean viral loads of each compartment. To this aim, we formally derive the compartmental model from an appropriate microscopic one. Firstly, we consider a multi-agent system in which individuals are identified by the epidemiological compartment to which they belong and by their viral load. Microscopic rules describe both the switch of compartment and the evolution of the viral load. In particular, in the binary interactions between susceptible and infectious individuals, the probability for the susceptible individual to get infected depends on the viral load of the infectious individual. Then, we implement the prescribed microscopic dynamics in appropriate kinetic equations, from which the macroscopic equations for the densities and viral load momentum of the compartments are eventually derived. In the macroscopic model, the rate of disease transmission turns out to be a function of the mean viral load of the infectious population. We analytically and numerically investigate the case that the transmission rate linearly depends on the viral load, which is compared to the classical case of constant transmission rate. A qualitative analysis is performed based on stability and bifurcation theory. Finally, numerical investigations concerning the model reproduction number and the epidemic dynamics are presented.
Collapse
Affiliation(s)
- Rossella Della Marca
- Mathematics Area, SISSA, International School for Advanced Studies, Via Bonomea 265, 34136, Trieste, Italy
| | - Nadia Loy
- Department of Mathematical Sciences "G. L. Lagrange", Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129, Torino, Italy.
| | - Andrea Tosin
- Department of Mathematical Sciences "G. L. Lagrange", Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129, Torino, Italy
| |
Collapse
|
236
|
Dinh C, Gallouche M, Terrisse H, Gam K, Giner C, Nemoz B, Larrat S, Giai J, Bosson JL, Landelle C. Risk factors for nosocomial COVID-19 in a French university hospital. Infect Dis Now 2023; 53:104695. [PMID: 36958692 PMCID: PMC10030266 DOI: 10.1016/j.idnow.2023.104695] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 02/09/2023] [Accepted: 03/15/2023] [Indexed: 03/24/2023]
Abstract
OBJECTIVES Prevention strategies implemented by hospitals to reduce nosocomial transmission of SARS-CoV-2 sometimes failed. Our aim was to determine the risk factors for nosocomial COVID-19. PATIENTS AND METHODS A case-control study was conducted (September 1, 2020-January 31, 2021) with adult patients hospitalized in medical or surgical units. Infants or patients hospitalized in ICU were excluded. Cases were patients with nosocomial COVID-19 (clinical symptoms and RT-PCR+ for SARS-CoV-2 or RT-PCR+ for SARS-CoV-2 with Ct ≤28 more than 5days after admission); controls were patients without infection (RT-PCR- for SARS-CoV-2 >5 days after admission). They were matched according to length of stay before diagnosis and period of admission. Analyses were performed with a conditional logistic regression. RESULTS A total of 281 cases and 441 controls were included. In the bivariate analysis, cases were older (OR per 10years: 1.22; 95%CI [1.10;1.36]), had more often shared a room (OR: 1.74; 95%CI [1.25;2.43]) or a risk factor for severe COVID-19 (OR: 1.94; 95%CI [1.09;3.45]), were more often hospitalized in medical units [OR: 1.59; 95%CI [1.12;2.25]), had higher exposure to contagious health care workers (HCW; OR per 1person-day: 1.12; 95%CI [1.08;1.17]) and patients (OR per 1 person-day: 1.11; 95%CI [1.08;1.14]) than controls. In an adjusted model, risk factors for nosocomial COVID-19 were exposure to contagious HCW (aOR per 1person-day: 1.08; 95%CI [1.03;1.14]) and to contagious patients (aOR per 1person-day: 1.10; 95%CI [1.07;1.13]). CONCLUSIONS Exposure to contagious professionals and patients are the main risk factors for nosocomial COVID-19.
Collapse
Affiliation(s)
- C Dinh
- Grenoble Alpes university/CNRS, Grenoble INP, MESP TIM-C UMR 5525, Grenoble, France
| | - M Gallouche
- Grenoble Alpes university/CNRS, Grenoble INP, MESP TIM-C UMR 5525, Grenoble, France; Infection Control Unit, Grenoble Alpes University Hospital, Grenoble, France
| | - H Terrisse
- Grenoble Alpes university/CNRS, Grenoble INP, MESP TIM-C UMR 5525, Grenoble, France
| | - K Gam
- Grenoble Alpes university/CNRS, Grenoble INP, MESP TIM-C UMR 5525, Grenoble, France
| | - C Giner
- Infection Control Unit, Grenoble Alpes University Hospital, Grenoble, France
| | - B Nemoz
- Virology Laboratory, Grenoble Alpes University Hospital, Grenoble, France; Antibodies and Infectious Diseases, Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - S Larrat
- Virology Laboratory, Grenoble Alpes University Hospital, Grenoble, France
| | - J Giai
- Grenoble Alpes university/CNRS, Grenoble INP, MESP TIM-C UMR 5525, Grenoble, France; Public Health department, Grenoble Alpes University Hospital, Grenoble, France
| | - J L Bosson
- Grenoble Alpes university/CNRS, Grenoble INP, MESP TIM-C UMR 5525, Grenoble, France; Public Health department, Grenoble Alpes University Hospital, Grenoble, France
| | - C Landelle
- Grenoble Alpes university/CNRS, Grenoble INP, MESP TIM-C UMR 5525, Grenoble, France; Infection Control Unit, Grenoble Alpes University Hospital, Grenoble, France.
