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Shi H, Sun J, Zeng Y, Wang X, Liu S, Zhang L, Shao E. Immune escape of SARS-CoV-2 variants to therapeutic monoclonal antibodies: a system review and meta-analysis. Virol J 2023; 20:266. [PMID: 37968649 PMCID: PMC10652597 DOI: 10.1186/s12985-023-01977-5] [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: 08/05/2022] [Accepted: 01/25/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND Omicron's high transmissibility and variability present new difficulties for COVID-19 vaccination prevention and therapy. In this article, we analyzed the sensitivity of vaccine-induced antibodies as well as the effect of booster vaccinations against Omicron sublineages. METHODS We looked for Randomized Controlled Trials and cohort studies that reported the COVID-19 vaccines against Omicron sublineages up to 28 July 2022 through PubMed, the Cochrane Library, EMBASE, and Web of Science. Quantitative synthesis was carried out using Stata 16.0 and RevMa5.3, then the serum NT50 and antibody sensitivity to neutralize Omicron sublineages were assessed before and after booster vaccination. This study was registered with PROSPERO number CRD42022350477. RESULTS This meta-analysis included 2138 patients from 20 studies, and the booster vaccination against Omicron sublineages showed a significant difference compared to 2 dosage: BA.1/BA.1.1 (SMD = 0.80, 95% CI: 0.75-0.85, P = 0.00), BA.2/BA.2.12.1 (SMD = 0.77, 95% CI: 0.69-0.85, P = 0.00), BA.3 (SMD = 0.91, 95% CI: 0.83-1.0, P = 0.00), and BA.4/5 (SMD = 0.77, 95% CI: 0.60-0.94, P = 0.00). The sensitivity of vaccines-induced antibodies decreased by at least 5-folds after booster vaccination, particularly in the case of BA.4/5 which had the most notable decline in vaccine effectiveness. CONCLUSION After the booster vaccination, the NT50 and the neutralization ability of vaccine-induced antibodies increased, but the susceptibility of antibodies decreased compared with the control virus, which may be a clue for future Omicron sublineages prevention.
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Affiliation(s)
- Huichun Shi
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Jiajia Sun
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450099, China
| | - Yigang Zeng
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Xiaomeng Wang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Shanshan Liu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Lijun Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
| | - Enming Shao
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
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Hyams C, Qian G, Nava G, Challen R, Begier E, Southern J, Lahuerta M, Nguyen JL, King J, Morley A, Clout M, Maskell N, Jodar L, Oliver J, Ellsbury G, McLaughlin JM, Gessner BD, Finn A, Danon L, Dodd JW. Impact of SARS-CoV-2 infective exacerbation of chronic obstructive pulmonary disease on clinical outcomes in a prospective cohort study of hospitalised adults. J R Soc Med 2023; 116:371-385. [PMID: 37404021 PMCID: PMC10686205 DOI: 10.1177/01410768231184162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/04/2023] [Indexed: 07/06/2023] Open
Abstract
OBJECTIVES To determine whether acute exacerbations of chronic obstructive pulmonary disease (AECOPD) triggered by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), have worse outcomes than AECOPD caused by other infectious agents or non-infective AECOPD (NI-COPD). DESIGN A two-hospital prospective cohort study of adults hospitalised with acute respiratory disease. We compared outcomes with AECOPD and a positive test for SARS-CoV-2 (n = 816), AECOPD triggered by other infections (n = 3038) and NI-COPD (n = 994). We used multivariable modelling to adjust for potential confounders and assessed variation by seasons associated with different SARS-CoV-2 variants. SETTING Bristol UK, August 2020-May 2022. PARTICIPANTS Adults (≥18 y) hospitalised with AECOPD. MAIN OUTCOME MEASURES We determined the risk of positive pressure support, longer hospital admission and mortality following hospitalisation with AECOPD due to non-SARS-CoV-2 infection compared with SARS-CoV-2 AECOPD and NI-COPD. RESULTS Patients with SARS-CoV-2 AECOPD, in comparison to non-SARS-CoV-2 infective AECOPD or NI-COPD, more frequently required positive pressure support (18.5% and 7.5% vs. 11.7%, respectively), longer hospital stays (median [interquartile range, IQR]: 7 [3-15] and 5 [2-10] vs. 4 [2-9] days, respectively) and had higher 30-day mortality (16.9% and 11.1% vs. 5.9%, respectively) (all p < 0.001). In adjusted analyses, SARS-CoV-2 AECOPD was associated with a 55% (95% confidence interval [95% CI]: 24-93), 26% (95% CI: 15-37) and 35% (95% CI: 10-65) increase in the risk of positive pressure support, hospitalisation length and 30-day mortality, respectively, relative to non-SARS-CoV-2 infective AECOPD. The difference in risk remained similar during periods of wild-type, Alpha and Delta SARS-CoV-2 strain dominance, but diminished during Omicron dominance. CONCLUSIONS SARS-CoV-2-related AECOPD had worse patient outcomes compared with non-SARS-CoV-2 AECOPD or NI-AECOPD, although the difference in risks was less pronounced during Omicron dominance.
