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Wu JH, Wang CC, Lu FL, Huang SC, Yen TY, Lu CY, Chang LY, Wu ET. Clinical characteristics and outcomes of children with COVID-19 in pediatric intensive care units during the Omicron wave in Taiwan. J Formos Med Assoc 2024:S0929-6646(24)00345-0. [PMID: 39117546 DOI: 10.1016/j.jfma.2024.07.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 06/03/2024] [Accepted: 07/22/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Since April 2022, the SARS-CoV-2 Omicron variant has caused a notable increase in pediatric COVID-19 cases in Taiwan. During the acute phase of infection, some children required admissions to pediatric intensive care units (PICU). This study aimed to analyze their clinical presentations and outcomes while exploring associated factors. METHODS Medical records were retrospectively collected from patients with COVID-19 (aged <18 years) admitted to our PICU from April 2022-March 2023. Early stage is defined as the period without adequate vaccination and treatment guidelines for children from April-June 2022, and the remaining months are referred to as late stage. Clinical characteristics and outcomes were compared between patients in early and late stages. RESULTS We enrolled 78 children with COVID-19, with a median length of stay (LOS) in PICU of 3 days and a 5% mortality rate. Patients admitted during the early stage had lower vaccination rates (7% vs. 50%), higher pediatric logistic organ dysfunction scores (2 vs. 0.1), and longer LOS in the PICU (6 vs. 2 days) than those admitted during the late stage. Multivariate analysis identified admission during the early stage as a risk factor for prolonged LOS (>7 days) in the PICU (odds ratio: 3.65, p = 0.047). CONCLUSION Without available vaccinations and suitable treatment guidelines, children with COVID-19 tended to have more severe illness and prolonged LOS in the PICU. These observations highlight the importance of vaccinations and familiarity of medical providers with adequate management of this newly-emerging infectious disease.
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Affiliation(s)
- Jeng-Hung Wu
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Medicine, National Taiwan University Hospital, Jinshan Branch, New Taipei City, Taiwan
| | - Ching-Chia Wang
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Frank Leigh Lu
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shu-Chien Huang
- Department of Surgery, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Ting-Yu Yen
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chun-Yi Lu
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Luan-Yin Chang
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - En-Ting Wu
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan.
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2
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Judson SD, Dowdy DW. Modeling zoonotic and vector-borne viruses. Curr Opin Virol 2024; 67:101428. [PMID: 39047313 PMCID: PMC11292992 DOI: 10.1016/j.coviro.2024.101428] [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: 02/02/2024] [Accepted: 07/06/2024] [Indexed: 07/27/2024]
Abstract
The 2013-2016 Ebola virus disease epidemic and the coronavirus disease 2019 pandemic galvanized tremendous growth in models for emerging zoonotic and vector-borne viruses. Therefore, we have reviewed the main goals and methods of models to guide scientists and decision-makers. The elements of models for emerging viruses vary across spectrums: from understanding the past to forecasting the future, using data across space and time, and using statistical versus mechanistic methods. Hybrid/ensemble models and artificial intelligence offer new opportunities for modeling. Despite this progress, challenges remain in translating models into actionable decisions, particularly in areas at highest risk for viral disease outbreaks. To address this issue, we must identify gaps in models for specific viruses, strengthen validation, and involve policymakers in model development.
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Affiliation(s)
- Seth D Judson
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
| | - David W Dowdy
- Division of Infectious Disease Epidemiology, Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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3
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Rolff J, Bonhoeffer S, Kloft C, Leistner R, Regoes R, Hochberg ME. Forecasting antimicrobial resistance evolution. Trends Microbiol 2024; 32:736-745. [PMID: 38238231 DOI: 10.1016/j.tim.2023.12.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 08/09/2024]
Abstract
Antimicrobial resistance (AMR) is a major global health issue. Current measures for tackling it comprise mainly the prudent use of drugs, the development of new drugs, and rapid diagnostics. Relatively little attention has been given to forecasting the evolution of resistance. Here, we argue that forecasting has the potential to be a great asset in our arsenal of measures to tackle AMR. We argue that, if successfully implemented, forecasting resistance will help to resolve the antibiotic crisis in three ways: it will (i) guide a more sustainable use (and therefore lifespan) of antibiotics and incentivize investment in drug development, (ii) reduce the spread of AMR genes and pathogenic microbes in the environment and between patients, and (iii) allow more efficient treatment of persistent infections, reducing the continued evolution of resistance. We identify two important challenges that need to be addressed for the successful establishment of forecasting: (i) the development of bespoke technology that allows stakeholders to empirically assess the risks of resistance evolving during the process of drug development and therapeutic/preventive use, and (ii) the transformative shift in mindset from the current praxis of mostly addressing the problem of antibiotic resistance a posteriori to a concept of a priori estimating, and acting on, the risks of resistance.
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Affiliation(s)
- Jens Rolff
- Evolutionary Biology, Institute of Biology, Freie Universität Berlin, Berlin, Germany.
| | | | - Charlotte Kloft
- Clinical Pharmacy and Biochemistry, Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Rasmus Leistner
- Charité-Universitätsmedizin Berlin Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Berlin, Germany
| | - Roland Regoes
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Michael E Hochberg
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, 34095 Montpellier, France; Santa Fe Institute, Santa Fe, NM 87501, USA
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4
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Saad-Roy CM, Morris SE, Boots M, Baker RE, Lewis BL, Farrar J, Marathe MV, Graham AL, Levin SA, Wagner CE, Metcalf CJE, Grenfell BT. Impact of waning immunity against SARS-CoV-2 severity exacerbated by vaccine hesitancy. PLoS Comput Biol 2024; 20:e1012211. [PMID: 39102402 PMCID: PMC11299835 DOI: 10.1371/journal.pcbi.1012211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 05/29/2024] [Indexed: 08/07/2024] Open
Abstract
The SARS-CoV-2 pandemic has generated a considerable number of infections and associated morbidity and mortality across the world. Recovery from these infections, combined with the onset of large-scale vaccination, have led to rapidly-changing population-level immunological landscapes. In turn, these complexities have highlighted a number of important unknowns related to the breadth and strength of immunity following recovery or vaccination. Using simple mathematical models, we investigate the medium-term impacts of waning immunity against severe disease on immuno-epidemiological dynamics. We find that uncertainties in the duration of severity-blocking immunity (imparted by either infection or vaccination) can lead to a large range of medium-term population-level outcomes (i.e. infection characteristics and immune landscapes). Furthermore, we show that epidemiological dynamics are sensitive to the strength and duration of underlying host immune responses; this implies that determining infection levels from hospitalizations requires accurate estimates of these immune parameters. More durable vaccines both reduce these uncertainties and alleviate the burden of SARS-CoV-2 in pessimistic outcomes. However, heterogeneity in vaccine uptake drastically changes immune landscapes toward larger fractions of individuals with waned severity-blocking immunity. In particular, if hesitancy is substantial, more robust vaccines have almost no effects on population-level immuno-epidemiology, even if vaccination rates are compensatorily high among vaccine-adopters. This pessimistic scenario for vaccination heterogeneity arises because those few individuals that are vaccine-adopters are so readily re-vaccinated that the duration of vaccinal immunity has no appreciable consequences on their immune status. Furthermore, we find that this effect is heightened if vaccine-hesitants have increased transmissibility (e.g. due to riskier behavior). Overall, our results illustrate the necessity to characterize both transmission-blocking and severity-blocking immune time scales. Our findings also underline the importance of developing robust next-generation vaccines with equitable mass vaccine deployment.
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Affiliation(s)
- Chadi M. Saad-Roy
- Miller Institute for Basic Research in Science, University of California, Berkeley, California, United States of America
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
| | - Sinead E. Morris
- Department of Pathology and Cell Biology, Columbia University Medical Center, Columbia University, New York, New York, United States of America
| | - Mike Boots
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
- Department of Biosciences, University of Exeter, Penryn, United Kingdom
| | - Rachel E. Baker
- Department of Epidemiology, Brown School of Public Health, Brown University, Providence, Rhode Island, United States of America
| | - Bryan L. Lewis
- Network Systems Science and Advanced Computing Division, Biocomplexity Institute, University of Virginia, Charlottesville, Virginia, United States of America
| | | | - Madhav V. Marathe
- Network Systems Science and Advanced Computing Division, Biocomplexity Institute, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Computer Science, University of Virginia, Charlottesville, Virginia, United States of America
| | - Andrea L. Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Simon A. Levin
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | | | - C. Jessica E. Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- School of Public and International Affairs, Princeton University, Princeton, New Jersey, United States of America
| | - Bryan T. Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- School of Public and International Affairs, Princeton University, Princeton, New Jersey, United States of America
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5
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Kulin D, Shah A, Fairlie T, Wong RK, Fang X, Ghoshal UC, Kashyap PC, Mulak A, Lee YY, Talley NJ, Koloski N, Jones MP, Holtmann GJ. The COVID-19 pandemic as a modifier of DGBI symptom severity: A systematic review and meta-analysis. Neurogastroenterol Motil 2024:e14878. [PMID: 39056447 DOI: 10.1111/nmo.14878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/24/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024]
Abstract
BACKGROUND This SRMA reviewed and assessed the changes in the severity of disorders of gut-brain interaction (DGBI) symptoms during the COVID-19 pandemic, and evaluated factors associated with symptom severity changes. METHODS Electronic databases were searched until February 2024, for articles reporting on changes in symptom severity in DGBI patients during the COVID-19 pandemic. The proportion of DGBI patients who reported a change in their symptom severity were pooled using a random-effects model, and subgroup analyses were conducted to assess the effect of socio-cultural modifiers on symptom severity in DGBI. KEY RESULTS Twelve studies including 3610 DGBI patients found that 31.4% (95% CI, 15.9-52.5) of DGBI patients experienced symptom deterioration, while 24.3% (95% CI, 10.2-47.5) experienced improvement. Countries with high gross domestic product (GDP) had a 43.5% (95% CI, 16.3-75.2) likelihood of symptom deterioration, compared to 9.2% (95% CI, 1.4-42.2) in lower GDP countries. Similarly, countries with low COVID fatality rates had a 60.1% (95% CI, 19.7-90.3) likelihood of symptom deterioration, compared to 18.3% (95% CI, 7.8-36.9) in higher fatality rate countries. Countries with lenient COVID policies had a 58.4% (95% CI, 14.1-92.3) likelihood of symptom deterioration, compared to 19% (95% CI, 8.2-38.1) in countries with stricter policies. Patients in high vaccine hesitancy countries had a 51.4% (95% CI, 19.5-82.2) likelihood of symptom deterioration, compared to 10.6% (95% CI, 2.7-33.4) in low vaccine hesitancy countries. CONCLUSIONS & INFERENCES This meta-analysis reveals that a significantly higher proportion of DGBI patients experienced deterioration of symptoms during the COVID-19 pandemic. Various sociocultural, economic and environmental factors potentially modify the effects of the COVID-19 pandemic on DGBI.
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Affiliation(s)
- Dmitrii Kulin
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
- Department of Gastroenterology & Hepatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Ayesha Shah
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
- Department of Gastroenterology & Hepatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Thomas Fairlie
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
- Department of Gastroenterology & Hepatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Reuben K Wong
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xiucai Fang
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Uday C Ghoshal
- Institute of Gastrosciences and Liver Transplantation, Apollo Multispeciality Hospitals, Kolkata, India
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Agata Mulak
- Department of Gastroenterology and Hepatology, Wroclaw Medical University, Wroclaw, Poland
| | - Yeong Yeh Lee
- School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu, Malaysia
- GI Function & Motility Unit, Hospital Universiti Sains Malaysia, Kota Bharu, Malaysia
| | - Nicholas J Talley
- School of Medicine and Public Health, and Hunter Medical Research Institute, The University of Newcastle, Newcastle, New South Wales, Australia
| | - Natasha Koloski
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
- Department of Gastroenterology & Hepatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Michael P Jones
- Macquarie University, School of Psychological Sciences, Sydney, New South Wales, Australia
| | - Gerald J Holtmann
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
- Department of Gastroenterology & Hepatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
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6
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Mai W, Shen J, Ma F, Zhu J, Chen L, Lei Y, Yu P, Niu C, Wang F, Yan S, Mai X, He P, Liao L, Xiong X, Zheng Y, Liu Q, Huang Y, Wang Q, Liang J, Ji T. Specific humoral immune response and XBB variants re-infection risk of hemodialysis patients after Omicron BA.5 infection in China. Vaccine 2024:126108. [PMID: 39048466 DOI: 10.1016/j.vaccine.2024.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 06/08/2024] [Accepted: 07/02/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND Currently, there is limited understanding of the specific humoral immune response in BA.5-infected hemodialysis patients (BA.5-CHDPs) with previous COVID-19 vaccination. Additionally, the relevant risk factors for reinfection with XBB variants in BA.5-CHDPs have yet to be elucidated. METHOD A total of 178 BA.5-CHDPs were enrolled in this study among 53 patients who had previous vaccination. To compare hemodialysis patients in both unvaccinated and vaccinated for their immune response to the BA.5 subtype infection, we assessed serum levels of anti-ancestral-S1-IgG, anti-BA.5-receptor binding domain (RBD)-IgG, and anti-XBB.1.16-RBD-IgG using enzyme-linked immunosorbent assay, the neutralizing antibody titer against BA.5 and XBB.1.16 was determined using pseudovirus neutralization assays. Univariate and multivariate binary logistic regression analyses were conducted to identify factors associated with severe infection, the magnitude of specific humoral immunity and susceptibility to XBB variants reinfection. RESULT Our findings indicate that BA.5-CHDPs with full or booster vaccinations have higher levels of anti-ancestral-S1-IgG than unvaccinated individuals. However, levels of anti-BA.5-RBD-IgG and anti-XBB.1.16-RBD-IgG are much lower. Booster-vaccinated BA.5-CHDPs have significantly higher levels of BA.5 and XBB.1.16 specific antibodies and neutralizing antibodies than unvaccinated patients. Low globulin levels and shorter hemodialysis duration are independent risk factors for XBB reinfection in BA.5-CHDPs. CONCLUSION Although XBB.1.16 specific neutralizing antibody levels were low in BA.5-CHDPs, these levels cannot predict the risk of reinfection; other potential risk factors need to be investigated in the future.
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Affiliation(s)
- Weikang Mai
- State Key Laboratory of Respiratory Disease, Clinical Laboratory Medicine Department, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, PR China
| | - Jinwei Shen
- Nephrology Department, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, PR China
| | - Feifei Ma
- Obstetrical Department, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, PR China
| | - Jinhong Zhu
- State Key Laboratory of Respiratory Disease, Clinical Laboratory Medicine Department, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, PR China
| | - Lu Chen
- State Key Laboratory of Respiratory Disease, Clinical Laboratory Medicine Department, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, PR China
| | - Yu Lei
- State Key Laboratory of Respiratory Disease, Clinical Laboratory Medicine Department, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, PR China
| | - Pei Yu
- State Key Laboratory of Respiratory Disease, Clinical Laboratory Medicine Department, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, PR China
| | - Chanying Niu
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510535, PR China
| | - Feng Wang
- State Key Laboratory of Respiratory Disease, Clinical Laboratory Medicine Department, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, PR China
| | - Shuo Yan
- State Key Laboratory of Respiratory Disease, Clinical Laboratory Medicine Department, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, PR China
| | - Xiaorui Mai
- State Key Laboratory of Respiratory Disease, Clinical Laboratory Medicine Department, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, PR China
| | - Peng He
- Microbiology Detection Department, Guangzhou Center for Disease Control and Prevention, Guangzhou 510440, PR China
| | - Longhao Liao
- Department of Medical Laboratory, Guangdong Lingnan Institute of Technology, Guangzhou 510663, PR China
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510535, PR China
| | - Yu Zheng
- Urology Surgery Department, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, PR China
| | - Qiliang Liu
- College of Intelligent Medicine and Biotechnology, Guilin Medical University, Guilin, Guangxi 541100, PR China
| | - Ying Huang
- Nephrology Department, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, PR China.
| | - Qian Wang
- Guangzhou Laboratory, Guangzhou 510005, PR China.
| | - Jianbo Liang
- Nephrology Department, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, PR China.
| | - Tianxing Ji
- State Key Laboratory of Respiratory Disease, Clinical Laboratory Medicine Department, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, PR China.
