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Poniedziałek B, Rzymski P, Zarębska-Michaluk D, Flisiak R. Viral respiratory infections and air pollution: A review focused on research in Poland. CHEMOSPHERE 2024; 359:142256. [PMID: 38723686 DOI: 10.1016/j.chemosphere.2024.142256] [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: 02/22/2024] [Revised: 05/02/2024] [Accepted: 05/04/2024] [Indexed: 05/14/2024]
Abstract
The COVID-19 pandemic has reinforced an interest in the relationship between air pollution and respiratory viral infections, indicating that their burden can be increased under poor air quality. This paper reviews the pathways through which air pollutants can enhance susceptibility to such infections and aggravate their clinical course and outcome. It also summarizes the research exploring the links between various viral infections and exposure to solid and gaseous pollution in Poland, a region characterized by poor air quality, especially during a heating season. The majority of studies focused on concentrations of particulate matter (PM; 86.7%); the other pollutants, i.e., BaP, benzene, CO, NOx, O3, and SO2, were studied less often and sometimes only in the context of a particular infection type. Most research concerned COVID-19, showing that elevated levels of PM and NO2 correlated with higher morbidity and mortality, while increased PM2.5 and benzo[a]pyrene levels were related to worse clinical course and outcome in hospitalized, regardless of age and dominant SARS-CoV-2 variant. PM10 and PM2.5 levels were also associated with the incidence of influenza-like illness and, along with NO2 concentrations, with a higher rate of children's hospitalizations due to lower respiratory tract RSV infections. Higher levels of air pollutants also increased hospitalization due to bronchitis (PM, NOx, and O3) and emergency department admission due to viral croup (PM10, PM2.5, NOx, CO, and benzene). Although the conducted studies imply only correlations and have other limitations, as discussed in the present paper, it appears that improving air quality through reducing combustion processes in energy production in Poland should be perceived as a part of multilayered protection measures against respiratory viral infections, decreasing the healthcare costs of COVID-19, lower tract RSV infections, influenza, and other respiratory viral diseases prevalent between autumn and early spring, in addition to other health and climate benefits.
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Affiliation(s)
- Barbara Poniedziałek
- Department of Environmental Medicine, Poznan University of Medical Sciences, Poznań, Poland.
| | - Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, Poznań, Poland.
| | | | - Robert Flisiak
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, Białystok, Poland.
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2
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Schmidt PW. Inference under superspreading: Determinants of SARS-CoV-2 transmission in Germany. Stat Med 2024; 43:1933-1954. [PMID: 38422989 DOI: 10.1002/sim.10046] [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: 08/03/2022] [Revised: 01/11/2024] [Accepted: 02/10/2024] [Indexed: 03/02/2024]
Abstract
Superspreading, under-reporting, reporting delay, and confounding complicate statistical inference on determinants of disease transmission. A model that accounts for these factors within a Bayesian framework is estimated using German Covid-19 surveillance data. Compartments based on date of symptom onset, location, and age group allow to identify age-specific changes in transmission, adjusting for weather, reported prevalence, and testing and tracing. Several factors were associated with a reduction in transmission: public awareness rising, information on local prevalence, testing and tracing, high temperature, stay-at-home orders, and restaurant closures. However, substantial uncertainty remains for other interventions including school closures and mandatory face coverings. The challenge of disentangling the effects of different determinants is discussed and examined through a simulation study. On a broader perspective, the study illustrates the potential of surveillance data with demographic information and date of symptom onset to improve inference in the presence of under-reporting and reporting delay.
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Wells CR, Pandey A, Moghadas SM, Fitzpatrick MC, Singer BH, Galvani AP. Evaluation of Strategies for Transitioning to Annual SARS-CoV-2 Vaccination Campaigns in the United States. Ann Intern Med 2024; 177:609-617. [PMID: 38527289 DOI: 10.7326/m23-2451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND The U.S. Food and Drug Administration has proposed administering annual SARS-CoV-2 vaccines. OBJECTIVE To evaluate the effectiveness of an annual SARS-CoV-2 vaccination campaign, quantify the health and economic benefits of a second dose provided to children younger than 2 years and adults aged 50 years or older, and optimize the timing of a second dose. DESIGN An age-structured dynamic transmission model. SETTING United States. PARTICIPANTS A synthetic population reflecting demographics and contact patterns in the United States. INTERVENTION Vaccination against SARS-CoV-2 with age-specific uptake similar to that of influenza vaccination. MEASUREMENTS Incidence, hospitalizations, deaths, and direct health care cost. RESULTS The optimal timing between the first and second dose delivered to children younger than 2 years and adults aged 50 years or older in an annual vaccination campaign was estimated to be 5 months. In direct comparison with a single-dose campaign, a second booster dose results in 123 869 fewer hospitalizations (95% uncertainty interval [UI], 121 994 to 125 742 fewer hospitalizations) and 5524 fewer deaths (95% UI, 5434 to 5613 fewer deaths), averting $3.63 billion (95% UI, $3.57 billion to $3.69 billion) in costs over a single year. LIMITATIONS Population immunity is subject to degrees of immune evasion for emerging SARS-CoV-2 variants. The model was implemented in the absence of nonpharmaceutical interventions and preexisting vaccine-acquired immunity. CONCLUSION The direct health care costs of SARS-CoV-2, particularly among adults aged 50 years or older, would be substantially reduced by administering a second dose 5 months after the initial dose. PRIMARY FUNDING SOURCE Natural Sciences and Engineering Research Council of Canada, Notsew Orm Sands Foundation, National Institutes of Health, Centers for Disease Control and Prevention, and National Science Foundation.
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Affiliation(s)
- Chad R Wells
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, New Haven, Connecticut (C.R.W., A.P., A.P.G.)
| | - Abhishek Pandey
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, New Haven, Connecticut (C.R.W., A.P., A.P.G.)
| | - Seyed M Moghadas
- Agent-Based Modelling Laboratory, York University, Toronto, Ontario, Canada (S.M.M.)
| | - Meagan C Fitzpatrick
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland (M.C.F.)
| | - Burton H Singer
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida (B.H.S.)
| | - Alison P Galvani
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, New Haven, Connecticut (C.R.W., A.P., A.P.G.)
