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Kulmala I, Taipale A, Sanmark E, Lastovets N, Sormunen P, Nuorti P, Saari S, Luoto A, Säämänen A. Estimated relative potential for airborne SARS-CoV-2 transmission in a day care centre. Heliyon 2024; 10:e30724. [PMID: 38756615 PMCID: PMC11096945 DOI: 10.1016/j.heliyon.2024.e30724] [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: 08/20/2023] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/18/2024] Open
Abstract
We estimated the hourly probability of airborne severe acute respiratory coronavirus 2 (SARS-CoV-2) transmission and further the estimated number of persons at transmission risk in a day care centre by calculating the inhaled dose for airborne pathogens based on their concentration, exposure time and activity. Information about the occupancy and activity of the rooms was collected from day care centre personnel and building characteristics were obtained from the design values. The generation rate of pathogens was calculated as a product of viral load of the respiratory fluids and the emission of the exhaled airborne particles, considering the prevalence of the disease and the activity of the individuals. A well-mixed model was used in the estimation of the concentration of pathogens in the air. The Wells-Riley model was used for infection probability. The approach presented in this study was utilised in the identification of hot spots and critical events in the day care centre. Large variation in the infection probabilities and estimated number of persons at transmission risk was observed when modelling a normal day at the centre. The estimated hourly infection probabilities between the worst hour in the worst room and the best hour in the best room varied in the ratio of 100:1. Similarly, the number of persons at transmission risk between the worst and best cases varied in the ratio 1000:1. Although there are uncertainties in the input values affecting the absolute risk estimates the model proved to be useful in ranking and identifying the hot spots and events in the building and implementing effective control measures.
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Affiliation(s)
- Ilpo Kulmala
- VTT Smart Energy and Built Environment, Visiokatu 4, PO Box 1300, FI-33101, Tampere, Finland
| | - Aimo Taipale
- VTT Smart Energy and Built Environment, Visiokatu 4, PO Box 1300, FI-33101, Tampere, Finland
| | - Enni Sanmark
- Helsinki University Hospital, Department of Otorhinolaryngology and Phoniatrics – Head and Neck Surgery, Helsinki, Finland
- University of Helsinki, Helsinki, Finland
| | - Natalia Lastovets
- Tampere University, Faculty of Built Environment, Civil Engineering Unit, Korkeakoulunkatu 5D, FI-33720, Tampere, Finland
| | - Piia Sormunen
- Tampere University, Faculty of Built Environment, Civil Engineering Unit, Korkeakoulunkatu 5D, FI-33720, Tampere, Finland
| | - Pekka Nuorti
- Tampere University, Faculty of Social Sciences, Health Sciences Unit, Arvo Ylpön Katu 34, 33520, Tampere, Finland
| | - Sampo Saari
- Tampere University of Applied Sciences, Kuntokatu 3, 33520, Tampere, Finland
| | - Anni Luoto
- Granlund Oy, Malminkaari 21, 00700, Helsinki, Finland
| | - Arto Säämänen
- VTT Smart Energy and Built Environment, Visiokatu 4, PO Box 1300, FI-33101, Tampere, Finland
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Kim JM, Kim D, Lee NJ, Woo SH, Lee J, Lee H, Park AK, Kim JA, Lee CY, Kim ,IH, Yoo CK, Kim EJ. Increased viral load in patients infected with severe acute respiratory syndrome coronavirus 2 Omicron variant in the Republic of Korea. Osong Public Health Res Perspect 2023; 14:272-278. [PMID: 37652682 PMCID: PMC10493702 DOI: 10.24171/j.phrp.2023.0024] [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: 01/25/2023] [Revised: 05/12/2023] [Accepted: 06/12/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) has been declared a global pandemic owing to the rapid spread of the causative agent, severe acute respiratory syndrome coronavirus 2. Its Delta and Omicron variants are more transmissible and pathogenic than other variants. Some debates have emerged on the mechanism of variants of concern. In the COVID-19 wave that began in December 2021, the Omicron variant, first reported in South Africa, became identifiable in most cases globally. The aim of this study was to provide data to inform effective responses to the transmission of the Omicron variant. METHODS The Delta variant and the spike protein D614G mutant were compared with the Omicron variant. Viral loads from 5 days after symptom onset were compared using epidemiological data collected at the time of diagnosis. RESULTS The Omicron variant exhibited a higher viral load than other variants, resulting in greater transmissibility within 5 days of symptom onset. CONCLUSION Future research should focus on vaccine efficacy against the Omicron variant and compare trends in disease severity associated with its high viral load.