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7
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Bayhan Gİ, Altan I, Mercan H, Özkaya Parlakay A, Coşkun ZN, Dinç B, Gülhan B, Kanık-Yüksek S. Is SARS-CoV-2 Now More Like the Seasonal Coronaviruses Following Its Evolution? Pediatr Infect Dis J 2024; 43:682-686. [PMID: 38534261 DOI: 10.1097/inf.0000000000004327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
BACKGROUND SARS-CoV-2 has evolved significantly since the beginning of the COVID-19 pandemic. COVID-19 mortality has decreased due to increased population immunity and possibly the reduced intrinsic severity of the new variants. SARS-CoV-2 is now considered an endemic virus, but the extent to which its clinical findings resemble those of seasonal coronaviruses (sCoV) is not fully understood. METHODS Pediatric patients under 18 years of age who were sent for SARS-CoV-2 polymerase chain reaction real-time reverse transcription polymerase chain reaction between January 1, 2022 and January 14, 2023 and whose results were positive were included in this study. To include only symptomatic COVID-19 patients in the study, asymptomatic patients who were positive in their screening tests were excluded. For the sCoV patients' group, patients who had a respiratory viral polymerase chain reaction assay between January 10, 2022 and January 11, 2023 and were positive for any type of sCoV were included in the study. The 2 groups were compared for clinical and laboratory characteristics. RESULTS The study included 213 patients with COVID-19 and 194 patients with sCoV infection. Fever was a more common symptom in patients with COVID-19. sCoV was associated with lower respiratory involvement while increasing age was protective. The likelihood of hospitalization was decreased by increasing age but increased by the presence of comorbid conditions and lower respiratory tract involvement. The type of virus had no effect on the likelihood of hospitalization. CONCLUSIONS In conclusion, sCoV infections carry a higher risk for lower respiratory involvement than COVID-19, and COVID-19 has a milder course than sCoV infections in children.
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Affiliation(s)
- Gülsüm İclal Bayhan
- From the Department of Pediatric Infectious Disease, Faculty of Medicine, Ankara Yıldırım Beyazıt University
| | | | | | - Aslınur Özkaya Parlakay
- From the Department of Pediatric Infectious Disease, Faculty of Medicine, Ankara Yıldırım Beyazıt University
| | | | - Bedia Dinç
- Department of Microbiology, Ankara City Hospital, Ankara, Turkey
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8
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Mirska B, Zenczak M, Nowis K, Stolarek I, Podkowiński J, Rakoczy M, Marcinkowska-Swojak M, Koralewska N, Zmora P, Lenartowicz Onyekaa E, Osuch M, Łasińska K, Kuczma-Napierała J, Jaworska M, Madej Ł, Ciechomska M, Jamsheer A, Kurowski K, Figlerowicz M, Handschuh L. The landscape of the COVID-19 pandemic in Poland emerging from epidemiological and genomic data. Sci Rep 2024; 14:14416. [PMID: 38909091 PMCID: PMC11193717 DOI: 10.1038/s41598-024-65468-5] [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: 01/11/2024] [Accepted: 06/20/2024] [Indexed: 06/24/2024] Open
Abstract
The COVID-19 pandemic has profoundly affected all aspects of our lives. Through real-time monitoring and rapid vaccine implementation, we succeeded in suppressing the spread of the disease and mitigating its consequences. Finally, conclusions can be summarized and drawn. Here, we use the example of Poland, which was seriously affected by the pandemic. Compared to other countries, Poland has not achieved impressive results in either testing or vaccination, which may explain its high mortality (case fatality rate, CFR 1.94%). Through retrospective analysis of data collected by the COVID-19 Data Portal Poland, we found significant regional differences in the number of tests performed, number of cases detected, number of COVID-19-related deaths, and vaccination rates. The Masovian, Greater Poland, and Pomeranian voivodeships, the country's leaders in vaccination, reported high case numbers but low death rates. In contrast, the voivodeships in the eastern and southern parts of Poland (Subcarpathian, Podlaskie, Lublin, Opole), which documented low vaccination levels and low case numbers, had higher COVID-19-related mortality rates. The strong negative correlation between the CFR and the percentage of the population that was vaccinated in Poland supports the validity of vaccination. To gain insight into virus evolution, we sequenced more than 500 genomes and analyzed nearly 80 thousand SARS-CoV-2 genome sequences deposited in GISAID by Polish diagnostic centers. We showed that the SARS-CoV-2 variant distribution over time in Poland reflected that in Europe. Haplotype network analysis allowed us to follow the virus transmission routes and identify potential superspreaders in each pandemic wave.
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Affiliation(s)
- Barbara Mirska
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Michal Zenczak
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Katarzyna Nowis
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Ireneusz Stolarek
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Jan Podkowiński
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Magdalena Rakoczy
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | | | - Natalia Koralewska
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Paweł Zmora
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | | | - Marcin Osuch
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | | | | | | | - Łukasz Madej
- Regional Science and Technology Center, Podzamcze, Poland
| | - Marzena Ciechomska
- National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland
| | - Aleksander Jamsheer
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
- Centers for Medical Genetics GENESIS, Poznan, Poland
| | - Krzysztof Kurowski
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Luiza Handschuh
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland.
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9
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Funk A, Florin TA, Kuppermann N, Finkelstein Y, Kazakoff A, Baldovsky M, Tancredi DJ, Breslin K, Bergmann KR, Gardiner M, Pruitt CM, Liu DR, Neuman MI, Wilkinson M, Ambroggio L, Pang XL, Cauchemez S, Malley R, Klassen TP, Lee BE, Payne DC, Mahmud SM, Freedman SB. Household Transmission Dynamics of Asymptomatic SARS-CoV-2-Infected Children: A Multinational, Controlled Case-Ascertained Prospective Study. Clin Infect Dis 2024; 78:1522-1530. [PMID: 38530249 PMCID: PMC11175701 DOI: 10.1093/cid/ciae069] [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: 11/01/2023] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Asymptomatic SARS-CoV-2 infection in children is highly prevalent but its acute and chronic implications have been minimally described. METHODS In this controlled case-ascertained household transmission study, we recruited asymptomatic children <18 years with SARS-CoV-2 nucleic acid testing performed at 12 tertiary care pediatric institutions in Canada and the United States. We attempted to recruit all test-positive children and 1 to 3 test-negative, site-matched controls. After 14 days' follow-up we assessed the clinical (ie, symptomatic) and combined (ie, test-positive, or symptomatic) secondary attack rates (SARs) among household contacts. Additionally, post-COVID-19 condition (PCC) was assessed in SARS-CoV-2-positive participating children after 90 days' follow-up. RESULTS A total of 111 test-positive and 256 SARS-CoV-2 test-negative asymptomatic children were enrolled between January 2021 and April 2022. After 14 days, excluding households with co-primary cases, the clinical SAR among household contacts of SARS-CoV-2-positive and -negative index children was 10.6% (19/179; 95% CI: 6.5%-16.1%) and 2.0% (13/663; 95% CI: 1.0%-3.3%), respectively (relative risk = 5.4; 95% CI: 2.7-10.7). In households with a SARS-CoV-2-positive index child, age <5 years, being pre-symptomatic (ie, developed symptoms after test), and testing positive during Omicron and Delta circulation periods (vs earlier) were associated with increased clinical and combined SARs among household contacts. Among 77 asymptomatic SARS-CoV-2-infected children with 90-day follow-up, 6 (7.8%; 95% CI: 2.9%-16.2%) reported PCC. CONCLUSIONS Asymptomatic SARS-CoV-2-infected children, especially those <5 years, are important contributors to household transmission, with 1 in 10 exposed household contacts developing symptomatic illness within 14 days. Asymptomatic SARS-CoV-2-infected children may develop PCC.
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Affiliation(s)
- Anna Funk
- Department of Obstetrics and Gynecology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Todd A Florin
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Division of Emergency Medicine, Ann and Robert H. Lurie Children's Hospital Chicago, Chicago, Illinois, USA
| | - Nathan Kuppermann
- Department of Emergency Medicine, University of California, Davis School of Medicine, Sacramento, California, USA
- Department of Pediatrics, University of California, Davis School of Medicine, Sacramento, California, USA
| | - Yaron Finkelstein
- Divisions of Emergency Medicine and Clinical Pharmacology and Toxicology, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Alissa Kazakoff
- Faculty of Kinesiology, University of Calgary, Calgary, Alberta, Canada
| | - Michael Baldovsky
- Division of Pediatric Emergency Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Daniel J Tancredi
- Department of Pediatrics, University of California, Davis School of Medicine, Sacramento, California, USA
| | - Kristen Breslin
- Division of Emergency Medicine, Children's National Hospital, Washington, D.C., USA
| | - Kelly R Bergmann
- Department of Pediatric Emergency Medicine, Children's Minnesota, Minneapolis, Minnesota, USA
| | - Michael Gardiner
- Department of Pediatrics, University of California, San Diego School of Medicine, San Diego, California, USA
- Division of Emergency Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Christopher M Pruitt
- Department of Pediatrics, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Deborah R Liu
- Division of Emergency Medicine, Department of Pediatrics, Children's Hospital Los Angeles, Keck USC School of Medicine, Los Angeles, California, USA
| | - Mark I Neuman
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Division of Emergency Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Matthew Wilkinson
- Department of Pediatrics, University of Texas at Austin, Dell Medical School, Austin, Texas, USA
| | - Lilliam Ambroggio
- Department of Pediatrics, University of Colorado, Aurora, Colorado, USA
- Section of Emergency Medicine, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Xiao-Li Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Paris, France
| | - Richard Malley
- Division of Infectious Diseases, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Terry P Klassen
- Children's Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Bonita E Lee
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Daniel C Payne
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Salaheddin M Mahmud
- Dept of Community Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Stephen B Freedman
- Section of Pediatric Emergency Medicine, Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Section of Gastroenterology, Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Emergency Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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10
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Kakee S, Kanai K, Tsuneki-Tokunaga A, Okuno K, Namba N, Tomita K, Chikumi H, Kageyama S. Difference in TMPRSS2 usage by Delta and Omicron variants of SARS-CoV-2: Implication for a sudden increase among children. PLoS One 2024; 19:e0299445. [PMID: 38870131 PMCID: PMC11175390 DOI: 10.1371/journal.pone.0299445] [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: 02/11/2024] [Accepted: 05/07/2024] [Indexed: 06/15/2024] Open
Abstract
It has been postulated from a combination of evidence that a sudden increase in COVID-19 cases among pediatric patients after onset of the Omicron wave was attributed to a reduced requirement for TMPRSS2-mediated entry in pediatric airways with lower expression levels of TMPRSS2. Epidemic strains were isolated from the indigenous population in an area, and the levels of TMPRSS2 required for Delta and Omicron variants were assessed. As a result, Delta variants proliferated fully in cultures of TMPRSS2-positive Vero cells but not in TMPRSS2-negative Vero cell culture (350-fold, Delta vs 9.6-fold, Omicron). There was no obvious age-dependent selection of Omicron strains affected by the TMPRSS2 (9.6-fold, Adults vs. 12-fold, Children). A phylogenetic tree was generated and Blast searches (up to 100 references) for the spread of strains in the study area showed that each strain had almost identical homology (>99.5%) with foreign isolates, although indigenous strains had obvious differences from each other. This suggested that the differences had been present abroad for a long period. Therefore, the lower requirement for TMPRSS2 by Omicron strains might be applicable to epidemic strains globally. In conclusion, the property of TMPRSS2-independent cleavage makes Omicron proliferate with ease and allows epidemics among children with fewer TMPRSS2 on epithelial surfaces of the respiratory organs.
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Affiliation(s)
- Sosuke Kakee
- Division of Virology, Department of Microbiology and Immunology, Faculty of Medicine, Tottori University, Yonago, Japan
- Division of Pediatrics and Perinatology, Department of Multidisciplinary Internal Medicine, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Kyosuke Kanai
- Division of Virology, Department of Microbiology and Immunology, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Akeno Tsuneki-Tokunaga
- Division of Virology, Department of Microbiology and Immunology, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Keisuke Okuno
- Division of Pediatrics and Perinatology, Department of Multidisciplinary Internal Medicine, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Noriyuki Namba
- Division of Pediatrics and Perinatology, Department of Multidisciplinary Internal Medicine, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Katsuyuki Tomita
- Department of Respiratory Medicine, National Hospital Organization Yonago Medical Center, Yonago, Japan
| | | | - Seiji Kageyama
- Division of Virology, Department of Microbiology and Immunology, Faculty of Medicine, Tottori University, Yonago, Japan
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11
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Tian H, Kong X, Han F, Xing F, Zhu S, Xu T, Wang W, Song N, Wu Y. Liver Iron Overload Drives COVID-19 Mortality: a Two-Sample Mendelian Randomization Study. Biol Trace Elem Res 2024; 202:2509-2517. [PMID: 37814169 DOI: 10.1007/s12011-023-03878-8] [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: 07/23/2023] [Accepted: 09/19/2023] [Indexed: 10/11/2023]
Abstract
Iron overload has been associated with an increased risk of COVID-19 severity and mortality in observational studies, but it remains unclear whether these associations represent causal effects. We performed a two-sample Mendelian randomization (MR) to determine associations between genetic liability to iron overload and the risk of COVID-19 severity and mortality. From genome-wide association studies of European ancestry, single-nucleotide polymorphisms associated with liver iron (n = 32,858) and ferritin (n = 23,986) were selected as exposure instruments, and summary statistics of the hospitalization (n = 16,551) and mortality (n = 15,815) of COVID-19 were utilized as the outcome. We used the inverse-variance weighted (IVW) method as the primary analysis to estimate causal effects, and other alternative approaches as well as comprehensive sensitivity analysis were conducted for estimating the robustness of identified associations. Genetically predicted high liver iron levels were associated with an increased risk of COVID-19 mortality based on the results of IVW analysis (OR = 1.38, 95% CI: 1.05-1.82, P = 0.02). Likewise, sensitivity analyses showed consistent and robust results in general (all P > 0.05). A higher risk of COVID-19 hospitalization trend was also observed in patients with high liver iron levels without statistical significance. This study suggests that COVID-19 mortality might be partially driven by the iron accumulation in the liver, supporting the classification of iron overload as one of the independent death risk factors. Therefore, avoiding iron overload and maintaining normal iron levels may be a powerful measure to reduce COVID-19 mortality.