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4
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Dewald F, Steger G, Fish I, Torre-Lage I, Hellriegel C, Milz E, Kolb-Bastigkeit A, Heger E, Fries M, Buess M, Marizy N, Michaelis B, Suárez I, Rubio Quintanares GH, Pirkl M, Aigner A, Oberste M, Hellmich M, Wong A, Orduz JC, Fätkenheuer G, Dötsch J, Kossow A, Moench EM, Quade G, Neumann U, Kaiser R, Schranz M, Klein F. SARS-CoV-2 Test-to-Stay in Daycare. Pediatrics 2024; 153:e2023064668. [PMID: 38596855 DOI: 10.1542/peds.2023-064668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/24/2024] [Indexed: 04/11/2024] Open
Abstract
BACKGROUND AND OBJECTIVES Test-to-stay concepts apply serial testing of children in daycare after exposure to SARS-CoV-2 without use of quarantine. This study aims to assess the safety of a test-to-stay screening in daycare facilities. METHODS 714 daycare facilities and approximately 50 000 children ≤6 years in Cologne, Germany participated in a SARS-CoV-2 Pool-polymerase chain reaction (PCR) screening from March 2021 to April 2022. The screening initially comprised post-exposure quarantine and was adapted to a test-to-stay approach during its course. To assess safety of the test-to-stay approach, we explored potential changes in frequencies of infections among children after the adaptation to the test-to-stay approach by applying regression discontinuity in time (RDiT) analyses. To this end, PCR-test data were linked with routinely collected data on reported infections in children and analyzed using ordinary least squares regressions. RESULTS 219 885 Pool-PCRs and 352 305 Single-PCRs were performed. 6440 (2.93%) Pool-PCRs tested positive, and 17 208 infections in children were reported. We estimated that during a period of 30 weeks, the test-to-stay concept avoided between 7 and 20 days of quarantine per eligible daycare child. RDiT revealed a 26% reduction (Exp. Coef: 0.74, confidence interval 0.52-1.06) in infection frequency among children and indicated no significant increase attributable to the test-to-stay approach. This result was not sensitive to adjustments for 7-day incidence, season, SARS-CoV-2 variant, and socioeconomic status. CONCLUSIONS Our analyses provide evidence that suggest safety of the test-to-stay approach compared with quarantine measures. This approach offers a promising option to avoid use of quarantine after exposure to respiratory pathogens in daycare settings.
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Affiliation(s)
- Felix Dewald
- Institute of Virology, Faculty of Medicine and University Hospital Cologne
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Public Health, Berlin, Germany
- German Center for Infection Research (DZIF), Partner site Bonn-Cologne, Cologne, Germany
| | - Gertrud Steger
- Institute of Virology, Faculty of Medicine and University Hospital Cologne
| | - Irina Fish
- Institute of Virology, Faculty of Medicine and University Hospital Cologne
| | - Ivonne Torre-Lage
- Institute of Virology, Faculty of Medicine and University Hospital Cologne
| | | | - Esther Milz
- Institute of Virology, Faculty of Medicine and University Hospital Cologne
| | | | - Eva Heger
- Institute of Virology, Faculty of Medicine and University Hospital Cologne
| | - Mira Fries
- Health department of Cologne, Cologne, Germany
| | | | | | | | - Isabelle Suárez
- Department I of Internal Medicine, Division of Infectious Diseases, Faculty of Medicine, University Hospital Cologne
| | | | - Martin Pirkl
- Institute of Virology, Faculty of Medicine and University Hospital Cologne
| | - Annette Aigner
- Institute of Biometry and Clinical Epidemiology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Max Oberste
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University Hospital Cologne
| | - Martin Hellmich
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University Hospital Cologne
| | - Anabelle Wong
- Institute of Public Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Infectious Disease Epidemiology Group, Max Planck Institute for Infection Biology, Berlin, Germany
| | | | - Gerd Fätkenheuer
- Department I of Internal Medicine, Division of Infectious Diseases, Faculty of Medicine, University Hospital Cologne
| | - Jörg Dötsch
- Department of Pediatrics, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Annelene Kossow
- Health department of Cologne, Cologne, Germany
- Institute for Hygiene, University Hospital Münster, Münster, Germany
| | | | - Gustav Quade
- MVZ Labor Dr. Quade and Kollegen GmbH, Cologne, Germany
| | - Udo Neumann
- Youth Welfare Office of Cologne, Cologne, Germany
| | - Rolf Kaiser
- Institute of Virology, Faculty of Medicine and University Hospital Cologne
- German Center for Infection Research (DZIF), Partner site Bonn-Cologne, Cologne, Germany
| | - Madlen Schranz
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Public Health, Berlin, Germany
- Robert Koch Institute, Department for Infectious Disease Epidemiology, Berlin, Germany
| | - Florian Klein
- Institute of Virology, Faculty of Medicine and University Hospital Cologne
- Center for Molecular Medicine Cologne (CMMC), University of Cologne
- German Center for Infection Research (DZIF), Partner site Bonn-Cologne, Cologne, Germany
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de Rioja VL, Basile L, Perramon-Malavez A, Martínez-Solanas É, López D, Medina Maestro S, Coma E, Fina F, Prats C, Mendioroz Peña J, Alvarez-Lacalle E. Severity of Omicron Subvariants and Vaccine Impact in Catalonia, Spain. Vaccines (Basel) 2024; 12:466. [PMID: 38793717 PMCID: PMC11125683 DOI: 10.3390/vaccines12050466] [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: 03/19/2024] [Revised: 04/18/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
In the current COVID-19 landscape dominated by Omicron subvariants, understanding the timing and efficacy of vaccination against emergent lineages is crucial for planning future vaccination campaigns, yet detailed studies stratified by subvariant, vaccination timing, and age groups are scarce. This retrospective study analyzed COVID-19 cases from December 2021 to January 2023 in Catalonia, Spain, focusing on vulnerable populations affected by variants BA.1, BA.2, BA.5, and BQ.1 and including two national booster campaigns. Our database includes detailed information such as dates of diagnosis, hospitalization and death, last vaccination, and cause of death, among others. We evaluated the impact of vaccination on disease severity by age, variant, and vaccination status, finding that recent vaccination significantly mitigated severity across all Omicron subvariants, although efficacy waned six months post-vaccination, except for BQ.1, which showed more stable levels. Unvaccinated individuals had higher hospitalization and mortality rates. Our results highlight the importance of periodic vaccination to reduce severe outcomes, which are influenced by variant and vaccination timing. Although the seasonality of COVID-19 is uncertain, our analysis suggests the potential benefit of annual vaccination in populations >60 years old, probably in early fall, if COVID-19 eventually exhibits a major peak similar to other respiratory viruses.