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Affiliation(s)
- Jeong-Min Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Dongju Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Nam-Joo Lee
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Sang Hee Woo
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Jaehee Lee
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Hyeokjin Lee
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Ae Kyung Park
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Jeong-Ah Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Chae Young Lee
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - , Il-Hwan Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Cheon Kwon Yoo
- Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Eun-Jin Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
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Choi G, Lim AY, Choi S, Park K, Lee SY, Kim JH. Viral shedding patterns of symptomatic SARS-CoV-2 infections by periods of variant predominance and vaccination status in Gyeonggi Province, Korea. Epidemiol Health 2022; 45:e2023008. [PMID: 36596734 PMCID: PMC10581894 DOI: 10.4178/epih.e2023008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/21/2022] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVES We compared the viral cycle threshold (Ct) values of infected patients to better understand viral kinetics by vaccination status during different periods of variant predominance in Gyeonggi Province, Korea. METHODS We obtained case-specific data from the coronavirus disease 2019 (COVID-19) surveillance system, Gyeonggi in-depth epidemiological report system, and Health Insurance Review & Assessment Service from January 2020 to January 2022. We defined periods of variant predominance and explored Ct values by analyzing viral sequencing test results. Using a generalized additive model, we performed a nonlinear regression analysis to determine viral kinetics over time. RESULTS Cases in the Delta variant's period of predominance had higher viral shedding patterns than cases in other periods. The temporal change of viral shedding did not vary by vaccination status in the Omicron-predominant period, but viral shedding decreased in patients who had completed their third vaccination in the Delta-predominant period. During the Delta-predominant and Omicron-predominant periods, the time from symptom onset to peak viral shedding based on the E gene was approximately 2.4 days (95% confidence interval [CI], 2.2 to 2.5) and 2.1 days (95% CI, 2.0 to 2.1), respectively. CONCLUSIONS In one-time tests conducted to diagnose COVID-19 in a large population, although no adjustment for individual characteristics was conducted, it was confirmed that viral shedding differed by the predominant strain and vaccination history. These results show the value of utilizing hundreds of thousands of test data produced at COVID-19 screening test centers.
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Affiliation(s)
- Gawon Choi
- Gyeonggi Infectious Disease Control Center, Health Bureau, Gyeonggi Provincial Government, Suwon, Korea
| | - Ah-Young Lim
- Department of Social and Preventive Medicine, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Sojin Choi
- Gyeonggi Infectious Disease Control Center, Health Bureau, Gyeonggi Provincial Government, Suwon, Korea
| | - Kunhee Park
- Gyeonggi Infectious Disease Control Center, Health Bureau, Gyeonggi Provincial Government, Suwon, Korea
| | - Soon Young Lee
- Department of Preventive Medicine and Public Health, Ajou University School of Medicine, Suwon, Korea
| | - Jong-Hun Kim
- Gyeonggi Infectious Disease Control Center, Health Bureau, Gyeonggi Provincial Government, Suwon, Korea
- Department of Social and Preventive Medicine, Sungkyunkwan University School of Medicine, Suwon, Korea
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Meurisse M, Van Oyen H, Blot K, Catteau L, Serrien B, Klamer S, Cauët E, Robert A, Van Goethem N. Evaluating methodological approaches to assess the severity of infection with SARS-CoV-2 variants: scoping review and applications on Belgian COVID-19 data. BMC Infect Dis 2022; 22:839. [DOI: 10.1186/s12879-022-07777-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Differences in the genetic material of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants may result in altered virulence characteristics. Assessing the disease severity caused by newly emerging variants is essential to estimate their impact on public health. However, causally inferring the intrinsic severity of infection with variants using observational data is a challenging process on which guidance is still limited. We describe potential limitations and biases that researchers are confronted with and evaluate different methodological approaches to study the severity of infection with SARS-CoV-2 variants.
Methods
We reviewed the literature to identify limitations and potential biases in methods used to study the severity of infection with a particular variant. The impact of different methodological choices is illustrated by using real-world data of Belgian hospitalized COVID-19 patients.