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Affiliation(s)
- Huimin Tian
- Zhonglou District Center for Disease Control and Prevention, Changzhou, Jiangsu, China.
| | - Xiangjie Kong
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, Shandong, China
| | - Fulei Han
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, Shandong, China
| | - Fangjie Xing
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, Shandong, China
| | - Shuai Zhu
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, Shandong, China
| | - Tao Xu
- Department of Pulmonary and Critical Care Medicine, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Weijing Wang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, Shandong, China
| | - Ning Song
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorder, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Yili Wu
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, Shandong, China
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12
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Moore S, Cavany S, Perkins TA, España GFC. Projecting the future impact of emerging SARS-CoV-2 variants under uncertainty: Modeling the initial Omicron outbreak. Epidemics 2024; 47:100759. [PMID: 38452455 DOI: 10.1016/j.epidem.2024.100759] [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: 08/18/2023] [Revised: 01/26/2024] [Accepted: 03/01/2024] [Indexed: 03/09/2024] Open
Abstract
Over the past several years, the emergence of novel SARS-CoV-2 variants has led to multiple waves of increased COVID-19 incidence. When the Omicron variant emerged, there was considerable concern about its potential impact in the winter of 2021-2022 due to its increased fitness. However, there was also considerable uncertainty regarding its likely impact due to questions about its relative transmissibility, severity, and degree of immune escape. We sought to evaluate the ability of an agent-based model to forecast incidence in the context of this emerging pathogen variant. To project COVID-19 cases and deaths in Indiana, we calibrated our model to COVID-19 hospitalizations, deaths, and test-positivity rates through November 2021, and then projected COVID-19 incidence through April 2022 under four different scenarios that covered the plausible ranges of Omicron's severity, transmissibility, and degree of immune escape. Our initial projections from December 2021 through March 2022 indicated that under a pessimistic scenario with high disease severity, the peak in weekly COVID-19 deaths in Indiana would be larger than the previous peak in December 2020. However, retrospective analyses indicate that Omicron's severity was closer to the optimistic scenario, and even though cases and hospitalizations reached a new peak, fewer deaths occurred than during the previous peak. According to our results, Omicron's rapid spread was consistent with a combination of higher transmissibility and immune escape relative to earlier variants. Our updated projections starting in January 2022 accurately predicted that cases would peak in mid-January and decline rapidly over the next several months. The performance of our projections shows that following the emergence of a new pathogen variant, models can help quantify the potential range of outbreak magnitudes and trajectories. Agent-based models are particularly useful in these scenarios because they can efficiently track individual vaccination and infection histories with multiple variants with varying degrees of cross-protection.
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Affiliation(s)
- Sean Moore
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, United States.
| | - Sean Cavany
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, United States
| | - T Alex Perkins
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Guido Felipe Camargo España
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, United States
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13
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Li H, Zhao J, Xing Y, Chen J, Wen Z, Ma R, Han F, Huang B, Wang H, Li C, Chen Y, Ning X. Identification of Age-Related Characteristic Genes Involved in Severe COVID-19 Infection Among Elderly Patients Using Machine Learning and Immune Cell Infiltration Analysis. Biochem Genet 2024:10.1007/s10528-024-10802-9. [PMID: 38656671 DOI: 10.1007/s10528-024-10802-9] [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: 01/01/2024] [Accepted: 04/05/2024] [Indexed: 04/26/2024]
Abstract
Elderly patients infected with severe acute respiratory syndrome coronavirus 2 are at higher risk of severe clinical manifestation, extended hospitalization, and increased mortality. Those patients are more likely to experience persistent symptoms and exacerbate the condition of basic diseases with long COVID-19 syndrome. However, the molecular mechanisms underlying severe COVID-19 in the elderly patients remain unclear. Our study aims to investigate the function of the interaction between disease-characteristic genes and immune cell infiltration in patients with severe COVID-19 infection. COVID-19 datasets (GSE164805 and GSE180594) and aging dataset (GSE69832) were obtained from the Gene Expression Omnibus database. The combined different expression genes (DEGs) were subjected to Gene Ontology (GO) functional enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Diseases Ontology functional enrichment analysis, Gene Set Enrichment Analysis, machine learning, and immune cell infiltration analysis. GO and KEGG enrichment analyses revealed that the eight DEGs (IL23A, PTGER4, PLCB1, IL1B, CXCR1, C1QB, MX2, ALOX12) were mainly involved in inflammatory mediator regulation of TRP channels, coronavirus disease-COVID-19, and cytokine activity signaling pathways. Three-degree algorithm (LASSO, SVM-RFE, KNN) and correlation analysis showed that the five DEGs up-regulated the immune cells of macrophages M0/M1, memory B cells, gamma delta T cell, dendritic cell resting, and master cell resisting. Our study identified five hallmark genes that can serve as disease-characteristic genes and target immune cells infiltrated in severe COVID-19 patients among the elderly population, which may contribute to the study of pathogenesis and the evaluation of diagnosis and prognosis in aging patients infected with severe COVID-19.
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Affiliation(s)
- Huan Li
- Department of Geriatrics, Xijing Hospital, Fourth Military Medical University, No. 127 Chang le West Road, Xi'an, 710032, Shaanxi, China
- Department of Nephrology, The Second People's Hospital of Shaan xi Province, Xi'an, China
| | - Jin Zhao
- Department of Geriatrics, Xijing Hospital, Fourth Military Medical University, No. 127 Chang le West Road, Xi'an, 710032, Shaanxi, China
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yan Xing
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Jia Chen
- Xi'an Medical University, Xi'an, China
| | | | - Rui Ma
- Department of Geriatrics, Xijing Hospital, Fourth Military Medical University, No. 127 Chang le West Road, Xi'an, 710032, Shaanxi, China
| | - Fengxia Han
- Department of Geriatrics, Xijing Hospital, Fourth Military Medical University, No. 127 Chang le West Road, Xi'an, 710032, Shaanxi, China
| | - Boyong Huang
- Department of Geriatrics, Xijing Hospital, Fourth Military Medical University, No. 127 Chang le West Road, Xi'an, 710032, Shaanxi, China
| | - Hao Wang
- Department of Geriatrics, Xijing Hospital, Fourth Military Medical University, No. 127 Chang le West Road, Xi'an, 710032, Shaanxi, China
| | - Cui Li
- Department of Geriatrics, Xijing Hospital, Fourth Military Medical University, No. 127 Chang le West Road, Xi'an, 710032, Shaanxi, China
| | - Yang Chen
- Department of Geriatrics, Xijing Hospital, Fourth Military Medical University, No. 127 Chang le West Road, Xi'an, 710032, Shaanxi, China
| | - Xiaoxuan Ning
- Department of Geriatrics, Xijing Hospital, Fourth Military Medical University, No. 127 Chang le West Road, Xi'an, 710032, Shaanxi, China.
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14
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Yin Q, Liu W, Jiang Y, Feng Q, Wang X, Dou H, Liu Z, He F, Fan Y, Jiao B, Jiao B. Comprehensive genomic analysis of the SARS-CoV-2 Omicron variant BA.2.76 in Jining City, China, 2022. BMC Genomics 2024; 25:378. [PMID: 38632523 PMCID: PMC11022347 DOI: 10.1186/s12864-024-10246-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 03/21/2024] [Indexed: 04/19/2024] Open
Abstract
OBJECTIVE This study aims to analyze the molecular characteristics of the novel coronavirus (SARS-CoV-2) Omicron variant BA.2.76 in Jining City, China. METHODS Whole-genome sequencing was performed on 87 cases of SARS-CoV-2 infection. Evolutionary trees were constructed using bioinformatics software to analyze sequence homology, variant sites, N-glycosylation sites, and phosphorylation sites. RESULTS All 87 SARS-CoV-2 whole-genome sequences were classified under the evolutionary branch of the Omicron variant BA.2.76. Their similarity to the reference strain Wuhan-Hu-1 ranged from 99.72 to 99.74%. In comparison to the reference strain Wuhan-Hu-1, the 87 sequences exhibited 77-84 nucleotide differences and 27 nucleotide deletions. A total of 69 amino acid variant sites, 9 amino acid deletions, and 1 stop codon mutation were identified across 18 proteins. Among them, the spike (S) protein exhibited the highest number of variant sites, and the ORF8 protein showed a Q27 stop mutation. Multiple proteins displayed variations in glycosylation and phosphorylation sites. CONCLUSION SARS-CoV-2 continues to evolve, giving rise to new strains with enhanced transmission, stronger immune evasion capabilities, and reduced pathogenicity. The application of high-throughput sequencing technologies in the epidemic prevention and control of COVID-19 provides crucial insights into the evolutionary and variant characteristics of the virus at the genomic level, thereby holding significant implications for the prevention and control of the COVID-19 pandemic.
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Affiliation(s)
- Qiang Yin
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Wei Liu
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Yajuan Jiang
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Qiang Feng
- Department of Laboratory, Rencheng Center for Disease Control and Prevention, Jining, China
| | - Xiaoyu Wang
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Huixin Dou
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Zanzan Liu
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Feifei He
- Computer Information Technology, Northern Arizona University, Arizona, USA
| | - Yingying Fan
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
| | - Baihai Jiao
- Department of Medicine, School of Medicine, University of Connecticut Health Center, Farmington, CT, USA.
| | - Boyan Jiao
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
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15
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Plumb ID, Briggs Hagen M, Wiegand R, Dumyati G, Myers C, Harland KK, Krishnadasan A, James Gist J, Abedi G, Fleming-Dutra KE, Chea N, Lee JE, Kellogg M, Edmundson A, Britton A, Wilson LE, Lovett SA, Ocampo V, Markus TM, Smithline HA, Hou PC, Lee LC, Mower W, Rwamwejo F, Steele MT, Lim SC, Schrading WA, Chinnock B, Beiser DG, Faine B, Haran JP, Nandi U, Chipman AK, LoVecchio F, Eucker S, Femling J, Fuller M, Rothman RE, Curlin ME, Talan DA, Mohr NM. Effectiveness of a bivalent mRNA vaccine dose against symptomatic SARS-CoV-2 infection among U.S. Healthcare personnel, September 2022-May 2023. Vaccine 2024; 42:2543-2552. [PMID: 37973512 PMCID: PMC10994739 DOI: 10.1016/j.vaccine.2023.10.072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Bivalent mRNA vaccines were recommended since September 2022. However, coverage with a recent vaccine dose has been limited, and there are few robust estimates of bivalent VE against symptomatic SARS-CoV-2 infection (COVID-19). We estimated VE of a bivalent mRNA vaccine dose against COVID-19 among eligible U.S. healthcare personnel who had previously received monovalent mRNA vaccine doses. METHODS We conducted a case-control study in 22 U.S. states, and enrolled healthcare personnel with COVID-19 (case-participants) or without COVID-19 (control-participants) during September 2022-May 2023. Participants were considered eligible for a bivalent mRNA dose if they had received 2-4 monovalent (ancestral-strain) mRNA vaccine doses, and were ≥67 days after the most recent vaccine dose. We estimated VE of a bivalent mRNA dose using conditional logistic regression, accounting for matching by region and four-week calendar period. We adjusted estimates for age group, sex, race and ethnicity, educational level, underlying health conditions, community COVID-19 exposure, prior SARS-CoV-2 infection, and days since the last monovalent mRNA dose. RESULTS Among 3,647 healthcare personnel, 1,528 were included as case-participants and 2,119 as control-participants. Participants received their last monovalent mRNA dose a median of 404 days previously; 1,234 (33.8%) also received a bivalent mRNA dose a median of 93 days previously. Overall, VE of a bivalent dose was 34.1% (95% CI, 22.6%-43.9%) against COVID-19 and was similar by product, days since last monovalent dose, number of prior doses, age group, and presence of underlying health conditions. However, VE declined from 54.8% (95% CI, 40.7%-65.6%) after 7-59 days to 21.6% (95% CI 5.6%-34.9%) after ≥60 days. CONCLUSIONS Bivalent mRNA COVID-19 vaccines initially conferred approximately 55% protection against COVID-19 among U.S. healthcare personnel. However, protection waned after two months. These findings indicate moderate initial protection against symptomatic SARS-CoV-2 infection by remaining up-to-date with COVID-19 vaccines.
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Affiliation(s)
- Ian D Plumb
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control & Prevention, Atlanta, GA, USA.
| | - Melissa Briggs Hagen
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control & Prevention, Atlanta, GA, USA
| | - Ryan Wiegand
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control & Prevention, Atlanta, GA, USA
| | - Ghinwa Dumyati
- University of Rochester Medical Center, Rochester, NY, USA
| | | | | | | | - Jade James Gist
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control & Prevention, Atlanta, GA, USA
| | - Glen Abedi
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control & Prevention, Atlanta, GA, USA
| | - Katherine E Fleming-Dutra
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control & Prevention, Atlanta, GA, USA
| | - Nora Chea
- National Center for Emerging and Zoonotic Diseases, Centers for Disease Control & Prevention, USA
| | - Jane E Lee
- California Emerging Infections Program, Oakland, CA, USA
| | | | - Alexandra Edmundson
- Connecticut Emerging Infections Program, Yale School of Public Health, CT, USA
| | - Amber Britton
- Georgia Emerging Infections Program and Emory University School of Medicine, Atlanta, GA, USA
| | - Lucy E Wilson
- Maryland Emerging Infections Program, Maryland Department of Health and University of Maryland, Baltimore, MD, USA
| | | | - Valerie Ocampo
- Public Health Division, Oregon Health Authority, OR, USA
| | | | | | - Peter C Hou
- Brigham and Women's Hospital, Boston, MA, USA
| | | | | | | | - Mark T Steele
- University of Missouri-Kansas City, Kansas City, MO, USA
| | - Stephen C Lim
- University Medical Center New Orleans, LSU Health Sciences Center, New Orleans, LA, USA
| | | | | | | | | | - John P Haran
- University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Utsav Nandi
- University of Mississippi Medical Center, Jackson, MS, USA
| | | | | | | | - Jon Femling
- University of New Mexico Health Science Center, USA
| | | | - Richard E Rothman
- Department of Emergency Medicine, Johns Hopkins University, Baltimore, MD, USA
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16
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Lina A, Keith H, Jenny H, Mariana M, Gregorio T, Laure WV, Paolo T. Facing SARS-CoV-2 emergence on the animal health perspective: The role of the World Organisation for Animal Health in preparedness and official reporting of disease occurrence. Zoonoses Public Health 2024. [PMID: 38584342 DOI: 10.1111/zph.13133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 03/17/2024] [Accepted: 03/19/2024] [Indexed: 04/09/2024]
Abstract
AIMS Current data suggest that SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) emerged from an animal source. However, to date, there is insufficient scientific evidence to identify the source of SARS-CoV-2 or to explain the original route of transmission to humans. A wide range of mammalian species have been shown to be susceptible to the virus through experimental infection, and in natural environments when in contact with infected humans. The main objective of this work was to provide a summary of the official data shared by countries on SARS-CoV-2 in animals with the World Organisation for Animal Health (WOAH), to highlight the role of WOAH as an international organization in coordinating scientific information actions and to discuss the implications and impact of these activities. METHODS AND RESULTS Between January 2020 and December 2022, 36 countries in Europe, the Americas, Asia and Africa officially reported SARS-CoV-2 identification in 26 animal species. Affected countries were generally responsive in confirming the pathogen (median of 5 days after onset) and reporting to WOAH (median of 7 days after confirmation). CONCLUSIONS During the pandemic, WOAH, supported by its network of experts, played a crucial role in collecting, analysing and disseminating veterinary scientific information, acting as the reference organization on these issues, thus avoiding misinformation and disinformation. Future perspectives to avoid new emerging threats are discussed.