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Affiliation(s)
- Víctor López de Rioja
- Department of Physics, Universitat Politècnica de Catalunya, Castelldefels, 08860 Barcelona, Spain; (A.P.-M.); (C.P.); (E.A.-L.)
| | - Luca Basile
- Public Health Agency of Catalonia, Department of Health, 08005 Barcelona, Spain; (L.B.); (S.M.M.); (J.M.P.)
| | - Aida Perramon-Malavez
- Department of Physics, Universitat Politècnica de Catalunya, Castelldefels, 08860 Barcelona, Spain; (A.P.-M.); (C.P.); (E.A.-L.)
| | | | - Daniel López
- Department of Physics, Universitat Politècnica de Catalunya, Castelldefels, 08860 Barcelona, Spain; (A.P.-M.); (C.P.); (E.A.-L.)
| | - Sergio Medina Maestro
- Public Health Agency of Catalonia, Department of Health, 08005 Barcelona, Spain; (L.B.); (S.M.M.); (J.M.P.)
| | - Ermengol Coma
- Primary Care Services Information System (SISAP), Institut Català de la Salut, 08007 Barcelona, Spain; (E.C.)
| | - Francesc Fina
- Primary Care Services Information System (SISAP), Institut Català de la Salut, 08007 Barcelona, Spain; (E.C.)
| | - Clara Prats
- Department of Physics, Universitat Politècnica de Catalunya, Castelldefels, 08860 Barcelona, Spain; (A.P.-M.); (C.P.); (E.A.-L.)
| | - Jacobo Mendioroz Peña
- Public Health Agency of Catalonia, Department of Health, 08005 Barcelona, Spain; (L.B.); (S.M.M.); (J.M.P.)
- University of Vic—Central University of Catalonia (UVic-UCC), 08500 Vic, Spain
| | - Enric Alvarez-Lacalle
- Department of Physics, Universitat Politècnica de Catalunya, Castelldefels, 08860 Barcelona, Spain; (A.P.-M.); (C.P.); (E.A.-L.)
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6
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Jung SM, Loo SL, Howerton E, Contamin L, Smith CP, Carcelén EC, Yan K, Bents SJ, Levander J, Espino J, Lemaitre JC, Sato K, McKee CD, Hill AL, Chinazzi M, Davis JT, Mu K, Vespignani A, Rosenstrom ET, Rodriguez-Cartes SA, Ivy JS, Mayorga ME, Swann JL, España G, Cavany S, Moore SM, Perkins TA, Chen S, Paul R, Janies D, Thill JC, Srivastava A, Aawar MA, Bi K, Bandekar SR, Bouchnita A, Fox SJ, Meyers LA, Porebski P, Venkatramanan S, Adiga A, Hurt B, Klahn B, Outten J, Chen J, Mortveit H, Wilson A, Hoops S, Bhattacharya P, Machi D, Vullikanti A, Lewis B, Marathe M, Hochheiser H, Runge MC, Shea K, Truelove S, Viboud C, Lessler J. Potential impact of annual vaccination with reformulated COVID-19 vaccines: Lessons from the US COVID-19 scenario modeling hub. PLoS Med 2024; 21:e1004387. [PMID: 38630802 PMCID: PMC11062554 DOI: 10.1371/journal.pmed.1004387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 05/01/2024] [Accepted: 03/27/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Coronavirus Disease 2019 (COVID-19) continues to cause significant hospitalizations and deaths in the United States. Its continued burden and the impact of annually reformulated vaccines remain unclear. Here, we present projections of COVID-19 hospitalizations and deaths in the United States for the next 2 years under 2 plausible assumptions about immune escape (20% per year and 50% per year) and 3 possible CDC recommendations for the use of annually reformulated vaccines (no recommendation, vaccination for those aged 65 years and over, vaccination for all eligible age groups based on FDA approval). METHODS AND FINDINGS The COVID-19 Scenario Modeling Hub solicited projections of COVID-19 hospitalization and deaths between April 15, 2023 and April 15, 2025 under 6 scenarios representing the intersection of considered levels of immune escape and vaccination. Annually reformulated vaccines are assumed to be 65% effective against symptomatic infection with strains circulating on June 15 of each year and to become available on September 1. Age- and state-specific coverage in recommended groups was assumed to match that seen for the first (fall 2021) COVID-19 booster. State and national projections from 8 modeling teams were ensembled to produce projections for each scenario and expected reductions in disease outcomes due to vaccination over the projection period. From April 15, 2023 to April 15, 2025, COVID-19 is projected to cause annual epidemics peaking November to January. In the most pessimistic scenario (high immune escape, no vaccination recommendation), we project 2.1 million (90% projection interval (PI) [1,438,000, 4,270,000]) hospitalizations and 209,000 (90% PI [139,000, 461,000]) deaths, exceeding pre-pandemic mortality of influenza and pneumonia. In high immune escape scenarios, vaccination of those aged 65+ results in 230,000 (95% confidence interval (CI) [104,000, 355,000]) fewer hospitalizations and 33,000 (95% CI [12,000, 54,000]) fewer deaths, while vaccination of all eligible individuals results in 431,000 (95% CI: 264,000-598,000) fewer hospitalizations and 49,000 (95% CI [29,000, 69,000]) fewer deaths. CONCLUSIONS COVID-19 is projected to be a significant public health threat over the coming 2 years. Broad vaccination has the potential to substantially reduce the burden of this disease, saving tens of thousands of lives each year.
