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Al Khalaf R, Bernasconi A, Pinoli P. Systematic analysis of SARS-CoV-2 Omicron subvariants' impact on B and T cell epitopes. PLoS One 2024; 19:e0307873. [PMID: 39298436 PMCID: PMC11412522 DOI: 10.1371/journal.pone.0307873] [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: 03/22/2024] [Accepted: 07/14/2024] [Indexed: 09/21/2024] Open
Abstract
INTRODUCTION Epitopes are specific structures in antigens that are recognized by the immune system. They are widely used in the context of immunology-related applications, such as vaccine development, drug design, and diagnosis / treatment / prevention of disease. The SARS-CoV-2 virus has represented the main point of interest within the viral and genomic surveillance community in the last four years. Its ability to mutate and acquire new characteristics while it reorganizes into new variants has been analyzed from many perspectives. Understanding how epitopes are impacted by mutations that accumulate on the protein level cannot be underrated. METHODS With a focus on Omicron-named SARS-CoV-2 lineages, including the last WHO-designated Variants of Interest, we propose a workflow for data retrieval, integration, and analysis pipeline for conducting a database-wide study on the impact of lineages' characterizing mutations on all T cell and B cell linear epitopes collected in the Immune Epitope Database (IEDB) for SARS-CoV-2. RESULTS Our workflow allows us to showcase novel qualitative and quantitative results on 1) coverage of viral proteins by deposited epitopes; 2) distribution of epitopes that are mutated across Omicron variants; 3) distribution of Omicron characterizing mutations across epitopes. Results are discussed based on the type of epitope, the response frequency of the assays, and the sample size. Our proposed workflow can be reproduced at any point in time, given updated variant characterizations and epitopes from IEDB, thereby guaranteeing to observe a quantitative landscape of mutations' impact on demand. CONCLUSION A big data-driven analysis such as the one provided here can inform the next genomic surveillance policies in combatting SARS-CoV-2 and future epidemic viruses.
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Affiliation(s)
- Ruba Al Khalaf
- Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, Milano, Italia
| | - Anna Bernasconi
- Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, Milano, Italia
| | - Pietro Pinoli
- Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, Milano, Italia
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Pander J, Beekman-Hendriks W, Coolen N, van de Flier V, Senster J, Rovers CP. No more government-imposed societal-level COVID-19 control measures but still significant self-experienced burden for severely immunocompromised individuals - A cross-sectional survey in the Netherlands. Prev Med Rep 2024; 45:102827. [PMID: 39114410 PMCID: PMC11304848 DOI: 10.1016/j.pmedr.2024.102827] [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: 04/08/2024] [Revised: 07/02/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
Objectives In March 2023, all societal-level COVID-19 control measures were lifted by the Dutch government. This study was performed to understand the self-experienced burden of this new phase of COVID-19 on the perspectives and behaviors of severely immunocompromised individuals. Methods This is an observational, descriptive, cross-sectional study in The Netherlands. An online survey was completed by severely immunocompromised individuals, to capture their general well-being (score from 1 = worst to 10 = best), mental and physical health, and daily and social activities during survey conduct and retrospectively for before onset of COVID-19. The survey was open for completion from May 24th until August 7nd, 2023. Results Of the 236 respondents, 96.6 % had been vaccinated against COVID-19 and 24.6 % were shielding to avoid COVID-19 during survey conduct. The general well-being score for all respondents was 7.5 (±1.2 SD) before onset of the COVID-19 pandemic and 6.9 (±1.6 SD) during survey conduct (P<0.001). For the shielding group (n = 58), these scores were 7.6 (±1.0 SD) and 5.7 (±1.6 SD), respectively (P<0.001). Generally, for all questions about mental and physical health and daily and social activities, there was a trend towards more negative answers during survey conduct, compared with before onset of the COVID-19 pandemic, which was more pronounced for the shielding group. Conclusions Despite absence of government-imposed societal measures, COVID-19 avoidance still had a self-experienced burden on perspectives and behaviors of immunocompromised individuals in The Netherlands, with a significantly lower general well-being during survey conduct, compared with before onset of COVID-19.
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Affiliation(s)
- Jan Pander
- AstraZeneca BV, PO Box 93015, 2509AA Den Haag, the Netherlands
| | | | - Neeltje Coolen
- AstraZeneca BV, PO Box 93015, 2509AA Den Haag, the Netherlands
| | | | - Jeroen Senster
- Motivaction BV, PO Box 15262, 1001MG Amsterdam, the Netherlands
| | - Chantal P. Rovers
- Radboud University Medical Center, Department of Internal Medicine/Division of Infectious Diseases, PO Box 9101, 6500HB Nijmegen, the Netherlands
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Harrigan SP, Velásquez García HA, Abdia Y, Wilton J, Prystajecky N, Tyson J, Fjell C, Hoang L, Kwong JC, Mishra S, Wang L, Sander B, Janjua NZ, Sbihi H. The Clinical Severity of COVID-19 Variants of Concern: Retrospective Population-Based Analysis. JMIR Public Health Surveill 2024; 10:e45513. [PMID: 39190434 PMCID: PMC11387920 DOI: 10.2196/45513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/28/2024] [Accepted: 06/06/2024] [Indexed: 08/28/2024] Open
Abstract
BACKGROUND SARS-CoV-2 variants of concern (VOCs) emerged and rapidly replaced the original strain worldwide. The increased transmissibility of these new variants led to increases in infections, hospitalizations, and mortality. However, there is a scarcity of retrospective investigations examining the severity of all the main VOCs in presence of key public health measures and within various social determinants of health (SDOHs). OBJECTIVE This study aims to provide a retrospective assessment of the clinical severity of COVID-19 VOCs in the context of heterogenous SDOHs and vaccination rollout. METHODS We used a population-based retrospective cohort design with data from the British Columbia COVID-19 Cohort, a linked provincial surveillance platform. To assess the relative severity (hospitalizations, intensive care unit [ICU] admissions, and deaths) of Gamma, Delta, and Omicron infections during 2021 relative to Alpha, we used inverse probability treatment weighted Cox proportional hazard modeling. We also conducted a subanalysis among unvaccinated individuals, as assessed severity differed across VOCs and SDOHs. RESULTS We included 91,964 individuals infected with a SARS-CoV-2 VOC (Alpha: n=20,487, 22.28%; Gamma: n=15,223, 16.55%; Delta: n=49,161, 53.46%; and Omicron: n=7093, 7.71%). Delta was associated with the most severe disease in terms of hospitalization, ICU admissions, and deaths (hospitalization: adjusted hazard ratio [aHR] 2.00, 95% CI 1.92-2.08; ICU: aHR 2.05, 95% CI 1.91-2.20; death: aHR 3.70, 95% CI 3.23-4.25 relative to Alpha), followed generally by Gamma and then Omicron and Alpha. The relative severity by VOC remained similar in the unvaccinated individual subanalysis, although the proportion of individuals infected with Delta and Omicron who were hospitalized was 2 times higher in those unvaccinated than in those fully vaccinated. Regarding SDOHs, the proportion of hospitalized individuals was higher in areas with lower income across all VOCs, whereas among Alpha and Gamma infections, 2 VOCs that cocirculated, differential distributions of hospitalizations were found among racially minoritized groups. CONCLUSIONS Our study provides robust severity estimates for all VOCs during the COVID-19 pandemic in British Columbia, Canada. Relative to Alpha, we found Delta to be the most severe, followed by Gamma and Omicron. This study highlights the importance of targeted testing and sequencing to ensure timely detection and accurate estimation of severity in emerging variants. It further sheds light on the importance of vaccination coverage and SDOHs in the context of pandemic preparedness to support the prioritization of allocation for resource-constrained or minoritized groups.
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Affiliation(s)
- Sean P Harrigan
- BC Centre for Disease Control, Vancouver, BC, Canada
- University of British Columbia Centre for Disease Control, Vancouver, BC, Canada
| | | | - Younathan Abdia
- University of British Columbia Centre for Disease Control, Vancouver, BC, Canada
| | - James Wilton
- BC Centre for Disease Control, Vancouver, BC, Canada
| | - Natalie Prystajecky
- BC Centre for Disease Control, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - John Tyson
- BC Centre for Disease Control, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Chris Fjell
- BC Centre for Disease Control, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Linda Hoang
- BC Centre for Disease Control, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jeffrey C Kwong
- Institute for Clinical Evaluative Sciences, Toronto, ON, Canada
- Public Health Ontario, Toronto, ON, Canada
- Department of Family and Community Medicine, University of Toronto, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Sharmistha Mishra
- Institute for Clinical Evaluative Sciences, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- MAP Centre for Urban Health Solutions, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Linwei Wang
- MAP Centre for Urban Health Solutions, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada
| | - Beate Sander
- Institute for Clinical Evaluative Sciences, Toronto, ON, Canada
- Public Health Ontario, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Toronto Health Economics and Technology Assessment Collaborative, University Health Network, Toronto, ON, Canada
| | - Naveed Z Janjua
- BC Centre for Disease Control, Vancouver, BC, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
- Centre for Advancing Health Outcomes, St Paul's Hospital, Vancouver, BC, Canada
| | - Hind Sbihi
- BC Centre for Disease Control, Vancouver, BC, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
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Qiu H, Yuan XY, Holloway K, Wood H, Cabral T, Grant C, McQueen P, Westmacott G, Beniac DR, Lin L, Carpenter M, Kobasa D, Gräfenhan T, Cheney IW. Development and characterization of monoclonal antibodies recognizing nucleocapsid protein of multiple SARS-CoV-2 variants. Heliyon 2024; 10:e35325. [PMID: 39170261 PMCID: PMC11336563 DOI: 10.1016/j.heliyon.2024.e35325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 07/25/2024] [Accepted: 07/26/2024] [Indexed: 08/23/2024] Open
Abstract
Rapid antigen test (RAT) is widely used for SARS-CoV-2 infection diagnostics. However, test sensitivity has decreased recently due to the emergence of the Omicron variant and its sublineages. Here we developed a panel of SARS-CoV-2 nucleocapsid protein (NP) specific mouse monoclonal antibodies (mAbs) and assessed their sensitivity and specificity to important SARS-CoV-2 variants. We identified seven mAbs that exhibited strong reactivity to SARS-CoV-2 variants and recombinant NP (rNP) by Western immunoblot or ELISA. Their specificity to SARS-CoV-2 was confirmed by negative or low reactivity to rNPs from SARS-CoV-1, MERS, and common human coronaviruses (HCoV-HKU1, HCoV-CO43, HCoV-NL63, and HCoV-229E). These seven mAbs were further tested by immunoplaque assay against selected variants of concern (VOCs), including two Omicron sublineages, and five mAbs (F461G13, F461G7, F459G7, F457G3, and F461G6), showed strong reactions, warranting further suitability testing for the development of diagnostic assay.
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Affiliation(s)
- Hongyu Qiu
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada
| | - Xin-Yong Yuan
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada
| | - Kimberly Holloway
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada
| | - Heidi Wood
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada
| | - Teresa Cabral
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada
| | - Chris Grant
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada
| | - Peter McQueen
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada
| | - Garrett Westmacott
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada
| | - Daniel R. Beniac
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada
| | - Lisa Lin
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada
| | - Michael Carpenter
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada
| | - Darwyn Kobasa
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada
| | | | - Ian Wayne Cheney
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada
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Santosa A, Oras J, Li H, Nwaru C, Kirui B, Nyberg F. Survival of Critically Ill COVID-19 Patients in Sweden During the First Two and a Half Years of the Pandemic. Crit Care Med 2024; 52:1194-1205. [PMID: 38546287 PMCID: PMC11239088 DOI: 10.1097/ccm.0000000000006271] [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] [Indexed: 07/13/2024]
Abstract
OBJECTIVES Some studies have examined survival trends among critically ill COVID-19 patients, but most were case reports, small cohorts, and had relatively short follow-up periods. We aimed to examine the survival trend among critically ill COVID-19 patients during the first two and a half years of the pandemic and investigate potential predictors across different variants of concern periods. DESIGN Prospective cohort study. SETTING Swedish ICUs, between March 6, 2020, and December 31, 2022. PATIENTS Adult COVID-19 ICU patients of 18 years old or older from the Swedish Intensive Care Register (SIR) that were linked to multiple other national registers. MEASUREMENT AND MAIN RESULTS Survival probability and predictors of COVID-19 death were estimated using Kaplan-Meier and Cox regression analysis. Of 8975 patients, 2927 (32.6%) died. The survival rate among COVID-19 critically ill patients appears to have changed over time, with a worse survival in the Omicron period overall. The adjusted hazard ratios (aHRs) comparing older and younger ages were consistently strong but slightly attenuated in the Omicron period. After adjustment, the aHR of death was significantly higher for men, older age (40+ yr), low income, and with comorbid chronic heart disease, chronic lung disease, impaired immune disease, chronic renal disease, stroke, and cancer, and for those requiring invasive or noninvasive respiratory supports, who developed septic shock or had organ failures ( p < 0.05). In contrast, foreign-born patients, those with booster vaccine, and those who had taken steroids had better survival (aHR = 0.87; 95% CI, 0.80-0.95; 0.74, 0.65-0.84, and 0.91, 0.84-0.98, respectively). Observed associations were similar across different variant periods. CONCLUSIONS In this nationwide Swedish cohort covering over two and a half years of the pandemic, ICU survival rates changed over time. Older age was a strong predictor across all periods. Furthermore, most other mortality predictors remained consistent across different variant periods.
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Affiliation(s)
- Ailiana Santosa
- School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Västra Götaland, Sweden
| | - Jonatan Oras
- Department of Anaesthesiology and Intensive Care, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Västra Götaland, Sweden
- Department of Anaesthesiology and Intensive Care, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Västra Götaland, Sweden
| | - Huiqi Li
- School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Västra Götaland, Sweden
| | - Chioma Nwaru
- School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Västra Götaland, Sweden
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Brian Kirui
- School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Västra Götaland, Sweden
| | - Fredrik Nyberg
- School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Västra Götaland, Sweden
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Yamanaga S, Shimata K, Ohfuji S, Yoshikawa M, Natori Y, Hibi T, Yuzawa K, Egawa H. Excess mortality in COVID-19-affected solid organ transplant recipients across the pandemic. Am J Transplant 2024; 24:1495-1508. [PMID: 38514016 DOI: 10.1016/j.ajt.2024.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 03/05/2024] [Accepted: 03/12/2024] [Indexed: 03/23/2024]
Abstract
The excess mortality of coronavirus disease 2019 (COVID-19) solid organ transplant recipients (SOTRs) throughout the pandemic remains unclear. This prospective cohort study based on the Japanese nationwide registry included 1632 SOTRs diagnosed with COVID-19 between February 1, 2020, and July 31, 2022, categorized based on dominant phases of variants of concern (VOCs): Waves 1 to 3 (Beta), 4 (Alpha), 5 (Delta), 6 (Omicron BA.1/BA.2), and 7 (Omicron BA.5). Excess mortality of COVID-19-affected SOTRs was analyzed by calculating standardized mortality ratios (SMRs). Overall, 1632 COVID-19-confirmed SOTRs included 1170 kidney, 408 liver, 25 lung, 20 heart, 1 small intestine, and 8 multiorgan recipients. Although disease severity and all-cause mortality decreased as VOCs transitioned, SMRs of SOTRs were consistently higher than those of the general population throughout the pandemic, showing a U-shaped gap that peaked toward the Omicron BA.5 phase; SMR (95% CI): 6.2 (3.1-12.5), 4.0 (1.5-10.6), 3.0 (1.3-6.7), 8.8 (5.3-14.5), and 21.9 (5.5-87.6) for Waves 1 to 3 (Beta), Wave 4 (Alpha), Wave 5 (Delta), Wave 6 (Omicron BA.1/2), and Wave 7 (Omicron BA.5), respectively. In conclusion, COVID-19 SOTRs had greater SMRs than the general population across the pandemic. Vaccine boosters, immunosuppression optimization, and other protective measures, particularly for older SOTRs, are paramount.
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Affiliation(s)
- Shigeyoshi Yamanaga
- Department of Surgery, Japanese Red Cross Kumamoto Hospital, Nagamine-Minami, Higashi Ward, Kumamoto, Japan
| | - Keita Shimata
- Department of Pediatric Surgery and Transplantation, Kumamoto University Graduate School of Medical Sciences, Honjō, Chuo Ward, Kumamoto, Japan
| | - Satoko Ohfuji
- Department of Public Health, Osaka Metropolitan University Graduate School of Medicine, Asahimachi, Abeno Ward, Osaka, Japan
| | - Mikiko Yoshikawa
- Organ Transplantation and General Surgery, Kyoto Prefectural University of Medicine, Kajiichō, Kamigyo Ward, Kyoto, Japan
| | - Yoichiro Natori
- Solid Organ Transplant Infectious Diseases, Miami Transplant Institute, Jackson Health System, Miami, Florida, USA; Division of Infectious Diseases, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Taizo Hibi
- Department of Pediatric Surgery and Transplantation, Kumamoto University Graduate School of Medical Sciences, Honjō, Chuo Ward, Kumamoto, Japan.
| | - Kenji Yuzawa
- Department of Transplantation Surgery, National Hospital Organization Mito Medical Center, Sakuranosato, Ibaraki, Higashiibaraki District, Ibaraki, Japan
| | - Hiroto Egawa
- Department of Surgery, Tokyo Women's Medical University, Kawadacho, Shinjuku Ward, Tokyo, Japan
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Livieratos A, Gogos C, Akinosoglou K. SARS-CoV-2 Variants and Clinical Outcomes of Special Populations: A Scoping Review of the Literature. Viruses 2024; 16:1222. [PMID: 39205196 PMCID: PMC11359867 DOI: 10.3390/v16081222] [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: 06/07/2024] [Revised: 07/20/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024] Open
Abstract
The ongoing COVID-19 pandemic has significantly impacted special populations, including immunocompromised individuals, people living with HIV (PLWHIV), pediatric patients, and those with chronic liver disease (CLD). This scoping review aims to map the clinical outcomes of these vulnerable groups when infected with various SARS-CoV-2 variants. The review identifies trends and patterns, noting that early variants, such as Alpha and Delta, are associated with more severe outcomes, including higher hospitalization and mortality rates. In contrast, the Omicron variant, despite its increased transmissibility, tends to cause milder clinical manifestations. The review highlights the necessity for ongoing surveillance and tailored healthcare interventions due to the heterogeneity of patient populations and the evolving nature of the virus. Continuous monitoring and adaptive healthcare strategies are essential to mitigate the impact of COVID-19 on these high-risk groups.
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Affiliation(s)
| | - Charalambos Gogos
- Department of Medicine, University of Patras, 26504 Rio, Greece; (C.G.); (K.A.)
| | - Karolina Akinosoglou
- Department of Medicine, University of Patras, 26504 Rio, Greece; (C.G.); (K.A.)