| |
Collapse
|
237
|
Van der Feltz-Cornelis CM, Moriarty AS, Strain WD. Neurological Dysfunction in Long COVID Should Not Be Labelled as Functional Neurological Disorder. Viruses 2023; 15:783. [PMID: 36992491 PMCID: PMC10059786 DOI: 10.3390/v15030783] [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: 03/01/2023] [Accepted: 03/17/2023] [Indexed: 03/22/2023] Open
Abstract
There have been suggestions that Long COVID might be purely functional (meaning psychological) in origin. Labelling patients with neurological dysfunction in Long COVID as having functional neurological disorder (FND) in the absence of proper testing may be symptomatic of that line of thought. This practice is problematic for Long COVID patients, as motor and balance symptoms have been reported to occur in Long COVID frequently. FND is characterized by the presentation of symptoms that seem neurological but lack compatibility of the symptom with a neurological substrate. Although diagnostic classification according to the ICD-11 and DSM-5-TR is dependent predominantly on the exclusion of any other medical condition that could account for the symptoms, current neurological practice of FND classification allows for such comorbidity. As a consequence, Long COVID patients with motor and balance symptoms mislabeled as FND have no longer access to Long COVID care, whereas treatment for FND is seldom provided and is ineffective. Research into underlying mechanisms and diagnostic methods should explore how to determine whether motor and balance symptoms currently diagnosed as FND should be considered one part of Long COVID symptoms, in other words, one component of symptomatology, and in which cases they correctly represent FND. Research into rehabilitation models, treatment and integrated care are needed, which should take into account biological underpinnings as well as possible psychological mechanisms and the patient perspective.
Collapse
Affiliation(s)
| | - Andrew S. Moriarty
- Department of Health Sciences, Hull York Medical School, (HYMS), University of York, York YO10 5DD, UK
| | - William David Strain
- Diabetes and Vascular Medicine Research Centre, Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter EX2 5AX, UK
| |
Collapse
|
238
|
Gao S, Shen M, Wang X, Wang J, Martcheva M, Rong L. A multi-strain model with asymptomatic transmission: Application to COVID-19 in the US. J Theor Biol 2023; 565:111468. [PMID: 36940811 PMCID: PMC10027298 DOI: 10.1016/j.jtbi.2023.111468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 02/08/2023] [Accepted: 03/16/2023] [Indexed: 03/23/2023]
Abstract
COVID-19, induced by the SARS-CoV-2 infection, has caused an unprecedented pandemic in the world. New variants of the virus have emerged and dominated the virus population. In this paper, we develop a multi-strain model with asymptomatic transmission to study how the asymptomatic or pre-symptomatic infection influences the transmission between different strains and control strategies that aim to mitigate the pandemic. Both analytical and numerical results reveal that the competitive exclusion principle still holds for the model with the asymptomatic transmission. By fitting the model to the COVID-19 case and viral variant data in the US, we show that the omicron variants are more transmissible but less fatal than the previously circulating variants. The basic reproduction number for the omicron variants is estimated to be 11.15, larger than that for the previous variants. Using mask mandate as an example of non-pharmaceutical interventions, we show that implementing it before the prevalence peak can significantly lower and postpone the peak. The time of lifting the mask mandate can affect the emergence and frequency of subsequent waves. Lifting before the peak will result in an earlier and much higher subsequent wave. Caution should also be taken to lift the restriction when a large portion of the population remains susceptible. The methods and results obtained her e may be applied to the study of the dynamics of other infectious diseases with asymptomatic transmission using other control measures.
Collapse
Affiliation(s)
- Shasha Gao
- School of Mathematics and Statistics, Jiangxi Normal University, Nanchang, 330000, China; Department of Mathematics, University of Florida, Gainesville, FL 32611, United States of America
| | - Mingwang Shen
- China-Australia Joint Research Centre for Infectious Diseases, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Xueying Wang
- Department of Mathematics and Statistics, Washington State University, Pullman, WA 99163, United States of America
| | - Jin Wang
- Department of Mathematics, University of Tennessee at Chattanooga, Chattanooga, TN 37403, United States of America
| | - Maia Martcheva
- Department of Mathematics, University of Florida, Gainesville, FL 32611, United States of America
| | - Libin Rong
- Department of Mathematics, University of Florida, Gainesville, FL 32611, United States of America.