Results
We observed different ways of defining coronavirus disease 2019 (COVID-19) disease severity (e.g., admission to the hospital or intensive care unit versus the occurrence of severe complications or death) and exposure to a variant (e.g., linkage of the sequencing or genotyping result with the patient data through a unique identifier versus categorization of patients based on time periods). Different potential selection biases (e.g., overcontrol bias, endogenous selection bias, sample truncation bias) and factors fluctuating over time (e.g., medical expertise and therapeutic strategies, vaccination coverage and natural immunity, pressure on the healthcare system, affected population groups) according to the successive waves of COVID-19, dominated by different variants, were identified. Using data of Belgian hospitalized COVID-19 patients, we were able to document (i) the robustness of the analyses when using different variant exposure ascertainment methods, (ii) indications of the presence of selection bias and (iii) how important confounding variables are fluctuating over time.
Conclusions
When estimating the unbiased marginal effect of SARS-CoV-2 variants on the severity of infection, different strategies can be used and different assumptions can be made, potentially leading to different conclusions. We propose four best practices to identify and reduce potential bias introduced by the study design, the data analysis approach, and the features of the underlying surveillance strategies and data infrastructure.
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Loh D, Reiter RJ. Melatonin: Regulation of Viral Phase Separation and Epitranscriptomics in Post-Acute Sequelae of COVID-19. Int J Mol Sci 2022; 23:8122. [PMID: 35897696 PMCID: PMC9368024 DOI: 10.3390/ijms23158122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/09/2022] [Accepted: 07/20/2022] [Indexed: 01/27/2023] Open
Abstract
The relentless, protracted evolution of the SARS-CoV-2 virus imposes tremendous pressure on herd immunity and demands versatile adaptations by the human host genome to counter transcriptomic and epitranscriptomic alterations associated with a wide range of short- and long-term manifestations during acute infection and post-acute recovery, respectively. To promote viral replication during active infection and viral persistence, the SARS-CoV-2 envelope protein regulates host cell microenvironment including pH and ion concentrations to maintain a high oxidative environment that supports template switching, causing extensive mitochondrial damage and activation of pro-inflammatory cytokine signaling cascades. Oxidative stress and mitochondrial distress induce dynamic changes to both the host and viral RNA m6A methylome, and can trigger the derepression of long interspersed nuclear element 1 (LINE1), resulting in global hypomethylation, epigenetic changes, and genomic instability. The timely application of melatonin during early infection enhances host innate antiviral immune responses by preventing the formation of "viral factories" by nucleocapsid liquid-liquid phase separation that effectively blockades viral genome transcription and packaging, the disassembly of stress granules, and the sequestration of DEAD-box RNA helicases, including DDX3X, vital to immune signaling. Melatonin prevents membrane depolarization and protects cristae morphology to suppress glycolysis via antioxidant-dependent and -independent mechanisms. By restraining the derepression of LINE1 via multifaceted strategies, and maintaining the balance in m6A RNA modifications, melatonin could be the quintessential ancient molecule that significantly influences the outcome of the constant struggle between virus and host to gain transcriptomic and epitranscriptomic dominance over the host genome during acute infection and PASC.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA;
| | - Russel J. Reiter
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA
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Jang YR, Kim JM, Rhee JE, Kim D, Lee NJ, Lee H, Kim JH, Kim EJ, Kim JY. Clinical Features and Duration of Viral Shedding Individuals with SARS-CoV-2 Omicron Variant Infection. Open Forum Infect Dis 2022; 9:ofac237. [PMID: 35855961 PMCID: PMC9129180 DOI: 10.1093/ofid/ofac237] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/07/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
We analyzed the duration of infectivity of the SARS-CoV-2 Omicron variant by the viral culture of respiratory samples collected daily from isolated patients with SARS-CoV-2 infection. The culture positivity rate of the Omicron variant was higher than that of the Delta variant within 8 days after symptom onset.
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Affiliation(s)
- Young R. Jang
- Division of Infectious Diseases, Department of Internal Medicine, Incheon Medical Center, Incheon, South Korea
| | - Jeong-Min Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Jee E. Rhee
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Dongju Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Nam-Joo Lee
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Hyeokjin Lee
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Jong-Hun Kim
- Department of Social and Preventive Medicine, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Eun-Jin Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Jin Y. Kim
- Division of Infectious Diseases, Department of Internal Medicine, Incheon Medical Center, Incheon, South Korea
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