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Affiliation(s)
- Sung-mok Jung
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sara L. Loo
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Emily Howerton
- The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Lucie Contamin
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Claire P. Smith
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Erica C. Carcelén
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Katie Yan
- The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Samantha J. Bents
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John Levander
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jessi Espino
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Joseph C. Lemaitre
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Koji Sato
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Clifton D. McKee
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Alison L. Hill
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Matteo Chinazzi
- Northeastern University, Boston, Massachusetts, United States of America
| | - Jessica T. Davis
- Northeastern University, Boston, Massachusetts, United States of America
| | - Kunpeng Mu
- Northeastern University, Boston, Massachusetts, United States of America
| | | | - Erik T. Rosenstrom
- North Carolina State University, Raleigh, North Carolina, United States of America
| | | | - Julie S. Ivy
- North Carolina State University, Raleigh, North Carolina, United States of America
| | - Maria E. Mayorga
- North Carolina State University, Raleigh, North Carolina, United States of America
| | - Julie L. Swann
- North Carolina State University, Raleigh, North Carolina, United States of America
| | - Guido España
- University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Sean Cavany
- University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Sean M. Moore
- University of Notre Dame, Notre Dame, Indiana, United States of America
| | - T. Alex Perkins
- University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Shi Chen
- University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Rajib Paul
- University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Daniel Janies
- University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Jean-Claude Thill
- University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Ajitesh Srivastava
- University of Southern California, Los Angeles, California, United States of America
| | - Majd Al Aawar
- University of Southern California, Los Angeles, California, United States of America
| | - Kaiming Bi
- University of Texas at Austin, Austin, Texas, United States of America
| | | | - Anass Bouchnita
- University of Texas at El Paso, El Paso, Texas, United States of America
| | - Spencer J. Fox
- University of Georgia, Athens, Georgia, United States of America
| | | | | | | | - Aniruddha Adiga
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Benjamin Hurt
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Brian Klahn
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Joseph Outten
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Jiangzhuo Chen
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Henning Mortveit
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Amanda Wilson
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Stefan Hoops
- University of Virginia, Charlottesville, Virginia, United States of America
| | | | - Dustin Machi
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Anil Vullikanti
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Bryan Lewis
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Madhav Marathe
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Harry Hochheiser
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michael C. Runge
- U.S. Geological Survey, Laurel, Maryland, United States of America
| | - Katriona Shea
- The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Shaun Truelove
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Cécile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Justin Lessler
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
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7
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Scarpa F, Branda F, Petrosillo N, Ciccozzi M. On the SARS-CoV-2 Variants. Infect Dis Rep 2024; 16:289-297. [PMID: 38667750 PMCID: PMC11050187 DOI: 10.3390/idr16020024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/09/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
The evolutionary dynamics of viruses, particularly exemplified by SARS-CoV-2 during the ongoing COVID-19 pandemic, underscore the intricate interplay between genetics, host adaptation, and viral spread. This paper delves into the genetic evolution of SARS-CoV-2, emphasizing the implications of viral variants on global health. Initially emerging from the Wuhan-Hu-1 lineage, SARS-CoV-2 rapidly diversified into numerous variants, each characterized by distinct mutations in the spike protein and other genomic regions. Notable variants such as B.1.1.7 (α), B.1.351 (β), P.1 (γ), B.1.617.2 (δ), and the Omicron variant have garnered significant attention due to their heightened transmissibility and immune evasion capabilities. In particular, the Omicron variant has presented a myriad of subvariants, raising concerns about its potential impact on public health. Despite the emergence of numerous variants, the vast majority have exhibited limited expansion capabilities and have not posed significant threats akin to early pandemic strains. Continued genomic surveillance is imperative to identify emerging variants of concern promptly. While genetic adaptation is intrinsic to viral evolution, effective public health responses must be grounded in empirical evidence to navigate the evolving landscape of the pandemic with resilience and precision.
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy
| | - Francesco Branda
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, 00128 Rome, Italy; (F.B.); (M.C.)
| | - Nicola Petrosillo
- Infection Prevention Control/Infectious Disease Service, Fondazione Policlinico Universitario Campus Bio-Medico, 00127 Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, 00128 Rome, Italy; (F.B.); (M.C.)
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8
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Rigatou A, Sultana MC. SARS-CoV-2 Pandemic: A Comparison Between the Epidemiological Situation in Greece and Romania. Cureus 2024; 16:e54460. [PMID: 38510869 PMCID: PMC10953612 DOI: 10.7759/cureus.54460] [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: 02/18/2024] [Indexed: 03/22/2024] Open
Abstract
Introduction Since the onset of the SARS-CoV-2 pandemic, there seems to be scarce data targeting the comparison of epidemiological data among different countries. In an attempt to reveal and characterize the epidemiological profile in the Balkan peninsula, a cross-sectional study has been conducted, aiming to retrospectively collect all the existing information regarding the SARS-CoV-2 pandemic over a period of three years, starting from March 2020 until March 2023. The comparative analysis of the epidemiological features and the main indicators between Romania and Greece can generate a good overview of the factors that can influence public health and create an adequate system of measures to limit the COVID-19 pandemic in the area. A retrospective comparative study aiming to detect and associate the main indicators determining the evolution of the SARS-CoV-2 pandemic data with the control measures adopted in Romania and Greece was performed. Methods Publicly available data were obtained from official sources such as the World Health Organization, the European Centre for Disease Control, the Romanian and Greek Ministries of Health, and the Romanian National Centre for Surveillance and Control of Communicable Diseases. The reported number of cases, in total and in conjunction with the age distribution, total number of deaths, and vaccination coverage, from the onset of the pandemic in March 2020 until March 2023, were collected. All officially reported cases of COVID-19 were included in this analysis. Reports with missing or incomplete values regarding the timeframe, age distribution, and vaccination status were excluded. Results During the timeframe of the study, from March 2020 until March 2023, Greece reported a higher number of confirmed SARS-CoV-2 cases as compared to Romania (5,910,103 cases and 3,352,356 cases, respectively). Still, in terms of the overall death toll, Romania recorded a higher mortality rate than Greece during the pandemic (67.773 deaths vs. 36.372 deaths). Concerning both cumulative incidence rates and the 14-day case notification rate per 100.000 inhabitants, it is evident that Romania exhibited greater numbers throughout the course of the pandemic. Although it is not clearly stated, the compulsory vaccination of elderly people that was set as a high priority in Greece may have contributed to the above results. In terms of the 14-day death notification rate per 100.000 inhabitants in 2020 and 2021, Romania showed a higher rate than Greece, while Greece reported a greater rate in 2022 and up until March 2023. Between 2020 and 2023, Greece presented both a higher number of vaccinated individuals and a higher vaccination coverage with two doses (7,034,695 individuals, 70% of the general population), as compared to Romania (6,467,804 individuals, 33.68% of the general population, p<0.0001). Conclusions Despite the similar restrictions and preventive actions adopted by Romania and Greece, some of the epidemiological data between the two countries tends to differ. It must not be ignored that every nation should be considered a unique entity with distinct features, including individuals, customs, and policies, rather than being categorized with other countries based on geographic proximity or regionalization.