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Affiliation(s)
- Awada Lina
- World Organisation for Animal Health (WOAH), Paris, France
| | - Hamilton Keith
- World Organisation for Animal Health (WOAH), Paris, France
| | | | | | | | | | - Tizzani Paolo
- World Organisation for Animal Health (WOAH), Paris, France
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17
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Erazo-Oliveras A, Muñoz-Vega M, Salinas ML, Wang X, Chapkin RS. Dysregulation of cellular membrane homeostasis as a crucial modulator of cancer risk. FEBS J 2024; 291:1299-1352. [PMID: 36282100 PMCID: PMC10126207 DOI: 10.1111/febs.16665] [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: 06/18/2022] [Revised: 09/09/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2022]
Abstract
Cellular membranes serve as an epicentre combining extracellular and cytosolic components with membranous effectors, which together support numerous fundamental cellular signalling pathways that mediate biological responses. To execute their functions, membrane proteins, lipids and carbohydrates arrange, in a highly coordinated manner, into well-defined assemblies displaying diverse biological and biophysical characteristics that modulate several signalling events. The loss of membrane homeostasis can trigger oncogenic signalling. More recently, it has been documented that select membrane active dietaries (MADs) can reshape biological membranes and subsequently decrease cancer risk. In this review, we emphasize the significance of membrane domain structure, organization and their signalling functionalities as well as how loss of membrane homeostasis can steer aberrant signalling. Moreover, we describe in detail the complexities associated with the examination of these membrane domains and their association with cancer. Finally, we summarize the current literature on MADs and their effects on cellular membranes, including various mechanisms of dietary chemoprevention/interception and the functional links between nutritional bioactives, membrane homeostasis and cancer biology.
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Affiliation(s)
- Alfredo Erazo-Oliveras
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Mónica Muñoz-Vega
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Michael L. Salinas
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Xiaoli Wang
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Robert S. Chapkin
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
- Center for Environmental Health Research; Texas A&M University; College Station, Texas, 77843; USA
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18
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Li S, Zhang F, Lin R, Sun Q, Qu L, Zhong L. Shared Immune Associations Between COVID-19 and Inflammatory Bowel Disease: A Cross-Sectional Observational Study in Shanghai, China. J Inflamm Res 2024; 17:1929-1940. [PMID: 38558943 PMCID: PMC10981870 DOI: 10.2147/jir.s449746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
Purpose The rapid global spread of the SARS-CoV-2 Omicron variant introduces a novel complication: the emergence of IBD (inflammatory bowel disease)-like ulcers in certain patients. This research delves into this new challenge by juxtaposing the clinical manifestations and genetic expression patterns of individuals affected by the Omicron variant of COVID-19 with those diagnosed with IBD. It aims to decode the link between these conditions, potentially shedding light on previously unexplored facets of COVID-19 pathophysiology. This investigation emphasizes gene expression analysis as a key tool to identify wider disease correlations and innovative therapeutic avenues. Patients and Methods From March to December 2022, patients with SARS-CoV-2 Omicron infection and inflammatory bowel disease and healthy controls were recruited in Shanghai East Hospital, Shanghai, China. The epidemiological and clinical characteristics of the patients were compared. Four RNA sequencing datasets (GSE205244, GSE201530, GSE174159, and GSE186507) were extracted from the Gene Expression Omnibus database to detect mutually differentially expressed genes and common pathways in patients with SARS-CoV-2 infection and inflammatory bowel disease. Results Compared to patients with active inflammatory bowel disease, patients with SARS-CoV-2 infection were more likely to have elevated interferon-α levels and an increased lymphocyte count and less likely to have high interleukin-6, tumor necrosis factor-α, and C-reactive protein levels and an elevated neutrophil count. A total of 51 common differentially expressed genes were identified in the four RNA-sequencing datasets. Enrichment analysis suggested that these genes were related to inflammation and the immune response, especially the innate immune response and nucleotide oligomerization domain-like receptor signaling pathway. Conclusion The inflammation and immune-response pathways in COVID-19 and inflammatory bowel disease have several similarities and some differences. The study identifies the NLR signaling pathway's key role in both COVID-19 and IBD, suggesting its potential as a target for therapeutic intervention and vaccine development.
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Affiliation(s)
- Shan Li
- Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China
| | - Fengdi Zhang
- Department of Infectious Diseases, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China
| | - Ritian Lin
- Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China
| | - Qinjuan Sun
- Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China
| | - Lihong Qu
- Department of Infectious Diseases, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China
| | - Lan Zhong
- Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China
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19
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Quek ZBR, Ng SH. Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology. Pathogens 2024; 13:275. [PMID: 38668230 PMCID: PMC11054155 DOI: 10.3390/pathogens13040275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 04/29/2024] Open
Abstract
High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover sufficient sequences for downstream analyses (e.g., identification and genome characterisation). To circumvent this, hybrid-capture target enrichment (HC) is able to enrich pathogen nucleic acids across multiple scales of divergences and taxa, depending on the panel used. In this review, we outline the applications of HC in human pathogens-bacteria, fungi, parasites and viruses-including identification, genomic epidemiology, antimicrobial resistance genotyping, and evolution. Importantly, we explored the applicability of HC to clinical metagenomics, which ultimately requires more work before it is a reliable and accurate tool for clinical diagnosis. Relatedly, the utility of HC was exemplified by COVID-19, which was used as a case study to illustrate the maturity of HC for recovering pathogen sequences. As we unravel the origins of COVID-19, zoonoses remain more relevant than ever. Therefore, the role of HC in biosurveillance studies is also highlighted in this review, which is critical in preparing us for the next pandemic. We also found that while HC is a popular tool to study viruses, it remains underutilised in parasites and fungi and, to a lesser extent, bacteria. Finally, weevaluated the future of HC with respect to bait design in the eukaryotic groups and the prospect of combining HC with long-read HTS.
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Affiliation(s)
- Z. B. Randolph Quek
- Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore
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20
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Drouin A, Plumb ID, McCullough M, James Gist J, Liu S, Theberge M, Katz J, Moreida M, Flaherty S, Chatwani B, Briggs Hagen M, Midgley CM, Fusco D. Clinical and laboratory characteristics of patients hospitalized with severe COVID-19 in New Orleans, August 2020 to September 2021. Sci Rep 2024; 14:6539. [PMID: 38503862 PMCID: PMC10951213 DOI: 10.1038/s41598-024-57306-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/17/2024] [Indexed: 03/21/2024] Open
Abstract
Louisiana experienced high morbidity and mortality from COVID-19. To assess possible explanatory factors, we conducted a cohort study (ClinSeqSer) of patients hospitalized with COVID-19 in New Orleans during August 2020-September 2021. Following enrollment, we reviewed medical charts, and performed SARS-CoV-2 RT-PCR testing on nasal and saliva specimens. We used multivariable logistic regression to assess associations between patient characteristics and severe illness, defined as ≥ 6 L/min oxygen or intubation. Among 456 patients, median age was 56 years, 277 (60.5%) were Black non-Hispanic, 436 (95.2%) had underlying health conditions, and 358 were unvaccinated (92.0% of 389 verified). Overall, 187 patients (40.1%) had severe illness; 60 (13.1%) died during admission. In multivariable models, severe illness was associated with age ≥ 65 years (OR 2.08, 95% CI 1.22-3.56), hospitalization > 5 days after illness onset (OR 1.49, 95% CI 1.01-2.21), and SARS CoV-2 cycle threshold (Ct) result of < 32 in saliva (OR 4.79, 95% CI 1.22-18.77). Among patients who were predominantly Black non-Hispanic, unvaccinated and with underlying health conditions, approximately 1 in 3 patients had severe COVID-19. Older age and delayed time to admission might have contributed to high case-severity. An association between case-severity and low Ct value in saliva warrants further investigation.
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Affiliation(s)
- Arnaud Drouin
- Department of Medicine, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA, 70130, USA
- University Medical Center, New Orleans, LA, USA
| | - Ian D Plumb
- Applied Epidemiology Studies Team, Epidemiology Branch, and on detail to the Global Respiratory Viruses Branch Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control, Atlanta, GA, USA
| | | | | | - Sharon Liu
- Department of Medicine, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA, 70130, USA
| | - Marc Theberge
- Department of Medicine, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA, 70130, USA
| | - Joshua Katz
- Department of Medicine, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA, 70130, USA
| | - Matthew Moreida
- Department of Medicine, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA, 70130, USA
| | - Shelby Flaherty
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Bhoomija Chatwani
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Melissa Briggs Hagen
- Applied Epidemiology Studies Team, Epidemiology Branch, and on detail to the Global Respiratory Viruses Branch Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control, Atlanta, GA, USA
| | - Claire M Midgley
- Applied Epidemiology Studies Team, Epidemiology Branch, and on detail to the Global Respiratory Viruses Branch Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control, Atlanta, GA, USA
| | - Dahlene Fusco
- Department of Medicine, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA, 70130, USA.
- University Medical Center, New Orleans, LA, USA.
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA.
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21
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Jia F, Han J. COVID-19 related neurological manifestations in Parkinson's disease: has ferroptosis been a suspect? Cell Death Discov 2024; 10:146. [PMID: 38503730 PMCID: PMC10951317 DOI: 10.1038/s41420-024-01915-6] [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: 06/06/2023] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 03/21/2024] Open
Abstract
A rising number of patient cases point to a probable link between SARS-CoV-2 infection and Parkinson's disease (PD), yet the mechanisms by which SARS-CoV-2 affects the brain and generates neuropsychiatric symptoms in COVID-19 patients remain unknown. Ferroptosis, a distinct iron-dependent non-apoptotic type of cell death characterized by lipid peroxidation and glutathione depletion, a key factor in neurological disorders. Ferroptosis may have a pathogenic role in COVID-19, according to recent findings, however its potential contributions to COVID-19-related PD have not yet been investigated. This review covers potential paths for SARS-CoV-2 infection of the brain. Among these putative processes, ferroptosis may contribute to the etiology of COVID-19-associated PD, potentially providing therapeutic methods.
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Affiliation(s)
- Fengju Jia
- School of Nursing, Qingdao University, No. 308 Ningxia Road, Qingdao, 266071, China.
| | - Jing Han
- School of Nursing, Qingdao University, No. 308 Ningxia Road, Qingdao, 266071, China
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22
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Poland GA, Raina MacIntyre C. Celebrating vaccines: The 2023 Nobel prize in medicine or physiology. Vaccine 2024; 42:1409-1410. [PMID: 38365486 DOI: 10.1016/j.vaccine.2023.10.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 02/18/2024]
Affiliation(s)
- Gregory A Poland
- Mayo Vaccine Research Group, 200 First Street, SW, Guggenheim 611B, Mayo Clinic, Rochester, MN 55905, United States.
| | - C Raina MacIntyre
- Biosecurity Program, The Kirby Institute for Infection and Immunity, UNSW Sydney, Australia
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23
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Khan RS, Ordog T, Hong SD, Schmitz AH, Thattaliyath B, Sharathkumar AA. Evolution of Cardiovascular Findings in Multisystem Inflammatory Syndrome in Children (MIS-C) Across COVID-19 Variants: Common Trends and Unusual Presentations. Pediatr Cardiol 2024; 45:552-559. [PMID: 38261062 DOI: 10.1007/s00246-023-03397-2] [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: 11/17/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024]
Abstract
Multisystem inflammatory syndrome in children (MIS-C) is a rare condition following COVID-19 infection. Cardiac involvement is common and includes left ventricular systolic dysfunction, cardiac marker elevation, electrocardiogram (ECG) changes, and coronary artery dilation. This single-center retrospective cohort study compares cardiovascular disease between three major SARS-CoV-2 variants and describes the evolution of findings in medium-term follow-up. Of 69 total children (mean age 9.2 years, 58% male), 60 (87%) had cardiovascular involvement with the most common features being troponin elevation in 33 (47%) and left ventricular dysfunction in 22 (32%). Based on presumed infection timing, 61 patients were sorted into variant cohorts of Alpha, Delta, and Omicron. Hospitalization was longer for the Delta group (7.7 days) vs Alpha (5.1 days, p = 0.0065) and Omicron (4.9 days, p = 0.012). Troponin elevation was more common in Delta compared to Alpha (13/20 vs 7/25, p = 0.18), and cumulative evidence of cardiac injury (echocardiographic abnormality and/or troponin elevation) was more common in Delta (17/20) compared with Alpha (12/25, p = 0.013) or Omicron (8/16, p = 0.034). Forty-nine (77%) of the original cohort (n = 69) had no cardiac symptoms or findings beyond 3 months post-hospitalization. Cardiac MRI was performed in 28 patients (between 3 and 6 months post-hospitalization) and was normal in 25 patients (89%). The differences in the variant cohorts may be due to alteration of the immune landscape with higher severity of COVID-19 infection. Despite overall reassuring cardiac outcomes, it is important to note the variability of presentation and remain vigilant with future variants.
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Affiliation(s)
- Rabia S Khan
- Division of Pediatric Cardiology, Department of Pediatrics, UCLA Health Sciences, Los Angeles, CA, USA.
| | | | - Sandy D Hong
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Anna H Schmitz
- Division of Hospital Medicine, Department of Pediatrics, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Bijoy Thattaliyath
- Division of Pediatric Cardiology, Department of Pediatrics, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Anjali A Sharathkumar
- Division of Pediatric Hematology, Department of Pediatrics, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
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24
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Sala S, Nitschke P, Masuda R, Gray N, Lawler NG, Wood JM, Buckler JN, Berezhnoy G, Bolaños J, Boughton BA, Lonati C, Rössler T, Singh Y, Wilson ID, Lodge S, Morillon AC, Loo RL, Hall D, Whiley L, Evans GB, Grove TL, Almo SC, Harris LD, Holmes E, Merle U, Trautwein C, Nicholson JK, Wist J. Integrative Molecular Structure Elucidation and Construction of an Extended Metabolic Pathway Associated with an Ancient Innate Immune Response in COVID-19 Patients. J Proteome Res 2024; 23:956-970. [PMID: 38310443 PMCID: PMC10913068 DOI: 10.1021/acs.jproteome.3c00654] [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: 10/06/2023] [Revised: 12/01/2023] [Accepted: 12/29/2023] [Indexed: 02/05/2024]
Abstract
We present compelling evidence for the existence of an extended innate viperin-dependent pathway, which provides crucial evidence for an adaptive response to viral agents, such as SARS-CoV-2. We show the in vivo biosynthesis of a family of novel endogenous cytosine metabolites with potential antiviral activities. Two-dimensional nuclear magnetic resonance (NMR) spectroscopy revealed a characteristic spin-system motif, indicating the presence of an extended panel of urinary metabolites during the acute viral replication phase. Mass spectrometry additionally enabled the characterization and quantification of the most abundant serum metabolites, showing the potential diagnostic value of the compounds for viral infections. In total, we unveiled ten nucleoside (cytosine- and uracil-based) analogue structures, eight of which were previously unknown in humans allowing us to propose a new extended viperin pathway for the innate production of antiviral compounds. The molecular structures of the nucleoside analogues and their correlation with an array of serum cytokines, including IFN-α2, IFN-γ, and IL-10, suggest an association with the viperin enzyme contributing to an ancient endogenous innate immune defense mechanism against viral infection.