- Department of Internal Medicine and Infectious Diseases, University General Hospital of Patras, 26504 Rio, Greece
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Murthy SC, Gordon SM, Lowry AM, Blackstone EH. Evolution of serious and life-threatening COVID-19 pneumonia as the SARS-CoV-2 pandemic progressed: an observational study of mortality to 60 days after admission to a 15-hospital US health system. BMJ Open 2024; 14:e075028. [PMID: 38977360 PMCID: PMC11256047 DOI: 10.1136/bmjopen-2023-075028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 05/13/2024] [Indexed: 07/10/2024] Open
Abstract
OBJECTIVE In order to predict at hospital admission the prognosis of patients with serious and life-threatening COVID-19 pneumonia, we sought to understand the clinical characteristics of hospitalised patients at admission as the SARS-CoV-2 pandemic progressed, document their changing response to the virus and its variants over time, and identify factors most importantly associated with mortality after hospital admission. DESIGN Observational study using a prospective hospital systemwide COVID-19 database. SETTING 15-hospital US health system. PARTICIPANTS 26 872 patients admitted with COVID-19 to our Northeast Ohio and Florida hospitals from 1 March 2020 to 1 June 2022. MAIN OUTCOME MEASURES 60-day mortality (highest risk period) after hospital admission analysed by random survival forests machine learning using demographics, medical history, and COVID-19 vaccination status, and viral variant, symptoms, and routine laboratory test results obtained at hospital admission. RESULTS Hospital mortality fell from 11% in March 2020 to 3.7% in March 2022, a 66% decrease (p<0.0001); 60-day mortality fell from 17% in May 2020 to 4.7% in May 2022, a 72% decrease (p<0.0001). Advanced age was the strongest predictor of 60-day mortality, followed by admission laboratory test results. Risk-adjusted 60-day mortality had all patients been admitted in March 2020 was 15% (CI 3.0% to 28%), and had they all been admitted in May 2022, 12% (CI 2.2% to 23%), a 20% decrease (p<0.0001). Dissociation between observed and predicted decrease in mortality was related to temporal change in admission patient profile, particularly in laboratory test results, but not vaccination status or viral variant. CONCLUSIONS Hospital mortality from COVID-19 decreased substantially as the pandemic evolved but persisted after hospital discharge, eclipsing hospital mortality by 50% or more. However, after accounting for the many, even subtle, changes across the pandemic in patients' demographics, medical history and particularly admission laboratory results, a patient admitted early in the pandemic and predicted to be at high risk would remain at high risk of mortality if admitted tomorrow.
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Affiliation(s)
- Sudish C Murthy
- Thoracic and Cardiovascular Surgery, Cleveland Clinic, Cleveland, Ohio, USA
| | | | - Ashley M Lowry
- Quantitative Health Sciences, Cleveland Clinic, Cleveland, Ohio, USA
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9
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von Falkenhausen AS, Geipel S, Gail A, Scherer C, Stockhausen S, Sams LE, Becker F, Doldi PM, Lemmermöhle E, de Villèle P, Schleef M, Becker M, Lauterbach M, Massberg S, Kääb S, Sinner MF. Telemedical management of symptomatic COVID-19 outpatients. ERJ Open Res 2024; 10:00277-2024. [PMID: 39135664 PMCID: PMC11317893 DOI: 10.1183/23120541.00277-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 04/16/2024] [Indexed: 08/15/2024] Open
Abstract
Background COVID-19 remains a challenge to individual health and healthcare resources worldwide. Telemedical surveillance might minimise hospitalisation and direct patient-physician contacts. Yet, randomised clinical trials evaluating telemedical management of COVID-19 patients are lacking. Methods COVID-SMART is a randomised, open-label, controlled clinical trial investigating whether telemedicine reduces the primary end-point of hospitalisation or any unscheduled utilisation of an emergency medical service within 30 days of follow-up. Key secondary end-points included mortality and primary end-point components. We enrolled acutely infected SARS-CoV-2 patients suitable for outpatient care. All presented with ≥1 risk factor for an adverse COVID-19 course. Patients were randomised 1:1 into a control group receiving standard of care and an intervention group receiving smartphone-based assessment of oxygen saturation, heart rate and electrocardiogram, and telemedical counselling via a 24/7 emergency hotline. Results Of 607 enrolled patients (mean±sd age 46.7±13.5 years), 304 were randomised into the intervention and 303 into the control group. The primary end-point occurred in 6.9% (n=21) of the intervention and in 9.6% (n=29) of the control group (hazard ratio (HR) 0.72, 95% confidence interval (CI) 0.41-1.26; p=0.24). No deaths occurred during follow-up. Fewer intervention group participants utilised outpatient-based emergency medical services (HR 0.43, 95% CI 0.20-0.90; p=0.03). Conclusions COVID-SMART is the first randomised clinical trial assessing the benefit of telemedicine in an acute respiratory infectious disease. Whereas telemedical management did not reduce the primary end-point of hospitalisation, fewer intervention group patients used outpatient-based emergency services, suggesting a potential benefit for less-acutely infected individuals.
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Affiliation(s)
- Aenne S. von Falkenhausen
- Department of Medicine I, LMU University Hospital, LMU Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
| | - Scott Geipel
- Department of Medicine I, LMU University Hospital, LMU Munich, Munich, Germany
| | - Antonia Gail
- Department of Medicine I, LMU University Hospital, LMU Munich, Munich, Germany
| | - Clemens Scherer
- Department of Medicine I, LMU University Hospital, LMU Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
| | - Sven Stockhausen
- Department of Medicine I, LMU University Hospital, LMU Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
| | - Lauren E. Sams
- Department of Medicine I, LMU University Hospital, LMU Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
| | - Finn Becker
- Department of Medicine I, LMU University Hospital, LMU Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
| | - Philipp M. Doldi
- Department of Medicine I, LMU University Hospital, LMU Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
| | - Eric Lemmermöhle
- Department of Medicine I, LMU University Hospital, LMU Munich, Munich, Germany
| | | | | | | | | | - Steffen Massberg
- Department of Medicine I, LMU University Hospital, LMU Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
| | - Stefan Kääb
- Department of Medicine I, LMU University Hospital, LMU Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
- These authors share senior authorship
| | - Moritz F. Sinner
- Department of Medicine I, LMU University Hospital, LMU Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
- These authors share senior authorship
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10
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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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11
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Zygmunt A, Warsame K, Mather RG, McKinnon L, Philipneri A, Li S, Menon S. COVID-19 in correctional facilities in Ontario, Canada: a retrospective epidemiological analysis from 15 January 2020 to 31 December 2022. INTERNATIONAL JOURNAL OF PRISON HEALTH 2024; ahead-of-print. [PMID: 38888194 DOI: 10.1108/ijoph-01-2024-0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
PURPOSE The physical environment of correctional facilities promote infectious disease transmission and outbreaks. The purpose of this study is to compare the COVID-19 burden between the correctional facility (incarcerated individuals and staff members) and non-correctional facility population in Ontario during the COVID-19 pandemic. DESIGN/METHODOLOGY/APPROACH All individuals in Ontario with a laboratory confirmation of SARS-CoV-2 between 15 January 2020 and 31 December 2022 and entered into the provincial COVID-19 data were included. Cases were classified as a correctional facility case (living or working in a correctional facility) or a non-correctional facility case. COVID-19 vaccination status was obtained from the provincial COVID-19 vaccine registry. Statistics Canada census data were used to calculate COVID-19 incidence and hospitalization rates for incarcerated cases and the non-correctional facility population. FINDINGS Between 15 January 2020 and 31 December 2022, there were 1,550,045 COVID-19 cases in Ontario of which 8,292 (0.53%) cases were reported in correctional (63.8% amongst incarcerated individuals, 18.6% amongst staff and 17.7% amongst an unknown classification) and 1,541,753 (99.47%) were non-correctional facility cases. Most cases in correctional facilities were men (83.8%) and aged 20-59 years (93.1%). COVID-19 incidence and hospitalization rates were generally higher among incarcerated individuals compared to the non-correctional facility population throughout the study period. COVID-19 incidence peaked in January 2022 for both the correctional facility population (21,543.8 per 100,000 population) and the non-correctional facility population (1915.1 per 100,000 population). The rate of COVID-19 hospitalizations peaked for the correctional facility population aged 20-59 in March 2021 (70.7 per 100,000 population) and in April 2021 for the non-correctional facility population aged 20-59 (19.8 per 100,000 population). A greater percentage of incarcerated individuals (73.0%) were unvaccinated at time of their COVID-19 diagnosis compared to the non-correctional facility population (49.3%). Deaths amongst correctional facility cases were rare (0.1%, 6 / 8,292) compared to 1.0% of non-correctional facility cases (n = 15,787 / 1,541,753). ORIGINALITY/VALUE During the COVID-19 pandemic, individuals incarcerated in correctional facilities in Ontario had higher COVID-19 incidence and hospitalization rates compared to the non-correctional facility population. These results support prioritizing incarcerated individuals for public health interventions to mitigate COVID-19 impacts in correctional facilities.
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Affiliation(s)
- Austin Zygmunt
- Public Health Ontario, Toronto, Canada and Department of Family Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | | | - Richard G Mather
- Public Health Ontario, Toronto, Canada and Department of Family Medicine, Queen's University School of Medicine, Kingston, Canada
| | | | | | - Stone Li
- Public Health and Preventive Medicine Residency Program, Northern Ontario School of Medicine, Thunder Bay, Canada
| | - Sandya Menon
- Region of Peel Public Health, Mississauga, Canada
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12
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Kwiatkowska R, Chatzilena A, King J, Clout M, McGuinness S, Maskell N, Oliver J, Challen R, Hickman M, Finn A, Hyams C, Danon L. Syndromic case definitions for lower respiratory tract infection (LRTI) are less sensitive in older age: an analysis of symptoms among hospitalised adults. BMC Infect Dis 2024; 24:568. [PMID: 38849730 PMCID: PMC11157799 DOI: 10.1186/s12879-024-09425-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/21/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Lower Respiratory Tract Infections (LRTI) pose a serious threat to older adults but may be underdiagnosed due to atypical presentations. Here we assess LRTI symptom profiles and syndromic (symptom-based) case ascertainment in older (≥ 65y) as compared to younger adults (< 65y). METHODS We included adults (≥ 18y) with confirmed LRTI admitted to two acute care Trusts in Bristol, UK from 1st August 2020- 31st July 2022. Logistic regression was used to assess whether age ≥ 65y reduced the probability of meeting syndromic LRTI case definitions, using patients' symptoms at admission. We also calculated relative symptom frequencies (log-odds ratios) and evaluated how symptoms were clustered across different age groups. RESULTS Of 17,620 clinically confirmed LRTI cases, 8,487 (48.1%) had symptoms meeting the case definition. Compared to those not meeting the definition these cases were younger, had less severe illness and were less likely to have received a SARS-CoV-2 vaccination or to have active SARS-CoV-2 infection. Prevalence of dementia/cognitive impairment and levels of comorbidity were lower in this group. After controlling for sex, dementia and comorbidities, age ≥ 65y significantly reduced the probability of meeting the case definition (aOR = 0.67, 95% CI:0.63-0.71). Cases aged ≥ 65y were less likely to present with fever and LRTI-specific symptoms (e.g., pleurisy, sputum) than younger cases, and those aged ≥ 85y were characterised by lack of cough but frequent confusion and falls. CONCLUSIONS LRTI symptom profiles changed considerably with age in this hospitalised cohort. Standard screening protocols may fail to detect older and frailer cases of LRTI based on their symptoms.
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Affiliation(s)
- Rachel Kwiatkowska
- Population Health Sciences, University of Bristol, Bristol, UK
- NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK
| | | | - Jade King
- Clinical Research and Imaging Centre, UHBW NHS Trust, Bristol, UK
| | | | | | - Nick Maskell
- Academic Respiratory Unit, Southmead Hospital, University of Bristol, Bristol, UK
| | | | - Robert Challen
- Dept of Engineering Mathematics, University of Bristol, Bristol, UK
| | - Matthew Hickman
- Population Health Sciences, University of Bristol, Bristol, UK
- NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK
| | - Adam Finn
- Population Health Sciences, University of Bristol, Bristol, UK
- NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK
- Bristol Vaccine Centre, University of Bristol, Bristol, UK
- Cellular & Molecular Medicine, University of Bristol, Bristol, UK
| | - Catherine Hyams
- Population Health Sciences, University of Bristol, Bristol, UK
- Clinical Research and Imaging Centre, UHBW NHS Trust, Bristol, UK
- Bristol Vaccine Centre, University of Bristol, Bristol, UK
- North Bristol NHS Trust, Southmead Hospital, Bristol, UK
| | - Leon Danon
- Dept of Engineering Mathematics, University of Bristol, Bristol, UK.
- Bristol Vaccine Centre, University of Bristol, Bristol, UK.
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13
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Hu L, Zhang H, Huang C, Shen T, Feng Z, Mu F, Xu L, Lin Y, Yue C, Guo K, Tian M, Shi J, Zhang C, Wen P, Cao S, Wang Y, Zhang J, Shi X, Wang Z, He Y, Zhang X, Liu X, Lv Y, Liu Z, Guo W, Wang B. Effect of ursodeoxycholic acid on preventing SARS-CoV-2 infection in patients with liver transplantation: a multicenter retrospective cohort study. QJM 2024; 117:339-347. [PMID: 37950449 DOI: 10.1093/qjmed/hcad254] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/06/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Immunosuppressed recipients of liver transplantation (LT) are more likely to develop coronavirus disease 2019 (COVID-19) and may have an increased risk of developing worse outcomes. AIM To assess the effect of ursodeoxycholic acid (UDCA) on preventing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in LT recipients. DESIGN Adult patients (aged ≥ 18 years) who underwent LT between 1 January 2015 and 31 December 2022 were included and categorized into two groups according to their use of UDCA. METHODS The prevalence and severity of COVID-19 among transplantation patients between the UDCA and non-UDCA groups were estimated and compared. RESULTS Among the 897 LT patients who met the inclusion criteria, infection rate of SARS-CoV-2 was 78.4%, and the rate of severe illness was 5.1% from January 2022 to January 2023 in China. In the multivariate analysis, only UDCA treatment (P = 0.006) was found to be a protective factor against SARS-CoV-2 infection. After propensity score matching, the SARS-CoV-2 infection rate in the UDCA group was lower than that in the non-UDCA group (74.1% vs. 84.6%, P = 0.002). This rate was further reduced to 62.1% (P = 0.002) when the oral administration dose was >15 mg/kg/day. There was no difference in the rates of severe COVID-19 illness, ICU admission, or ventilation rate or length of hospital stay with or without UDCA treatment (all P > 0.05). CONCLUSIONS The use of UDCA in LT patients significantly reduced the SARS-CoV-2 infection rate and showed a dose-dependent protective effect.
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Affiliation(s)
- L Hu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - H Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - C Huang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - T Shen
- Department of General Surgery, The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710061, China
| | - Z Feng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - F Mu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - L Xu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Y Lin
- Department of Plastic, Aesthetic and Maxillofacial Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - C Yue
- Department of Biology, York University, Toronto, ON M3J1P3, Canada
| | - K Guo
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - M Tian
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - J Shi
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - C Zhang
- Department of Surgical Intensive Care Unit, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - P Wen
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - S Cao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Y Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - J Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - X Shi
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Z Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Y He
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - X Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - X Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Y Lv
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Z Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - W Guo
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - B Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
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14
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Zher-Wen, Zhen S, Yu R. Moral characteristics predicting COVID-19 vaccination. J Pers 2024; 92:820-836. [PMID: 37899552 DOI: 10.1111/jopy.12892] [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: 10/31/2022] [Revised: 09/18/2023] [Accepted: 10/02/2023] [Indexed: 10/31/2023]
Abstract
OBJECTIVE The current study aims to assess, for the first time, whether vaccination is predicted by different behavioral and cognitive aspects of moral decision-making. BACKGROUND Studies linking moral factors to vaccination have largely examined whether vaccination decisions can be explained by individual differences in the endorsement of various principles and norms central to deontology-based arguments in vaccination ethics. However, these studies have overlooked whether individuals prioritize norms over other considerations when making decisions, such as maximizing consequences (utilitarianism). METHOD In a sample of 1492 participants, the current study assessed whether vaccination is explained by individual differences in three aspects of moral decision-making (consequence sensitivity, norm sensitivity, and action tendency), while also considering ethics position (idealism, relativism) and moral identity. RESULTS Supportive vaccination (vaccine uptake accompanied by a positive attitude toward vaccines) was associated with utilitarianism (increased consequence sensitivity) and increased tolerance to risks and harm toward others. Meanwhile, although those in the non-vaccinated group was associated with higher harm sensitivities, they neither supported nor received the COVID vaccines (when vaccines prevent harm from infection). CONCLUSION Pro-vaccination messages may be made more effective by addressing perceptions of harms associated with vaccines and infections, respectively.
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Affiliation(s)
- Zher-Wen
- Department of Management, Marketing, and Information Systems, Hong Kong Baptist University, Hong Kong, China
| | - Shanshan Zhen
- Department of Social and Behavioural Sciences, City University of Hong Kong, Hong Kong, China
| | - Rongjun Yu
- Department of Management, Marketing, and Information Systems, Hong Kong Baptist University, Hong Kong, China
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15
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Van Nam L, Dien TC, Bang LVN, Thach PN, Van Duyet L. Genetic features of SARS-CoV-2 Alpha, Delta, and Omicron variants and their association with the clinical severity of COVID-19 in Vietnam. IJID REGIONS 2024; 11:100348. [PMID: 38601946 PMCID: PMC11004080 DOI: 10.1016/j.ijregi.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 04/12/2024]
Abstract
Objectives We investigated the genetic variations in the Alpha, Delta, and Omicron variants of SARS-CoV-2 and their association with clinical status and treatment outcomes in patients with COVID-19. Methods MiSeq was used to sequence the Alpha, Delta, and Omicron genomes, and MEGA 6.6 was used to define the nucleotide variations. We determined the association between clinical severity and treatment outcomes for the SARS-CoV-2 variants. Results The BA.1.1 and BA.2 lineages of the Omicron variant had 57-59 mutations, which is 2-2.7-fold higher than that of the B.1.1.7 (Alpha), B.1.617.2, and AY.57 (Delta) lineages. We found distinct mutations in SARS-CoV-2: five in Alpha (C26305T, G26558T, G7042T, C14120T, and C27509T); seven in Delta (C26408T, C1403T, C5184T, C9891T, T11418C, C11514T, and C22227T); and three in Omicron (C26408T, C8991T, and C25810T). Patients with the Delta variant had a severe rate of 23.8%, a critical rate of 53.7%, and a mortality rate of 38.9%, which were significantly higher than those with the Omicron and Alpha variants. Conclusions The Alpha, Delta, and Omicron variants in this study had genetic diversity and differed from the strains reported in other countries, with the Delta variant producing significantly more clinical severity and mortality than the Alpha and Omicron variants.
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Affiliation(s)
- Le Van Nam
- Departments of Infectious Disease, Military Hospital, Hanoi, Vietnam
| | - Trinh Cong Dien
- Departments of Infectious Disease, Military Hospital, Hanoi, Vietnam
| | | | - Pham Ngoc Thach
- Micobiology and Molecular Biology Department, National Hospital for Tropical Diseases, Hanoi, Vietnam
| | - Le Van Duyet
- Micobiology and Molecular Biology Department, National Hospital for Tropical Diseases, Hanoi, Vietnam
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16
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Rong N, Wu J, Zhao B, Peng W, Yang H, Zhang G, Ruan D, Wei X, Liu J. Comparison of the pathogenicity and neutrophil and monocyte response between SARS-CoV-2 prototype and Omicron BA.1 in a lethal mouse model. Animal Model Exp Med 2024. [PMID: 38760905 DOI: 10.1002/ame2.12419] [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: 01/09/2024] [Accepted: 04/02/2024] [Indexed: 05/20/2024] Open
Abstract
BACKGROUND SARS-CoV-2, first identified in late 2019, has given rise to numerous variants of concern (VOCs), posing a significant threat to human health. The emergence of Omicron BA.1.1 towards the end of 2021 led to a pandemic in early 2022. At present, the lethal mouse model for the study of SARS-CoV-2 needs supplementation, and the alterations in neutrophils and monocytes caused by different strains remain to be elucidated. METHODS Human ACE2 transgenic mice were inoculated with the SARS-CoV-2 prototype and Omicron BA.1, respectively. The pathogenicity of the two strains was evaluated by observing clinical symptoms, viral load and pathology. Complete blood count, immunohistochemistry and flow cytometry were performed to detect the alterations of neutrophils and monocytes caused by the two strains. RESULTS Our findings revealed that Omicron BA.1 exhibited significantly lower virulence compared to the SARS-CoV-2 prototype in the mouse model. Additionally, we observed a significant increase in the proportion of neutrophils late in infection with the SARS-CoV-2 prototype and Omicron BA.1. We found that the proportion of monocytes increased at first and then decreased. The trends in the changes in the proportions of neutrophils and monocytes induced by the two strains were similar. CONCLUSION Our study provides valuable insights into the utility of mouse models for simulating the severe disease of SARS-CoV-2 prototype infection and the milder manifestation associated with Omicron BA.1. SARS-CoV-2 prototype and Omicron BA.1 resulted in similar trends in the changes in neutrophils and monocytes.