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Affiliation(s)
- Anastasia Rigatou
- Virology, "St. S. Nicolau" Institute of Virology, Carol Davila University of Medicine and Pharmacy, Bucharest, ROU
| | - Madalina Camelia Sultana
- Virology, "St. S. Nicolau" Institute of Virology, Carol Davila University of Medicine and Pharmacy, Bucharest, ROU
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9
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Jung SM, Loo SL, Howerton E, Contamin L, Smith CP, Carcelén EC, Yan K, Bents SJ, Levander J, Espino J, Lemaitre JC, Sato K, McKee CD, Hill AL, Chinazzi M, Davis JT, Mu K, Vespignani A, Rosenstrom ET, Rodriguez-Cartes SA, Ivy JS, Mayorga ME, Swann JL, España G, Cavany S, Moore SM, Perkins A, Chen S, Paul R, Janies D, Thill JC, Srivastava A, Al Aawar M, Bi K, Bandekar SR, Bouchnita A, Fox SJ, Meyers LA, Porebski P, Venkatramanan S, Adiga A, Hurt B, Klahn B, Outten J, Chen J, Mortveit H, Wilson A, Hoops S, Bhattacharya P, Machi D, Vullikanti A, Lewis B, Marathe M, Hochheiser H, Runge MC, Shea K, Truelove S, Viboud C, Lessler J. Potential impact of annual vaccination with reformulated COVID-19 vaccines: lessons from the U.S. COVID-19 Scenario Modeling Hub. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.26.23297581. [PMID: 37961207 PMCID: PMC10635209 DOI: 10.1101/2023.10.26.23297581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Importance COVID-19 continues to cause significant hospitalizations and deaths in the United States. Its continued burden and the impact of annually reformulated vaccines remain unclear. Objective To project COVID-19 hospitalizations and deaths from April 2023-April 2025 under two plausible assumptions about immune escape (20% per year and 50% per year) and three possible CDC recommendations for the use of annually reformulated vaccines (no vaccine recommendation, vaccination for those aged 65+, vaccination for all eligible groups). Design The COVID-19 Scenario Modeling Hub solicited projections of COVID-19 hospitalization and deaths between April 15, 2023-April 15, 2025 under six scenarios representing the intersection of considered levels of immune escape and vaccination. State and national projections from eight modeling teams were ensembled to produce projections for each scenario. Setting The entire United States. Participants None. Exposure Annually reformulated vaccines assumed to be 65% effective against strains circulating on June 15 of each year and to become available on September 1. Age and state specific coverage in recommended groups was assumed to match that seen for the first (fall 2021) COVID-19 booster. Main outcomes and measures Ensemble estimates of weekly and cumulative COVID-19 hospitalizations and deaths. Expected relative and absolute reductions in hospitalizations and deaths due to vaccination over the projection period. Results From April 15, 2023-April 15, 2025, COVID-19 is projected to cause annual epidemics peaking November-January. In the most pessimistic scenario (high immune escape, no vaccination recommendation), we project 2.1 million (90% PI: 1,438,000-4,270,000) hospitalizations and 209,000 (90% PI: 139,000-461,000) deaths, exceeding pre-pandemic mortality of influenza and pneumonia. In high immune escape scenarios, vaccination of those aged 65+ results in 230,000 (95% CI: 104,000-355,000) fewer hospitalizations and 33,000 (95% CI: 12,000-54,000) fewer deaths, while vaccination of all eligible individuals results in 431,000 (95% CI: 264,000-598,000) fewer hospitalizations and 49,000 (95% CI: 29,000-69,000) fewer deaths. Conclusion and Relevance COVID-19 is projected to be a significant public health threat over the coming two years. Broad vaccination has the potential to substantially reduce the burden of this disease.
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Affiliation(s)
- Sung-mok Jung
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Sara L. Loo
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Emily Howerton
- The Pennsylvania State University, State College, Pennsylvania
| | | | - Claire P. Smith
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Erica C. Carcelén
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Katie Yan
- The Pennsylvania State University, State College, Pennsylvania
| | - Samantha J. Bents
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland
| | | | - Jessi Espino
- University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Joseph C. Lemaitre
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Koji Sato
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Clif D. McKee
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Alison L. Hill
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | | | - Kunpeng Mu
- University of Massachusetts Amherst, Amherst, Massachusetts
| | | | | | | | - Julie S. Ivy
- North Carolina State University, Raleigh, North Carolina
| | | | - Julie L. Swann
- North Carolina State University, Raleigh, North Carolina
| | | | - Sean Cavany
- University of Notre Dame, Notre Dame, Indiana
| | | | | | - Shi Chen
- University of North Carolina at Charlotte, Charlotte, North Carolina
| | - Rajib Paul
- University of North Carolina at Charlotte, Charlotte, North Carolina
| | - Daniel Janies
- University of North Carolina at Charlotte, Charlotte, North Carolina
| | - Jean-Claude Thill
- University of North Carolina at Charlotte, Charlotte, North Carolina
| | | | - Majd Al Aawar
- University of Southern California, Los Angeles, California
| | - Kaiming Bi
- University of Texas at Austin, Austin, Texas
| | | | | | | | | | | | | | | | | | - Brian Klahn
- University of Virginia, Charlottesville, Virginia
| | | | | | | | | | - Stefan Hoops
- University of Virginia, Charlottesville, Virginia
| | | | - Dustin Machi
- University of Virginia, Charlottesville, Virginia
| | | | - Bryan Lewis
- University of Virginia, Charlottesville, Virginia
| | | | | | | | - Katriona Shea
- The Pennsylvania State University, State College, Pennsylvania
| | - Shaun Truelove
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Cécile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland
| | - Justin Lessler
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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10
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Rzymski P, Pokorska-Śpiewak M, Jackowska T, Kuchar E, Nitsch-Osuch A, Pawłowska M, Babicki M, Jaroszewicz J, Szenborn L, Wysocki J, Flisiak R. Key Considerations during the Transition from the Acute Phase of the COVID-19 Pandemic: A Narrative Review. Vaccines (Basel) 2023; 11:1502. [PMID: 37766178 PMCID: PMC10537111 DOI: 10.3390/vaccines11091502] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
The COVID-19 pandemic has been met with an unprecedented response from the scientific community, leading to the development, investigation, and authorization of vaccines and antivirals, ultimately reducing the impact of SARS-CoV-2 on global public health. However, SARS-CoV-2 is far from being eradicated, continues to evolve, and causes substantial health and economic burdens. In this narrative review, we posit essential points on SARS-CoV-2 and its responsible management during the transition from the acute phase of the COVID-19 pandemic. As discussed, despite Omicron (sub)variant(s) causing clinically milder infections, SARS-CoV-2 is far from being a negligible pathogen. It requires continued genomic surveillance, particularly if one considers that its future (sub)lineages do not necessarily have to be milder. Antivirals and vaccines remain the essential elements in COVID-19 management. However, the former could benefit from further development and improvements in dosing, while the seasonal administration of the latter requires simplification to increase interest and tackle vaccine hesitancy. It is also essential to ensure the accessibility of COVID-19 pharmaceuticals and vaccines in low-income countries and improve the understanding of their use in the context of the long-term goals of SARS-CoV-2 management. Regardless of location, the primary role of COVID-19 awareness and education must be played by healthcare workers, who directly communicate with patients and serve as role models for healthy behaviors.