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Affiliation(s)
- Samuele Sala
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Philipp Nitschke
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Reika Masuda
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Nicola Gray
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Nathan G. Lawler
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - James M. Wood
- Ferrier
Research Institute, Victoria University
of Wellington, Wellington 6012, New Zealand
- The
Maurice Wilkins Centre for Molecular Biodiscovef Wellington, Welry, The University of Auckland, Auckland 1010, New Zealand
| | - Joshua N. Buckler
- Ferrier
Research Institute, Victoria University
of Wellington, Wellington 6012, New Zealand
| | - Georgy Berezhnoy
- Department
of Preclinical Imaging and Radiopharmacy, Werner Siemens Imaging Center, University Hospital Tübingen, 72074 Tübingen, Germany
| | - Jose Bolaños
- Chemistry
Department, Universidad del Valle, Cali 76001, Colombia
| | - Berin A. Boughton
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Caterina Lonati
- Center
for Preclinical Research, Fondazione IRCCS
Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Titus Rössler
- Department
of Preclinical Imaging and Radiopharmacy, Werner Siemens Imaging Center, University Hospital Tübingen, 72074 Tübingen, Germany
| | - Yogesh Singh
- Institute
of Medical Genetics and Applied Genomics, University Hospital Tübingen, 72074 Tübingen, Germany
| | - Ian D. Wilson
- Division
of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, Burlington Danes Building, Du Cane Road, London W12 0NN, U.K.
| | - Samantha Lodge
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Aude-Claire Morillon
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Ruey Leng Loo
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Drew Hall
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Luke Whiley
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Gary B. Evans
- Ferrier
Research Institute, Victoria University
of Wellington, Wellington 6012, New Zealand
- The
Maurice Wilkins Centre for Molecular Biodiscovef Wellington, Welry, The University of Auckland, Auckland 1010, New Zealand
| | - Tyler L. Grove
- Department
of Biochemistry, Albert Einstein College
of Medicine, Bronx, New York 10461, United States
| | - Steven C. Almo
- Department
of Biochemistry, Albert Einstein College
of Medicine, Bronx, New York 10461, United States
| | - Lawrence D. Harris
- Ferrier
Research Institute, Victoria University
of Wellington, Wellington 6012, New Zealand
- The
Maurice Wilkins Centre for Molecular Biodiscovef Wellington, Welry, The University of Auckland, Auckland 1010, New Zealand
| | - Elaine Holmes
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
- Division
of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, Burlington Danes Building, Du Cane Road, London W12 0NN, U.K.
| | - Uta Merle
- Department
of Internal Medicine IV, University Hospital
Heidelberg, 69120 Heidelberg, Germany
| | - Christoph Trautwein
- Department
of Preclinical Imaging and Radiopharmacy, Werner Siemens Imaging Center, University Hospital Tübingen, 72074 Tübingen, Germany
| | - Jeremy K. Nicholson
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
- Institute
of Global Health Innovation, Faculty of
Medicine, Imperial College London, Level 1, Faculty Building, South Kensington Campus, London SW7 2NA, U.K.
| | - Julien Wist
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
- Chemistry
Department, Universidad del Valle, Cali 76001, Colombia
- Faculty of Medicine, Department of Metabolism,
Digestion and Reproduction,
Division of Digestive Diseases at Imperial College, London SW7 2AZ, U.K.
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25
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Gerashchenko GV, Hryshchenko NV, Melnichuk NS, Marchyshak TV, Chernushyn SY, Demchyshina IV, Chernenko LM, Kuzin IV, Tkachuk ZY, Kashuba VI, Tukalo MA. Genetic characteristics of SARS-CoV-2 virus variants observed upon three waves of the COVID-19 pandemic in Ukraine between February 2021-January 2022. Heliyon 2024; 10:e25618. [PMID: 38380034 PMCID: PMC10877268 DOI: 10.1016/j.heliyon.2024.e25618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 12/06/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024] Open
Abstract
The aim of our study was to identify and characterize the SARS-CoV-2 variants in COVID-19 patients' samples collected from different regions of Ukraine to determine the relationship between SARS-CoV-2 phylogenetics and COVID-19 epidemiology. Patients and methods Samples were collected from COVID-19 patients during 2021 and the beginning of 2022 (401 patients). The SARS-CoV-2 genotyping was performed by parallel whole genome sequencing. Results The obtained SARS-CoV-2 genotypes showed that three waves of the COVID-19 pandemic in Ukraine were represented by three main variants of concern (VOC), named Alpha, Delta and Omicron; each VOC successfully replaced the earlier variant. The VOC Alpha strain was presented by one B.1.1.7 lineage, while VOC Delta showed a spectrum of 25 lineages that had different prevalence in 19 investigated regions of Ukraine. The VOC Omicron in the first half of the pandemic was represented by 13 lines that belonged to two different clades representing B.1 and B.2 Omicron strains. Each of the three epidemic waves (VOC Alpha, Delta, and Omicron) demonstrated their own course of disease, associated with genetic changes in the SARS-CoV-2 genome. The observed epidemiological features are associated with the genetic characteristics of the different VOCs, such as point mutations, deletions and insertions in the viral genome. A phylogenetic and transmission analysis showed the different mutation rates; there were multiple virus sources with a limited distribution between regions. Conclusions The evolution of SARS-CoV-2 virus and high levels of morbidity due to COVID-19 are still registered in the world. Observed multiple virus sourses with the limited distribution between regions indicates the high efficiency of the anti-epidemic policy pursued by the Ministry of Health of Ukraine to prevent the spread of the epidemic, despite the low level of vaccination of the Ukrainian population.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Zenovii Yu Tkachuk
- Institute of Molecular Biology and Genetics of NAS of Ukraine, Kyiv, Ukraine
| | - Vladimir I. Kashuba
- Institute of Molecular Biology and Genetics of NAS of Ukraine, Kyiv, Ukraine
| | - Mykhailo A. Tukalo
- Institute of Molecular Biology and Genetics of NAS of Ukraine, Kyiv, Ukraine
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26
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Chen MP, Jiang DX, Rang JX, Zhuo HB, Zhou ZG. Comparison of azvudine, molnupiravir, and nirmatrelvir/ritonavir in adult patients with mild-to-moderate COVID-19: a retrospective cohort study. Sci Rep 2024; 14:3318. [PMID: 38337014 PMCID: PMC10858188 DOI: 10.1038/s41598-024-53862-y] [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: 07/21/2023] [Accepted: 02/06/2024] [Indexed: 02/12/2024] Open
Abstract
This study aimed to explore the effectiveness and safety of azvudine, nirmatrelvir/ritonavir, and molnupiravir in adult patients with mild-to-moderate COVID-19. This retrospective cohort study included patients with mild-to-moderate COVID-19 (asymptomatic, mild, and common types) at the First Hospital of Changsha (Hunan Province, China) between March and November 2022. Eligible patients were classified into the azvudine, nirmatrelvir/ritonavir, or molnupiravir groups according to the antiviral agents they received. The outcomes were the times to nucleic acid negative conversion (NANC). This study included 157 patients treated with azvudine (n = 66), molnupiravir (n = 66), or nirmatrelvir/ritonavir (n = 25). There were no statistically significant differences in the time from diagnosis to NANC among the azvudine, molnupiravir, and nirmatrelvir/ritonavir groups [median, 9 (95% CI 9-11) vs. 11 (95% CI 10-12) vs. 9 (95% CI 8-12) days, P = 0.15], time from administration to NANC [median, 9 (95% CI 8-10) vs. 10 (95% CI 9.48-11) vs. 8.708 (95% CI 7.51-11) days, P = 0.50], or hospital stay [median, 11 (95% CI 11-13) vs. 13 (95% CI 12-14) vs. 12 (95% CI 10-14) days, P = 0.14], even after adjustment for sex, age, COVID-19 type, comorbidities, Ct level, time from diagnosis to antiviral treatment, and number of symptoms. The cumulative NANC rates in the azvudine, molnupiravir, and nirmatrelvir/ritonavir groups were 15.2%/12.3%/16.0% at day 5 (P = 0.858), 34.8%/21.5%/32.0% at day 7 (P = 0.226), 66.7%/52.3%/60.0% at 10 days (P = 0.246), and 86.4%/86.2%/80.0% at day 14 (P = 0.721). No serious adverse events were reported. Azvudine may be comparable to nirmatrelvir/ritonavir and molnupiravir in adult patients with mild-to-moderate COVID-19 regarding time to NANC, hospital stay, and AEs.
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Affiliation(s)
- Mei-Ping Chen
- Department of Infectious Disease, The Affiliated Changsha Hospital of Xiangya School of Medicine, Central South University (The First Hospital of Changsha), Changsha, 410000, People's Republic of China
| | - Di-Xuan Jiang
- Department of Respiratory and Critical Care Medicine, The Affiliated Changsha Hospital of Xiangya School of Medicine, Central South University (The First Hospital of Changsha), Changsha, 410000, People's Republic of China
| | - Jia-Xi Rang
- Department of Nurse, The Affiliated Changsha Hospital of Xiangya School of Medicine, Central South University (The First Hospital of Changsha), Changsha, 410000, People's Republic of China
| | - Hai-Bo Zhuo
- Department of Respiratory and Critical Care Medicine, The Affiliated Changsha Hospital of Xiangya School of Medicine, Central South University (The First Hospital of Changsha), Changsha, 410000, People's Republic of China
| | - Zhi-Guo Zhou
- Department of Respiratory and Critical Care Medicine, The Affiliated Changsha Hospital of Xiangya School of Medicine, Central South University (The First Hospital of Changsha), Changsha, 410000, People's Republic of China.
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Boldea O, Alipoor A, Pei S, Shaman J, Rozhnova G. Age-specific transmission dynamics of SARS-CoV-2 during the first 2 years of the pandemic. PNAS NEXUS 2024; 3:pgae024. [PMID: 38312225 PMCID: PMC10837015 DOI: 10.1093/pnasnexus/pgae024] [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: 11/24/2023] [Accepted: 01/09/2024] [Indexed: 02/06/2024]
Abstract
During its first 2 years, the SARS-CoV-2 pandemic manifested as multiple waves shaped by complex interactions between variants of concern, non-pharmaceutical interventions, and the immunological landscape of the population. Understanding how the age-specific epidemiology of SARS-CoV-2 has evolved throughout the pandemic is crucial for informing policy decisions. In this article, we aimed to develop an inference-based modeling approach to reconstruct the burden of true infections and hospital admissions in children, adolescents, and adults over the seven waves of four variants (wild-type, Alpha, Delta, and Omicron BA.1) during the first 2 years of the pandemic, using the Netherlands as the motivating example. We find that reported cases are a considerable underestimate and a generally poor predictor of true infection burden, especially because case reporting differs by age. The contribution of children and adolescents to total infection and hospitalization burden increased with successive variants and was largest during the Omicron BA.1 period. However, the ratio of hospitalizations to infections decreased with each subsequent variant in all age categories. Before the Delta period, almost all infections were primary infections occurring in naive individuals. During the Delta and Omicron BA.1 periods, primary infections were common in children but relatively rare in adults who experienced either reinfections or breakthrough infections. Our approach can be used to understand age-specific epidemiology through successive waves in other countries where random community surveys uncovering true SARS-CoV-2 dynamics are absent but basic surveillance and statistics data are available.
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Affiliation(s)
- Otilia Boldea
- Department of Econometrics and OR, Tilburg School of Economics and Management, Tilburg University, Tilburg 5037 AB, The Netherlands
| | - Amir Alipoor
- Department of Econometrics and OR, Tilburg School of Economics and Management, Tilburg University, Tilburg 5037 AB, The Netherlands
| | - Sen Pei
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Jeffrey Shaman
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
- Columbia Climate School, Columbia University, New York, NY 10025, USA
| | - Ganna Rozhnova
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht 3584 CX, The Netherlands
- Center for Complex Systems Studies (CCSS), Utrecht University, Utrecht 3584 CE, The Netherlands
- Faculdade de Ciências, Universidade de Lisboa, Lisbon PT1749-016, Portugal
- BioISI—Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon PT1749-016, Portugal
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Ma J, Wang Y, Liu J, Wu Y, Zhang S, Li X, Zha D, Zhou J, Xia Y, Zhang X. Impact of perioperative SARS-CoV-2 Omicron infection on postoperative complications in liver cancer hepatectomy: A single-center matched study. Int J Infect Dis 2024; 139:101-108. [PMID: 38065317 DOI: 10.1016/j.ijid.2023.12.002] [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: 09/29/2023] [Revised: 11/29/2023] [Accepted: 12/03/2023] [Indexed: 12/21/2023] Open
Abstract
OBJECTIVES To explore the effects of perioperative SARS-CoV-2 Omicron infection on postoperative complications in patients with liver cancer. METHODS A propensity-matched study was conducted, which included patients with primary liver cancer who underwent hepatectomy from September 01, 2022 to January 20, 2023. Patients who infected SARS-CoV-2 Omicron during the perioperative period (7 days before to 30 days after surgery) were matched 1:1 with noninfected patients. The primary outcomes, which were COVID-19-related major complications and liver resection-specific complications, were analyzed using multivariate logistic regression. RESULTS A total of 243 patients were included, with 63 cases of perioperative infections, of which 62 were postoperative infections. The overall 30-day postoperative mortality rate was 1.6% (4/243). Compared to noninfected patients, those with perioperative infections showed no significant difference in the occurrence of adverse postoperative outcomes. However, they had a higher rate of 30-day readmission after surgery (11.1% vs 0%, P = 0.013). Perioperative SARS-CoV-2 infection was not associated with "major cardiorespiratory complications" or "liver resection-specific complications", but age, pre-existing comorbidities, and tumor type were related to these outcomes. CONCLUSION Perioperative SARS-CoV-2 Omicron infection did not increase the incidence of postoperative complications in patients with liver cancer. However, those patients had a higher rate of 30-day readmission after surgery.
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Affiliation(s)
- Junyong Ma
- Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai, China
| | - Yizhou Wang
- Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai, China
| | - Jian Liu
- Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai, China
| | - Yali Wu
- Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai, China; Clinical Graduate School, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Shichao Zhang
- Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai, China
| | - Xifeng Li
- Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai, China
| | - Daoxi Zha
- Department of Anesthesiology, Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai, China
| | - Jun Zhou
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai, China
| | - Yong Xia
- Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai, China
| | - Xiaofeng Zhang
- Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai, China.