| |
Collapse
|
239
|
Huberts NFD, Thijssen JJJ. Optimal timing of non-pharmaceutical interventions during an epidemic. EUROPEAN JOURNAL OF OPERATIONAL RESEARCH 2023; 305:1366-1389. [PMID: 35765314 PMCID: PMC9221090 DOI: 10.1016/j.ejor.2022.06.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/15/2022] [Indexed: 05/10/2023]
Abstract
In response to the recent outbreak of the SARS-CoV-2 virus governments have aimed to reduce the virus's spread through, inter alia, non-pharmaceutical intervention. We address the question when such measures should be implemented and, once implemented, when to remove them. These issues are viewed through a real-options lens and we develop an SIRD-like continuous-time Markov chain model to analyze a sequence of options: the option to intervene and introduce measures and, after intervention has started, the option to remove these. Measures can be imposed multiple times. We implement our model using estimates from empirical studies and, under fairly general assumptions, our main conclusions are that: (1) measures should be put in place not long after the first infections occur; (2) if the epidemic is discovered when there are many infected individuals already, then it is optimal never to introduce measures; (3) once the decision to introduce measures has been taken, these should stay in place until the number of susceptible or infected members of the population is close to zero; (4) it is never optimal to introduce a tier system to phase-in measures but it is optimal to use a tier system to phase-out measures; (5) a more infectious variant may reduce the duration of measures being in place; (6) the risk of infections being brought in by travelers should be curbed even when no other measures are in place. These results are robust to several variations of our base-case model.
Collapse
Affiliation(s)
- Nick F D Huberts
- Management School, University of York, Heslington, York YO10 5ZF, United Kingdom
| | - Jacco J J Thijssen
- Management School, University of York, Heslington, York YO10 5ZF, United Kingdom
- Department of Mathematics, University of York, Heslington, York YO10 5ZF, United Kingdom
| |
Collapse
|
240
|
Gorji H, Stauffer N, Lunati I, Caduff A, Bühler M, Engel D, Chung HR, Loukas O, Feig S, Renz H. Projection of healthcare demand in Germany and Switzerland urged by Omicron wave (January-March 2022). Epidemics 2023; 43:100680. [PMID: 36963246 PMCID: PMC10011028 DOI: 10.1016/j.epidem.2023.100680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 02/22/2023] [Accepted: 03/07/2023] [Indexed: 03/18/2023] Open
Abstract
In January 2022, after the implementation of broad vaccination programs, the Omicron wave was propagating across Europe. There was an urgent need to understand how population immunity affects the dynamics of the COVID-19 pandemic when the loss of vaccine protection was concurrent with the emergence of a new variant of concern. In particular, assessing the risk of saturation of the healthcare systems was crucial to manage the pandemic and allow a transition towards the endemic course of SARS-CoV-2 by implementing more refined mitigation strategies that shield the most vulnerable groups and protect the healthcare systems. We investigated the epidemic dynamics by means of compartmental models that describe the age-stratified social-mixing and consider vaccination status, type, and waning of the efficacy. In response to the acute situation, our model aimed at (i) providing insight into the plausible scenarios that were likely to occur in Switzerland and Germany in the midst of the Omicron wave, (ii) informing public health authorities, and (iii) helping take informed decisions to minimize negative consequences of the pandemic. Despite the unprecedented numbers of new positive cases, our results suggested that, in all plausible scenarios, the wave was unlikely to create an overwhelming healthcare demand; due to the lower hospitalization rate and the effectiveness of the vaccines in preventing a severe course of the disease. This prediction came true and the healthcare systems in Switzerland and Germany were not pushed to the limit, despite the unprecedentedly large number of infections. By retrospective comparison of the model predictions with the official reported data of the epidemic dynamic, we demonstrate the ability of the model to capture the main features of the epidemic dynamic and the corresponding healthcare demand. In a broader context, our framework can be applied also to endemic scenarios, offering quantitative support for refined public health interventions in response to recurring waves of COVID-19 or other infectious diseases.
Collapse
Affiliation(s)
- Hossein Gorji
- Laboratory of Multiscale Studies in Building Physics, Empa, Dübendorf, Switzerland.
| | - Noé Stauffer
- Laboratory of Multiscale Studies in Building Physics, Empa, Dübendorf, Switzerland
| | - Ivan Lunati
- Laboratory of Multiscale Studies in Building Physics, Empa, Dübendorf, Switzerland
| | - Alexa Caduff
- Department of Justice, Security and Health, Canton Grisons, Switzerland
| | - Martin Bühler
- Department of Justice, Security and Health, Canton Grisons, Switzerland
| | - Doortje Engel
- Department of Justice, Security and Health, Canton Grisons, Switzerland
| | - Ho Ryun Chung
- Institute of Bioinformatics and Biostatistics, Philipps University Marburg, Marburg, Germany
| | - Orestis Loukas
- Institute of Bioinformatics and Biostatistics, Philipps University Marburg, Marburg, Germany
| | - Sabine Feig
- Institute of Laboratory Medicine and Pathobiochemistry Molecular Diagnostics, Philipps University Marburg, Marburg, Germany
| | - Harald Renz
- Institute of Laboratory Medicine and Pathobiochemistry Molecular Diagnostics, Philipps University Marburg, Marburg, Germany
| |
Collapse
|
241
|
Ridenti MA, Teles LK, Maranhão A, Teles VK. Mathematical modeling and investigation on the role of demography and contact patterns in social distancing measures effectiveness in COVID-19 dissemination. MATHEMATICAL MEDICINE AND BIOLOGY : A JOURNAL OF THE IMA 2023; 40:73-95. [PMID: 36373595 DOI: 10.1093/imammb/dqac015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/30/2022] [Accepted: 10/03/2022] [Indexed: 11/15/2022]
Abstract
In this article, we investigate the importance of demography and contact patterns in determining the spread of COVID-19 and to the effectiveness of social distancing policies. We investigate these questions proposing an augmented epidemiological model with an age-structured model, with the population divided into susceptible (S), exposed (E), asymptomatic infectious (A), hospitalized (H), symptomatic infectious (I) and recovered individuals (R), to simulate COVID-19 dissemination. The simulations were carried out using six combinations of four types of isolation policies (work restrictions, isolation of the elderly, community distancing and school closures) and four representative fictitious countries generated over alternative demographic transition stage patterns (aged developed, developed, developing and least developed countries). We concluded that the basic reproduction number depends on the age profile and the contact patterns. The aged developed country had the lowest basic reproduction number ($R0=1.74$) due to the low contact rate among individuals, followed by the least developed country ($R0=2.00$), the developing country ($R0=2.43$) and the developed country ($R0=2.64$). Because of these differences in the basic reproduction numbers, the same intervention policies had higher efficiencies in the aged and least developed countries. Of all intervention policies, the reduction in work contacts and community distancing were the ones that produced the highest decrease in the $R0$ value, prevalence, maximum hospitalization demand and fatality rate. The isolation of the elderly was more effective in the developed and aged developed countries. The school closure was the less effective intervention policy, though its effects were not negligible in the least developed and developing countries.