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Affiliation(s)
- Na Rong
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Jing Wu
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Binbin Zhao
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Wanjun Peng
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Hekai Yang
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Gengxin Zhang
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | | | - Xiaohui Wei
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Jiangning Liu
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
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17
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Han HJ, Kim SW, Kim H, So J, Lee EJ, Lim YM, Lee JH, Lee MA, Kim BJ, Baek SH, Lee HS, Sohn E, Kim S, Park JS, Kang M, Park HJ, Yoon BA, Kim JK, Seok HY, Kim S, Min JH, Chung YH, Cho JH, Kim JE, Oh SI, Shin HY. Impact of COVID-19 Infection and Its Association With Previous Vaccination in Patients With Myasthenia Gravis in Korea: A Multicenter Retrospective Study. J Korean Med Sci 2024; 39:e150. [PMID: 38742290 PMCID: PMC11091230 DOI: 10.3346/jkms.2024.39.e150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/10/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND During the coronavirus disease 2019 (COVID-19) pandemic, patients with myasthenia gravis (MG) were more susceptible to poor outcomes owing to respiratory muscle weakness and immunotherapy. Several studies conducted in the early stages of the COVID-19 pandemic reported higher mortality in patients with MG compared to the general population. This study aimed to investigate the clinical course and prognosis of COVID-19 in patients with MG and to compare these parameters between vaccinated and unvaccinated patients in South Korea. METHODS This multicenter, retrospective study, which was conducted at 14 tertiary hospitals in South Korea, reviewed the medical records and identified MG patients who contracted COVID-19 between February 2022 and April 2022. The demographic and clinical characteristics associated with MG and vaccination status were collected. The clinical outcomes of COVID-19 infection and MG were investigated and compared between the vaccinated and unvaccinated patients. RESULTS Ninety-two patients with MG contracted COVID-19 during the study. Nine (9.8%) patients required hospitalization, 4 (4.3%) of whom were admitted to the intensive care unit. Seventy-five of 92 patients were vaccinated before contracting COVID-19 infection, and 17 were not. During the COVID-19 infection, 6 of 17 (35.3%) unvaccinated patients were hospitalized, whereas 3 of 75 (4.0%) vaccinated patients were hospitalized (P < 0.001). The frequencies of ICU admission and mechanical ventilation were significantly lower in the vaccinated patients than in the unvaccinated patients (P = 0.019 and P = 0.032, respectively). The rate of MG deterioration was significantly lower in the vaccinated patients than in the unvaccinated patients (P = 0.041). Logistic regression after weighting revealed that the risk of hospitalization and MG deterioration after COVID-19 infection was significantly lower in the vaccinated patients than in the unvaccinated patients. CONCLUSION This study suggests that the clinical course and prognosis of patients with MG who contracted COVID-19 during the dominance of the omicron variant of COVID-19 may be milder than those at the early phase of the COVID-19 pandemic when vaccination was unavailable. Vaccination may reduce the morbidity of COVID-19 in patients with MG and effectively prevent MG deterioration induced by COVID-19 infection.
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Affiliation(s)
- Hee Jo Han
- Department of Neurology, Yonsei University College of Medicine, Seoul, Korea
| | - Seung Woo Kim
- Department of Neurology, Yonsei University College of Medicine, Seoul, Korea
| | - Hyunjin Kim
- Department of Neurology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jungmin So
- Department of Neurology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Eun-Jae Lee
- Department of Neurology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Young-Min Lim
- Department of Neurology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jung Hwan Lee
- Department of Neurology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Myung Ah Lee
- Department of Neurology, Uijeongbu St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Byung-Jo Kim
- Department of Neurology, Korea University Anam Hospital, Seoul, Korea
| | - Seol-Hee Baek
- Department of Neurology, Korea University Anam Hospital, Seoul, Korea
| | - Hyung-Soo Lee
- Department of Neurology, National Medical Center, Seoul, Korea
| | - Eunhee Sohn
- Department of Neurology, Chungnam National University Hospital, Chungnam National University College of Medicine, Daejeon, Korea
| | - Sooyoung Kim
- Department of Neurology, Chungnam National University Hospital, Chungnam National University College of Medicine, Daejeon, Korea
| | - Jin-Sung Park
- Department of Neurology, Kyungpook National University Chilgok Hospital, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Minsung Kang
- Department of Neurology, Kyungpook National University Chilgok Hospital, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Hyung Jun Park
- Department of Neurology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Byeol-A Yoon
- Department of Neurology, Dong-A University College of Medicine, Busan, Korea
| | - Jong Kuk Kim
- Department of Neurology, Dong-A University College of Medicine, Busan, Korea
| | - Hung Youl Seok
- Department of Neurology, Keimyung University Dongsan Hospital, Keimyung University School of Medicine, Daegu, Korea
| | - Sohyeon Kim
- Department of Neurology, Keimyung University Dongsan Hospital, Keimyung University School of Medicine, Daegu, Korea
| | - Ju-Hong Min
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yeon Hak Chung
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jeong Hee Cho
- Department of Neurology, National Health Insurance Service Ilsan Hospital, Goyang, Korea
| | - Jee-Eun Kim
- Department of Neurology, Ewha Womans University Seoul Hospital, Ewha Womans University College of Medicine, Seoul, Korea
| | - Seong-Il Oh
- Department of Neurology, Kyung Hee University Hospital, Kyung Hee University College of Medicine, Seoul, Korea
| | - Ha Young Shin
- Department of Neurology, Yonsei University College of Medicine, Seoul, Korea.
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18
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Song Q, Liu H, Tan H, Yang B, Zhang H, Liu L, Fan C. Prophylactic-dose direct oral anticoagulants for non-hospitalised people with COVID-19: A meta-analysis of randomised controlled trials. J Glob Health 2024; 14:05015. [PMID: 38665058 PMCID: PMC11046256 DOI: 10.7189/jogh.14.05015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024] Open
Abstract
Background Several reviews have been conducted on thromboprophylaxis in non-hospitalised patients with coronavirus disease 2019 (COVID-19). In this systematic review and meta-analysis, we sought to investigate the impact of prophylactic-dose direct oral anticoagulants (DOACs) in this population. Methods We searched PubMed, Web of Science, EMBASE and Cochrane Library for randomised controlled trials (RCTs) comparing prophylactic-dose DOACs with placebo or no treatment in non-hospitalised patients with COVID-19 until September 2023. The primary efficacy outcome was a composite of all-cause mortality and thromboembolic events, while major bleeding events were the primary safety outcome. We expressed continuous outcome data as mean differences (MDs) with 95% confidence intervals (CIs) and dichotomous outcome data as risk ratios (RRs) with 95% CIs. Results We included six RCTs involving 4307 patients. Prophylactic-dose DOAC therapy compared with placebo or no treatment was associated with significantly decreased risks of the composite outcome of all-cause mortality and thromboembolic events (1.43% vs 2.67% (RR = 0.53; 95% CI = 0.34-0.82, P = 0.004, I2 = 3%)). Major bleeding events were infrequent, and we detected no significant differences between patients assigned to prophylactic-dose DOACs vs placebo or no treatment (0.19% vs 0.05% (RR = 2.50; 95% CI = 0.49-12.87, P = 0.27, I2 = 0%)). The use of prophylactic-dose DOACs was also associated with a reduction in venous thromboembolism, with no difference in all-cause mortality, arterial thromboembolism, hospitalisations, and clinically relevant nonmajor bleeding between two groups. Sensitivity analyses with the leave-one-out method for the primary efficacy and safety outcome did not change the effect estimate substantially. Conclusions We found that prophylaxis-dose DOACs could significantly improve clinical outcomes and reduce venous thrombotic events without increasing the risk of major bleeding events compared with placebo or no treatment in non-hospitalised patients with COVID-19. Registration PROSPERO: CRD42023466889.
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Affiliation(s)
- Qingchun Song
- Department of Cardiovascular Surgery, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongduan Liu
- Department of Cardiovascular Surgery, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Haoyu Tan
- Department of Cardiovascular Surgery, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Benli Yang
- Department of Cardiovascular Surgery, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hao Zhang
- Department of Cardiovascular Surgery, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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19
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Ray A, Minh Tran TT, Santos Natividade RD, Moreira RA, Simpson JD, Mohammed D, Koehler M, L Petitjean SJ, Zhang Q, Bureau F, Gillet L, Poma AB, Alsteens D. Single-Molecule Investigation of the Binding Interface Stability of SARS-CoV-2 Variants with ACE2. ACS NANOSCIENCE AU 2024; 4:136-145. [PMID: 38644967 PMCID: PMC11027127 DOI: 10.1021/acsnanoscienceau.3c00060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 04/23/2024]
Abstract
The SARS-CoV-2 pandemic spurred numerous research endeavors to comprehend the virus and mitigate its global severity. Understanding the binding interface between the virus and human receptors is pivotal to these efforts and paramount to curbing infection and transmission. Here we employ atomic force microscopy and steered molecular dynamics simulation to explore SARS-CoV-2 receptor binding domain (RBD) variants and angiotensin-converting enzyme 2 (ACE2), examining the impact of mutations at key residues upon binding affinity. Our results show that the Omicron and Delta variants possess strengthened binding affinity in comparison to the Mu variant. Further, using sera from individuals either vaccinated or with acquired immunity following Delta strain infection, we assess the impact of immunity upon variant RBD/ACE2 complex formation. Single-molecule force spectroscopy analysis suggests that vaccination before infection may provide stronger protection across variants. These results underscore the need to monitor antigenic changes in order to continue developing innovative and effective SARS-CoV-2 abrogation strategies.
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Affiliation(s)
- Ankita Ray
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Thu Thi Minh Tran
- Faculty
of Materials Science and Technology, University
of Science—VNU HCM, 227 Nguyen Van Cu Street, District 5, 700000 Ho Chi Minh City, Vietnam
- Vietnam
National University, 700000 Ho Chi Minh City, Vietnam
| | - Rita dos Santos Natividade
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Rodrigo A. Moreira
- Basque
Center for Applied Mathematics, Mazarredo 14, 48009 Bilbao, Spain
| | - Joshua D. Simpson
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Danahe Mohammed
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Melanie Koehler
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Simon J. L Petitjean
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Qingrong Zhang
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Fabrice Bureau
- Laboratory
of Cellular and Molecular Immunology, GIGA Institute, Liège University, 4000 Liège, Belgium
| | - Laurent Gillet
- Immunology-Vaccinology
Lab of the Faculty of Veterinary Medicine, Liège University, 4000 Liège, Belgium
| | - Adolfo B. Poma
- Institute
of Fundamental Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland
| | - David Alsteens
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
- WELBIO
department, WEL Research Institute, 1300 Wavre, Belgium
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20
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Ørbo HS, Bjørlykke KH, Sexton J, Jyssum I, Tveter AT, Christensen IE, Mjaaland S, Kvien TK, Grødeland G, Kro GB, Jahnsen J, Haavardsholm EA, Munthe LA, Provan SA, Vaage JT, Goll GL, Jørgensen KK, Syversen SW. Incidence and outcome of COVID-19 following vaccine and hybrid immunity in patients on immunosuppressive therapy: identification of protective post-immunisation anti-RBD antibody levels in a prospective cohort study. RMD Open 2024; 10:e003545. [PMID: 38599653 PMCID: PMC11015197 DOI: 10.1136/rmdopen-2023-003545] [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: 07/28/2023] [Accepted: 02/15/2024] [Indexed: 04/12/2024] Open
Abstract
OBJECTIVES To assess incidence, severity and predictors of COVID-19, including protective post-vaccination levels of antibodies to the receptor-binding domain of SARS-CoV-2 spike protein (anti-RBD), informing further vaccine strategies for patients with immune-mediated inflammatory diseases (IMIDs) on immunosuppressive medication. METHODS IMIDs on immunosuppressives and healthy controls (HC) receiving SARS-CoV-2 vaccines were included in this prospective observational study. COVID-19 and outcome were registered and anti-RBD antibodies measured 2-5 weeks post-immunisation. RESULTS Between 15 February 2021 and 15 February 2023, 1729 IMIDs and 350 HC provided blood samples and self-reported COVID-19. The incidence of COVID-19 was 66% in patients and 67% in HC, with re-infection occurring in 12% of patients. Severe COVID-19 was recorded in 22 (2%) patients and no HC. No COVID-19-related deaths occurred. Vaccine-induced immunity gave higher risk of COVID-19 (HR 5.89 (95% CI 4.45 to 7.80)) than hybrid immunity. Post-immunisation anti-RBD levels <6000 binding antibody units/mL were associated with an increased risk of COVID-19 following three (HR 1.37 (95% CI 1.08 to 1.74)) and four doses (HR 1.28 (95% CI 1.02 to 1.62)), and of COVID-19 re-infection (HR 4.47 (95% CI 1.87 to 10.67)). CONCLUSION Vaccinated patients with IMID have a low risk of severe COVID-19. Hybrid immunity lowers the risk of infection. High post-immunisation anti-RBD levels protect against COVID-19. These results suggest that knowledge on COVID-19 history, and assessment of antibody levels post-immunisation can help individualise vaccination programme series in high-risk individuals. TRIAL REGISTRATION NUMBER NCT04798625.
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Affiliation(s)
- Hilde S Ørbo
- Center for treatment of Rheumatic and Musculoskeletal Diseases (REMEDY), Diakonhjemmet Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Kristin H Bjørlykke
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - Joseph Sexton
- Center for treatment of Rheumatic and Musculoskeletal Diseases (REMEDY), Diakonhjemmet Hospital, Oslo, Norway
| | - Ingrid Jyssum
- Center for treatment of Rheumatic and Musculoskeletal Diseases (REMEDY), Diakonhjemmet Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anne T Tveter
- Center for treatment of Rheumatic and Musculoskeletal Diseases (REMEDY), Diakonhjemmet Hospital, Oslo, Norway
| | - Ingrid E Christensen
- Center for treatment of Rheumatic and Musculoskeletal Diseases (REMEDY), Diakonhjemmet Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Siri Mjaaland
- Division of Infection Control, Section for Immunology, Norwegian Institute of Public Health, Oslo, Norway
| | - Tore K Kvien
- Center for treatment of Rheumatic and Musculoskeletal Diseases (REMEDY), Diakonhjemmet Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Gunnveig Grødeland
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Grete B Kro
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Jørgen Jahnsen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - Espen A Haavardsholm
- Center for treatment of Rheumatic and Musculoskeletal Diseases (REMEDY), Diakonhjemmet Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ludvig A Munthe
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, University of Oslo, Oslo, Norway
| | - Sella A Provan
- Center for treatment of Rheumatic and Musculoskeletal Diseases (REMEDY), Diakonhjemmet Hospital, Oslo, Norway
- Section for Public Health, Inland Norway University of Applied Sciences, Elverum, Norway
| | - John T Vaage
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Guro Løvik Goll
- Center for treatment of Rheumatic and Musculoskeletal Diseases (REMEDY), Diakonhjemmet Hospital, Oslo, Norway
- Institute of Health and Society, University of Oslo, Oslo, Norway
| | | | - Silje Watterdal Syversen
- Center for treatment of Rheumatic and Musculoskeletal Diseases (REMEDY), Diakonhjemmet Hospital, Oslo, Norway
- Institute of Health and Society, University of Oslo, Oslo, Norway
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21
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Lv J, Liping C, Huaying W. The Diagnostic and Predictive Value of Biomarkers for Pulmonary Fibrosis in Patients with Coronavirus Disease 2019. J Glob Infect Dis 2024; 16:45-53. [PMID: 39081507 PMCID: PMC11286082 DOI: 10.4103/jgid.jgid_150_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/11/2023] [Accepted: 01/15/2024] [Indexed: 08/02/2024] Open
Abstract
Introduction In coronavirus disease 2019 (COVID-19), particularly in older people, dysregulated immune response and aberrant repair can result in varied severity secondary pulmonary fibrosis (PF). By detecting some indicators, the occurrence and prognosis of fibrosis can be measured, providing directions for COVID-19 treatment. Methods The research study lasted for 3 months and involved 88 COVID-19 patients. According to the chest radiological examination, 47 (53.41%) individuals were found to have no PF, while 41 (46.59%) showed PF. Clinical data such as inflammation markers, imaging findings, blood gas analysis, and hospital stay length were collected. Results With area under the curve values of 0.7413, 0.7741, and 0.7048, respectively, and the study of the receiver operating characteristic curve demonstrated that mucin 1 (MUC1), carcinoembryonic antigen (CEA), and CXC chemokine receptor 10 (CXCL10) could diagnose the presence of COVID-19 PF. To evaluate the possibility of PF following severe acute respiratory syndrome coronavirus-2 infection, we established particular values for MUC1, CEA, and CXCL10 (1.296 ng/ml, 4.315 ng/ml, and 32.77 ng/ml, respectively). The survival curve for hospital days indicated that the length of hospital stays positively correlated with these three factors (P < 0.01). Transforming growth factor-beta did not correlate significantly with the severity of COVID-19 or PF. Conclusion The results of this study suggested that the MUC1, CEA, and CXCL10 can be employed to explore the severity of secondary PF in COVID-19.
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Affiliation(s)
- Jiapei Lv
- Department of Respiratory and Critical Care Medicine, The People’s Hospital Affiliated to Ningbo University, Ningbo, China
| | - Chen Liping
- Department of Respiratory and Critical Care Medicine, The People’s Hospital Affiliated to Ningbo University, Ningbo, China
| | - Wang Huaying
- Department of Respiratory and Critical Care Medicine, The People’s Hospital Affiliated to Ningbo University, Ningbo, China
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22
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Schlosser T, Krasselt M, Elsing L, Hecker M, Holler B, Hoffmeister A. Symptoms and Severity of COVID-19 in Patients with Immune-Mediated Inflammatory Diseases: Experience of a University Medical Center. Autoimmune Dis 2024; 2024:6627035. [PMID: 38571561 PMCID: PMC10990649 DOI: 10.1155/2024/6627035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/31/2024] [Accepted: 02/14/2024] [Indexed: 04/05/2024] Open
Abstract
Background The pandemic situation of the novel coronavirus (severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)) and its associated disease (coronavirus disease 2019 (COVID-19)) represents a challenging condition with a plethora of aspects. The course of COVID-19 in patients with immune-mediated inflammatory diseases (IMID) such as inflammatory bowel disease (IBD) and rheumatic diseases (RD) is not well known. Our study is one step toward closing this gap by collecting data on vaccination rates, infection-free survival, and individual symptom severity. Methods We conducted a prospective questionnaire-based study between April 2022 and October 2022 at our university hospital. Outward patients over the age of 18 years were screened for participation and reported about their infection/infection-free survival since the start of the pandemic. Results Finally, 156 patients were included in the study, 117 (75.0%) of which had inflammatory bowel disease and 39 (25.0%) patients with rheumatic disease. Altogether, 143 (91.7%) persons had received at least one vaccination against SARS-CoV-2. A total of 153 patients provided information regarding their COVID-19 history: 81 patients (52.0%) self-reported about their SARS-CoV-2 infection. In general, courses of infection were mild: only two patients (2.5% of patients with reported COVID-19) were hospitalized due to COVID-19 with one (1.2%) of the two needing intensive care. Asymptomatic COVID-19 had been described by 7 persons (8.6% of patients with reported COVID-19). Acute COVID-19 was accompanied by fatigue/tiredness in 58 persons (71.6% of patients with history of COVID-19) as the most frequent symptom. Other complaints were common cold (55 patients = 67.9%), cough (51 patients = 63.0%), headache (44 patients = 54.3%), and fever (35 patients = 43.2%). Stratified by vaccination status (unvaccinated vs. at least once vaccinated), the time to infection differed significantly (logrank test: p = 0.04, Chi2 4.1). At least once vaccinated people had a median COVID-19-free survival of 28.5 months (confidence interval (CI): 23.6 months-not reached). Without any vaccination, the estimated time to infection was 25.1 months (CI: 23.6 months-not reached). Conclusion Our IMID patients have a high rate of vaccination against SARS-CoV-2. Data show a significantly longer infection-free survival in vaccinated IMID patients as compared to unvaccinated patients. Discrimination between symptoms of COVID-19 and a concomitant inflammatory disease is difficult as complaints might be overlapping. This trial is registered with DRKS00028880.