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Larsen SL, Kraay ANM. Transparent transmission models for informing public health policy: the role of trust and generalizability. Proc Biol Sci 2024; 291:20232273. [PMID: 38264775 PMCID: PMC10806397 DOI: 10.1098/rspb.2023.2273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/20/2023] [Indexed: 01/25/2024] Open
Affiliation(s)
- Sophie L. Larsen
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alicia N. M. Kraay
- Department of Kinesiology and Community Health, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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30
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Kim SH, Kim J, Jung S, Noh JY, Kim J, Park H, Song YG, Peck KR, Park SH, Park MS, Ko JH, Song JY, Choi JY, Jung MK, Shin EC. Omicron BA.2 breakthrough infection elicits CD8 + T cell responses recognizing the spike of later Omicron subvariants. Sci Immunol 2024; 9:eade6132. [PMID: 38241400 DOI: 10.1126/sciimmunol.ade6132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 12/14/2023] [Indexed: 01/21/2024]
Abstract
Here, we examine peripheral blood memory T cell responses against the SARS-CoV-2 BA.4/BA.5 variant spike among vaccinated individuals with or without Omicron breakthrough infections. We provide evidence supporting a lack of original antigenic sin in CD8+ T cell responses targeting the spike. We show that BNT162b2-induced memory T cells respond to the BA.4/BA.5 spike. Among individuals with BA.1/BA.2 breakthrough infections, IFN-γ-producing CD8+ T cell responses against the BA.4/BA.5 spike increased. In a subgroup with BA.2 breakthrough infections, IFN-γ-producing CD8+ T cell responses against the BA.2-mutated spike region increased and correlated directly with responses against the BA.4/BA.5 spike, indicating that BA.2 spike-specific CD8+ T cells elicited by BA.2 breakthrough infection cross-react with the BA.4/BA.5 spike. We identified CD8+ T cell epitope peptides that are present in the spike of BA.2 and BA.4/BA.5 but not the original spike. These peptides are fully conserved in the spike of now-dominant XBB lineages. Our study shows that breakthrough infection by early Omicron subvariants elicits CD8+ T cell responses that recognize epitopes within the spike of newly emerging subvariants.
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Affiliation(s)
- Sang-Hoon Kim
- Center for Viral Immunology, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Jihye Kim
- Center for Viral Immunology, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Sungmin Jung
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Ji Yun Noh
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul 08308, Republic of Korea
| | - Jinnam Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Heedo Park
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Young Goo Song
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Kyong Ran Peck
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Su-Hyung Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Jae-Hoon Ko
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Joon Young Song
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul 08308, Republic of Korea
| | - Jun Yong Choi
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Min Kyung Jung
- Center for Viral Immunology, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Eui-Cheol Shin
- Center for Viral Immunology, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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Shaw SY, Kindrachuk J, McKinnon L, Biegun JCS, Reimer JN, Loeppky C, Wei YJ, Bullard J, Van Caeseele P, Stein DR. The descriptive epidemiology of pre-omicron SARS-CoV-2 breakthrough infections and severe outcomes in Manitoba, Canada. FRONTIERS IN EPIDEMIOLOGY 2024; 3:1248847. [PMID: 38455896 PMCID: PMC10911002 DOI: 10.3389/fepid.2023.1248847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/12/2023] [Indexed: 03/09/2024]
Abstract
Introduction Vaccination plays a key role in curbing severe outcomes resulting from COVID-19 disease. With the Omicron variant and the relaxing of public health protections breakthrough infections are increasingly common, and certain groups remain at higher risk for severe outcomes from breakthrough infections. We analysed population-based public health data from Manitoba, Canada to understand characteristics of those experiencing breakthrough infections and severe outcomes from breakthrough infections. Data from previous pandemic stages can provide valuable information regarding severe outcomes associated with breakthrough infection in the Omicron and future phases. Methods Positive SARS-CoV-2 PCR tests from Cadham Provincial Laboratory were linked to case information from the population-based Public Health Information Management System. A retrospective design was used with time-to-event analyses to examine severe outcomes among those experiencing breakthrough infection. Results Breakthrough cases were more likely to have 2 + chronic conditions, compared to age-, sex-, and time-period matched unvaccinated cases (24% vs. 17%), with hypertension (30%), diabetes (17%), and asthma (14%) being the most prevalent chronic conditions amongst breakthrough cases. Severe outcomes resulting from breakthrough infection was associated with age and chronic conditions, with those with 2 + chronic conditions at higher risk of severe outcomes (adjusted hazard ratio: 3.6, 95% confidence intervals: 2.0-6.4). Risk of severe outcomes varied by age group, with those 70 + years at over 13 times the risk of severe outcomes (95% CI: 4.5-39.8), compared to those 18-29 years of age. Discussion Our results demonstrate the impact of chronic conditions on the likelihood of, and severity of outcomes from breakthrough infections. These findings underscore the importance of vaccination programs prioritizing vulnerable populations.
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Affiliation(s)
- Souradet Y. Shaw
- Department of CommunityHealth Sciences, University of Manitoba, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Jason Kindrachuk
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Lyle McKinnon
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Jeffery C. S. Biegun
- Department of Sociology and Criminology, University of Manitoba, Winnipeg, MB, Canada
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Zaidi AK, Singh RB. Epidemiology of COVID-19. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 202:25-38. [PMID: 38237988 DOI: 10.1016/bs.pmbts.2023.09.002] [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: 01/23/2024]
Abstract
This chapter provides a detailed exploration of the epidemiology of COVID-19, focusing on several key aspects that offer valuable insights into the disease progression. A comprehensive comparison is made between the three related coronaviruses: SARS-CoV, MERS-CoV, and SARS-CoV-2, elucidating their similarities and differences in terms of transmission dynamics, clinical presentation, laboratory and radiological findings, infection mechanisms, and mortality rates. The concept of herd immunity is then discussed, exploring its relevance and potential implications for controlling the spread of COVID-19. Next, the chapter delves into the changing epidemiology of the disease, examining how various factors such as human behavior, public health interventions, and viral mutations have influenced its transmission patterns and severity over time. Finally, the timelines and evolution of COVID-19 are outlined, tracing the origins of the virus, its rapid global spread, and the emergence of new variants.
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Affiliation(s)
| | - Rohan Bir Singh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United State; Department of Population, Policy and Practice, Greater Ormond Street Institute of Child Health, University College London, United Kingdom; Discipline of Ophthalmology and Visual Sciences, Adelaide Medical School, University of Adelaide, Australia
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33
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Zhao D, Liu W, Zhang Z, Li Y, Luo J, Zheng W, Sun R. Timing of general anesthesia for pediatric patients recovering from COVID-19: a prospective cohort study. BMC Anesthesiol 2024; 24:11. [PMID: 38166732 PMCID: PMC10759690 DOI: 10.1186/s12871-023-02390-9] [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: 10/11/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
OBJECTIVE To explore the timing of general anesthesia for pediatric patients who have recovered from novel coronavirus infection and summarize anesthesia-related complications. METHODS We summarized the perioperative management of children under 14 years of age who underwent general anesthesia in our hospital according to national epidemic prevention and control requirements. We compared the incidence of postoperative pulmonary complications within 2 weeks (Group A), 3-4 weeks (Group B), and 5-6 weeks (Group C) after COVID-19 recovery. RESULTS There were differences among the three groups in terms of decreased blood oxygen saturation (< 94%), secretions, and coughing during the PACU period. The risk of low blood oxygen saturation during PACU decreased as the time of COVID-19 recovery extended in the three groups. Compared to Group A, the risk of low blood oxygen saturation was lower in Group B. The presence of respiratory symptoms and a body temperature above 40℃ increased the risk of decreased blood oxygen saturation. The proportion of children aged 11-14 years and children with high fever experiencing decreased blood oxygen saturation during PACU was higher in Groups A and B. Among the three groups, children with respiratory symptoms and longer illness duration had a higher proportion of decreased blood oxygen saturation during PACU. CONCLUSION Pediatric patients who have recovered from COVID-19 for more than 2 weeks have a lower risk of postoperative complications after general anesthesia. For children with respiratory system symptoms or high fever, there is a higher risk of transient blood oxygen saturation decrease during PACU. For older children, those with high fever, respiratory system symptoms, or longer illness duration, it is recommended to appropriately extend the time from COVID-19 recovery to surgery.
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Affiliation(s)
- Dinghuan Zhao
- Department of Anesthesiology, Tianjin Eye Hospital, No. 4 Gansu Road, Heping District, Tianjin, 300022, China
| | - Wei Liu
- Department of Anesthesiology, Tianjin Eye Hospital, No. 4 Gansu Road, Heping District, Tianjin, 300022, China
| | - Zhao Zhang
- Department of Anesthesiology, Tianjin Eye Hospital, No. 4 Gansu Road, Heping District, Tianjin, 300022, China
| | - Yuting Li
- Department of Anesthesiology, Tianjin Eye Hospital, No. 4 Gansu Road, Heping District, Tianjin, 300022, China
| | - Jun Luo
- Department of Anesthesiology, Tianjin Eye Hospital, No. 4 Gansu Road, Heping District, Tianjin, 300022, China
| | - Weiqiang Zheng
- Department of Anesthesiology, Tianjin Eye Hospital, No. 4 Gansu Road, Heping District, Tianjin, 300022, China
| | - Ruiqiang Sun
- Department of Anesthesiology, Tianjin Eye Hospital, No. 4 Gansu Road, Heping District, Tianjin, 300022, China.
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Martin R, Maleche A, Gay J, Fatima H. Lessons learnt from COVID-19 to reduce mortality and morbidity in the Global South: addressing global vaccine equity for future pandemics. BMJ Glob Health 2024; 9:e013680. [PMID: 38167259 PMCID: PMC10773420 DOI: 10.1136/bmjgh-2023-013680] [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: 08/09/2023] [Accepted: 11/06/2023] [Indexed: 01/05/2024] Open
Abstract
COVID-19, which killed more than 6 million people, will not be the last pandemic. Vaccines are key to preventing and ending pandemics. Therefore, it is critical to move now, before the next pandemic, towards global vaccine equity with shared goals, intermediate steps and long-term advocacy goals. Scientific integrity, ethical development, transparency, accountability and communication are critical. Countries can draw on lessons learnt from their response to the HIV pandemics, which has been at the vanguard of ensuring equitable access to rights-based services, to create shared goals and engage communities to increase access to and delivery of safe, quality vaccines. Access can be increased by: fostering the spread of mRNA intellectual property (IP) rights, with mRNA vaccine manufacturing on more continents; creating price transparency for vaccines; creating easily understandable, accessible and transparent data on vaccines; creating demand for a new international legal framework that allows IP rights to be waived quickly once a global pandemic is identified; and drawing on scientific expertise from around the world. Delivery can be improved by: creating strong public health systems that can deliver vaccines through the lifespan; creating or strengthening national regulatory agencies and independent national scientific advisory committees for vaccines; disseminating information from reliable, transparent national and subnational surveillance systems; improving global understanding that as more scientific data become available, this may result in changes to public health guidance; prioritising access to vaccines based on scientific criteria during an epidemic; and developing strategies to vaccinate those at highest risk with available vaccines.
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Affiliation(s)
- Rebecca Martin
- Global Health Institute, Emory University, Atlanta, Georgia, USA
| | - Allan Maleche
- Kenya Legal & Ethical Issues Network on HIV and AIDS (KELIN), Nairobi, Kenya
| | - Jill Gay
- Global Health Institute, Emory University, Atlanta, Georgia, USA
- J Gay Associates, Takoma Park, Maryland, USA
| | - Haram Fatima
- Global Health Institute, Emory University, Atlanta, Georgia, USA
- Georgia State University, Atlanta, Georgia, USA
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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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Rout M, Mishra S, Panda S, Dehury B, Pati S. Lipid and cholesterols modulate the dynamics of SARS-CoV-2 viral ion channel ORF3a and its pathogenic variants. Int J Biol Macromol 2024; 254:127986. [PMID: 37944718 DOI: 10.1016/j.ijbiomac.2023.127986] [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: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023]
Abstract
SARS-CoV-2 accessory protein, ORF3a is a putative ion channel which immensely contributes to viral pathogenicity by modulating host immune responses and virus-host interactions. Relatively high expression of ORF3a in diseased individuals and implication with inflammasome activation, apoptosis and autophagy inhibition, ratifies as an effective target for developing vaccines and therapeutics. Herein, we present the elusive dynamics of ORF3a-dimeric state using all-atoms molecular dynamics (MD) simulations at μ-seconds scale in a heterogeneous lipid-mimetic system in multiple replicates. Additionally, we also explore the effect of non-synonymous pathogenic mutations on ORF3a ion channel activity and viral pathogenicity in different SARS-CoV-2 variants using various structure-based protein stability (ΔΔG) tools and computational saturation mutagenesis. Our study ascertains the role of phosphatidylcholines and cholesterol in modulating the structure of ORF3a, which perturbs the size and flexibility of the polar cavity that allows permeation of large cations. Discrete trend in ion channel pore radius and area per lipid arises the premise that presence of lipids might also affect the overall conformation of ORF3a. MD structural-ensembles, in some replicates rationalize the crucial role of TM2 in maintaining the native structure of ORF3a. We also infer that loss of structural stability primarily grounds for pathogenicity in more than half of the pathogenic variants of ORF3a. Overall, the effect of mutation on alteration of ion permeability of ORF3a, proposed in this study brings mechanistic insights into variant consequences on viral membrane proteins of SARS-CoV-2, which can be utilized for the development of novel therapeutics to treat COVID-19 and other coronavirus diseases.
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Affiliation(s)
- Madhusmita Rout
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Chandrasekharpur, Bhubaneswar 751023, Odisha, India
| | - Sarbani Mishra
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Chandrasekharpur, Bhubaneswar 751023, Odisha, India
| | - Sunita Panda
- Mycology Division, ICMR-Regional Medical Research Centre, Chandrasekharpur, Bhubaneswar 751023, Odisha, India
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Chandrasekharpur, Bhubaneswar 751023, Odisha, India.
| | - Sanghamitra Pati
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Chandrasekharpur, Bhubaneswar 751023, Odisha, India.
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Sipowicz K, Pietras T, Mosiołek A, Sobstyl M, Ring M, Kamecki K, Stefańczyk I, Kosmalski M. The sense of loneliness and meaning in life in post-COVID convalescents-a preliminary study. Front Psychiatry 2023; 14:1296385. [PMID: 38188044 PMCID: PMC10768000 DOI: 10.3389/fpsyt.2023.1296385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/30/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction The COVID-19 epidemic has provided opportunity to study the impact of a well-defined severe illness on the development of a depressive episode and the associated sense of loneliness and lack of meaning in life. Materials and Methods The aim of the study was to assess the occurrence of a reactive depressive episode, the severity of depression, a sense of loneliness and meaning in life in subjects who approximately a year earlier than the date of the study had suffered from a pulmonary form of SARS-CoV-2 infection with radiologically documented interstitial lesions of the lungs, requiring and not requiring hospitalization compared to people who did not develop the disease as a result of infection with that virus. The study included 63 subjects hospitalized for pulmonary lesions, 67 not hospitalized and 60 healthy controls. The severity of depressive symptoms was measured using a Polish-language standardized version of the Beck Depression Inventory, a sense of loneliness using the De Jong Gierveld Loneliness Scale, and a sense of meaning in life using the Life Attitude Profile-Revised. Results The frequency of depression and its severity were found to be the highest in hospitalized patients compared to those treated at home and healthy people. A significant difference in the frequency of depression and its severity between outpatients and healthy people was also observed. The feeling of loneliness turned out to be greatest in the group of hospitalized people. Also, the severity of loneliness was found to be higher in the outpatient compared to the control group. The sense of meaning in life reached its lowest level among hospitalized patients, was moderately reduced in the outpatient group, and typical of the Polish population in the control group. Discussion Both pulmonary SARS-CoV-2 infection and hospitalization have been shown to be a risk factor for depression, increased feeling of loneliness and a reduced sense of meaning in life. The effect of trauma and the presence of depression can be the explanation for the increased sense of loneliness after the illness and the partial breakdown of the lifeline manifested by a decrease in the sense of meaning in life.