Collapse
Affiliation(s)
- Marco A Ridenti
- Physics Department, Aeronautics Institute of Technology, Marechal Eduardo Gomes, 50 Vila das Acácias, 12228-900, SP, Brazil
| | - Lara K Teles
- Physics Department, Aeronautics Institute of Technology, Marechal Eduardo Gomes, 50 Vila das Acácias, 12228-900, SP, Brazil
| | - Alexandre Maranhão
- Physics Department, Aeronautics Institute of Technology, Marechal Eduardo Gomes, 50 Vila das Acácias, 12228-900, SP, Brazil
| | - Vladimir K Teles
- Sao Paulo School of Economics, FGV-SP, Rua Itapeva, 474 Bela Vista, 01332-000, SP, Brazil
| |
Collapse
|
242
|
Kuhlmeier E, Chan T, Meli ML, Willi B, Wolfensberger A, Reitt K, Hüttl J, Jones S, Tyson G, Hosie MJ, Zablotski Y, Hofmann-Lehmann R. A Risk Factor Analysis of SARS-CoV-2 Infection in Animals in COVID-19-Affected Households. Viruses 2023; 15:731. [PMID: 36992440 PMCID: PMC10051903 DOI: 10.3390/v15030731] [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: 02/08/2023] [Revised: 02/28/2023] [Accepted: 03/07/2023] [Indexed: 03/18/2023] Open
Abstract
A higher prevalence of SARS-CoV-2 infections in animals that have close contact with SARS-CoV-2-positive humans ("COVID-19 households") has been demonstrated in several countries. This prospective study aimed to determine the SARS-CoV-2 prevalence in animals from Swiss COVID-19 households and to assess the potential risk factors for infection. The study included 226 companion animals (172 cats, 76.1%; 49 dogs, 21.7%; and 5 other animals, 2.2%) from 122 COVID-19 households with 336 human household members (including 230 SARS-CoV-2-positive people). The animals were tested for viral RNA using an RT-qPCR and/or serologically for antibodies and neutralizing activity. Additionally, surface samples from animal fur and beds underwent an RT-qPCR. A questionnaire about hygiene, animal hygiene, and contact intensity was completed by the household members. A total of 49 of the 226 animals (21.7%) from 31 of the 122 households (25.4%) tested positive/questionably positive for SARS-CoV-2, including 37 of the 172 cats (21.5%) and 12 of the 49 dogs (24.5%). The surface samples tested positive significantly more often in households with SARS-CoV-2-positive animals than in households with SARS-CoV-2-negative animals (p = 0.011). Significantly more animals tested positive in the multivariable analysis for households with minors. For cats, a shorter length of outdoor access and a higher frequency of removing droppings from litterboxes were factors that were significantly associated with higher infection rates. The study emphasizes that the behavior of owners and the living conditions of animals can influence the likelihood of a SARS-CoV-2 infection in companion animals. Therefore, it is crucial to monitor the infection transmission and dynamics in animals, as well as to identify the possible risk factors for animals in infected households.
Collapse
Affiliation(s)
- Evelyn Kuhlmeier
- Clinical Laboratory, Vetsuisse Faculty, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland; (T.C.); (M.L.M.); (R.H.-L.)
| | - Tatjana Chan
- Clinical Laboratory, Vetsuisse Faculty, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland; (T.C.); (M.L.M.); (R.H.-L.)
| | - Marina L. Meli
- Clinical Laboratory, Vetsuisse Faculty, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland; (T.C.); (M.L.M.); (R.H.-L.)
| | - Barbara Willi
- Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland;
| | - Aline Wolfensberger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Rämistrasse 100, 8091 Zurich, Switzerland;
| | - Katja Reitt
- Center for Laboratory Medicine, Veterinary Diagnostic Services, Frohbergstrasse 3, 9001 St. Gallen, Switzerland; (K.R.); (J.H.)
| | - Julia Hüttl
- Center for Laboratory Medicine, Veterinary Diagnostic Services, Frohbergstrasse 3, 9001 St. Gallen, Switzerland; (K.R.); (J.H.)
| | - Sarah Jones
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow G61 1QH, UK; (S.J.); (G.T.)