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Affiliation(s)
- Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, 60-806 Poznań, Poland
| | - Maria Pokorska-Śpiewak
- Department of Children’s Infectious Diseases, Medical University of Warsaw, 02-091 Warsaw, Poland;
| | - Teresa Jackowska
- Department of Pediatrics, Centre for Postgraduate Medical Education, 01-813 Warsaw, Poland;
| | - Ernest Kuchar
- Department of Pediatrics with Clinical Assessment Unit, Medical University of Warsaw, 02-091 Warsaw, Poland;
| | - Aneta Nitsch-Osuch
- Department of Social Medicine and Public Health, Medical University of Warsaw, 02-007 Warsaw, Poland;
| | - Małgorzata Pawłowska
- Department of Infectious Diseases and Hepatology, Faculty of Medicine, Collegium Medicum, Nicolaus Copernicus University, 85-067 Bydgoszcz, Poland;
| | - Mateusz Babicki
- Department of Family Medicine, Wroclaw Medical University, 51-141 Wroclaw, Poland;
| | - Jerzy Jaroszewicz
- Department of Infectious Diseases and Hepatology, Medical University of Silesia, 41-902 Bytom, Poland;
| | - Leszek Szenborn
- Department of Pediatric Infectious Diseases, Wrocław Medical University, 50-367 Wroclaw, Poland;
| | - Jacek Wysocki
- Department of Preventive Medicine, Poznan University of Medical Sciences, 61-701 Poznań, Poland;
| | - Robert Flisiak
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, 15-089 Bialystok, Poland;
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11
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Chrysostomou AC, Vrancken B, Haralambous C, Alexandrou M, Gregoriou I, Ioannides M, Ioannou C, Kalakouta O, Karagiannis C, Marcou M, Masia C, Mendris M, Papastergiou P, Patsalis PC, Pieridou D, Shammas C, Stylianou DC, Zinieri B, Lemey P, Network TCOMESSAR, Kostrikis LG. Unraveling the Dynamics of Omicron (BA.1, BA.2, and BA.5) Waves and Emergence of the Deltacton Variant: Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus (Oct 2021-Oct 2022). Viruses 2023; 15:1933. [PMID: 37766339 PMCID: PMC10535466 DOI: 10.3390/v15091933] [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: 08/31/2023] [Revised: 09/09/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Commencing in December 2019 with the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), three years of the coronavirus disease 2019 (COVID-19) pandemic have transpired. The virus has consistently demonstrated a tendency for evolutionary adaptation, resulting in mutations that impact both immune evasion and transmissibility. This ongoing process has led to successive waves of infections. This study offers a comprehensive assessment spanning genetic, phylogenetic, phylodynamic, and phylogeographic dimensions, focused on the trajectory of the SARS-CoV-2 epidemic in Cyprus. Based on a dataset comprising 4700 viral genomic sequences obtained from affected individuals between October 2021 and October 2022, our analysis is presented. Over this timeframe, a total of 167 distinct lineages and sublineages emerged, including variants such as Delta and Omicron (1, 2, and 5). Notably, during the fifth wave of infections, Omicron subvariants 1 and 2 gained prominence, followed by the ascendancy of Omicron 5 in the subsequent sixth wave. Additionally, during the fifth wave (December 2021-January 2022), a unique set of Delta sequences with genetic mutations associated with Omicron variant 1, dubbed "Deltacron", was identified. The emergence of this phenomenon initially evoked skepticism, characterized by concerns primarily centered around contamination or coinfection as plausible etiological contributors. These hypotheses were predominantly disseminated through unsubstantiated assertions within the realms of social and mass media, lacking concurrent scientific evidence to validate their claims. Nevertheless, the exhaustive molecular analyses presented in this study have demonstrated that such occurrences would likely lead to a frameshift mutation-a genetic aberration conspicuously absent in our provided sequences. This substantiates the accuracy of our initial assertion while refuting contamination or coinfection as potential etiologies. Comparable observations on a global scale dispelled doubt, eventually leading to the recognition of Delta-Omicron variants by the scientific community and their subsequent monitoring by the World Health Organization (WHO). As our investigation delved deeper into the intricate dynamics of the SARS-CoV-2 epidemic in Cyprus, a discernible pattern emerged, highlighting the major role of international connections in shaping the virus's local trajectory. Notably, the United States and the United Kingdom were the central conduits governing the entry and exit of the virus to and from Cyprus. Moreover, notable migratory routes included nations such as Greece, South Korea, France, Germany, Brazil, Spain, Australia, Denmark, Sweden, and Italy. These empirical findings underscore that the spread of SARS-CoV-2 within Cyprus was markedly influenced by the influx of new, highly transmissible variants, triggering successive waves of infection. This investigation elucidates the emergence of new waves of infection subsequent to the advent of highly contagious and transmissible viral variants, notably characterized by an abundance of mutations localized within the spike protein. Notably, this discovery decisively contradicts the hitherto hypothesis of seasonal fluctuations in the virus's epidemiological dynamics. This study emphasizes the importance of meticulously examining molecular genetics alongside virus migration patterns within a specific region. Past experiences also emphasize the substantial evolutionary potential of viruses such as SARS-CoV-2, underscoring the need for sustained vigilance. However, as the pandemic's dynamics continue to evolve, a balanced approach between caution and resilience becomes paramount. This ethos encourages an approach founded on informed prudence and self-preservation, guided by public health authorities, rather than enduring apprehension. Such an approach empowers societies to adapt and progress, fostering a poised confidence rooted in well-founded adaptation.