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Affiliation(s)
- Kasper Sipowicz
- Department of Interdisciplinary Disability Studies, The Maria Grzegorzewska University in Warsaw, Warsaw, Poland
| | - Tadeusz Pietras
- The Second Department of Psychiatry, Institute of Psychiatry and Neurology in Warsaw, Warsaw, Poland
- Department of Clinical Pharmacology, Medical University of Lodz, Lodz, Poland
| | - Anna Mosiołek
- Department of Forensic Psychiatry, Institute of Psychiatry and Neurology in Warsaw, Warsaw, Poland
| | - Michał Sobstyl
- Neurosurgery Department, Institute of Psychiatry and Neurology in Warsaw, Warsaw, Poland
| | - Michał Ring
- The Second Department of Psychiatry, Institute of Psychiatry and Neurology in Warsaw, Warsaw, Poland
| | - Krystian Kamecki
- The Second Department of Psychiatry, Institute of Psychiatry and Neurology in Warsaw, Warsaw, Poland
| | - Ignacy Stefańczyk
- The Second Department of Psychiatry, Institute of Psychiatry and Neurology in Warsaw, Warsaw, Poland
| | - Marcin Kosmalski
- Department of Clinical Pharmacology, Medical University of Lodz, Lodz, Poland
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Valdano E, Colombi D, Poletto C, Colizza V. Epidemic graph diagrams as analytics for epidemic control in the data-rich era. Nat Commun 2023; 14:8472. [PMID: 38123580 PMCID: PMC10733371 DOI: 10.1038/s41467-023-43856-1] [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: 01/18/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023] Open
Abstract
COVID-19 highlighted modeling as a cornerstone of pandemic response. But it also revealed that current models may not fully exploit the high-resolution data on disease progression, epidemic surveillance and host behavior, now available. Take the epidemic threshold, which quantifies the spreading risk throughout epidemic emergence, mitigation, and control. Its use requires oversimplifying either disease or host contact dynamics. We introduce the epidemic graph diagrams to overcome this by computing the epidemic threshold directly from arbitrarily complex data on contacts, disease and interventions. A grammar of diagram operations allows to decompose, compare, simplify models with computational efficiency, extracting theoretical understanding. We use the diagrams to explain the emergence of resistant influenza variants in the 2007-2008 season, and demonstrate that neglecting non-infectious prodromic stages of sexually transmitted infections biases the predicted epidemic risk, compromising control. The diagrams are general, and improve our capacity to respond to present and future public health challenges.
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Affiliation(s)
- Eugenio Valdano
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F75012, Paris, France
| | | | - Chiara Poletto
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Vittoria Colizza
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F75012, Paris, France.
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Baboo S, Diedrich JK, Torres JL, Copps J, Singh B, Garrett PT, Ward AB, Paulson JC, Yates JR. Evolving spike-protein N-glycosylation in SARS-CoV-2 variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539897. [PMID: 37214937 PMCID: PMC10197516 DOI: 10.1101/2023.05.08.539897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Since >3 years, SARS-CoV-2 has plunged humans into a colossal pandemic. Henceforth, multiple waves of infection have swept through the human population, led by variants that were able to partially evade acquired immunity. The co-evolution of SARS-CoV-2 variants with human immunity provides an excellent opportunity to study the interaction between viral pathogens and their human hosts. The heavily N-glycosylated spike-protein of SARS-CoV-2 plays a pivotal role in initiating infection and is the target for host immune-response, both of which are impacted by host-installed N-glycans. Using highly-sensitive DeGlyPHER approach, we compared the N-glycan landscape on spikes of the SARS-CoV-2 Wuhan-Hu-1 strain to seven WHO-defined variants of concern/interest, using recombinantly expressed, soluble spike-protein trimers, sharing same stabilizing-mutations. We found that N-glycan processing is conserved at most sites. However, in multiple variants, processing of N-glycans from high mannose- to complex-type is reduced at sites N165, N343 and N616, implicated in spike-protein function.
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Affiliation(s)
- Sabyasachi Baboo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jolene K. Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jonathan L. Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Bhavya Singh
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Patrick T. Garrett
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - James C. Paulson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - John R. Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
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Lv Y, Xiang Q, Jiang X, Zhang B, Wu J, Cao H. Effectiveness of inspector mechanism for the emergency infection prevention and control in the SARS-CoV-2 epidemic period: a self-control real-word study. BMC Infect Dis 2023; 23:858. [PMID: 38057717 DOI: 10.1186/s12879-023-08682-2] [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: 07/19/2023] [Accepted: 10/07/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND To ensure emergency infection prevention and control (IPC) can be fully supervised and monitored in coronavirus disease (COVID-19) epidemic period, a three-level inspector mechanism called "Internal self-check, Departmental cross-check, and Verification of outstanding key and difficult issues" was established in southwest China. The present study aimed to explore the effectiveness of inspector mechanism for the emergency IPC. METHODS A self-control real-world study was conducted during COVID-19 epidemic period from 2020 to 2022. An innovative designed mobile phone application was used to realize paperless information transmission and data management. Data were compared between inspection levels using SPSS 19.0 software. RESULTS A total of 2,800,132 supervision records were collected, including 149,137 comprehensive epidemic IPC projects, 1,410,093 personal protective equipment (PPE) use, 1,223,595 wearing and removing process of PPE and 17,307 ultraviolet light-detectable fluorescent (UV/F) surface marker. During the study period, the inspectors and subjects explored many optimized IPC measures. The compliance rate of check items has exceeded 98%, and internal self-check has a statistically significant higher rate than departmental cross-check (99.95% versus 98.74%, χ2 = 26111.479, P < 0.001). Compare with the failure rate in internal self check, the failure rate of PPE usage and wearing/removing process was statistically higher in departmental cross-check (χ2 = 1957.987, P < 0.001, χ2 = 465.610, P < 0.001, respectively). The overall clearance rate of UV/F surface markers is 87.88%, but there is no statistically significant difference over the three years of the present study (F = 2.902, P = 0.071). CONCLUSIONS Inspector mechanism for the emergency IPC completed an incredible inspection workload and offered creative assistance to combat the COVID-19 outbreak. These methods and accumulated experiences should be helpful for us to strengthen IPC for future epidemic.
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Affiliation(s)
- Yu Lv
- Healthcare-Associated Infection Control Center, Sichuan Provincial People's Hospital, school of medicine, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, P. R. China
| | - Qian Xiang
- Healthcare-Associated Infection Control Center, Sichuan Provincial People's Hospital, school of medicine, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, P. R. China
| | - Xiaoyan Jiang
- Healthcare-Associated Infection Control Center, Sichuan Provincial People's Hospital, school of medicine, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, P. R. China
| | - Bo Zhang
- Development Department, Chengdu Yiou Technology Co. LTD, Chengdu, 610000, Sichuan, P. R. China
| | - Jiayu Wu
- Healthcare-Associated Infection Control Center, Sichuan Provincial People's Hospital, school of medicine, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, P. R. China.
| | - Hongrong Cao
- Healthcare-Associated Infection Control Center, Sichuan Provincial People's Hospital, school of medicine, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, P. R. China.
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Xu C, Zhang Z, Huang X, Cheng K, Guo S, Wang X, Liu M, Liu X. A study on the transmission dynamics of COVID-19 considering the impact of asymptomatic infection. JOURNAL OF BIOLOGICAL DYNAMICS 2023; 17:2244980. [PMID: 37656780 DOI: 10.1080/17513758.2023.2244980] [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: 12/22/2022] [Accepted: 08/01/2023] [Indexed: 09/03/2023]
Abstract
The COVID-19 epidemic has been spreading around the world for nearly three years, and asymptomatic infections have exacerbated the spread of the epidemic. To analyse and evaluate the role of asymptomatic infections in the spread of the epidemic, we establish an improved COVID-19 infectious disease dynamics model. We fit the epidemic data in the four time periods corresponding to the selected 614G, Alpha, Delta and Omicron variants and obtain the proportion of asymptomatic persons among the infected persons gradually increased and with the increase of the detection ratio, the cumulative number of cases has dropped significantly, but the decline in the proportion of asymptomatic infections is not obvious. Therefore, in view of the hidden transmission of asymptomatic infections, the cooperation between various epidemic prevention and control policies is required to effectively curb the spread of the epidemic.
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Affiliation(s)
- Chuanqing Xu
- School of Science, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Zonghao Zhang
- School of Science, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Xiaotong Huang
- School of Science, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Kedeng Cheng
- School of Science, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Songbai Guo
- School of Science, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Xiaojing Wang
- School of Science, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Maoxing Liu
- School of Science, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Xiaoling Liu
- Mathematics department, Hanshan Normal University, Chaozhou, People's Republic of China
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Woodward A, Rivers C. Building Case Investigation and Contact Tracing Programs in US State and Local Health Departments: A Conceptual Framework. Disaster Med Public Health Prep 2023; 17:e540. [PMID: 38031272 DOI: 10.1017/dmp.2023.205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
OBJECTIVE At the onset of the COVID-19 pandemic, and to this day, US state, tribal, local, and territorial health departments lacked comprehensive case investigation and contact tracing (CI/CT) guidelines that clearly define the capabilities and capacities of CI/CT programs and how to scale up these programs to respond to outbreaks. This research aims to identify the capabilities and capacities of CI/CT programs and to develop a conceptual framework that represents the relationships between these program components. METHODS This study conducted a narrative literature review and qualitative interviews with 10 US state and local health departments and 4 public health experts to identify and characterize the capacities and capabilities of CI/CT programs. RESULTS This research resulted in the first comprehensive analysis of the capabilities and capacities of CI/CT programs and a conceptual framework that illustrates the interrelationships between the capacities, capabilities, outcomes, and impacts of CI/CT programs. CONCLUSIONS Our findings highlight the need for further guidance to assist jurisdictional health departments in shifting CI/CT program goals as outbreaks evolve. Training the public health workforce on making decisions around CI/CT program implementation during outbreaks is critical to ensure readiness for a variety of outbreak scenarios.
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Affiliation(s)
- Alexandra Woodward
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Johns Hopkins Center for Health Security, Baltimore, MD, USA
| | - Caitlin Rivers
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Johns Hopkins Center for Health Security, Baltimore, MD, USA
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43
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Rudin C, Bollen N, Hong SL, Wegner F, Politi L, Mellou K, Geenen C, Gorissen S, Verhasselt B, Durkin K, Henin C, Logist AS, Dellicour S, Resa T, Stadler T, Maes P, Cuypers L, André E, Egli A, Baele G. Investigation of an international water polo tournament in Czechia as a potential source for early introduction of the SARS-CoV-2 Omicron variant into Belgium, Switzerland and Germany, November 2021. Euro Surveill 2023; 28:2300018. [PMID: 37943503 PMCID: PMC10636743 DOI: 10.2807/1560-7917.es.2023.28.45.2300018] [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: 12/29/2022] [Accepted: 06/28/2023] [Indexed: 11/10/2023] Open
Abstract
BackgroundThe earliest recognised infections by the SARS-CoV-2 Omicron variant (Pango lineage B.1.1.529) in Belgium and Switzerland suggested a connection to an international water polo tournament, held 12-14 November 2021 in Brno, Czechia.AimTo study the arrival and subsequent spread of the Omicron variant in Belgium and Switzerland, and understand the overall importance of this international sporting event on the number of infections in the two countries.MethodsWe performed intensive forward and backward contact tracing in both countries, supplemented by phylogenetic investigations using virus sequences of the suspected infection chain archived in public databases.ResultsThrough contact tracing, we identified two and one infected athletes of the Belgian and Swiss water polo teams, respectively, and subsequently also three athletes from Germany. In Belgium and Switzerland, four and three secondary infections, and three and one confirmed tertiary infections were identified. Phylogenetic investigation demonstrated that this sporting event played a role as the source of infection, but without a direct link with infections from South Africa and not as a superspreading event; the virus was found to already be circulating at that time in the countries involved.ConclusionThe SARS-CoV-2 Omicron variant started to circulate in Europe several weeks before its identification in South Africa on 24 November 2021. Accordingly, it can be assumed that travel restrictions are usually implemented too late to prevent the spread of newly detected SARS-CoV-2 variants to other regions. Phylogenetic analysis may modify the perception of an apparently clear result of intensive contact tracing.
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Affiliation(s)
| | - Nena Bollen
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Samuel L Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Fanny Wegner
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Lida Politi
- Department of Microbial Resistance and Infections in Health Care Settings, Directorate of Surveillance and Prevention of Infectious Diseases, Hellenic National Public Health Organization (EODY), Athens, Greece
- European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Kassiani Mellou
- Directorate of Epidemiological Surveillance and Intervention for Infectious Diseases, Hellenic National Public Health Organization (EODY), Athens, Greece
| | - Caspar Geenen
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Microbiology, KU Leuven, Leuven, Belgium
| | - Sarah Gorissen
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Microbiology, KU Leuven, Leuven, Belgium
| | - Bruno Verhasselt
- Department of Diagnostic Sciences, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Keith Durkin
- Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
| | - Coralie Henin
- Federal testing platform COVID-19, Université libre de Bruxelles, Bruxelles, Belgium
| | - Anne-Sophie Logist
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Tobias Resa
- Cantonal Office of Public Health Basel-Landschaft, Liestal, Switzerland
| | - Tanja Stadler
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Piet Maes
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Lize Cuypers
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Microbiology, KU Leuven, Leuven, Belgium
| | - Emmanuel André
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Microbiology, KU Leuven, Leuven, Belgium
| | - Adrian Egli
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Swiss Pathogen Surveillance Platform (https://spsp.ch)
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
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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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Saad-Roy CM, Traulsen A. Dynamics in a behavioral-epidemiological model for individual adherence to a nonpharmaceutical intervention. Proc Natl Acad Sci U S A 2023; 120:e2311584120. [PMID: 37889930 PMCID: PMC10622941 DOI: 10.1073/pnas.2311584120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
The SARS-CoV-2 pandemic has highlighted the importance of behavioral drivers in epidemic dynamics. With the relaxation of mandated nonpharmaceutical interventions (NPIs) formerly in place to decrease transmission, such as mask-wearing or social distancing, adherence to an NPI is now the result of individual decision-making. To study these coupled dynamics, we embed a game-theoretic model for individual NPI adherence within an epidemiological model. When the disease is endemic, we find that our model has multiple (but none concurrently stable) equilibria: one each with zero, complete, or partial NPI adherence. Surprisingly, for the equilibrium with partial NPI adherence, the number of infections is independent of the transmission rate. Therefore, in that regime, a change in the rate of pathogen transmission, e.g., due to another (mandated) NPI or a new variant, has no effect on endemic infection levels. On the other hand, we show that vaccination successfully decreases endemic infection levels, and, unexpectedly, also reduces the number of susceptibles at equilibrium when there is partial adherence. From a game-theoretic perspective, we find that highly effective NPIs lead at most to partial adherence. As this effectiveness decreases, partially effective NPIs initially lead to increases in population-level adherence, especially if the risk is high enough. However, a completely ineffective NPI results in no adherence. Furthermore, we identify parameter regions where the individual incentives may not align with those of society as a whole. Overall, our findings illustrate complexities that can arise due to behavioral-epidemiological feedback and suggest appropriate measures to avoid more pessimistic population-level outcomes.