- MRC-University of Glasgow Centre for Virus, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow G61 1QH, UK
| | - Grace Tyson
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow G61 1QH, UK; (S.J.); (G.T.)
| | - Margaret J. Hosie
- MRC-University of Glasgow Centre for Virus, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow G61 1QH, UK
| | - Yury Zablotski
- Clinic of Small Animal Medicine, Centre for Clinical Veterinary Medicine, LMU Munich, 80539 Munich, Germany;
| | - Regina Hofmann-Lehmann
- Clinical Laboratory, Vetsuisse Faculty, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland; (T.C.); (M.L.M.); (R.H.-L.)
| |
Collapse
|
243
|
Xu J, Carruthers J, Finnie T, Hall I. Simplified within-host and Dose-response Models of SARS-CoV-2. J Theor Biol 2023; 565:111447. [PMID: 36898624 PMCID: PMC9993737 DOI: 10.1016/j.jtbi.2023.111447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/20/2023] [Accepted: 02/24/2023] [Indexed: 03/12/2023]
Abstract
Understanding the mechanistic dynamics of transmission is key to designing more targeted and effective interventions to limit the spread of infectious diseases. A well-described within-host model allows explicit simulation of how infectiousness changes over time at an individual level. This can then be coupled with dose-response models to investigate the impact of timing on transmission. We collected and compared a range of within-host models used in previous studies and identified a minimally-complex model that provides suitable within-host dynamics while keeping a reduced number of parameters to allow inference and limit unidentifiability issues. Furthermore, non-dimensionalised models were developed to further overcome the uncertainty in estimates of the size of the susceptible cell population, a common problem in many of these approaches. We will discuss these models, and their fit to data from the human challenge study (see Killingley et al. (2022)) for SARS-CoV-2 and the model selection results, which has been performed using ABC-SMC. The parameter posteriors have then used to simulate viral-load based infectiousness profiles via a range of dose-response models, which illustrate the large variability of the periods of infection window observed for COVID-19.
Collapse
Affiliation(s)
- Jingsi Xu
- Department of Mathematics, University of Manchester, United Kingdom.
| | | | - Thomas Finnie
- PHAGE Joint Modelling Team, UK Health Security Agency, United Kingdom
| | - Ian Hall
- Department of Mathematics, University of Manchester, United Kingdom; PHAGE Joint Modelling Team, UK Health Security Agency, United Kingdom.
| |
Collapse
|
244
|
Khanizadeh S, Malekshahi A, Hanifehpour H, Birjandi M, Fallahi S. Rapid, sensitive, and specific detection of SARS-CoV-2 in nasopharyngeal swab samples of suspected patients using a novel one-step loop-mediated isothermal amplification (one-step LAMP) technique. BMC Microbiol 2023; 23:63. [PMID: 36882699 PMCID: PMC9989590 DOI: 10.1186/s12866-023-02806-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 02/23/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND In the absence of effective antiviral drugs or vaccines, early and accurate detection of SARS-CoV-2 infection is essential to the COVID-19 pandemic. This study developed and evaluated a novel rapid One-Step LAMP assay to directly detect the SARS-CoV-2 RNA from nasopharyngeal (NP) swab samples of patients with suspected SARS-CoV-2 infection living in deprived areas in comparison to One-Step Real-time PCR. METHODS Two hundred fifty-four NP swab samples from patients suspected of COVID-19 infection living in deprived western areas of Iran were tested by TaqMan One-Step RT-qPCR and fast One-Step LAMP assays. Tenfold serial dilutions of SARS-CoV-2 RNA standard strain where the viral copy number in each dilution was previously determined using the qPCR and various templates were used to investigate the analytical sensitivity and specificity of the One-Step LAMP assay in triplicate. Also, the efficacy and reliability of the method compared to TaqMan One-Step RT-qPCR were evaluated using SARS-CoV-2 positive and negative clinical samples. RESULTS The results of the One-Step RT-qPCR and One-Step LAMP tests were positive in 131 (51.6%) and 127 (50%) participants, respectively. Based on Cohen's kappa coefficient (κ), the agreement between the two tests was 97%, which was statistically significant (P < 0.001). The detection limit for the One-Step LAMP assay was 1 × 101 copies of standard SARS-CoV-2 RNA per reaction in less than an hour in triplicates. Negative results in all samples with non-SARS-CoV-2 templates represent 100% specificity. CONCLUSIONS The results showed that the One-Step LAMP assay is an efficient consistent technique for detecting SARS-CoV-2 among suspected individuals due to its simplicity, speed, low cost, sensitivity, and specificity. Therefore, it has great potential as a useful diagnostic tool for disease epidemic control, timely treatment, and public health protection, especially in poor and underdeveloped countries.