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Affiliation(s)
- Tobias Schlosser
- Department of Oncology, Gastroenterology, Hepatology, Pneumology and Infectious Diseases, Division of Gastroenterology, University Medical Center, Leipzig, Germany
| | - Marco Krasselt
- Department of Endocrinology, Nephrology and Rheumatology, Division of Rheumatology, University Medical Center, Leipzig, Germany
| | - Louis Elsing
- Department of Oncology, Gastroenterology, Hepatology, Pneumology and Infectious Diseases, Division of Gastroenterology, University Medical Center, Leipzig, Germany
| | - Martin Hecker
- Department of Oncology, Gastroenterology, Hepatology, Pneumology and Infectious Diseases, Division of Gastroenterology, University Medical Center, Leipzig, Germany
| | - Babett Holler
- Department of Oncology, Gastroenterology, Hepatology, Pneumology and Infectious Diseases, Division of Gastroenterology, University Medical Center, Leipzig, Germany
| | - Albrecht Hoffmeister
- Department of Oncology, Gastroenterology, Hepatology, Pneumology and Infectious Diseases, Division of Gastroenterology, University Medical Center, Leipzig, Germany
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23
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Sila T, Suriyaamorn W, Toh C, Rajborirug S, Surasombatpattana S, Thongsuksai P, Kongkamol C, Chusri S, Sornsenee P, Wuthisuthimethawee P, Chaowanawong R, Sangkhathat S, Ingviya T. Factors associated with the worsening of COVID-19 symptoms among cohorts in community- or home-isolation care in southern Thailand. Front Public Health 2024; 12:1350304. [PMID: 38572011 PMCID: PMC10987961 DOI: 10.3389/fpubh.2024.1350304] [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: 12/05/2023] [Accepted: 02/09/2024] [Indexed: 04/05/2024] Open
Abstract
Introduction This study aimed to investigate factors associated with time-to-referral due to worsening symptoms in patients with laboratory-confirmed COVID-19 in southern Thailand. While underlying diseases have been evaluated to assess COVID-19 severity, the influence of vaccinations and treatments is also crucial. Methods A cohort of 8,638 patients quarantined in home or community isolation with laboratory-confirmed COVID-19 was analyzed. Survival analysis and the Cox proportional hazard ratio were employed to assess factors influencing time-toreferral. Results Age ≥ 60 years, neurologic disorders, cardiovascular disease, and human immunodeficiency virus infection were identified as significant risk factors for severe COVID-19 referral. Patients who received full- or booster-dose vaccinations had a lower risk of experiencing severe symptoms compared to unvaccinated patients. Notably, individuals vaccinated during the Omicron-dominant period had a substantially lower time-to-referral than those unvaccinated during the Delta-dominant period. Moreover, patients vaccinated between 1 and 6 months prior to infection had a significantly lower risk of time-to-referral than the reference group. Discussion These findings demonstrate early intervention in high-risk COVID-19 patients and the importance of vaccination efficacy to reduce symptom severity. The study provides valuable insights for guiding future epidemic management strategies and optimising patient care during infectious disease outbreaks.
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Affiliation(s)
- Thanit Sila
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
- Department of Health Science and Clinical Research, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Wisanuwee Suriyaamorn
- Division of Digital Innovation and Data Analytics, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Chanavee Toh
- Department of Health Science and Clinical Research, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Songyos Rajborirug
- Department of Epidemiology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | | | - Paramee Thongsuksai
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
- Department of Health Science and Clinical Research, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Chanon Kongkamol
- Division of Digital Innovation and Data Analytics, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
- Department of Family Medicine and Preventive Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Sarunyou Chusri
- Department of Internal Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Phoomjai Sornsenee
- Faculty of Medicine, Department of Family Medicine and Preventive Medicine, Prince of Songkla University, Hat Yai, Songkla, Thailand
| | - Prasit Wuthisuthimethawee
- Department of Emergency Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Raya Chaowanawong
- Faculty of Nursing, Prince of Songkla University, Hat Yai, Songkla, Thailand
| | - Surasak Sangkhathat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
- Faculty of Medicine, Translational Medicine Research Center, Prince of Songkla University, Songkhla, Thailand
| | - Thammasin Ingviya
- Division of Digital Innovation and Data Analytics, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
- Department of Family Medicine and Preventive Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
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24
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Kumwichar P, Poonsiri C, Botwright S, Sirichumroonwit N, Loharjun B, Thawillarp S, Cheewaruangroj N, Chokchaisiripakdee A, Teerawattananon Y, Chongsuvivatwong V. Durability of the Effectiveness of Heterologous COVID-19 Vaccine Regimens in Thailand: Retrospective Cohort Study Using National Registration Data. JMIR Public Health Surveill 2024; 10:e48255. [PMID: 38441923 PMCID: PMC10951833 DOI: 10.2196/48255] [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: 04/17/2023] [Revised: 10/31/2023] [Accepted: 02/08/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND The durability of heterologous COVID-19 vaccine effectiveness (VE) has been primarily studied in high-income countries, while evaluation of heterologous vaccine policies in low- and middle-income countries remains limited. OBJECTIVE We aimed to evaluate the duration during which the VE of heterologous COVID-19 vaccine regimens in mitigating serious outcomes, specifically severe COVID-19 and death following hospitalization with COVID-19, remains over 50%. METHODS We formed a dynamic cohort by linking records of Thai citizens aged ≥18 years from citizen vital, COVID-19 vaccine, and COVID-19 cases registry databases between May 2021 and July 2022. Encrypted citizen identification numbers were used to merge the data between the databases. This study focuses on 8 common heterologous vaccine sequences: CoronaVac/ChAdOx1, ChAdOx1/BNT162b2, CoronaVac/CoronaVac/ChAdOx1, CoronaVac/ChAdOx1/ChAdOx1, CoronaVac/ChAdOx1/BNT162b2, BBIBP-CorV/BBIBP-CorV/BNT162b2, ChAdOx1/ChAdOx1/BNT162b2, and ChAdOx1/ChAdOx1/mRNA-1273. Nonimmunized individuals were considered for comparisons. The cohort was stratified according to the vaccination status, age, sex, province location, month of vaccination, and outcome. Data analysis employed logistic regression to determine the VE, accounting for potential confounders and durability over time, with data observed over a follow-up period of 7 months. RESULTS This study includes 52,580,841 individuals, with approximately 17,907,215 and 17,190,975 receiving 2- and 3-dose common heterologous vaccines (not mutually exclusive), respectively. The 2-dose heterologous vaccinations offered approximately 50% VE against severe COVID-19 and death following hospitalization with COVID-19 for 2 months; however, the protection significantly declined over time. The 3-dose heterologous vaccinations sustained over 50% VE against both outcomes for at least 8 months, as determined by logistic regression with durability time-interaction modeling. The vaccine sequence consisting of CoronaVac/CoronaVac/ChAdOx1 demonstrated >80% VE against both outcomes, with no evidence of VE waning. The final monthly measured VE of CoronaVac/CoronaVac/ChAdOx1 against severe COVID-19 and death following hospitalization at 7 months after the last dose was 82% (95% CI 80.3%-84%) and 86.3% (95% CI 83.6%-84%), respectively. CONCLUSIONS In Thailand, within a 7-month observation period, the 2-dose regimens could not maintain a 50% VE against severe and fatal COVID-19 for over 2 months, but all of the 3-dose regimens did. The CoronaVac/CoronaVac/ChAdOx1 regimen showed the best protective effect against severe and fatal COVID-19. The estimated durability of 50% VE for at least 8 months across all 3-dose heterologous COVID-19 vaccine regimens supports the adoption of heterologous prime-boost vaccination strategies, with a primary series of inactivated virus vaccine and boosting with either a viral vector or an mRNA vaccine, to prevent similar pandemics in low- and middle-income countries.
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Affiliation(s)
- Ponlagrit Kumwichar
- Department of Epidemiology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Chittawan Poonsiri
- Health Intervention and Technology Assessment Program, Ministry of Public Health, Nonthaburi, Thailand
| | - Siobhan Botwright
- Health Intervention and Technology Assessment Program, Ministry of Public Health, Nonthaburi, Thailand
| | - Natchalaikorn Sirichumroonwit
- Department of Medical Services, Institute of Medical Research and Technology Assessment, Ministry of Public Health, Nonthaburi, Thailand
| | - Bootsakorn Loharjun
- Department of Medical Services, Institute of Medical Research and Technology Assessment, Ministry of Public Health, Nonthaburi, Thailand
| | | | | | | | - Yot Teerawattananon
- Health Intervention and Technology Assessment Program, Ministry of Public Health, Nonthaburi, Thailand
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25
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Yotsuyanagi H, Ohmagari N, Doi Y, Yamato M, Bac NH, Cha BK, Imamura T, Sonoyama T, Ichihashi G, Sanaki T, Tsuge Y, Uehara T, Mukae H. Efficacy and Safety of 5-Day Oral Ensitrelvir for Patients With Mild to Moderate COVID-19: The SCORPIO-SR Randomized Clinical Trial. JAMA Netw Open 2024; 7:e2354991. [PMID: 38335000 PMCID: PMC10858401 DOI: 10.1001/jamanetworkopen.2023.54991] [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] [Received: 08/31/2023] [Accepted: 12/14/2023] [Indexed: 02/10/2024] Open
Abstract
Importance Treatment options for COVID-19 are warranted irrespective of the presence of risk factors for severe disease. Objective To assess the efficacy and safety of ensitrelvir in patients with mild to moderate COVID-19. Design, Setting, and Participants This phase 3 part of a phase 2/3, double-blind, placebo-controlled randomized clinical trial was conducted from February 10 to July 10, 2022, with a 28-day follow-up period, at 92 institutions in Japan, Vietnam, and South Korea. Patients (aged 12 to <70 years) with mild to moderate COVID-19 within 120 hours of positive viral test results were studied. Interventions Patients were randomized (1:1:1) to receive 125 mg of once-daily ensitrelvir (375 mg on day 1), 250 mg of once-daily ensitrelvir (750 mg on day 1), or placebo for 5 days. Main Outcomes and Measures The primary end point was the time to resolution of the composite of 5 characteristic symptoms of SARS-CoV-2 Omicron infection, assessed using a Peto-Prentice generalized Wilcoxon test stratified by vaccination history. Virologic efficacy and safety were also assessed. Results A total of 1821 patients were randomized, of whom 1030 (347 in the 125-mg ensitrelvir group, 340 in the 250-mg ensitrelvir group, and 343 in the placebo group) were randomized in less than 72 hours of disease onset (primary analysis population). The mean (SD) age in this population was 35.2 (12.3) years, and 552 (53.6%) were men. A significant difference was observed between the 125-mg ensitrelvir group and the placebo group (P = .04 with a Peto-Prentice generalized Wilcoxon test). The difference in median time was approximately 1 day between the 125-mg ensitrelvir group and the placebo group (167.9 vs 192.2 hours; difference, -24.3 hours; 95% CI, -78.7 to 11.7 hours). Adverse events were observed in 267 of 604 patients (44.2%) in the 125-mg ensitrelvir group, 321 of 599 patients (53.6%) in the 250-mg ensitrelvir group, and 150 of 605 patients (24.8%) in the placebo group, which included a decrease in high-density lipoprotein level (188 [31.1%] in the 125-mg ensitrelvir group, 231 [38.6%] in the 250-mg ensitrelvir group, and 23 [3.8%] in the placebo group). No treatment-related serious adverse events were reported. Conclusions and Relevance In this randomized clinical trial, 125-mg ensitrelvir treatment reduced the time to resolution of the 5 typical COVID-19 symptoms compared with placebo in patients treated in less than 72 hours of disease onset; the absolute difference in median time to resolution was approximately 1 day. Ensitrelvir demonstrated clinical and antiviral efficacy without new safety concerns. Generalizability to populations outside Asia should be confirmed. Trial Registration Japan Registry of Clinical Trials Identifier: jRCT2031210350.
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Affiliation(s)
| | - Norio Ohmagari
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Departments of Microbiology and Infectious Diseases, Fujita Health University School of Medicine, Toyoake, Japan
| | - Masaya Yamato
- Infectious Diseases Center, Rinku General Medical Center, Izumisano, Japan
| | - Nguyen Hoang Bac
- Endoscopic Surgery Training Center, University Medical Center, University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Bong Ki Cha
- Department of Internal Medicine, Chung-Ang Medical Health Care System Hyundae Hospital, Gyeonggi-do, Republic of Korea
| | - Takumi Imamura
- Drug Development and Regulatory Science Division, Shionogi & Co, Ltd, Osaka, Japan
| | - Takuhiro Sonoyama
- Drug Development and Regulatory Science Division, Shionogi & Co, Ltd, Osaka, Japan
| | - Genki Ichihashi
- Drug Development and Regulatory Science Division, Shionogi & Co, Ltd, Osaka, Japan
| | - Takao Sanaki
- Research Division, Shionogi & Co, Ltd, Toyonaka, Japan
| | - Yuko Tsuge
- Drug Development and Regulatory Science Division, Shionogi & Co, Ltd, Osaka, Japan
| | - Takeki Uehara
- Drug Development and Regulatory Science Division, Shionogi & Co, Ltd, Osaka, Japan
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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26
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Sievers BL, Cheng MTK, Csiba K, Meng B, Gupta RK. SARS-CoV-2 and innate immunity: the good, the bad, and the "goldilocks". Cell Mol Immunol 2024; 21:171-183. [PMID: 37985854 PMCID: PMC10805730 DOI: 10.1038/s41423-023-01104-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023] Open
Abstract
An ancient conflict between hosts and pathogens has driven the innate and adaptive arms of immunity. Knowledge about this interplay can not only help us identify biological mechanisms but also reveal pathogen vulnerabilities that can be leveraged therapeutically. The humoral response to SARS-CoV-2 infection has been the focus of intense research, and the role of the innate immune system has received significantly less attention. Here, we review current knowledge of the innate immune response to SARS-CoV-2 infection and the various means SARS-CoV-2 employs to evade innate defense systems. We also consider the role of innate immunity in SARS-CoV-2 vaccines and in the phenomenon of long COVID.
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Affiliation(s)
| | - Mark T K Cheng
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kata Csiba
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Bo Meng
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
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Beppu H, Fukuda T, Otsubo N, Akihisa T, Kawanishi T, Ogawa T, Abe Y, Endo M, Hanawa T, Sugita C, Kikkawa Y, Yamada T, Wakai S. Comparative outcomes of hemodialysis patients facing pre-Omicron and Omicron COVID-19 epidemics. Ther Apher Dial 2024; 28:51-60. [PMID: 37724487 DOI: 10.1111/1744-9987.14067] [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: 04/20/2023] [Revised: 07/01/2023] [Accepted: 09/06/2023] [Indexed: 09/20/2023]
Abstract
INTRODUCTION This study elucidates factors affecting the severity and mortality in pre-Omicron and Omicron strains of SARS-CoV-2 and vaccination impact. METHODS This single-center retrospective observational study included 1598 hospitalized COVID-19 patients. Patients were grouped into "pre-Omicron" and "Omicron" periods. The endpoint was severe COVID-19 (oxygen saturation [SpO2 ] < 94%). Logistic regression examined associations between clinical factors, including hemodialysis (HD), and the endpoint. RESULTS The HD patient mortality rate dropped from 16% pre-Omicron to 4% during the Omicron epidemic. HD was significantly associated with the study endpoint in both epidemics. Unvaccinated patients had a greater risk of reaching the study endpoint among patients receiving HD. CONCLUSION These findings suggest that the Omicron variant, alongside vaccination and healthcare innovations, led to improved prognoses for HD patients with COVID-19. However, HD patients remain at a greater risk for severe COVID-19. Increased vaccination rates and optimized healthcare resources can improve this vulnerable population's prognoses.
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Affiliation(s)
- Hiroko Beppu
- Department of Nephrology, Tokyo Metropolitan Okubo Hospital, Tokyo, Japan
- Department of Cooperative Graduate School, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Tatsuya Fukuda
- Department of Endocrinology and Metabolism, Tokyo Metropolitan Okubo Hospital, Tokyo, Japan
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Naoya Otsubo
- Department of Endocrinology and Metabolism, Tokyo Metropolitan Okubo Hospital, Tokyo, Japan
| | - Taro Akihisa
- Department of Endocrinology and Metabolism, Tokyo Metropolitan Okubo Hospital, Tokyo, Japan
| | - Tomoko Kawanishi
- Department of Nephrology, Tokyo Metropolitan Okubo Hospital, Tokyo, Japan
| | - Toshie Ogawa
- Department of Nephrology, Tokyo Metropolitan Okubo Hospital, Tokyo, Japan
| | - Yasutomo Abe
- Department of Nephrology, Tokyo Metropolitan Okubo Hospital, Tokyo, Japan
| | - Mariko Endo
- Department of Nephrology, Tokyo Metropolitan Okubo Hospital, Tokyo, Japan
| | - Tomohide Hanawa
- Department of Pulmonary Medicine, Tokyo Metropolitan Okubo Hospital, Tokyo, Japan
| | - Chise Sugita
- Department of Pulmonary Medicine, Tokyo Metropolitan Okubo Hospital, Tokyo, Japan
| | - Yoshiaki Kikkawa
- Department of Cooperative Graduate School, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
- Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Tetsuya Yamada
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Sachiko Wakai
- Department of Nephrology, Tokyo Metropolitan Okubo Hospital, Tokyo, Japan
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28
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Baek S, Jeong YJ, Kim YH, Kim JY, Kim JH, Kim EY, Lim JK, Kim J, Kim Z, Kim K, Chung MJ. Development and Validation of a Robust and Interpretable Early Triaging Support System for Patients Hospitalized With COVID-19: Predictive Algorithm Modeling and Interpretation Study. J Med Internet Res 2024; 26:e52134. [PMID: 38206673 PMCID: PMC10811577 DOI: 10.2196/52134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/03/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Robust and accurate prediction of severity for patients with COVID-19 is crucial for patient triaging decisions. Many proposed models were prone to either high bias risk or low-to-moderate discrimination. Some also suffered from a lack of clinical interpretability and were developed based on early pandemic period data. Hence, there has been a compelling need for advancements in prediction models for better clinical applicability. OBJECTIVE The primary objective of this study was to develop and validate a machine learning-based Robust and Interpretable Early Triaging Support (RIETS) system that predicts severity progression (involving any of the following events: intensive care unit admission, in-hospital death, mechanical ventilation required, or extracorporeal membrane oxygenation required) within 15 days upon hospitalization based on routinely available clinical and laboratory biomarkers. METHODS We included data from 5945 hospitalized patients with COVID-19 from 19 hospitals in South Korea collected between January 2020 and August 2022. For model development and external validation, the whole data set was partitioned into 2 independent cohorts by stratified random cluster sampling according to hospital type (general and tertiary care) and geographical location (metropolitan and nonmetropolitan). Machine learning models were trained and internally validated through a cross-validation technique on the development cohort. They were externally validated using a bootstrapped sampling technique on the external validation cohort. The best-performing model was selected primarily based on the area under the receiver operating characteristic curve (AUROC), and its robustness was evaluated using bias risk assessment. For model interpretability, we used Shapley and patient clustering methods. RESULTS Our final model, RIETS, was developed based on a deep neural network of 11 clinical and laboratory biomarkers that are readily available within the first day of hospitalization. The features predictive of severity included lactate dehydrogenase, age, absolute lymphocyte count, dyspnea, respiratory rate, diabetes mellitus, c-reactive protein, absolute neutrophil count, platelet count, white blood cell count, and saturation of peripheral oxygen. RIETS demonstrated excellent discrimination (AUROC=0.937; 95% CI 0.935-0.938) with high calibration (integrated calibration index=0.041), satisfied all the criteria of low bias risk in a risk assessment tool, and provided detailed interpretations of model parameters and patient clusters. In addition, RIETS showed potential for transportability across variant periods with its sustainable prediction on Omicron cases (AUROC=0.903, 95% CI 0.897-0.910). CONCLUSIONS RIETS was developed and validated to assist early triaging by promptly predicting the severity of hospitalized patients with COVID-19. Its high performance with low bias risk ensures considerably reliable prediction. The use of a nationwide multicenter cohort in the model development and validation implicates generalizability. The use of routinely collected features may enable wide adaptability. Interpretations of model parameters and patients can promote clinical applicability. Together, we anticipate that RIETS will facilitate the patient triaging workflow and efficient resource allocation when incorporated into a routine clinical practice.