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Affiliation(s)
- Chadi M. Saad-Roy
- Miller Institute for Basic Research in Science, University of California, Berkeley, CA94720
- Department of Integrative Biology, University of California, Berkeley, CA94720
| | - Arne Traulsen
- Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön24306, Germany
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Zachreson C, Tobin R, Szanyi J, Walker C, Cromer D, Shearer FM, Conway E, Ryan G, Cheng A, McCaw JM, Geard N. Individual variation in vaccine immune response can produce bimodal distributions of protection. Vaccine 2023; 41:6630-6636. [PMID: 37793975 DOI: 10.1016/j.vaccine.2023.09.025] [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: 02/14/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 10/06/2023]
Abstract
The ability for vaccines to protect against infectious diseases varies among individuals, but computational models employed to inform policy typically do not account for this variation. Here we examine this issue: we implement a model of vaccine efficacy developed in the context of SARS-CoV-2 in order to evaluate the general implications of modelling correlates of protection on the individual level. Due to high levels of variation in immune response, the distributions of individual-level protection emerging from this model tend to be highly dispersed, and are often bimodal. We describe the specification of the model, provide an intuitive parameterisation, and comment on its general robustness. We show that the model can be viewed as an intermediate between the typical approaches that consider the mode of vaccine action to be either "all-or-nothing" or "leaky". Our view based on this analysis is that individual variation in correlates of protection is an important consideration that may be crucial to designing and implementing models for estimating population-level impacts of vaccination programs.
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Affiliation(s)
- Cameron Zachreson
- School of Computing and Information Systems, The University of Melbourne, Parkville, Victoria, Australia.
| | - Ruarai Tobin
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Joshua Szanyi
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Camelia Walker
- School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia
| | - Deborah Cromer
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Freya M Shearer
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia; Telethon Kids Institute, Nedlands, Western Australia, Australia
| | - Eamon Conway
- The Walter and Eliza Hall Institute, Melbourne, Victoria, Australia
| | - Gerard Ryan
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia; Telethon Kids Institute, Nedlands, Western Australia, Australia
| | - Allen Cheng
- Monash Infectious Diseases, Monash Health and School of Clinical Sciences, Monash University, Clayton, Victoria, Australia
| | - James M McCaw
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia; School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia
| | - Nicholas Geard
- School of Computing and Information Systems, The University of Melbourne, Parkville, Victoria, Australia
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Hart WS, Park H, Jeong YD, Kim KS, Yoshimura R, Thompson RN, Iwami S. Analysis of the risk and pre-emptive control of viral outbreaks accounting for within-host dynamics: SARS-CoV-2 as a case study. Proc Natl Acad Sci U S A 2023; 120:e2305451120. [PMID: 37788317 PMCID: PMC10576149 DOI: 10.1073/pnas.2305451120] [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: 04/13/2023] [Accepted: 09/07/2023] [Indexed: 10/05/2023] Open
Abstract
In the era of living with COVID-19, the risk of localised SARS-CoV-2 outbreaks remains. Here, we develop a multiscale modelling framework for estimating the local outbreak risk for a viral disease (the probability that a major outbreak results from a single case introduced into the population), accounting for within-host viral dynamics. Compared to population-level models previously used to estimate outbreak risks, our approach enables more detailed analysis of how the risk can be mitigated through pre-emptive interventions such as antigen testing. Considering SARS-CoV-2 as a case study, we quantify the within-host dynamics using data from individuals with omicron variant infections. We demonstrate that regular antigen testing reduces, but may not eliminate, the outbreak risk, depending on characteristics of local transmission. In our baseline analysis, daily antigen testing reduces the outbreak risk by 45% compared to a scenario without antigen testing. Additionally, we show that accounting for heterogeneity in within-host dynamics between individuals affects outbreak risk estimates and assessments of the impact of antigen testing. Our results therefore highlight important factors to consider when using multiscale models to design pre-emptive interventions against SARS-CoV-2 and other viruses.
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Affiliation(s)
- William S. Hart
- Mathematical Institute, University of Oxford, OxfordOX2 6GG, United Kingdom
- lnterdisciplinary Biology Laboratory, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya464-8602, Japan
| | - Hyeongki Park
- lnterdisciplinary Biology Laboratory, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya464-8602, Japan
| | - Yong Dam Jeong
- lnterdisciplinary Biology Laboratory, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya464-8602, Japan
- Department of Mathematics, Pusan National University, Busan46241, South Korea
| | - Kwang Su Kim
- lnterdisciplinary Biology Laboratory, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya464-8602, Japan
- Department of Scientific Computing, Pukyong National University, Busan48513, South Korea
| | - Raiki Yoshimura
- lnterdisciplinary Biology Laboratory, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya464-8602, Japan
| | - Robin N. Thompson
- Mathematical Institute, University of Oxford, OxfordOX2 6GG, United Kingdom
- Mathematics Institute, University of Warwick, CoventryCV4 7AL, United Kingdom
- Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, CoventryCV4 7AL, United Kingdom
| | - Shingo Iwami
- lnterdisciplinary Biology Laboratory, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya464-8602, Japan
- Institute of Mathematics for Industry, Kyushu University, Fukuoka819-0395, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto606-8501, Japan
- Interdisciplinary Theoretical and Mathematical Sciences Program, RIKEN, Saitama351-0198, Japan
- NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo135-8550, Japan
- Science Groove Inc., Fukuoka810-0041, Japan
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48
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Drummond PD, de Salles DB, de Souza NSH, Oliveira DCR, Guidoni DL, de Souza FSH. Profile and Outcomes of Hospitalized COVID-19 Patients during the Prevalence of the Omicron Variant According to the Brazilian Regions: A Retrospective Cohort Study from 2022. Vaccines (Basel) 2023; 11:1568. [PMID: 37896971 PMCID: PMC10610688 DOI: 10.3390/vaccines11101568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 10/29/2023] Open
Abstract
We investigated the clinical-epidemiological profile and outcomes of COVID-19 patients hospitalized in 2022, during the Omicron variant/subvariant prevalence, in different Brazilian regions to identify the most vulnerable subgroups requiring special attention. Data from COVID-19 patients were extracted from the national Information System for Epidemiological Surveillance of Influenza (SIVEP-Gripe database), and analyses stratified by region and age group were conducted. The constructed dataset encompassed clinical-epidemiological information, intensive care unit admission, invasive and non-invasive ventilation requirements, vaccination status, and evolution (cure or death). It was observed that there were significant differences in the vaccination rates between regions, in the occurrence of unfavorable outcomes, and in the pattern of comorbidities in young patients. The north region had higher rates of unvaccinated patients and a lower percentage of those vaccinated with three doses in all age groups compared to other regions. The northeast region had the highest rates of patients admitted to the ICU for all age groups, while the north and northeast were the most affected by IMV requirements and in-hospital death in all age groups. This study showed that extended vaccination coverage, especially booster doses, can protect different population segments from developing severe disease since lower vaccination coverage was observed in regions with higher fatality rates.
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Affiliation(s)
- Pedro Dutra Drummond
- Department of Computing, Federal University of Ouro Preto, Morro do Cruzeiro Campus, Ouro Preto 35400-000, MG, Brazil
| | - Daniel Bortot de Salles
- Department of Computing, Federal University of Ouro Preto, Morro do Cruzeiro Campus, Ouro Preto 35400-000, MG, Brazil
| | - Natália Satchiko Hojo de Souza
- Laboratory of Immunopathology, Oswaldo Cruz Foundation—Minas, Av. Augusto de Lima 1715, Belo Horizonte 30190-002, MG, Brazil
| | - Daniela Carine Ramires Oliveira
- Department of Mathematics and Statistics, Federal University of São João del-Rei, Praça Frei Orlando 170, São João del Rei 36307-352, MG, Brazil
| | - Daniel Ludovico Guidoni
- Department of Computing, Federal University of Ouro Preto, Morro do Cruzeiro Campus, Ouro Preto 35400-000, MG, Brazil
| | - Fernanda Sumika Hojo de Souza
- Department of Computing, Federal University of Ouro Preto, Morro do Cruzeiro Campus, Ouro Preto 35400-000, MG, Brazil
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49
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Carlini F, Lusi V, Rizzi C, Assogna F, Laroni A. Cladribine Tablets Mode of Action, Learning from the Pandemic: A Narrative Review. Neurol Ther 2023; 12:1477-1490. [PMID: 37421556 PMCID: PMC10444742 DOI: 10.1007/s40120-023-00520-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 06/16/2023] [Indexed: 07/10/2023] Open
Abstract
Multiple sclerosis (MS) is an immune-mediated disease of the central nervous system, characterized by chronic, inflammatory, demyelinating, and neurodegenerative processes. MS management relies on disease-modifying drugs that suppress/modulate the immune system. Cladribine tablets (CladT) have been approved by different health authorities for patients with various forms of relapsing MS. The drug has been demonstrated to deplete CD4+ and CD8+ T-cells, with a higher effect described in the former, and to decrease total CD19+, CD20+, and naive B-cell counts. COVID-19 is expected to become endemic, suggesting its potential infection risk for immuno-compromised patients, including MS patients treated with disease-modifying drugs. We report here the available data on disease-modifying drug-treated-MS patients and COVID-19 infection and vaccination, with a focus on CladT. MS patients treated with CladT are not at higher risk of developing severe COVID-19. While anti-SARS-CoV-2 vaccination is recommended in all MS patients with guidelines addressing vaccination timing according to the different disease-modifying drugs, no vaccination timing restrictions seem to be necessary for cladribine, based on its mechanism of action and available evidence. Published data suggest that CladT treatment does not impact the production of anti-SARS-CoV-2 antibodies after COVID-19 vaccination, possibly due to its relative sparing effect on naïve B-cells and the rapid B-cell reconstitution following treatment. Slightly lower specific T-cell responses are likely not impacting the risk of breakthrough COVID-19. It could be stated that cladribine's transient effect on innate immune cells likely contributes to maintaining an adequate first line of defense against the SARS-CoV-2 virus.
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Affiliation(s)
- Federico Carlini
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, Genoa, Italy
| | - Valeria Lusi
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, Genoa, Italy
| | - Caterina Rizzi
- Merck Serono S.P.A., Italy an Affiliate of Merck KGaA, Piazza del Pigneto 9, Rome, Italy
| | - Francesco Assogna
- Merck Serono S.P.A., Italy an Affiliate of Merck KGaA, Piazza del Pigneto 9, Rome, Italy
| | - Alice Laroni
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, Genoa, Italy.
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genova, Largo Daneo 3, Genoa, Italy.
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50
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Santos CNO, Caldas GC, de Oliveira FA, da Silva AM, da Silva JS, da Silva RLL, de Jesus AR, Magalhães LS, de Almeida RP. COVID-19 recurrence is related to disease-early profile T cells while detection of anti-S1 IgG is related to multifunctional T cells. Med Microbiol Immunol 2023; 212:339-347. [PMID: 37488347 DOI: 10.1007/s00430-023-00776-7] [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: 04/24/2023] [Accepted: 07/11/2023] [Indexed: 07/26/2023]
Abstract
COVID-19 is caused by SARS-CoV-2 infection and leads from asymptomatic to severe outcomes. The recurrence of the COVID-19 has been described, however, mechanisms involved remains unclear. Thus, the work aimed to investigate the role of multifunctional T cells in patients with recurrent COVID-19. We evaluated clinical characteristics, presence of anti-S1 and anti-Nucleocapsid IgG in patients' sera, and multifunctional T cells (for IFN-γ, IL-2, and TNF-α) in patients with multiple episodes of COVID-19 and controls. Data demonstrate that patients with recurrent COVID-19 have a T cell pattern predominantly related to IFN-γ production. Also, patients with COVID-19 history and absence of anti-S1 IgG had lower levels of CD4+ IFN + IL-2 + TNF + T cells independently of number of disease episodes. Complementary, vaccination changed the patterns of T cells phenotypes and induced IgG seroconversion, despite not induce higher levels of multifunctional T cells in all patients. In conclusion, the data suggest that recurrent disease is related to early-disease T cell profile and absence of anti-S1 IgG is related to lower multifunctional CD4 T cell response, what suggests possibility of new episodes of COVID-19 in these patients.
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Affiliation(s)
- Camilla Natália O Santos
- Laboratório de Imunologia e Biologia Molecular, Universidade Federal de Sergipe, Aracaju, Brazil
- Programa de Pós-Graduação em Ciências da Saúde, Universidade Federal de Sergipe, Aracaju, Brazil
| | - Gustavo C Caldas
- Laboratório de Imunologia e Biologia Molecular, Universidade Federal de Sergipe, Aracaju, Brazil
- Departamento de Medicina, Hospital Universitário, Universidade Federal de Sergipe, Aracaju, Brazil
| | - Fabricia A de Oliveira
- Laboratório de Imunologia e Biologia Molecular, Universidade Federal de Sergipe, Aracaju, Brazil
| | - Angela Maria da Silva
- Laboratório de Imunologia e Biologia Molecular, Universidade Federal de Sergipe, Aracaju, Brazil
- Programa de Pós-Graduação em Ciências da Saúde, Universidade Federal de Sergipe, Aracaju, Brazil
- Departamento de Medicina, Hospital Universitário, Universidade Federal de Sergipe, Aracaju, Brazil
| | - João S da Silva
- Plataforma de Medicina Translacional da Fundação Oswaldo Cruz e Faculdade de Medicina de Ribeirão Preto, Ribeirao Preto, Brazil
| | - Ricardo Luís L da Silva
- Laboratório de Imunologia e Biologia Molecular, Universidade Federal de Sergipe, Aracaju, Brazil
- Departamento de Educação em Saúde, Universidade Federal de Sergipe, Lagarto, Brazil
| | - Amélia R de Jesus
- Laboratório de Imunologia e Biologia Molecular, Universidade Federal de Sergipe, Aracaju, Brazil
- Programa de Pós-Graduação em Ciências da Saúde, Universidade Federal de Sergipe, Aracaju, Brazil
- Departamento de Medicina, Hospital Universitário, Universidade Federal de Sergipe, Aracaju, Brazil
- Instituto de Investigação em Imunologia (iii), Instituto Nacional de Ciência e Tecnologia, São Paulo, Brazil
| | - Lucas S Magalhães
- Laboratório de Imunologia e Biologia Molecular, Universidade Federal de Sergipe, Aracaju, Brazil.
- Programa de Pós-Graduação em Ciências da Saúde, Universidade Federal de Sergipe, Aracaju, Brazil.
- Setor de Parasitologia e Patologia, Instituto de Ciência Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Brazil.
| | - Roque P de Almeida
- Laboratório de Imunologia e Biologia Molecular, Universidade Federal de Sergipe, Aracaju, Brazil
- Programa de Pós-Graduação em Ciências da Saúde, Universidade Federal de Sergipe, Aracaju, Brazil
- Departamento de Medicina, Hospital Universitário, Universidade Federal de Sergipe, Aracaju, Brazil
- Instituto de Investigação em Imunologia (iii), Instituto Nacional de Ciência e Tecnologia, São Paulo, Brazil
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