Collapse
Affiliation(s)
- Sayyad Khanizadeh
- Hepatitis Research Center, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran.,Department of Virology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Asra Malekshahi
- Department of Virology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Hooman Hanifehpour
- Department of Microbiology, Cancer Biomedical Research Center (CBC), Tehran, Iran
| | - Mehdi Birjandi
- Department of Biostatistics and Epidemiology, School of Health and Nutrition, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Shirzad Fallahi
- Hepatitis Research Center, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran. .,Department of Parasitology and Mycology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran.
| |
Collapse
|
245
|
Tsang TK, Huang X, Wang C, Chen S, Yang B, Cauchemez S, Cowling BJ. The effect of variation of individual infectiousness on SARS-CoV-2 transmission in households. eLife 2023; 12:82611. [PMID: 36880191 PMCID: PMC9991055 DOI: 10.7554/elife.82611] [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: 08/11/2022] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Quantifying variation of individual infectiousness is critical to inform disease control. Previous studies reported substantial heterogeneity in transmission of many infectious diseases including SARS-CoV-2. However, those results are difficult to interpret since the number of contacts is rarely considered in such approaches. Here, we analyze data from 17 SARS-CoV-2 household transmission studies conducted in periods dominated by ancestral strains, in which the number of contacts was known. By fitting individual-based household transmission models to these data, accounting for number of contacts and baseline transmission probabilities, the pooled estimate suggests that the 20% most infectious cases have 3.1-fold (95% confidence interval: 2.2- to 4.2-fold) higher infectiousness than average cases, which is consistent with the observed heterogeneity in viral shedding. Household data can inform the estimation of transmission heterogeneity, which is important for epidemic management.
Collapse
Affiliation(s)
- Tim K Tsang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong KongHong KongChina
- Laboratory of Data Discovery for HealthHong KongChina
| | - Xiaotong Huang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong KongHong KongChina
| | - Can Wang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong KongHong KongChina
| | - Sijie Chen
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong KongHong KongChina
| | - Bingyi Yang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong KongHong KongChina
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut PasteurParisFrance
| | | |
Collapse
|
246
|
Karas M, Bernal I, Diaz O, Alshammari O, Baggett D, Bronk T, Chawdhury S, Eylon A, Garcia E, Haughton K, Kothe B, Joseph AM, Jacobs RJ. A Scoping Review of the Impact of COVID-19 on Kidney Transplant Patients in the United States. Cureus 2023; 15:e35725. [PMID: 37025740 PMCID: PMC10072165 DOI: 10.7759/cureus.35725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/03/2023] [Indexed: 03/06/2023] Open
Abstract
SARS-CoV-2, responsible for the COVID-19 pandemic, is a highly infectious virus that quickly became and continues to be a public health emergency, given the severe international implications. Immunocompromised patients, such as those undergoing kidney transplantation, are at an increased risk for severe illness from COVID-19 and require hospitalization for more aggressive treatment to ensure survival. COVID-19 has been infecting kidney transplant recipients (KTRs), affecting their treatment protocols, and threatening their survival. The objective of this scoping review was to summarize the published literature regarding the impact of COVID-19 on KTRs in the United States in terms of prevention, various treatment protocols, COVID-19 vaccination, and risk factors. The databases such as PubMed, MEDLINE/Ebsco, and Embase were used to search for peer-reviewed literature. The search was restricted to articles that were published on KTRs in the United States from January 1, 2019, to March 2022. The initial search yielded 1,023 articles after removing duplicates, leading to a final selection of 16 articles after screening with inclusion and exclusion criteria. Four domains emerged from the review: (1) impacts of COVID-19 on performing kidney transplants, (2) impacts of COVID-19 vaccinations on KTRs, (3) outcomes of treatment regiments for KTRs with COVID-19, and (4) risk factors associated with an increased mortality rate of COVID-19 in KTRs. Waitlisted patients for kidney transplants had a higher risk of mortality compared to nontransplant patients. COVID-19 vaccinations in KTRs are found to be safe, and the immune response can be improved by placing patients on a low dose of mycophenolate before vaccination. Withdrawal of immunosuppressants showed a mortality rate of 20% without increasing the rate of acute kidney injury (AKI). There is evidence to support that kidney transplantation with the accompanying immunosuppressant regimen can provide KTRs with better COVID-19 infection outcomes compared to waitlisted patients. Hospitalization, graft dysfunction, AKI, and respiratory failure were the most common risk factors that increased the risk of mortality in COVID-19-positive KTRs. Withdrawing KTRs from immunosuppressive drugs increased the mortality rate. Further studies are needed to investigate the effects of specific drugs and dosages on the severity and mortality rate of COVID-19 in KTRs.