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Affiliation(s)
- Sangwon Baek
- Medical AI Research Center, Samsung Medical Center, Seoul, Republic of Korea
- Center for Data Science, New York University, New York, NY, United States
| | - Yeon Joo Jeong
- Department of Radiology, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Republic of Korea
| | - Yun-Hyeon Kim
- Department of Radiology, Chonnam National University Hospital, Gwangju, Republic of Korea
| | - Jin Young Kim
- Department of Radiology, Keimyung University Dongsan Hospital, Daegu, Republic of Korea
| | - Jin Hwan Kim
- Department of Radiology, Chungnam National University Hospital, Daejeon, Republic of Korea
| | - Eun Young Kim
- Department of Radiology, Gachon University Gil Medical Center, Incheon, Republic of Korea
| | - Jae-Kwang Lim
- Department of Radiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jungok Kim
- Department of Infectious Diseases, Chungnam National University Sejong Hospital, Sejong, Republic of Korea
| | - Zero Kim
- Medical AI Research Center, Samsung Medical Center, Seoul, Republic of Korea
- Department of Data Convergence & Future Medicine, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyunga Kim
- Department of Data Convergence & Future Medicine, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Biomedical Statistics Center, Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
- Department of Digital Health, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Myung Jin Chung
- Medical AI Research Center, Samsung Medical Center, Seoul, Republic of Korea
- Department of Data Convergence & Future Medicine, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Department of Digital Health, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
- Department of Radiology, Samsung Medical Center, Seoul, Republic of Korea
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29
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Ng DCE, Liew CH, Tan KK, Chin L, Awang EHB, Chandirasekharan DA, Surdi Roslan MJB, Jamil MB, Zainol Abidin NZ, Cheah YK, Alias MFB, Khoo EJ. Clinical severity of Omicron and Delta SARS-CoV-2 infections in children. Pediatr Int 2024; 66:e15777. [PMID: 38863264 DOI: 10.1111/ped.15777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 02/05/2024] [Accepted: 03/28/2024] [Indexed: 06/13/2024]
Abstract
BACKGROUND We aimed to compare the clinical features and severity of the Omicron and Delta variant infections among children hospitalized for coronavirus disease 2019 (COVID-19). METHODS Children 12 years old or less hospitalized for COVID-19 across five hospitals between January 1, 2021 and March 31, 2022 were identified using the state's pediatric COVID-19 registry. Delta and Omicron-infected patients without previous COVID-19 infection, COVID-19 vaccination, or co-infections were propensity-score matched 1:1 to control for differences in baseline characteristics. Clinical manifestations, treatments, and outcomes were analyzed. Disease severity was assessed using an adapted WHO ordinal scale. RESULTS Of the initial 1367 patients, 668 had Delta infection and 699 had Omicron infection. Propensity-score matching produced 558 matched pairs. Patients with Omicron infection were more likely to present with croup (the odds ratio, OR, was 10.87, with a 95% confidence interval, CI, ranging from 2.54 to 46.59), lower respiratory tract infection (OR 2.32, 95% CI, 1.48-3.64) and seizures (OR 8.39, 95% CI, 5.04-13.99) compared with those with Delta infection. Omicron was associated with increased odds of moderate/severe disease (OR 6.14, 95% CI, 4.72-7.99) and a greater need for intravenous fluid therapy (OR 6.00, 95% CI, 4.29-8.39), corticosteroids (OR 3.08, 95% CI, 1.66-5.72), empirical antibiotics (OR 1.70, 95% CI, 1.10-2.64), and low-flow nasal oxygen therapy (OR 3.68, 95% CI, 2.17-6.22) in comparison with Delta. CONCLUSION Children hospitalized with Omicron infection demonstrated a distinct clinical profile compared to those with Delta infection, with increased likelihood of moderate/severe disease and higher utilization of health-care resources.
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Affiliation(s)
- David Chun-Ern Ng
- Department of Pediatrics, Hospital Tuanku Ja'afar, Seremban, Malaysia
| | | | - Kah Kee Tan
- Department of Pediatrics, Perdana University Seremban Clinical Academic Center, Seremban, Negeri Sembilan, Malaysia
| | - Ling Chin
- Department of Pediatrics, Hospital Tuanku Ja'afar, Seremban, Malaysia
| | | | | | | | - Munzir Bin Jamil
- Department of Pediatrics, Hospital Tuanku Ja'afar, Seremban, Malaysia
| | | | - Yee Keat Cheah
- Department of Pediatrics, Hospital Tuanku Ja'afar, Seremban, Malaysia
| | - Mohd Ferous Bin Alias
- Negeri Sembilan State Health Department, Ministry of Health Malaysia, Seremban, Malaysia
| | - Erwin Jiayuan Khoo
- Department of Pediatrics, International Medical University, Kuala Lumpur, Malaysia
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA
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30
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Ulrichs T, Rolland M, Wu J, Nunes MC, El Guerche-Séblain C, Chit A. Changing epidemiology of COVID-19: potential future impact on vaccines and vaccination strategies. Expert Rev Vaccines 2024; 23:510-522. [PMID: 38656834 DOI: 10.1080/14760584.2024.2346589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/19/2024] [Indexed: 04/26/2024]
Abstract
INTRODUCTION COVID-19 was an unprecedented challenge worldwide; however, disease epidemiology has evolved, and COVID-19 no longer constitutes a public health emergency of international concern. Nonetheless, COVID-19 remains a global threat and uncertainties remain, including definition of the end of the pandemic and transition to endemicity, and understanding true rates of SARS-CoV-2 infection/transmission. AREAS COVERED Six international experts convened (April 2023) to interpret changing COVID-19 epidemiology and public health challenges. We report the panel's recommendations and knowledge gaps in COVID-19 epidemiology, SARS-CoV-2 evolution, and future vaccination strategies, informed by peer-reviewed publications, surveillance data, health authority assessments, and clinical experience. EXPERT OPINION High population SARS-CoV-2 immunity indicates the likely end to the pandemic's acute phase. Continued emergence of variants/sublineages that can evade the vaccine-induced antibody response are likely, but widespread immunity reduces the risk of disease severity. Continued surveillance is required to capture transition to endemicity, seasonality, and emergence of novel variants/sublineages, to inform future vaccination strategies. COVID-19 vaccination should be integrated into routine vaccination programs throughout life. Co-circulation with other respiratory viruses should be monitored to avoid a combined peak, which could overrun healthcare systems. Effective, combined vaccines and improved education may help overcome vaccine hesitancy/booster fatigue and increase vaccination uptake.
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Affiliation(s)
- Timo Ulrichs
- Department of Global Health, Akkon University for Human Sciences, Berlin, Germany
| | - Morgane Rolland
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Viral Genomics Section & Systems Serology Core Laboratory, Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Jianhong Wu
- York Emergency Mitigation, Engagement, Response, and Governance Institute, York University, Toronto, Canada
| | - Marta C Nunes
- Université Claude Bernard Lyon, Lyon, France
- University of the Witwatersrand, Johannesburg, South Africa
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31
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SeyedAlinaghi S, Afsahi AM, Mirzapour P, Afzalian A, Shahidi R, Dashti M, Ghasemzadeh A, Paranjkhoo P, Parsaei Z, Pashaei A, Mohammadi P, Najafi MS, Mahrokhi S, Matini P, Moradi A, Karimi A, Afroughi S, Mehraeen E, Dadras O. Comparison of Omicron and Delta Variants of SARS-CoV-2: A Systematic Review of Current Evidence. Infect Disord Drug Targets 2024; 24:e050324227686. [PMID: 38445691 DOI: 10.2174/0118715265279242240216114548] [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: 10/23/2023] [Revised: 01/21/2024] [Accepted: 02/07/2024] [Indexed: 03/07/2024]
Abstract
INTRODUCTION Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) caused the outbreak of coronavirus disease 2019 (COVID-19) in late 2019 in Wuhan, China. In early 2020, the disease spread rapidly around the world. Since the pandemic, SARS-CoV-2 has evolved dramatically into a wide variety of variants endowed with devastating properties. As of March 6, 2022, five SARS-CoV-2 variants of concern, including Alpha, Beta, Gamma, Delta, and Omicron strains have been identified. Due to the crucial importance of understanding the differences between the Omicron and Delta variants, this systematic review was conducted. METHODS This systematic review investigated new variants of Omicron SARS-CoV-2 based on current studies. Online databases were searched for English articles as of January 03, 2023. Selection of publications was a two-step process of title/abstract and full-text assessment against eligibility criteria. The relevant data from the included articles were systematically collected and organized in a designed table for analysis. To ensure the quality of the review, the PRISMA checklist and Newcastle- Ottawa Scale (NOS) of quality assessment were utilized. RESULTS The data extracted from 58 articles were analyzed, including 10003 pieces of evidence. Lower risk of hospitalization, ICU admission, and mortality after vaccination were reported in the Omicron variant compared to the Delta variant. Additionally, the Delta variant led to more severe clinical symptoms in comparison to the Omicron variant. CONCLUSION The Omicron variant of SARS-CoV-2 results in less severe disease outcomes as compared to Delta. Nevertheless, it remains crucial to maintain ongoing monitoring, implement containment measures, and adapt vaccination protocols to effectively address the evolving variants.
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Affiliation(s)
- SeyedAhmad SeyedAlinaghi
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High-Risk Behaviors, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir Masoud Afsahi
- Department of Radiology, School of Medicine, University of California, San Diego (UCSD), California, USA
| | - Pegah Mirzapour
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High-Risk Behaviors, Tehran University of Medical Sciences, Tehran, Iran
| | - Arian Afzalian
- School of medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ramin Shahidi
- School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Mohsen Dashti
- Department of Radiology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Afsaneh Ghasemzadeh
- Department of Radiology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parinaz Paranjkhoo
- Turpanjian College of Health Sciences, American University of Armenia, Yerevan, 0019, Armenia
| | - Zahra Parsaei
- Health Information Technology Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ava Pashaei
- School of Nursing, University of British Columbia, Vancouver, British Columbia, Canada
| | - Parsa Mohammadi
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Sadeq Najafi
- Research Center for Advanced Technologies in Cardiovascular Medicine, Cardiovascular Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Sona Mahrokhi
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High-Risk Behaviors, Tehran University of Medical Sciences, Tehran, Iran
| | - Parisa Matini
- School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Moradi
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Amirali Karimi
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Solaiman Afroughi
- Department of Biostatistics and Epidemiology, School of Health and Social Determinants of Health Research Center, Postal Code 7591875114, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Esmaeil Mehraeen
- Department of Health Information Technology, Khalkhal University of Medical Sciences, Khalkhal, Iran
| | - Omid Dadras
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, 5007, Norway
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32
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Lustig G, Ganga Y, Rodel HE, Tegally H, Khairallah A, Jackson L, Cele S, Khan K, Jule Z, Reedoy K, Karim F, Bernstein M, Ndung’u T, Moosa MYS, Archary D, de Oliveira T, Lessells R, Neher RA, Abdool Karim SS, Sigal A. SARS-CoV-2 infection in immunosuppression evolves sub-lineages which independently accumulate neutralization escape mutations. Virus Evol 2023; 10:vead075. [PMID: 38361824 PMCID: PMC10868398 DOI: 10.1093/ve/vead075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/11/2023] [Accepted: 12/21/2023] [Indexed: 02/17/2024] Open
Abstract
One mechanism of variant formation may be evolution during long-term infection in immunosuppressed people. To understand the viral phenotypes evolved during such infection, we tested SARS-CoV-2 viruses evolved from an ancestral B.1 lineage infection lasting over 190 days post-diagnosis in an advanced HIV disease immunosuppressed individual. Sequence and phylogenetic analysis showed two evolving sub-lineages, with the second sub-lineage replacing the first sub-lineage in a seeming evolutionary sweep. Each sub-lineage independently evolved escape from neutralizing antibodies. The most evolved virus for the first sub-lineage (isolated day 34) and the second sub-lineage (isolated day 190) showed similar escape from ancestral SARS-CoV-2 and Delta-variant infection elicited neutralizing immunity despite having no spike mutations in common relative to the B.1 lineage. The day 190 isolate also evolved higher cell-cell fusion and faster viral replication and caused more cell death relative to virus isolated soon after diagnosis, though cell death was similar to day 34 first sub-lineage virus. These data show that SARS-CoV-2 strains in prolonged infection in a single individual can follow independent evolutionary trajectories which lead to neutralization escape and other changes in viral properties.
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Affiliation(s)
- Gila Lustig
- Centre for the AIDS Programme of Research in South Africa, 719 Umbilo Road, Durban 4001, South Africa
| | - Yashica Ganga
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
| | - Hylton E Rodel
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
- Division of Infection and Immunity, University College London, UCL Cruciform Building Gower Street, London WC1E 6BT, UK
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform, 719 Umbilo Road, Durban 4001, South Africa
- Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Francie Van Zijl Drive, Cape Town 7505, South Africa
| | - Afrah Khairallah
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
| | - Laurelle Jackson
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
| | - Sandile Cele
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
| | - Khadija Khan
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
| | - Zesuliwe Jule
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
| | - Kajal Reedoy
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
| | - Farina Karim
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
| | - Mallory Bernstein
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
| | - Thumbi Ndung’u
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
- Division of Infection and Immunity, University College London, UCL Cruciform Building Gower Street, London WC1E 6BT, UK
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
- HIV Pathogenesis Programme, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
- Ragon Institute of MGH, MIT and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Mahomed-Yunus S Moosa
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
| | - Derseree Archary
- Centre for the AIDS Programme of Research in South Africa, 719 Umbilo Road, Durban 4001, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform, 719 Umbilo Road, Durban 4001, South Africa
- Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Francie Van Zijl Drive, Cape Town 7505, South Africa
- Department of Global Health, University of Washington, 3980 15th Avenue NE, Seattle, WA 98105, USA
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform, 719 Umbilo Road, Durban 4001, South Africa
| | - Richard A Neher
- SIB Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, Lausanne 1015, Switzerland
- Biozentrum, University of Basel, Spitalstrasse 41 4056, Basel, Switzerland
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, 719 Umbilo Road, Durban 4001, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY 10032, United States
| | - Alex Sigal
- Centre for the AIDS Programme of Research in South Africa, 719 Umbilo Road, Durban 4001, South Africa
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
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Anastasopoulou A, Diamantopoulos PT, Kouzis P, Saridaki M, Sideris K, Samarkos M, Gogas H. COVID-19 in Patients with Melanoma: A Single-Institution Study. Cancers (Basel) 2023; 16:96. [PMID: 38201522 PMCID: PMC10778439 DOI: 10.3390/cancers16010096] [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: 12/06/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
We conducted a single-center, non-interventional retrospective study of melanoma patients with COVID-19 (1 March 2020 until 17 March 2023). The cohort was further divided into three groups according to the periods of SARS-CoV-2 variant dominance in Greece. We recorded demographics, comorbidities, vaccination data, cancer diagnosis/stage, types of systemic melanoma treatments, date of COVID-19 diagnosis and survival. We identified 121 patients. The vast majority (87.6%) had advanced disease (stages III or IV). A total of 80.1% of the patients were receiving immune checkpoint inhibitor-based therapies, 92.5% had asymptomatic/mild COVID-19 and 7.4% had moderate/severe/critical disease, while 83.5% contracted COVID-19 during the third period of the pandemic. Sixteen patients (13.2%) were hospitalized for COVID-19 with a median length of stay of 12 days (range: 1-55 days). Advanced age, heart failure, number of comorbidities (≤1 vs. >1), vaccination status and the time period of the infection correlated with more severe COVID-19, whereas only heart failure and time period were independently correlated with severity. The 30-day mortality rate after COVID-19 was 4.2%. With a median follow-up of 340 days post-COVID-19, 17.4% of patients were deceased. In this cohort of melanoma patients with COVID-19, the 30-day mortality rate was low. There was no association between melanoma stage, treatment receipt and type of treatment with COVID-19 severity.
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Affiliation(s)
- Amalia Anastasopoulou
- First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (P.T.D.); (P.K.); (M.S.); (K.S.); (M.S.); (H.G.)
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Torche F, Nobles J. Vaccination, immunity, and the changing impact of COVID-19 on infant health. Proc Natl Acad Sci U S A 2023; 120:e2311573120. [PMID: 38011548 DOI: 10.1073/pnas.2311573120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 10/19/2023] [Indexed: 11/29/2023] Open
Abstract
In utero exposure to COVID-19 infection may lead to large intergenerational health effects. The impact of infection exposure has likely evolved since the onset of the pandemic as new variants emerge, immunity from prior infection increases, vaccines become available, and vaccine hesitancy persists, such that when infection is experienced is as important as whether it is experienced. We examine the changing impact of COVID-19 infection on preterm birth and the moderating role of vaccination. We offer the first plausibly causal estimate of the impact of maternal COVID-19 infection by using population data with no selectivity, universal information on maternal COVID-19 infection, and linked sibling data. We then assess change in this impact from 2020 to 2023 and evaluate the protective role of COVID-19 vaccination on infant health. We find a substantial adverse effect of prenatal COVID-19 infection on the probability of preterm birth. The impact was large during the first 2 y of the pandemic but had fully disappeared by 2022. The harmful impact of COVID-19 infection disappeared almost a year earlier in zip codes with high vaccination rates, suggesting that vaccines might have prevented thousands of preterm births. The findings highlight the need to monitor the changing consequences of emerging infectious diseases over time and the importance of mitigation strategies to reduce the burden of infection on vulnerable populations.
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Affiliation(s)
- Florencia Torche
- Department of Sociology, Stanford University, Stanford, CA 94305
| | - Jenna Nobles
- Department of Sociology, Center for Demography and Ecology, University of Wisconsin-Madison, Madison, WI 53706
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Harte JV, Coleman-Vaughan C, Crowley MP, Mykytiv V. It's in the blood: a review of the hematological system in SARS-CoV-2-associated COVID-19. Crit Rev Clin Lab Sci 2023; 60:595-624. [PMID: 37439130 DOI: 10.1080/10408363.2023.2232010] [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: 04/10/2023] [Accepted: 06/27/2023] [Indexed: 07/14/2023]
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to an unprecedented global healthcare crisis. While SARS-CoV-2-associated COVID-19 affects primarily the respiratory system, patients with COVID-19 frequently develop extrapulmonary manifestations. Notably, changes in the hematological system, including lymphocytopenia, neutrophilia and significant abnormalities of hemostatic markers, were observed early in the pandemic. Hematological manifestations have since been recognized as important parameters in the pathophysiology of SARS-CoV-2 and in the management of patients with COVID-19. In this narrative review, we summarize the state-of-the-art regarding the hematological and hemostatic abnormalities observed in patients with SARS-CoV-2-associated COVID-19, as well as the current understanding of the hematological system in the pathophysiology of acute and chronic SARS-CoV-2-associated COVID-19.