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Affiliation(s)
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Christos Haralambous
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, 1148 Nicosia, Cyprus
| | - Maria Alexandrou
- Microbiology Department, Larnaca General Hospital, 6301 Larnaca, Cyprus
| | - Ioanna Gregoriou
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, 1148 Nicosia, Cyprus
| | | | - Costakis Ioannou
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, 5310 Paralimni, Cyprus
| | - Olga Kalakouta
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, 1148 Nicosia, Cyprus
| | | | - Markella Marcou
- Department of Microbiology, Archbishop Makarios III Hospital, 2012 Nicosia, Cyprus
| | - Christina Masia
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, 5310 Paralimni, Cyprus
| | - Michail Mendris
- Microbiology Department, Limassol General Hospital, 4131 Limassol, Cyprus
| | | | - Philippos C. Patsalis
- Medicover Genetics, 2409 Nicosia, Cyprus
- Medical School, University of Nicosia, 2417 Nicosia, Cyprus
| | - Despo Pieridou
- Microbiology Department, Nicosia General Hospital, 2029 Nicosia, Cyprus
| | - Christos Shammas
- S.C.I.N.A. Bioanalysis Sciomedical Centre Ltd., 4040 Limassol, Cyprus
| | - Dora C. Stylianou
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
| | - Barbara Zinieri
- Microbiology Department, Paphos General Hospital, Achepans, 8026 Paphos, Cyprus
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | | | - Leondios G. Kostrikis
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
- Cyprus Academy of Sciences, Letters, and Arts, 60-68 Phaneromenis Street, 1011 Nicosia, Cyprus
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12
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Flahault A, Calmy A, Costagliola D, Drapkina O, Eckerle I, Larson HJ, Legido-Quigley H, Noakes C, Kazatchkine M, Kluge H. No time for complacency on COVID-19 in Europe. Lancet 2023; 401:1909-1912. [PMID: 37230103 PMCID: PMC10202416 DOI: 10.1016/s0140-6736(23)01012-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 05/11/2023] [Indexed: 05/27/2023]
Affiliation(s)
- Antoine Flahault
- Institute of Global Health, Faculty of Medicine, University of Geneva, CH-1202, Geneva, Switzerland.
| | - Alexandra Calmy
- HIV/AIDS Unit, Division of Infectious Diseases, University Hospitals of Geneva and University of Geneva, Geneva, Switzerland; University Hospitals of Geneva and University of Geneva, Geneva, Switzerland
| | - Dominique Costagliola
- French Academy of Sciences and Institut Pierre Louis d'Epidémiologie et de Santé Publique, Sorbonne Université, INSERM Paris, France
| | - Oxana Drapkina
- National Medical Research Center for Therapy and Preventive Medicine of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Isabella Eckerle
- Geneva Centre for Emerging Viral Diseases, University Hospitals of Geneva and University of Geneva, Geneva, Switzerland
| | - Heidi J Larson
- Department of Anthropology and The Vaccine Confidence Project, London School of Hygiene & Tropical Medicine, London, UK; University of Antwerp, Antwerp, and KULeuven, Leuven, Belgium
| | - Helena Legido-Quigley
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore; Imperial College London, London, UK; George Institute for Global Health UK, London, UK
| | | | - Michel Kazatchkine
- Global Health Center, Graduate Institute for International Affairs and Development, Geneva, Switzerland
| | - Hans Kluge
- WHO Regional Office for Europe, UN City, Copenhagen, Denmark
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13
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Walmsley T, Rose A, John R, Wei D, Hlávka JP, Machado J, Byrd K. Macroeconomic consequences of the COVID-19 pandemic. ECONOMIC MODELLING 2023; 120:106147. [PMID: 36570545 PMCID: PMC9768433 DOI: 10.1016/j.econmod.2022.106147] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 11/30/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
We estimate the economic impacts of COVID-19 in the U.S. using a disaster economic consequence analysis framework implemented by a dynamic computable general equilibrium (CGE) model. This facilitates identification of relative influences of several causal factors as "shocks" to the model, including mandatory business closures, disease spread trajectories, behavioral responses, resilience, pent-up demand, and government stimulus packages. The analysis is grounded in primary data on avoidance behavior and healthcare parameters. The decomposition of the influence of various causal factors will help policymakers offset the negative influences and reinforce the positive ones during the remainder of this pandemic and future ones.
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Affiliation(s)
- Terrie Walmsley
- Center for Risk and Economic Analysis of Threats and Emergencies (CREATE), USC, Los Angeles, CA, USA
- Department of Economics, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California (USC), Los Angeles, CA, USA
| | - Adam Rose
- Center for Risk and Economic Analysis of Threats and Emergencies (CREATE), USC, Los Angeles, CA, USA
- Sol Price School of Public Policy, USC, Los Angeles, CA, USA
| | - Richard John
- Center for Risk and Economic Analysis of Threats and Emergencies (CREATE), USC, Los Angeles, CA, USA
- Department of Psychology, Dana and David Dornsife College of Letters, Arts and Sciences, USC, Los Angeles, CA, USA
| | - Dan Wei
- Center for Risk and Economic Analysis of Threats and Emergencies (CREATE), USC, Los Angeles, CA, USA
- Sol Price School of Public Policy, USC, Los Angeles, CA, USA
| | - Jakub P Hlávka
- Center for Risk and Economic Analysis of Threats and Emergencies (CREATE), USC, Los Angeles, CA, USA
- Sol Price School of Public Policy, USC, Los Angeles, CA, USA
- Leonard D. Schaeffer Center for Health Policy & Economics, USC, Los Angeles, CA, USA
| | - Juan Machado
- Center for Risk and Economic Analysis of Threats and Emergencies (CREATE), USC, Los Angeles, CA, USA
| | - Katie Byrd
- Center for Risk and Economic Analysis of Threats and Emergencies (CREATE), USC, Los Angeles, CA, USA
- Department of Psychology, Dana and David Dornsife College of Letters, Arts and Sciences, USC, Los Angeles, CA, USA
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14
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Greiner T, Aigner A, Tinnemann P. SARS-CoV-2 infection dynamics in the tourism season 2020 in North Frisia, Germany. FRONTIERS IN EPIDEMIOLOGY 2022; 2:1029807. [PMID: 38455296 PMCID: PMC10910935 DOI: 10.3389/fepid.2022.1029807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 11/07/2022] [Indexed: 03/09/2024]
Abstract
Background International tourist activities including air travel, holiday on cruise ships, and Après-ski parties played a prominent role in the early spread of the SARS-CoV-2 pandemic. However, the effects of national tourism on infection dynamics are unclear. Methods Data were analyzed from the health authorities in North Frisia, the northernmost district in Germany with prominent tourist hotspots such as Sylt, Amrum, and Föhr. Data were available for the time period April 2020-November 2020. Results During the tourist season (May-October 2020), PCR-confirmed SARS-CoV-2 case numbers were low with 0 to 10 cases per day. Case numbers rose in September and peaked end of October (2nd wave). Among the confirmed cases, 13 persons were returning travelers and none were national tourists. Overall, only a small proportion of cases were related to individuals with presumed tourist contact. Conclusion In summer 2020, the arrival of a large number of tourists apparently did not increase local case numbers, and tourism-related outbreaks were not reported. Thus, tourism presumably did not contribute substantially to SARS-CoV-2 infection dynamics in North Frisia. However, incidences were low countrywide and protective measures were in place.