Collapse
|
247
|
Akhtar E, Mily A, Sarker P, Chanda BC, Haque F, Kuddusi RU, Haq MA, Lourda M, Brighenti S, Raqib R. Immune cell landscape in symptomatic and asymptomatic SARS-CoV-2 infected adults and children in urban Dhaka, Bangladesh. Immunobiology 2023; 228:152350. [PMID: 36822063 PMCID: PMC9938758 DOI: 10.1016/j.imbio.2023.152350] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 09/08/2022] [Accepted: 02/11/2023] [Indexed: 02/21/2023]
Abstract
OBJECTIVES The study of cellular immunity to SARS-CoV-2 is crucial for evaluating the course of the COVID-19 disease and for improving vaccine development. We aimed to assess the phenotypic landscape of circulating lymphocytes and mononuclear cells in adults and children who were seropositive to SARS-CoV-2 in the past 6 months. METHODS Blood samples (n = 350) were collected in a cross-sectional study in Dhaka, Bangladesh (Oct 2020-Feb 2021). Plasma antibody responses to SARS-CoV-2 were determined by an electrochemiluminescence immunoassay while lymphocyte and monocyte responses were assessed using flow cytometry including dimensionality reduction and clustering algorithms. RESULTS SARS-CoV-2 seropositivity was observed in 52% of adults (18-65 years) and 56% of children (10-17 years). Seropositivity was associated with reduced CD3+T cells in both adults (beta(β) = -2.86; 95% Confidence Interval (CI) = -5.98, 0.27) and children (β = -8.78; 95% CI = -13.8, -3.78). The frequencies of T helper effector (CD4+TEFF) and effector memory cells (CD4+TEM) were increased in seropositive compared to seronegative children. In adults, seropositivity was associated with an elevated proportion of cytotoxic T central memory cells (CD8+TCM). Overall, diverse manifestations of immune cell dysregulations were more prominent in seropositive children compared to adults, who previously had COVID-like symptoms. These changes involved reduced frequencies of CD4+TEFF cells and CD163+CD64+ classical monocytes, but increased levels of intermediate or non-classical monocytes, as well as CD8+TEM cells in symptomatic children. CONCLUSION Seropositive individuals in convalescence showed increased central and effector memory T cell phenotypes and pro-resolving/healing monocyte phenotypes compared to seronegative subjects. However, seropositive children with a previous history of COVID-like symptoms, displayed an ongoing innate inflammatory trait.
Collapse
Affiliation(s)
- Evana Akhtar
- Infectious Diseases Division, icddrb, Dhaka 1212, Bangladesh
| | - Akhirunnesa Mily
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, 141 52, Huddinge, Sweden
| | - Protim Sarker
- Infectious Diseases Division, icddrb, Dhaka 1212, Bangladesh
| | | | - Farjana Haque
- Infectious Diseases Division, icddrb, Dhaka 1212, Bangladesh
| | | | - Md Ahsanul Haq
- Infectious Diseases Division, icddrb, Dhaka 1212, Bangladesh
| | - Magda Lourda
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, 141 52, Huddinge, Sweden; Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Susanna Brighenti
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, 141 52, Huddinge, Sweden
| | - Rubhana Raqib
- Infectious Diseases Division, icddrb, Dhaka 1212, Bangladesh.
| |
Collapse
|
248
|
Pasco R, Johnson K, Fox SJ, Pierce KA, Johnson-León M, Lachmann M, Morton DP, Meyers LA. COVID-19 Test Allocation Strategy to Mitigate SARS-CoV-2 Infections across School Districts. Emerg Infect Dis 2023; 29:501-510. [PMID: 36787729 PMCID: PMC9973671 DOI: 10.3201/eid2903.220761] [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] [Indexed: 02/16/2023] Open
Abstract
In response to COVID-19, schools across the United States closed in early 2020; many did not fully reopen until late 2021. Although regular testing of asymptomatic students, teachers, and staff can reduce transmission risks, few school systems consistently used proactive testing to safeguard return to classrooms. Socioeconomically diverse public school districts might vary testing levels across campuses to ensure fair, effective use of limited resources. We describe a test allocation approach to reduce overall infections and disparities across school districts. Using a model of SARS-CoV-2 transmission in schools fit to data from a large metropolitan school district in Texas, we reduced incidence between the highest and lowest risk schools from a 5.6-fold difference under proportional test allocation to 1.8-fold difference under our optimized test allocation. This approach provides a roadmap to help school districts deploy proactive testing and mitigate risks of future SARS-CoV-2 variants and other pathogen threats.