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Affiliation(s)
- James V Harte
- Department of Haematology, Cork University Hospital, Wilton, Cork, Ireland
- School of Biochemistry & Cell Biology, University College Cork, Cork, Ireland
| | | | - Maeve P Crowley
- Department of Haematology, Cork University Hospital, Wilton, Cork, Ireland
- Irish Network for Venous Thromboembolism Research (INViTE), Ireland
| | - Vitaliy Mykytiv
- Department of Haematology, Cork University Hospital, Wilton, Cork, Ireland
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Tan-Lhernould L, Tamandjou C, Deschamps G, Platon J, Sommen C, Chereau F, Parent du Châtelet I, Cauchemez S, Vaux S, Paireau J. Impact of vaccination against severe COVID-19 in the French population aged 50 years and above: a retrospective population-based study. BMC Med 2023; 21:426. [PMID: 37940955 PMCID: PMC10633992 DOI: 10.1186/s12916-023-03119-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/19/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Given the widespread implementation of COVID-19 vaccination to mitigate the pandemic from the end of 2020, it is important to retrospectively evaluate its impact, in particular by quantifying the number of severe outcomes prevented through vaccination. METHODS We estimated the number of hospitalizations, intensive care unit (ICU) admissions and deaths directly averted by vaccination in France, in people aged ≥ 50 years, from December 2020 to March 2022, based on (1) the number of observed events, (2) vaccination coverage, and (3) vaccine effectiveness. We accounted for the effect of primary vaccination and the first booster dose, the circulating variants, the age groups, and the waning of vaccine-induced protection over time. RESULTS An estimated 480,150 (95% CI: 260,072-582,516) hospitalizations, 132,156 (50,409-157,767) ICU admissions and 125,376 (53,792-152,037) deaths were directly averted by vaccination in people aged ≥ 50 years, which corresponds to a reduction of 63.2% (48.2-67.6), 68.7% (45.6-72.4) and 62.7% (41.9-67.1) respectively, compared to what would have been expected without vaccination over the study period. An estimated 5852 (2285-6853) deaths were directly averted among the 50-59 years old, 16,837 (6568-19,473) among the 60-69 years old, 32,136 (13,651-36,758) among the 70-79 years old and 70,551 (31,288-88,953) among the ≥ 80 years old. CONCLUSIONS The vaccination campaign in France considerably reduced COVID-19 morbidity and mortality, as well as stress on the healthcare system.
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Affiliation(s)
- Laetitia Tan-Lhernould
- Direction des Maladies Infectieuses, Santé publique France, 12 Rue du Val d'Osne, Saint-Maurice, 94415, France
| | - Cynthia Tamandjou
- Direction des Maladies Infectieuses, Santé publique France, 12 Rue du Val d'Osne, Saint-Maurice, 94415, France
| | - Guilhem Deschamps
- Direction Appui, Traitements et Analyses de données, Santé publique France, 12 Rue du Val d'Osne, Saint-Maurice, 94415, France
| | - Johnny Platon
- Direction Appui, Traitements et Analyses de données, Santé publique France, 12 Rue du Val d'Osne, Saint-Maurice, 94415, France
| | - Cécile Sommen
- Direction Appui, Traitements et Analyses de données, Santé publique France, 12 Rue du Val d'Osne, Saint-Maurice, 94415, France
| | - Fanny Chereau
- Direction des Maladies Infectieuses, Santé publique France, 12 Rue du Val d'Osne, Saint-Maurice, 94415, France
| | - Isabelle Parent du Châtelet
- Direction des Maladies Infectieuses, Santé publique France, 12 Rue du Val d'Osne, Saint-Maurice, 94415, France
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Paris, F-75015, France
| | - Sophie Vaux
- Direction des Maladies Infectieuses, Santé publique France, 12 Rue du Val d'Osne, Saint-Maurice, 94415, France
| | - Juliette Paireau
- Direction des Maladies Infectieuses, Santé publique France, 12 Rue du Val d'Osne, Saint-Maurice, 94415, France.
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Paris, F-75015, France.
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Figueira‐Gonçalves JM, García-Bello MÁ, Ramallo‐Fariña Y, Méndez R, Latorre Campos A, González-Jiménez P, Peces-Barba G, Molina-Molina M, España PP, García E, Domínguez-Pazos SDJ, García Clemente M, Panadero C, de la Rosa-Carrillo D, Sibila O, Martínez-Pitarch MD, Toledo-Pons N, López-Ramirez C, Almonte-Batista W, Macías-Paredes A, Badenes-Bonet D, Pérez-Rodas EN, Lázaro J, Quirós Fernández S, Cordovilla R, Cano-Pumarega I, Torres A, Menendez R. Persistent Respiratory Failure and Re-Admission in Patients with Chronic Obstructive Pulmonary Disease Following Hospitalization for COVID-19. Int J Chron Obstruct Pulmon Dis 2023; 18:2473-2481. [PMID: 37955022 PMCID: PMC10638925 DOI: 10.2147/copd.s428316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/30/2023] [Indexed: 11/14/2023] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) has been associated with worse clinical evolution/survival during a hospitalization for SARS-CoV2 (COVID-19). The objective of this study was to learn the situation of these patients at discharge as well as the risk of re-admission/mortality in the following 12 months. Methods We carried out a subanalysis of the RECOVID registry. A multicenter, observational study that retrospectively collected data on severe acute COVID-19 episodes and follow-up visits for up to a year in survivors. The data collection protocol includes general demographic data, smoking, comorbidities, pharmacological treatment, infection severity, complications during hospitalization and required treatment. At discharge, resting oxygen saturation (SpO2), dyspnea according to the mMRC (modified Medical Research Council) scale and long-term oxygen therapy prescription were recorded. The follow-up database included the clinical management visits at 6 and 12 months, where re-admission and mortality were recorded. Results A total of 2047 patients were included (5.6% had a COPD diagnosis). At discharge, patients with COPD had greater dyspnea and a greater need for prescription home oxygen. After adjusting for age, sex and Charlson comorbidity index, patients with COPD had a greater risk of hospital re-admission due to respiratory causes (HR 2.57 [1.35-4.89], p = 0.004), with no significant differences in survival. Conclusion Patients with COPD who overcome a serious SARS-CoV2 infection show a worse clinical situation at discharge and a greater risk of re-admission for respiratory causes.
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Affiliation(s)
- Juan Marco Figueira‐Gonçalves
- Pneumology and Thoracic Surgery Service, Unit for Patients with Highly Complex COPD, University Hospital Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- University Institute of Tropical Disease and Public Health of the Canary Islands, University of La Laguna, Santa Cruz de Tenerife, Spain
| | - Miguel Ángel García-Bello
- Evaluation Unit (SESCS), Canary Islands Health Research Institute Foundation (FIISC), Tenerife, Spain
- Network for Research on Chronicity, Primary Care, and Health Promotion (RICAPPS), Tenerife, Spain
| | - Yolanda Ramallo‐Fariña
- Evaluation Unit (SESCS), Canary Islands Health Research Institute Foundation (FIISC), Tenerife, Spain
- Network for Research on Chronicity, Primary Care, and Health Promotion (RICAPPS), Tenerife, Spain
- Health Services Research on Chronic Patients Network (REDISSEC), Madrid, Spain
| | - Raúl Méndez
- Pneumology Department, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Respiratory InFections, Instituto de Investigación Sanitaria La Fe (IISLAFE), Valencia, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Medicine Department, University of Valencia, Valencia, Spain
| | - Ana Latorre Campos
- Pneumology Department, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Respiratory InFections, Instituto de Investigación Sanitaria La Fe (IISLAFE), Valencia, Spain
| | - Paula González-Jiménez
- Pneumology Department, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Respiratory InFections, Instituto de Investigación Sanitaria La Fe (IISLAFE), Valencia, Spain
- Medicine Department, University of Valencia, Valencia, Spain
| | | | - María Molina-Molina
- ILD Unit, Respiratory Department, Hospital de Bellvitge, Hospitalet de Llobregat, Spain
| | | | - Estela García
- Respiratory Service, Hospital de Cabueñes, Gijón, Spain
| | | | | | | | | | - Oriol Sibila
- Respiratory Service, Hospital Clínic, Barcelona, Spain
| | | | | | - Cecilia López-Ramirez
- Medical Surgical Unit of Respiratory Diseases, Hospital Virgen del Rocío, Sevilla, Spain
| | | | | | | | | | - Javier Lázaro
- Respiratory Service, Hospital Royo Villanova, Zaragoza, Spain
| | | | - Rosa Cordovilla
- Respiratory Service, Hospital de Salamanca, Salamanca, Spain
| | - Irene Cano-Pumarega
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Respiratory Service, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
| | - Antoni Torres
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Respiratory Service, Hospital Clínic, Barcelona, Spain
| | - Rosario Menendez
- Pneumology Department, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Respiratory InFections, Instituto de Investigación Sanitaria La Fe (IISLAFE), Valencia, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Medicine Department, University of Valencia, Valencia, Spain
| | - On behalf of RECOVID
- Pneumology and Thoracic Surgery Service, Unit for Patients with Highly Complex COPD, University Hospital Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- University Institute of Tropical Disease and Public Health of the Canary Islands, University of La Laguna, Santa Cruz de Tenerife, Spain
- Evaluation Unit (SESCS), Canary Islands Health Research Institute Foundation (FIISC), Tenerife, Spain
- Network for Research on Chronicity, Primary Care, and Health Promotion (RICAPPS), Tenerife, Spain
- Health Services Research on Chronic Patients Network (REDISSEC), Madrid, Spain
- Pneumology Department, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Respiratory InFections, Instituto de Investigación Sanitaria La Fe (IISLAFE), Valencia, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Medicine Department, University of Valencia, Valencia, Spain
- Pulmonology Department, Hospital Fundación Jiménez Díaz, Madrid, Spain
- ILD Unit, Respiratory Department, Hospital de Bellvitge, Hospitalet de Llobregat, Spain
- Respiratory Service, Hospital de Galdakao-Usansolo, Galdakao, Spain
- Respiratory Service, Hospital de Cabueñes, Gijón, Spain
- Respiratory Service, Hospital Universitario de A Coruña, A Coruña, Spain
- Respiratory Service, Hospital Universitario Central de Asturias, Oviedo, Spain
- Respiratory Service, Hospital de Getafe, Getafe, Spain
- Respiratory Service, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
- Respiratory Service, Hospital Clínic, Barcelona, Spain
- Respiratory Service, Hospital Lluís Alcanyís, Játiva, Spain
- Respiratory Service, Hospital Son Espases, Palma, Spain
- Medical Surgical Unit of Respiratory Diseases, Hospital Virgen del Rocío, Sevilla, Spain
- Respiratory Service, Hospital de Albacete, Albacete, Spain
- Respiratory Service, Hospital de Sant Jaume, Calella, Spain
- Respiratory Service, Hospital del Mar, Barcelona, Spain
- Respiratory Service, Hospital Municipal de Badalona, Badalona, Spain
- Respiratory Service, Hospital Royo Villanova, Zaragoza, Spain
- Respiratory Service, Hospital Basurto, Bilbao, Spain
- Respiratory Service, Hospital de Salamanca, Salamanca, Spain
- Respiratory Service, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
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Attar Cohen H, Mesfin S, Ikejezie J, Kassamali Z, Campbell F, Adele S, Guinko N, Idoko F, Mirembe BB, Mitri ME, Nezu I, Shimizu K, Ngongheh AB, Sklenovska N, Gumede N, Mosha FS, Mohamed B, Corpuz A, Pebody R, Marklewitz M, Gresh L, Mendez Rico JA, Hundal K, Kato M, Babu A, Archer BN, le Polain de Waroux O, Van Kerkhove MD, Mahamud A, Subissi L, Pavlin BI. Surveillance for variants of SARS-CoV-2 to inform risk assessments. Bull World Health Organ 2023; 101:707-716. [PMID: 37961054 PMCID: PMC10630725 DOI: 10.2471/blt.23.290093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/18/2023] [Accepted: 08/31/2023] [Indexed: 11/15/2023] Open
Abstract
Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, numerous severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have emerged, some leading to large increases in infections, hospitalizations and deaths globally. The virus's impact on public health depends on many factors, including the emergence of new viral variants and their global spread. Consequently, the early detection and surveillance of variants and characterization of their clinical effects are vital for assessing their health risk. The unprecedented capacity for viral genomic sequencing and data sharing built globally during the pandemic has enabled new variants to be rapidly detected and assessed. This article describes the main variants circulating globally between January 2020 and June 2023, the genetic features driving variant evolution, and the epidemiological impact of these variants across countries and regions. Second, we report how integrating genetic variant surveillance with epidemiological data and event-based surveillance, through a network of World Health Organization partners, supported risk assessment and helped provide guidance on pandemic responses. In addition, given the evolutionary characteristics of circulating variants and the immune status of populations, we propose future directions for the sustainable genomic surveillance of SARS-CoV-2 variants, both nationally and internationally: (i) optimizing variant surveillance by including environmental monitoring; (ii) coordinating laboratory assessment of variant evolution and phenotype; (iii) linking data on circulating variants with clinical data; and (iv) expanding genomic surveillance to additional pathogens. Experience during the COVID-19 pandemic has shown that genomic surveillance of pathogens can provide essential, timely and evidence-based information for public health decision-making.
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Affiliation(s)
- Homa Attar Cohen
- World Health Organization (WHO) Health Emergencies Programme, WHO, Avenue Appia 20, 1211Geneva, Switzerland
| | - Samuel Mesfin
- World Health Organization (WHO) Health Emergencies Programme, WHO, Avenue Appia 20, 1211Geneva, Switzerland
| | - Juniorcaius Ikejezie
- World Health Organization (WHO) Health Emergencies Programme, WHO, Avenue Appia 20, 1211Geneva, Switzerland
| | - Zyleen Kassamali
- World Health Organization (WHO) Health Emergencies Programme, WHO, Avenue Appia 20, 1211Geneva, Switzerland
| | - Finlay Campbell
- World Health Organization (WHO) Health Emergencies Programme, WHO, Avenue Appia 20, 1211Geneva, Switzerland
| | - Sandra Adele
- World Health Organization (WHO) Health Emergencies Programme, WHO, Avenue Appia 20, 1211Geneva, Switzerland
| | - Noe Guinko
- World Health Organization (WHO) Health Emergencies Programme, WHO, Avenue Appia 20, 1211Geneva, Switzerland
| | - Friday Idoko
- World Health Organization (WHO) Health Emergencies Programme, WHO, Avenue Appia 20, 1211Geneva, Switzerland
| | - Bernadette Basuta Mirembe
- World Health Organization (WHO) Health Emergencies Programme, WHO, Avenue Appia 20, 1211Geneva, Switzerland
| | - Maria Elizabeth Mitri
- World Health Organization (WHO) Health Emergencies Programme, WHO, Avenue Appia 20, 1211Geneva, Switzerland
| | - Ingrid Nezu
- World Health Organization (WHO) Health Emergencies Programme, WHO, Avenue Appia 20, 1211Geneva, Switzerland
| | - Kazuki Shimizu
- World Health Organization (WHO) Health Emergencies Programme, WHO, Avenue Appia 20, 1211Geneva, Switzerland
| | - Ajong Brian Ngongheh
- World Health Organization (WHO) Health Emergencies Programme, WHO, Avenue Appia 20, 1211Geneva, Switzerland
| | - Nikola Sklenovska
- World Health Organization (WHO) Health Emergencies Programme, WHO, Avenue Appia 20, 1211Geneva, Switzerland
| | | | | | - Basant Mohamed
- WHO Regional Office for the Eastern Mediterranean, Cairo, Egypt
| | - Aura Corpuz
- WHO Regional Office for the Eastern Mediterranean, Cairo, Egypt
| | | | | | - Lionel Gresh
- Pan American Health Organization, WashingtonD.C., United States of America
| | | | - Kareena Hundal
- WHO Regional Office for the Western Pacific, Manila, Philippines
| | - Masaya Kato
- WHO Regional Office for South-East Asia, New Delhi, India
| | - Amarnath Babu
- WHO Regional Office for South-East Asia, New Delhi, India
| | - Brett N Archer
- World Health Organization (WHO) Health Emergencies Programme, WHO, Avenue Appia 20, 1211Geneva, Switzerland
| | | | - Maria D Van Kerkhove
- World Health Organization (WHO) Health Emergencies Programme, WHO, Avenue Appia 20, 1211Geneva, Switzerland
| | - Abdirahman Mahamud
- World Health Organization (WHO) Health Emergencies Programme, WHO, Avenue Appia 20, 1211Geneva, Switzerland
| | - Lorenzo Subissi
- World Health Organization (WHO) Health Emergencies Programme, WHO, Avenue Appia 20, 1211Geneva, Switzerland
| | - Boris I Pavlin
- World Health Organization (WHO) Health Emergencies Programme, WHO, Avenue Appia 20, 1211Geneva, Switzerland
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Hyams C, Qian G, Nava G, Challen R, Begier E, Southern J, Lahuerta M, Nguyen JL, King J, Morley A, Clout M, Maskell N, Jodar L, Oliver J, Ellsbury G, McLaughlin JM, Gessner BD, Finn A, Danon L, Dodd JW. Impact of SARS-CoV-2 infective exacerbation of chronic obstructive pulmonary disease on clinical outcomes in a prospective cohort study of hospitalised adults. J R Soc Med 2023; 116:371-385. [PMID: 37404021 PMCID: PMC10686205 DOI: 10.1177/01410768231184162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/04/2023] [Indexed: 07/06/2023] Open
Abstract
OBJECTIVES To determine whether acute exacerbations of chronic obstructive pulmonary disease (AECOPD) triggered by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), have worse outcomes than AECOPD caused by other infectious agents or non-infective AECOPD (NI-COPD). DESIGN A two-hospital prospective cohort study of adults hospitalised with acute respiratory disease. We compared outcomes with AECOPD and a positive test for SARS-CoV-2 (n = 816), AECOPD triggered by other infections (n = 3038) and NI-COPD (n = 994). We used multivariable modelling to adjust for potential confounders and assessed variation by seasons associated with different SARS-CoV-2 variants. SETTING Bristol UK, August 2020-May 2022. PARTICIPANTS Adults (≥18 y) hospitalised with AECOPD. MAIN OUTCOME MEASURES We determined the risk of positive pressure support, longer hospital admission and mortality following hospitalisation with AECOPD due to non-SARS-CoV-2 infection compared with SARS-CoV-2 AECOPD and NI-COPD. RESULTS Patients with SARS-CoV-2 AECOPD, in comparison to non-SARS-CoV-2 infective AECOPD or NI-COPD, more frequently required positive pressure support (18.5% and 7.5% vs. 11.7%, respectively), longer hospital stays (median [interquartile range, IQR]: 7 [3-15] and 5 [2-10] vs. 4 [2-9] days, respectively) and had higher 30-day mortality (16.9% and 11.1% vs. 5.9%, respectively) (all p < 0.001). In adjusted analyses, SARS-CoV-2 AECOPD was associated with a 55% (95% confidence interval [95% CI]: 24-93), 26% (95% CI: 15-37) and 35% (95% CI: 10-65) increase in the risk of positive pressure support, hospitalisation length and 30-day mortality, respectively, relative to non-SARS-CoV-2 infective AECOPD. The difference in risk remained similar during periods of wild-type, Alpha and Delta SARS-CoV-2 strain dominance, but diminished during Omicron dominance. CONCLUSIONS SARS-CoV-2-related AECOPD had worse patient outcomes compared with non-SARS-CoV-2 AECOPD or NI-AECOPD, although the difference in risks was less pronounced during Omicron dominance.