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Affiliation(s)
- Timo Greiner
- Berlin School of Public Health, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Annette Aigner
- Institute of Biometry and Clinical Epidemiology, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Peter Tinnemann
- Health Protection Authority of the City of Frankfurt am Main, Frankfurt am Main, Germany
- Institute for Social Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
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15
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Lawton K, Keller SM, Barnum S, Arredondo-Lopez C, Spann K, Pusterla N. Seroprevalence of SARS-CoV-2 in 1186 Equids Presented to a Veterinary Medical Teaching Hospital in California from 2020 to 2022. Viruses 2022; 14:v14112497. [PMID: 36423106 PMCID: PMC9696554 DOI: 10.3390/v14112497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
While some companion animals have been shown to be susceptible to SARS-CoV-2, their role in the COVID-19 pandemic has remained poorly investigated. Equids are susceptible to SARS-CoV-2 based on the similarity of the human ACE-2 receptor and reports of infection. Clinical disease and prevalence factors associated with SARS-CoV-2 infection in equids have not yet been investigated. The aim of this study was to determine the seroprevalence of SARS-CoV-2 and selected prevalence factors in 1186 equids presented for various conditions to a Veterinary Medical Teaching Hospital over a two-year period. Blood samples were tested for SARS-CoV-2 antibodies using an ELISA targeting the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. Further, selected prevalence factors (season, age, breed, sex, presenting complaint) were retrieved from the medical records. No information was available on whether the horses had come into contact with COVID-19-positive individuals. Among the study animals, 42/1186 (3.5%) horses had detectable SARS-CoV-2 antibodies. Amongst the prevalence factors investigated, only seasonality (spring) was associated with a greater frequency of seropositivity to SARS-CoV-2. Horses with medical and surgical complaints were more likely to test seropositive to SARS-CoV-2 compared to horses presented for routine health care procedures, suggesting more frequent and/or longer interactions with individuals with COVID-19. While horses can become infected with SARS-CoV-2 via the occasional spillover from COVID-19 individuals, clinical disease expression remains subclinical, making horses an unlikely contributor to the spread of SARS-CoV-2.
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Affiliation(s)
- Kaila Lawton
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Stefan M. Keller
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Samantha Barnum
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Christina Arredondo-Lopez
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Kennedy Spann
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Nicola Pusterla
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
- Correspondence:
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Mannsverk S, Bergholm J, Palanisamy N, Ellström P, Kaden R, Lindh J, Lennerstrand J. SARS-CoV-2 variants of concern and spike protein mutational dynamics in a Swedish cohort during 2021, studied by Nanopore sequencing. Virol J 2022; 19:164. [PMID: 36258215 DOI: 10.1186/s12985-022-01896-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/08/2022] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Since the beginning of the COVID-19 pandemic, new variants of significance to public health have emerged. Consequently, early detection of new mutations and variants through whole-genome sequencing remains crucial to assist health officials in employing appropriate public health measures. METHODS We utilized the ARTIC Network SARS-CoV-2 tiled amplicon approach and Nanopore sequencing to sequence 4,674 COVID-19 positive patient samples from Uppsala County, Sweden, between week 15 and 52 in 2021. Using this data, we mapped the circulating variants of concern (VOC) in the county over time and analysed the Spike (S) protein mutational dynamics in the Delta variant throughout 2021. RESULTS The distribution of the SARS-CoV-2 VOC matched the national VOC distribution in Sweden, in 2021. In the S protein of the Delta variant, we detected mutations attributable to variants under monitoring and variants of interest (e.g., E484Q, Q613H, Q677H, A222V and Y145H) and future VOC (e.g., T95I and Y144 deletion, which are signature mutations in the Omicron variant). We also frequently detected some less well-described S protein mutations in our Delta sequences, that might play a role in shaping future emerging variants. These include A262S, Q675K, I850L, Q1201H, V1228L and M1237I. Lastly, we observed that some of the Delta variant's signature mutations were underrepresented in our study due to artifacts of the used bioinformatics tools, approach and sequencing method. We therefore discuss some pitfalls and considerations when sequencing SARS-CoV-2 genomes. CONCLUSION Our results suggest that genomic surveillance in a small, representative cohort can be used to make predictions about the circulating variants nationally. Moreover, we show that detection of transient mutations in currently circulating variants can give valuable clues to signature mutations of future VOC. Here we suggest six such mutations, that we detected frequently in the Delta variant during 2021. Lastly, we report multiple systematic errors that occurred when following the ARTIC Network SARS-CoV-2 tiled amplicon approach using the V3 primers and Nanopore sequencing, which led to the masking of some of the important signature mutations in the Delta sequences.
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Affiliation(s)
- Steinar Mannsverk
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene, Uppsala University, 751 85, Uppsala, Sweden.,Department of Cell and Molecular Biology, Uppsala University, 752 37, Uppsala, Sweden
| | - Julia Bergholm
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene, Uppsala University, 751 85, Uppsala, Sweden
| | | | - Patrik Ellström
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene, Uppsala University, 751 85, Uppsala, Sweden
| | - René Kaden
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene, Uppsala University, 751 85, Uppsala, Sweden
| | - Johan Lindh
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene, Uppsala University, 751 85, Uppsala, Sweden
| | - Johan Lennerstrand
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene, Uppsala University, 751 85, Uppsala, Sweden.
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