Collapse
|
249
|
Gupta P, Maharaj T, Weiss M, Rahaman N, Alsdurf H, Minoyan N, Harnois-Leblanc S, Merckx J, Williams A, Schmidt V, St-Charles PL, Patel A, Zhang Y, Buckeridge DL, Pal C, Schölkopf B, Bengio Y. Proactive Contact Tracing. PLOS DIGITAL HEALTH 2023; 2:e0000199. [PMID: 36913342 PMCID: PMC10010527 DOI: 10.1371/journal.pdig.0000199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 01/25/2023] [Indexed: 03/14/2023]
Abstract
The COVID-19 pandemic has spurred an unprecedented demand for interventions that can reduce disease spread without excessively restricting daily activity, given negative impacts on mental health and economic outcomes. Digital contact tracing (DCT) apps have emerged as a component of the epidemic management toolkit. Existing DCT apps typically recommend quarantine to all digitally-recorded contacts of test-confirmed cases. Over-reliance on testing may, however, impede the effectiveness of such apps, since by the time cases are confirmed through testing, onward transmissions are likely to have occurred. Furthermore, most cases are infectious over a short period; only a subset of their contacts are likely to become infected. These apps do not fully utilize data sources to base their predictions of transmission risk during an encounter, leading to recommendations of quarantine to many uninfected people and associated slowdowns in economic activity. This phenomenon, commonly termed as "pingdemic," may additionally contribute to reduced compliance to public health measures. In this work, we propose a novel DCT framework, Proactive Contact Tracing (PCT), which uses multiple sources of information (e.g. self-reported symptoms, received messages from contacts) to estimate app users' infectiousness histories and provide behavioral recommendations. PCT methods are by design proactive, predicting spread before it occurs. We present an interpretable instance of this framework, the Rule-based PCT algorithm, designed via a multi-disciplinary collaboration among epidemiologists, computer scientists, and behavior experts. Finally, we develop an agent-based model that allows us to compare different DCT methods and evaluate their performance in negotiating the trade-off between epidemic control and restricting population mobility. Performing extensive sensitivity analysis across user behavior, public health policy, and virological parameters, we compare Rule-based PCT to i) binary contact tracing (BCT), which exclusively relies on test results and recommends a fixed-duration quarantine, and ii) household quarantine (HQ). Our results suggest that both BCT and Rule-based PCT improve upon HQ, however, Rule-based PCT is more efficient at controlling spread of disease than BCT across a range of scenarios. In terms of cost-effectiveness, we show that Rule-based PCT pareto-dominates BCT, as demonstrated by a decrease in Disability Adjusted Life Years, as well as Temporary Productivity Loss. Overall, we find that Rule-based PCT outperforms existing approaches across a varying range of parameters. By leveraging anonymized infectiousness estimates received from digitally-recorded contacts, PCT is able to notify potentially infected users earlier than BCT methods and prevent onward transmissions. Our results suggest that PCT-based applications could be a useful tool in managing future epidemics.
Collapse
Affiliation(s)
- Prateek Gupta
- Montréal Institute of Learning Algorithms (Mila), Montréal, Québec, Canada
- The Alan Turing Institute, London, United Kingdom
- Department of Engineering Science, University of Oxford, Oxford, United Kingdom
- * E-mail:
| | - Tegan Maharaj
- Montréal Institute of Learning Algorithms (Mila), Montréal, Québec, Canada
- Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec, Canada
| | - Martin Weiss
- Montréal Institute of Learning Algorithms (Mila), Montréal, Québec, Canada
- Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec, Canada
| | - Nasim Rahaman
- Montréal Institute of Learning Algorithms (Mila), Montréal, Québec, Canada
- Max Planck Institute for Intelligent Systems, Tübingen, Germany
| | - Hannah Alsdurf
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Nanor Minoyan
- Department of Social and Preventive Medicine, School of Public Health, Université de Montréal, Canada
| | - Soren Harnois-Leblanc
- Department of Social and Preventive Medicine, School of Public Health, Université de Montréal, Canada
| | - Joanna Merckx
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Canada
| | - Andrew Williams
- Montréal Institute of Learning Algorithms (Mila), Montréal, Québec, Canada
- Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec, Canada
| | - Victor Schmidt
- Montréal Institute of Learning Algorithms (Mila), Montréal, Québec, Canada
- Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec, Canada
| | | | - Akshay Patel
- Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada
| | - Yang Zhang
- Montréal Institute of Learning Algorithms (Mila), Montréal, Québec, Canada
| | - David L. Buckeridge
- Montréal Institute of Learning Algorithms (Mila), Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Canada
| | - Christopher Pal
- Montréal Institute of Learning Algorithms (Mila), Montréal, Québec, Canada
- Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec, Canada
| | - Bernhard Schölkopf
- Max Planck Institute for Intelligent Systems, Tübingen, Germany
- Fellow of the Canadian Institute for Advanced Research (CIFAR), Canada
| | - Yoshua Bengio
- Montréal Institute of Learning Algorithms (Mila), Montréal, Québec, Canada
- Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec, Canada
- Fellow of the Canadian Institute for Advanced Research (CIFAR), Canada
| |
Collapse
|
250
|
Charlotte N. High Rate of SARS-CoV-2 Transmission Due to Choir Practice in France at the Beginning of the COVID-19 Pandemic. J Voice 2023. [PMID: 33386191 DOI: 10.1101/2020.07.19.20145326] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
OBJECTIVE To document the case of a high transmission rate of SARS-CoV-2 generating a cluster linked to an indoor choir rehearsal hold at the beginning of the COVID-19 pandemic in France. METHOD Case study. Data were obtained via a questionnaire. RESULTS Twenty-seven participants, including 25 singers, 1 conductor and 1 accompanist attended a choir practice on March 12, 2020. The practice was indoor and took place in a non ventilated space of 45 m2. No choir member reported having been symptomatic for COVID-19 between March 2 and March 12.The mean age of the participants was 66.9 (range 35-86) years. The secondary attack rate was 70%: 19/27 participants were diagnosed with COVID-19 from 1 to 12 days after the rehearsal with a median of 5.1 days. Thirty-six percent of the cases needed a hospitalization (7/19), and 21% (4/19) were admitted to an ICU. The index cases were asymptomatic and possibly multiple. CONCLUSION In the absence of valid barrier measures to prevent COVID-19 transmission, indoor choir practice should be suspended during the SARSCoV-2 surging phases. Transmission of the virus among gatherings from asymptomatic cases is a crucial issue and a main challenge to COVID-19 control.
Collapse
|