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Affiliation(s)
- Catherine Hyams
- Academic Respiratory Unit and Bristol Vaccine Centre, University of Bristol, Bristol, BS15, UK
| | - George Qian
- Engineering Mathematics, University of Bristol, Bristol, Bristol, BS8, UK
| | - George Nava
- Academic Respiratory Unit, University of Bristol, Southmead Hospital, Bristol, Bristol, BS15, UK
| | - Robert Challen
- Engineering Mathematics, University of Bristol, Bristol, Bristol, BS8, UK
| | - Elizabeth Begier
- Vaccines Medical Development, Scientific and Clinical Affairs, Pfizer Inc., Collegeville, PA 19426, USA
| | - Jo Southern
- Vaccines Medical Development, Scientific and Clinical Affairs, Pfizer Inc., Collegeville, PA 19426, USA
| | - Maria Lahuerta
- Vaccines Medical Development, Scientific and Clinical Affairs, Pfizer Inc., Collegeville, PA 19426, USA
| | - Jennifer L Nguyen
- Vaccines Medical Development, Scientific and Clinical Affairs, Pfizer Inc., Collegeville, PA 19426, USA
| | - Jade King
- Clinical Research and Imaging Centre, UHBW NHS Trust, Bristol, Bristol, BS2, UK
| | - Anna Morley
- Academic Respiratory Unit, Southmead Hospital, Bristol, Bristol, BS15, UK
| | - Madeleine Clout
- Bristol Vaccine Centre and Population Health Sciences, University of Bristol, Bristol, BS2, UK
| | - Nick Maskell
- Academic Respiratory Unit, University of Bristol, Southmead Hospital, Bristol, Bristol, BS15, UK
| | - Luis Jodar
- Vaccines Medical Development, Scientific and Clinical Affairs, Pfizer Inc., Collegeville, PA 19426, USA
| | - Jennifer Oliver
- Bristol Vaccine Centre and Population Health Sciences, University of Bristol, Bristol, BS2, UK
| | | | - John M McLaughlin
- Vaccines Medical Development, Scientific and Clinical Affairs, Pfizer Inc., Collegeville, PA 19426, USA
| | - Bradford D Gessner
- Vaccines Medical Development, Scientific and Clinical Affairs, Pfizer Inc., Collegeville, PA 19426, USA
| | - Adam Finn
- Bristol Vaccine Centre, Cellular and Molecular Medicine and Population Health Sciences, University of Bristol, Bristol, BS2, UK
| | - Leon Danon
- Engineering Mathematics, University of Bristol, Bristol, Bristol, BS8, UK
| | - James W Dodd
- Academic Respiratory Unit and Population Health Sciences, University of Bristol, Southmead Hospital, Bristol, BS15, UK
| | - The Avon CAP Research Group
- Academic Respiratory Unit and Bristol Vaccine Centre, University of Bristol, Bristol, BS15, UK
- Engineering Mathematics, University of Bristol, Bristol, Bristol, BS8, UK
- Academic Respiratory Unit, University of Bristol, Southmead Hospital, Bristol, Bristol, BS15, UK
- Vaccines Medical Development, Scientific and Clinical Affairs, Pfizer Inc., Collegeville, PA 19426, USA
- Clinical Research and Imaging Centre, UHBW NHS Trust, Bristol, Bristol, BS2, UK
- Academic Respiratory Unit, Southmead Hospital, Bristol, Bristol, BS15, UK
- Bristol Vaccine Centre and Population Health Sciences, University of Bristol, Bristol, BS2, UK
- Vaccines Medical Affairs, Pfizer Ltd, Tadworth, KT20, UK
- Bristol Vaccine Centre, Cellular and Molecular Medicine and Population Health Sciences, University of Bristol, Bristol, BS2, UK
- Academic Respiratory Unit and Population Health Sciences, University of Bristol, Southmead Hospital, Bristol, BS15, UK
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Pitsillou E, Yu Y, Beh RC, Liang JJ, Hung A, Karagiannis TC. Chronicling the 3-year evolution of the COVID-19 pandemic: analysis of disease management, characteristics of major variants, and impacts on pathogenicity. Clin Exp Med 2023; 23:3277-3298. [PMID: 37615803 DOI: 10.1007/s10238-023-01168-0] [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: 04/24/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023]
Abstract
Announced on December 31, 2019, the novel coronavirus arising in Wuhan City, Hubei Province resulted in millions of cases and lives lost. Following intense tracking, coronavirus disease 2019 (COVID-19) was declared a pandemic by the World Health Organization (WHO) in 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the cause of COVID-19 and the continuous evolution of the virus has given rise to several variants. In this review, a comprehensive analysis of the response to the pandemic over the first three-year period is provided, focusing on disease management, development of vaccines and therapeutics, and identification of variants. The transmissibility and pathogenicity of SARS-CoV-2 variants including Alpha, Beta, Gamma, Delta, and Omicron are compared. The binding characteristics of the SARS-CoV-2 spike protein to the angiotensin-converting enzyme 2 (ACE2) receptor and reproduction numbers are evaluated. The effects of major variants on disease severity, hospitalisation, and case-fatality rates are outlined. In addition to the spike protein, open reading frames mutations are investigated. We also compare the pathogenicity of SARS-CoV-2 with SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Overall, this study highlights the strengths and weaknesses of the global response to the pandemic, as well as the importance of prevention and preparedness. Monitoring the evolution of SARS-CoV-2 is critical in identifying and potentially predicting the health outcomes of concerning variants as they emerge. The ultimate goal would be a position in which existing vaccines and therapeutics could be adapted to suit new variants in as close to real-time as possible.
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Affiliation(s)
- Eleni Pitsillou
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Yiping Yu
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Raymond C Beh
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Julia J Liang
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia.
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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41
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Meehan GR, Herder V, Allan J, Huang X, Kerr K, Mendonca DC, Ilia G, Wright DW, Nomikou K, Gu Q, Molina Arias S, Hansmann F, Hardas A, Attipa C, De Lorenzo G, Cowton V, Upfold N, Palmalux N, Brown JC, Barclay WS, Filipe ADS, Furnon W, Patel AH, Palmarini M. Phenotyping the virulence of SARS-CoV-2 variants in hamsters by digital pathology and machine learning. PLoS Pathog 2023; 19:e1011589. [PMID: 37934791 PMCID: PMC10656012 DOI: 10.1371/journal.ppat.1011589] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/17/2023] [Accepted: 10/30/2023] [Indexed: 11/09/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to evolve throughout the coronavirus disease-19 (COVID-19) pandemic, giving rise to multiple variants of concern (VOCs) with different biological properties. As the pandemic progresses, it will be essential to test in near real time the potential of any new emerging variant to cause severe disease. BA.1 (Omicron) was shown to be attenuated compared to the previous VOCs like Delta, but it is possible that newly emerging variants may regain a virulent phenotype. Hamsters have been proven to be an exceedingly good model for SARS-CoV-2 pathogenesis. Here, we aimed to develop robust quantitative pipelines to assess the virulence of SARS-CoV-2 variants in hamsters. We used various approaches including RNAseq, RNA in situ hybridization, immunohistochemistry, and digital pathology, including software assisted whole section imaging and downstream automatic analyses enhanced by machine learning, to develop methods to assess and quantify virus-induced pulmonary lesions in an unbiased manner. Initially, we used Delta and Omicron to develop our experimental pipelines. We then assessed the virulence of recent Omicron sub-lineages including BA.5, XBB, BQ.1.18, BA.2, BA.2.75 and EG.5.1. We show that in experimentally infected hamsters, accurate quantification of alveolar epithelial hyperplasia and macrophage infiltrates represent robust markers for assessing the extent of virus-induced pulmonary pathology, and hence virus virulence. In addition, using these pipelines, we could reveal how some Omicron sub-lineages (e.g., BA.2.75 and EG.5.1) have regained virulence compared to the original BA.1. Finally, to maximise the utility of the digital pathology pipelines reported in our study, we developed an online repository containing representative whole organ histopathology sections that can be visualised at variable magnifications (https://covid-atlas.cvr.gla.ac.uk). Overall, this pipeline can provide unbiased and invaluable data for rapidly assessing newly emerging variants and their potential to cause severe disease.
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Affiliation(s)
- Gavin R. Meehan
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Vanessa Herder
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Jay Allan
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Xinyi Huang
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Karen Kerr
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Diogo Correa Mendonca
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Georgios Ilia
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Derek W. Wright
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Kyriaki Nomikou
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Sergi Molina Arias
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Florian Hansmann
- Institute of Veterinary Pathology, Faculty of Veterinary Medicine, Leipzig University, Germany
| | - Alexandros Hardas
- Department of Pathobiology & Population Sciences, The Royal Veterinary College, North Mymms, United Kingdom
| | - Charalampos Attipa
- The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, United Kingdom
| | | | - Vanessa Cowton
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Nicole Upfold
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Natasha Palmalux
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Jonathan C. Brown
- Department of Infectious Disease, Imperial College London, United Kingdom
| | - Wendy S. Barclay
- Department of Infectious Disease, Imperial College London, United Kingdom
| | | | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
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Ngiam JN, Ng OT, Toh MPHS, Gao Q, Soong AJ, Teo JHW, Low S, Vasoo S, Li JH, Thoon KC, Oh H, Pada SKMS, Ooi ST, Soh J, Wong HM, Tambyah PA. Predictors of disease severity in SARS-CoV-2 omicron variant XBB sublineages and variants of interest. J Med Virol 2023; 95:e29204. [PMID: 37937705 DOI: 10.1002/jmv.29204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/20/2023] [Accepted: 10/18/2023] [Indexed: 11/09/2023]
Abstract
The Omicron variant has been reported to present with milder disease compared with Delta, although this may be due to immunity from vaccination and prior exposure. Predictors of severity with recent strains have not been well characterized. We retrospectively examined consecutive cases of moderate-to-severe COVID-19 (defined as requiring supplemental oxygenation, intensive care or mortality) admitted to seven tertiary hospitals across Singapore in April 2023. Whole genome sequencing was performed on each isolate to determine the sublineage, while baseline clinical, laboratory data and outcomes were tabulated. We reviewed 182 patients with moderate-to-severe illness and 466 controls hospitalized at the same time. Advanced age and presence of chronic kidney disease predicted adverse outcome. Previously reported markers such as radiographic evidence of pneumonia, elevated C-reactive protein and serum creatinine levels at presentation also correlated with adverse outcomes. There were no observable differences in outcomes with any specific Omicron XBB sublineage. We did not find any specific Omicron XBB sublineage that was associated with worse outcomes. Larger multinational studies would be important to track the clinical evolution of the virus in its current endemic state.
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Affiliation(s)
- Jinghao Nicholas Ngiam
- Division of Infectious Diseases, National University Health System, Singapore, Singapore
| | - Oon Tek Ng
- Department of Infectious Diseases, Tan Tock Seng Hospital and the National Centre for Infectious Diseases, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Matthias Paul Han Sim Toh
- National Public Health and Epidemiology Unit, National Centre for Infectious Diseases, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Qi Gao
- National Public Health and Epidemiology Unit, National Centre for Infectious Diseases, Singapore, Singapore
| | - Ai Jia Soong
- National Public Health and Epidemiology Unit, National Centre for Infectious Diseases, Singapore, Singapore
| | - Joel Han Wen Teo
- National Public Health and Epidemiology Unit, National Centre for Infectious Diseases, Singapore, Singapore
| | - Shannon Low
- National Public Health and Epidemiology Unit, National Centre for Infectious Diseases, Singapore, Singapore
| | - Shawn Vasoo
- Department of Infectious Diseases, Tan Tock Seng Hospital and the National Centre for Infectious Diseases, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Jia Hui Li
- Department of Paediatrics, Infectious Disease Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Koh Cheng Thoon
- Department of Paediatrics, Infectious Disease Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Helen Oh
- Department of Infectious Diseases, Changi General Hospital, Singapore, Singapore
| | | | - Say Tat Ooi
- Department of Infectious Diseases, Khoo Teck Puat Hospital, Singapore, Singapore
| | - Jade Soh
- Department of Infectious Diseases, Sengkang General Hospital, Singapore, Singapore
| | - Hei Man Wong
- Department of Infectious Diseases, Singapore General Hospital Singapore, Singapore, Singapore
| | - Paul Anantharajah Tambyah
- Division of Infectious Diseases, National University Health System, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, Infectious Diseases Translational Research Programme, National University of Singapore, Singapore, Singapore
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Carmola LR, Roebling AD, Khosravi D, Langsjoen RM, Bombin A, Bixler B, Reid A, Chen C, Wang E, Lu Y, Zheng Z, Zhang R, Nguyen PV, Arthur RA, Fitts E, Gulick DA, Higginbotham D, Taz A, Ahmed A, Crumpler JH, Kraft C, Lam WA, Babiker A, Waggoner JJ, Openo KP, Johnson LM, Westbrook A, Piantadosi A. Viral and host factors associated with SARS-CoV-2 disease severity in Georgia, USA. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.25.23297530. [PMID: 37961729 PMCID: PMC10635197 DOI: 10.1101/2023.10.25.23297530] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
While SARS-CoV-2 vaccines have shown strong efficacy, their suboptimal uptake combined with the continued emergence of new viral variants raises concerns about the ongoing and future public health impact of COVID-19. We investigated viral and host factors, including vaccination status, that were associated with SARS-CoV-2 disease severity in a setting with low vaccination rates. We analyzed clinical and demographic data from 1,957 individuals in the state of Georgia, USA, coupled with viral genome sequencing from 1,185 samples. We found no difference in disease severity between individuals infected with Delta and Omicron variants among the participants in this study, after controlling for other factors, and we found no specific mutations associated with disease severity. Compared to those who were unvaccinated, vaccinated individuals experienced less severe SARS-CoV-2 disease, and the effect was similar for both variants. Vaccination within 270 days before infection was associated with decreased odds of moderate and severe outcomes, with the strongest association observed at 91-270 days post-vaccination. Older age and underlying health conditions, especially immunosuppression and renal disease, were associated with increased disease severity. Overall, this study provides insights into the impact of vaccination status, variants/mutations, and clinical factors on disease severity in SARS-CoV-2 infection when vaccination rates are low. Understanding these associations will help refine and reinforce messaging around the crucial importance of vaccination in mitigating the severity of SARS-CoV-2 disease.
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Affiliation(s)
- Ludy R. Carmola
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Allison Dorothy Roebling
- Georgia Emerging Infections Program; Georgia Department of Health; Atlanta, GA, 30303; USA
- Atlanta Veterans Affairs Medical Center; Decatur, GA, 30033; USA
- Division of Infectious Diseases; Department of Medicine, Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Dara Khosravi
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Rose M. Langsjoen
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Andrei Bombin
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
- Division of Infectious Diseases; Department of Medicine, Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Bri Bixler
- Graduate Program in Genetics and Molecular Biology, Emory University; Atlanta, GA, 30322; USA
| | - Alex Reid
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Cara Chen
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Ethan Wang
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Yang Lu
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Ziduo Zheng
- Department of Biostatistics and Bioinformatics; Rollins School of Public Health, Emory University; Atlanta, GA, 30322; USA
| | - Rebecca Zhang
- Department of Biostatistics and Bioinformatics; Rollins School of Public Health, Emory University; Atlanta, GA, 30322; USA
| | - Phuong-Vi Nguyen
- Division of Infectious Diseases; Department of Medicine, Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Robert A. Arthur
- Emory Integrated Computational Core; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Eric Fitts
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Dalia Arafat Gulick
- Georgia Clinical & Translational Science Alliance; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Dustin Higginbotham
- Georgia Clinical & Translational Science Alliance; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Azmain Taz
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Alaa Ahmed
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
- Emory Integrated Genomics Core; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - John Hunter Crumpler
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Colleen Kraft
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
- Division of Infectious Diseases; Department of Medicine, Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Wilbur A. Lam
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies; Atlanta, GA, 30322; USA
- Department of Pediatrics, Emory University School of Medicine; Atlanta, GA, 30322; USA
- Aflac Cancer and Blood Disorders Center at Children’s Healthcare of Atlanta; Atlanta, GA, 30322; USA
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
| | - Ahmed Babiker
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
- Division of Infectious Diseases; Department of Medicine, Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Jesse J. Waggoner
- Division of Infectious Diseases; Department of Medicine, Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Kyle P. Openo
- Georgia Emerging Infections Program; Georgia Department of Health; Atlanta, GA, 30303; USA
- Atlanta Veterans Affairs Medical Center; Decatur, GA, 30033; USA
- Division of Infectious Diseases; Department of Medicine, Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Laura M. Johnson
- Pediatric Biostatistics Core; Department of Pediatrics; School of Medicine; Emory University; Atlanta, GA, 30322; USA
| | - Adrianna Westbrook
- Pediatric Biostatistics Core; Department of Pediatrics; School of Medicine; Emory University; Atlanta, GA, 30322; USA
| | - Anne Piantadosi
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
- Division of Infectious Diseases; Department of Medicine, Emory University School of Medicine; Atlanta, GA, 30322; USA
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Booysen P, Wilkinson KA, Sheerin D, Waters R, Coussens AK, Wilkinson RJ. Immune interaction between SARS-CoV-2 and Mycobacterium tuberculosis. Front Immunol 2023; 14:1254206. [PMID: 37841282 PMCID: PMC10569495 DOI: 10.3389/fimmu.2023.1254206] [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: 07/06/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
SARS-CoV-2 and Mycobacterium tuberculosis (Mtb) are major infectious causes of death, with meta-analyses and population-based studies finding increased mortality in co-infected patients simultaneously diagnosed with COVID-19 and tuberculosis (TB). There is a need to understand the immune interaction between SARS-CoV-2 and Mtb which impacts poor outcomes for those co-infected. We performed a PubMed and preprint search using keywords [SARS-CoV-2] AND [tuberculosis] AND [Immune response], including publications after January 2020, excluding reviews or opinions. Abstracts were evaluated by authors for inclusion of data specifically investigating the innate and/or acquired immune responses to SARS-CoV-2 and Mtb in humans and animal models, immunopathological responses in co-infection and both trials and investigations of potential protection against SARS-CoV-2 by Bacille Calmette Guérin (BCG). Of the 248 articles identified, 39 were included. Incidence of co-infection is discussed, considering in areas with a high burden of TB, where reported co-infection is likely underestimated. We evaluated evidence of the clinical association between COVID-19 and TB, discuss differences and similarities in immune responses in humans and in murine studies, and the implications of co-infection. SARS-CoV-2 and Mtb have both been shown to modulate immune responses, particularly of monocytes, macrophages, neutrophils, and T cells. Co-infection may result in impaired immunity to SARS-CoV-2, with an exacerbated inflammatory response, while T cell responses to Mtb may be modulated by SARS-CoV-2. Furthermore, there has been no proven potential COVID-19 clinical benefit of BCG despite numerous large-scale clinical trials.
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Affiliation(s)
- Petro Booysen
- Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Katalin A. Wilkinson
- Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Medicine, University of Cape Town, Cape Town, South Africa
- Tuberculosis Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Dylan Sheerin
- Infectious Diseases and Immune Defence Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Robyn Waters
- Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Anna K. Coussens
- Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Infectious Diseases and Immune Defence Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Robert J. Wilkinson
- Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Medicine, University of Cape Town, Cape Town, South Africa
- Tuberculosis Laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Infectious Diseases, Imperial College, London, United Kingdom
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Li JX, Liao PL, Wei JCC, Hsu SB, Yeh CJ. A chronological review of COVID-19 case fatality rate and its secular trend and investigation of all-cause mortality and hospitalization during the Delta and Omicron waves in the United States: a retrospective cohort study. Front Public Health 2023; 11:1143650. [PMID: 37799149 PMCID: PMC10548482 DOI: 10.3389/fpubh.2023.1143650] [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] [Received: 01/13/2023] [Accepted: 08/14/2023] [Indexed: 10/07/2023] Open
Abstract
Introduction Coronavirus disease 2019 (COVID-19) has caused more than 690 million deaths worldwide. Different results concerning the death rates of the Delta and Omicron variants have been recorded. We aimed to assess the secular trend of case fatality rate (CFR), identify risk factors associated with mortality following COVID-19 diagnosis, and investigate the risks of mortality and hospitalization during Delta and Omicron waves in the United States. Methods This study assessed 2,857,925 individuals diagnosed with COVID-19 in the United States from January 2020, to June 2022. The inclusion criterion was the presence of COVID-19 diagnostic codes in electronic medical record or a positive laboratory test of the SARS-CoV-2. Statistical analysis was bifurcated into two components, longitudinal analysis and comparative analysis. To assess the discrepancies in hospitalization and mortality rates for COVID-19, we identified the prevailing periods for the Delta and Omicron variants. Results Longitudinal analysis demonstrated four sharp surges in the number of deaths and CFR. The CFR was persistently higher in males and older age. The CFR of Black and White remained higher than Asians since January 2022. In comparative analysis, the adjusted hazard ratios for all-cause mortality and hospitalization were higher in Delta wave compared to the Omicron wave. Risk of all-cause mortality was found to be greater 14-30 days after a COVID-19 diagnosis, while the likelihood of hospitalization was higher in the first 14 days following a COVID-19 diagnosis in Delta wave compared with Omicron wave. Kaplan-Meier analysis revealed the cumulative probability of mortality was approximately 2-fold on day 30 in Delta than in Omicron cases (log-rank p < 0.001). The mortality risk ratio between the Delta and Omicron variants was 1.671 (95% Cl 1.615-1.729, log-rank p < 0.001). Delta also had a significantly increased mortality risk over Omicron in all age groups. The CFR of people aged above 80 years was extremely high as 17.33%. Conclusion Male sex and age seemed to be strong and independent risk factors of mortality in COVID-19. The Delta variant appears to cause more hospitalization and death than the Omicron variant.
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Affiliation(s)
- Jing-Xing Li
- Department of Internal Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
- Graduate Institute of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Pei-Lun Liao
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - James Cheng-Chung Wei
- Department of Nursing, Chung Shan Medical University, Taichung, Taiwan
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Allergy, Immunology & Rheumatology, Chung Shan Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Integrated Medicine, China Medical University, Taichung, Taiwan
| | - Shu-Bai Hsu
- College of Medicine, China Medical University, Taichung, Taiwan
- Department of Nursing, China Medical University Hospital, Taichung, Taiwan
| | - Chih-Jung Yeh
- Department of Public Health, Chung Shan Medical University, Taichung, Taiwan
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Candelli M, Sacco Fernandez M, Pignataro G, Merra G, Tullo G, Bronzino A, Piccioni A, Ojetti V, Gasbarrini A, Franceschi F. ANCOC Score to Predict Mortality in Different SARS-CoV-2 Variants and Vaccination Status. J Clin Med 2023; 12:5838. [PMID: 37762779 PMCID: PMC10532001 DOI: 10.3390/jcm12185838] [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: 08/05/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND More than three years after the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic outbreak, hospitals worldwide are still affected by coronavirus disease 19 (COVID-19). The availability of a clinical score that can predict the risk of death from the disease at the time of diagnosis and that can be used even if population characteristics change and the virus mutates can be a useful tool for emergency physicians to make clinical decisions. During the first COVID-19 waves, we developed the ANCOC (age, blood urea nitrogen, C-reactive protein, oxygen saturation, comorbidities) score, a clinical score based on five main parameters (age, blood urea nitrogen, C-reactive protein, oxygen saturation, comorbidities) that accurately predicts the risk of death in patients infected with SARS-CoV-2. A score of less than -1 was associated with 0% mortality risk, whereas a score of 6 was associated with 100% risk of death, with an overall accuracy of 0.920. The aim of our study is to internally validate the ANCOC score and evaluate whether it can predict 60-day mortality risk independent of vaccination status and viral variant. METHODS We retrospectively enrolled 843 patients admitted to the emergency department (ED) of our hospital with a diagnosis of COVID-19. A total of 515 patients were admitted from July 2021 to September 2021, when the Delta variant was prevalent, and 328 in January 2022, when the Omicron 1 variant was predominant. All patients included in the study had a diagnosis of COVID-19 confirmed by polymerase chain reaction (PCR) on an oropharyngeal swab. Demographic data, comorbidities, vaccination data, and various laboratory, radiographic, and blood gas parameters were collected from all patients to determine differences between the two waves. ANCOC scores were then calculated for each patient, ranging from -6 to 6. RESULTS Patients infected with the Omicron variant were significantly older and had a greater number of comorbidities, of which hypertension and chronic obstructive pulmonary disease (COPD) were the most common. Immunization was less common in Delta patients than in Omicron patients (34% and 56%, respectively). To assess the accuracy of mortality prediction, we constructed a receiver operating characteristic (ROC) curve and found that the area under the ROC curve was greater than 0.8 for both variants. These results suggest that the ANCOC score is able to predict 60-day mortality regardless of viral variant and whether the patient is vaccinated or not. CONCLUSION In a population with increasingly high vaccination rates, several parameters may be considered prognostic for the risk of fatal outcomes. This study suggests that the ANCOC score can be very useful for the clinician in an emergency setting to quickly understand the patient's evolution and provide proper attention and the most appropriate treatments.
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Affiliation(s)
- Marcello Candelli
- Emergency, Anesthesiological and Reanimation Sciences Department, Fondazione Policlinico Universitario A. Gemelli—IRCCS of Rome, 00168 Rome, Italy; (G.P.); (A.B.); (A.P.); (V.O.); (F.F.)
| | - Marta Sacco Fernandez
- Department of Emergency Medicine, Università Cattolica del Sacro Cuore of Rome, 00168 Rome, Italy; (M.S.F.); (G.T.)
| | - Giulia Pignataro
- Emergency, Anesthesiological and Reanimation Sciences Department, Fondazione Policlinico Universitario A. Gemelli—IRCCS of Rome, 00168 Rome, Italy; (G.P.); (A.B.); (A.P.); (V.O.); (F.F.)
| | - Giuseppe Merra
- Biomedicine and Prevention Department, Section of Clinical Nutrition and Nutrigenomics, Facoltà di Medicina e Chirurgia, Università degli Studi di Roma Tor Vergata, 00133 Rome, Italy;
| | - Gianluca Tullo
- Department of Emergency Medicine, Università Cattolica del Sacro Cuore of Rome, 00168 Rome, Italy; (M.S.F.); (G.T.)
| | - Alessandra Bronzino
- Emergency, Anesthesiological and Reanimation Sciences Department, Fondazione Policlinico Universitario A. Gemelli—IRCCS of Rome, 00168 Rome, Italy; (G.P.); (A.B.); (A.P.); (V.O.); (F.F.)
| | - Andrea Piccioni
- Emergency, Anesthesiological and Reanimation Sciences Department, Fondazione Policlinico Universitario A. Gemelli—IRCCS of Rome, 00168 Rome, Italy; (G.P.); (A.B.); (A.P.); (V.O.); (F.F.)
| | - Veronica Ojetti
- Emergency, Anesthesiological and Reanimation Sciences Department, Fondazione Policlinico Universitario A. Gemelli—IRCCS of Rome, 00168 Rome, Italy; (G.P.); (A.B.); (A.P.); (V.O.); (F.F.)
| | - Antonio Gasbarrini
- Medical, Abdominal Surgery and Endocrine-Metabolic Science Department, Fondazione Policlinico Universitario A. Gemelli—IRCCS of Rome, 00168 Rome, Italy;
| | - Francesco Franceschi
- Emergency, Anesthesiological and Reanimation Sciences Department, Fondazione Policlinico Universitario A. Gemelli—IRCCS of Rome, 00168 Rome, Italy; (G.P.); (A.B.); (A.P.); (V.O.); (F.F.)
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Flisiak R, Zarębska-Michaluk D, Dobrowolska K, Rorat M, Rogalska M, Kryńska JA, Moniuszko-Malinowska A, Czupryna P, Kozielewicz D, Jaroszewicz J, Sikorska K, Bednarska A, Piekarska A, Rzymski P. Change in the Clinical Picture of Hospitalized Patients with COVID-19 between the Early and Late Period of Dominance of the Omicron SARS-CoV-2 Variant. J Clin Med 2023; 12:5572. [PMID: 37685639 PMCID: PMC10488127 DOI: 10.3390/jcm12175572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
This study aimed to compare the clinical picture of COVID-19 in the initial and later period of Omicron dominance and to identify populations still at risk. A retrospective comparison of the clinical data of 965 patients hospitalized during the early period of Omicron's dominance (EO, January-June 2022) with 897 patients from a later period (LO, July 2022-April 2023) from the SARSTer database was performed. Patients hospitalized during LO, compared to EO, were older, had a better clinical condition on admission, had a lower need for oxygen and mechanical ventilation, had less frequent lung involvement in imaging, and showed much faster clinical improvement. Moreover, the overall mortality during EO was 14%, higher than that in LO-9%. Despite the milder course of the disease, mortality exceeding 15% was similar in both groups among patients with lung involvement. The accumulation of risk factors such as an age of 60+, comorbidities, lung involvement, and oxygen saturation <90% resulted in a constant need for oxygen in 98% of patients, an 8% risk of mechanical ventilation, and a 30% mortality rate in the LO period. Multiple logistic regression revealed lower odds of death during the LO phase. Despite the milder course of infections caused by the currently dominant subvariants, COVID-19 prophylaxis is necessary in people over 60 years of age, especially those with comorbidities, and in the case of pneumonia and respiratory failure.
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Affiliation(s)
- Robert Flisiak
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, 15-540 Białystok, Poland; (R.F.); (M.R.); (J.A.K.)
| | - Dorota Zarębska-Michaluk
- Department of Infectious Diseases and Allergology, Jan Kochanowski University, 25-317 Kielce, Poland;
| | | | - Marta Rorat
- Department of Infectious Diseases and Hepatology, Wrocław Medical University, 51-149 Wrocław, Poland;
- Department of Forensic Medicine, Wrocław Medical University, 50-367 Wrocław, Poland
| | - Magdalena Rogalska
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, 15-540 Białystok, Poland; (R.F.); (M.R.); (J.A.K.)
| | - Justyna Anna Kryńska
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, 15-540 Białystok, Poland; (R.F.); (M.R.); (J.A.K.)
| | - Anna Moniuszko-Malinowska
- Department of Infectious Diseases and Neuroinfections, Medical University of Białystok, 15-809 Białystok, Poland; (A.M.-M.); (P.C.)
| | - Piotr Czupryna
- Department of Infectious Diseases and Neuroinfections, Medical University of Białystok, 15-809 Białystok, Poland; (A.M.-M.); (P.C.)
| | - Dorota Kozielewicz
- Department of Infectious Diseases and Hepatology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Toruń, Poland;
| | - Jerzy Jaroszewicz
- Department of Infectious Diseases and Hepatology, Medical University of Silesia in Katowice, 41-902 Bytom, Poland;
| | - Katarzyna Sikorska
- Division of Tropical and Parasitic Diseases, Faculty of Health Sciences, Medical University of Gdańsk, 80-210 Gdańsk, Poland;
| | - Agnieszka Bednarska
- Department of Adult’s Infectious Diseases, Medical University of Warsaw, Hospital for Infectious Diseases, 02-091 Warsaw, Poland;
| | - Anna Piekarska
- Department of Infectious Diseases and Hepatology, Medical University of Łódź, 90-419 Łódź, Poland;
| | - Piotr Rzymski
- Department of Environmental Medicine, Poznań University of Medical Sciences, 60-806 Poznań, Poland;
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Schröder D, Müllenmeister C, Heinemann S, Hummers E, Klawonn F, Vahldiek K, Dopfer-Jablonka A, Steffens S, Mikuteit M, Niewolik J, Overbeck TR, Kallusky J, Königs G, Heesen G, Schmachtenberg T, Müller F. Social participation during the COVID-19 pandemic in persons with a high risk for a severe course of COVID-19 - results of a longitudinal, multi-center observational study in Germany. Health Psychol Behav Med 2023; 11:2249534. [PMID: 37645515 PMCID: PMC10461510 DOI: 10.1080/21642850.2023.2249534] [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: 02/28/2023] [Accepted: 08/11/2023] [Indexed: 08/31/2023] Open
Abstract
Objective The COVID-19 pandemic has affected how people go about their daily lives, often in various and substantial ways. This study aims to prospectively evaluate the changes in social participation during the COVID-19 pandemic in persons with a high risk for a severe COVID-19 course in Germany. Methods A paper-pencil-based survey was conducted starting at March 2021. Participants filled out questionnaires at four time points based on their COVID-19 vaccination status: before COVID-19 vaccination, one month, six months and twelve months after COVID-19 vaccination. Social participation measures included the Pandemic Social Participation Questionnaire (PSP-Q) and the Index for measuring participation restrictions (IMET). Repeated measures ANOVA and paired t-test were used to test for changes between time-points. Repeated measures correlation was used to assess the relationship between social participation and local COVID-19 incidences. Results Data from 245 participants was analyzed before and one month after COVID-19 vaccination. In addition, data from 156 participants was analyzed at time points one, six and twelve months after COVID-19. PSP-Q and IMET scores changed significantly after participants received a COVID-19 vaccination. Between one month and twelve months after vaccination, social participation improved significantly measured by PSP-Q. Social participation was negatively correlated with regional COVID-19 incidences before and after COVID-19 vaccination. Social participation was positively correlated with COVID-19 incidences between one month and twelve months after COVID-19 vaccination. Conclusions Social participation improved in persons with a high risk for a severe COVID-19 course during the pandemic. The local COVID-19 incidence showed a negative association with social participation only until the fall of 2021 when it was used as the sole metric to regulate COVID-19 protective measures. Although our data describes the trends in social participation, further studies are needed to identify the influencing factors for the observed increase in social participation.
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Affiliation(s)
- Dominik Schröder
- Department of General Practice, University Medical Center, Göttingen, Germany
| | | | - Stephanie Heinemann
- Department of General Practice, University Medical Center, Göttingen, Germany
- Department of Geriatrics, University Medical Center Göttingen, Göttingen, Germany
| | - Eva Hummers
- Department of General Practice, University Medical Center, Göttingen, Germany
| | - Frank Klawonn
- Department of Computer Science, Ostfalia University of Applied Sciences, Wolfenbuettel, Germany
- Biostatistics Group, Helmholtz Centre for Infecwetion Research, Braunschweig, Germany
| | - Kai Vahldiek
- Department of Computer Science, Ostfalia University of Applied Sciences, Wolfenbuettel, Germany
| | - Alexandra Dopfer-Jablonka
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Brunswick, Germany
| | - Sandra Steffens
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Marie Mikuteit
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Jacqueline Niewolik
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Tobias R. Overbeck
- Department of Hematology and Medical Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - Jonathan Kallusky
- Department of Hematology and Medical Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - Gloria Königs
- Department of General Practice, University Medical Center, Göttingen, Germany
| | - Gloria Heesen
- Department of General Practice, University Medical Center, Göttingen, Germany
| | - Tim Schmachtenberg
- Department of General Practice, University Medical Center, Göttingen, Germany
| | - Frank Müller
- Department of General Practice, University Medical Center, Göttingen, Germany
- Department of Family Medicine, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
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49
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Shukla N, Srivastava N, Gupta R, Srivastava P, Narayan J. COVID Variants, Villain and Victory: A Bioinformatics Perspective. Microorganisms 2023; 11:2039. [PMID: 37630599 PMCID: PMC10459809 DOI: 10.3390/microorganisms11082039] [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: 06/21/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 08/27/2023] Open
Abstract
The SARS-CoV-2 virus, a novel member of the Coronaviridae family, is responsible for the viral infection known as Coronavirus Disease 2019 (COVID-19). In response to the urgent and critical need for rapid detection, diagnosis, analysis, interpretation, and treatment of COVID-19, a wide variety of bioinformatics tools have been developed. Given the virulence of SARS-CoV-2, it is crucial to explore the pathophysiology of the virus. We intend to examine how bioinformatics, in conjunction with next-generation sequencing techniques, can be leveraged to improve current diagnostic tools and streamline vaccine development for emerging SARS-CoV-2 variants. We also emphasize how bioinformatics, in general, can contribute to critical areas of biomedicine, including clinical diagnostics, SARS-CoV-2 genomic surveillance and its evolution, identification of potential drug targets, and development of therapeutic strategies. Currently, state-of-the-art bioinformatics tools have helped overcome technical obstacles with respect to genomic surveillance and have assisted in rapid detection, diagnosis, and delivering precise treatment to individuals on time.
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Affiliation(s)
- Nityendra Shukla
- CSIR Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India; (N.S.); (R.G.)
| | - Neha Srivastava
- Amity Institute of Biotechnology, Amity University, Uttar Pradesh, Lucknow Campus, Lucknow 226010, India; (N.S.); (P.S.)
| | - Rohit Gupta
- CSIR Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India; (N.S.); (R.G.)
| | - Prachi Srivastava
- Amity Institute of Biotechnology, Amity University, Uttar Pradesh, Lucknow Campus, Lucknow 226010, India; (N.S.); (P.S.)
| | - Jitendra Narayan
- CSIR Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India; (N.S.); (R.G.)
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Mak WA, Visser W, van der Vliet M, Markus HY, Koeleman JGM, Ong DSY. Ancestral SARS-CoV-2 and Omicron BA.5-specific neutralizing antibody and T-cell responses after Omicron bivalent booster vaccination in previously infected and infection-naive individuals. J Med Virol 2023; 95:e28989. [PMID: 37565645 DOI: 10.1002/jmv.28989] [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: 05/01/2023] [Revised: 06/28/2023] [Accepted: 07/16/2023] [Indexed: 08/12/2023]
Abstract
Coronavirus disease-2019 (COVID-19) bivalent ancestral/Omicron messenger RNA (mRNA) booster vaccinations became available to boost and expand the immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron infections. In a prospective cohort study including 59 healthcare workers, we assessed SARS-CoV-2 ancestral and Omicron BA.5-specific neutralizing antibody and T-cell responses in previously infected and infection-naive individuals. Also, we assessed the effect of an ancestral/Omicron BA.1 bivalent mRNA booster vaccination on these immune responses. 10 months after previous monovalent mRNA vaccinations, ancestral SARS-CoV-2 S1-specific T-cell and anti-RBD IgG responses remained detectable in most individuals and a previous SARS-CoV-2 infection was associated with increased T-cell responses. T-cell responses, anti-RBD IgG, and Omicron BA.5 neutralization activity increased after receiving an ancestral/Omicron BA.1 bivalent booster mRNA vaccination. An Omicron BA.5 infection in addition to bivalent vaccination, led to a higher ratio of Omicron BA.5 to ancestral strain neutralization activity compared to no bivalent vaccination and no recent SARS-CoV-2 infection. In conclusion, SARS-CoV-2 T-cell and antibody responses persist for up to 10 months after a monovalent booster mRNA vaccination. An ancestral/Omicron BA.1 bivalent booster mRNA vaccination increases these immune responses and also induces Omicron BA.5 cross-neutralization antibody activity. Finally, our data indicate that hybrid immunity is associated with improved preservation of T-cell immunity.
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Affiliation(s)
- Willem A Mak
- Department of Medical Microbiology and Infection Control, Franciscus Gasthuis & Vlietland, Rotterdam, The Netherlands
| | - Wendy Visser
- Department of Medical Microbiology and Infection Control, Franciscus Gasthuis & Vlietland, Rotterdam, The Netherlands
| | - Marijke van der Vliet
- Department of Medical Microbiology and Infection Control, Franciscus Gasthuis & Vlietland, Rotterdam, The Netherlands
| | - Hilde Y Markus
- Department of Medical Microbiology and Infection Control, Franciscus Gasthuis & Vlietland, Rotterdam, The Netherlands
| | - Johannes G M Koeleman
- Department of Medical Microbiology and Infection Control, Franciscus Gasthuis & Vlietland, Rotterdam, The Netherlands
| | - David S Y Ong
- Department of Medical Microbiology and Infection Control, Franciscus Gasthuis & Vlietland, Rotterdam, The Netherlands
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
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