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Affiliation(s)
- Catherine Hyams
- Academic Respiratory Unit and Bristol Vaccine Centre, University of Bristol, Bristol, BS15, UK
| | - George Qian
- Engineering Mathematics, University of Bristol, Bristol, Bristol, BS8, UK
| | - George Nava
- Academic Respiratory Unit, University of Bristol, Southmead Hospital, Bristol, Bristol, BS15, UK
| | - Robert Challen
- Engineering Mathematics, University of Bristol, Bristol, Bristol, BS8, UK
| | - Elizabeth Begier
- Vaccines Medical Development, Scientific and Clinical Affairs, Pfizer Inc., Collegeville, PA 19426, USA
| | - Jo Southern
- Vaccines Medical Development, Scientific and Clinical Affairs, Pfizer Inc., Collegeville, PA 19426, USA
| | - Maria Lahuerta
- Vaccines Medical Development, Scientific and Clinical Affairs, Pfizer Inc., Collegeville, PA 19426, USA
| | - Jennifer L Nguyen
- Vaccines Medical Development, Scientific and Clinical Affairs, Pfizer Inc., Collegeville, PA 19426, USA
| | - Jade King
- Clinical Research and Imaging Centre, UHBW NHS Trust, Bristol, Bristol, BS2, UK
| | - Anna Morley
- Academic Respiratory Unit, Southmead Hospital, Bristol, Bristol, BS15, UK
| | - Madeleine Clout
- Bristol Vaccine Centre and Population Health Sciences, University of Bristol, Bristol, BS2, UK
| | - Nick Maskell
- Academic Respiratory Unit, University of Bristol, Southmead Hospital, Bristol, Bristol, BS15, UK
| | - Luis Jodar
- Vaccines Medical Development, Scientific and Clinical Affairs, Pfizer Inc., Collegeville, PA 19426, USA
| | - Jennifer Oliver
- Bristol Vaccine Centre and Population Health Sciences, University of Bristol, Bristol, BS2, UK
| | | | - John M McLaughlin
- Vaccines Medical Development, Scientific and Clinical Affairs, Pfizer Inc., Collegeville, PA 19426, USA
| | - Bradford D Gessner
- Vaccines Medical Development, Scientific and Clinical Affairs, Pfizer Inc., Collegeville, PA 19426, USA
| | - Adam Finn
- Bristol Vaccine Centre, Cellular and Molecular Medicine and Population Health Sciences, University of Bristol, Bristol, BS2, UK
| | - Leon Danon
- Engineering Mathematics, University of Bristol, Bristol, Bristol, BS8, UK
| | - James W Dodd
- Academic Respiratory Unit and Population Health Sciences, University of Bristol, Southmead Hospital, Bristol, BS15, UK
| | - The Avon CAP Research Group
- Academic Respiratory Unit and Bristol Vaccine Centre, University of Bristol, Bristol, BS15, UK
- Engineering Mathematics, University of Bristol, Bristol, Bristol, BS8, UK
- Academic Respiratory Unit, University of Bristol, Southmead Hospital, Bristol, Bristol, BS15, UK
- Vaccines Medical Development, Scientific and Clinical Affairs, Pfizer Inc., Collegeville, PA 19426, USA
- Clinical Research and Imaging Centre, UHBW NHS Trust, Bristol, Bristol, BS2, UK
- Academic Respiratory Unit, Southmead Hospital, Bristol, Bristol, BS15, UK
- Bristol Vaccine Centre and Population Health Sciences, University of Bristol, Bristol, BS2, UK
- Vaccines Medical Affairs, Pfizer Ltd, Tadworth, KT20, UK
- Bristol Vaccine Centre, Cellular and Molecular Medicine and Population Health Sciences, University of Bristol, Bristol, BS2, UK
- Academic Respiratory Unit and Population Health Sciences, University of Bristol, Southmead Hospital, Bristol, BS15, UK
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Rohde G, Stenglein S, Prozesky H, Manudhane G, Sandulescu O, Bauer M, Overend T, Koch W, Neuschwander D, Planz O, Torres A, Witzenrath M. Efficacy and safety of zapnometinib in hospitalised adult patients with COVID-19 (RESPIRE): a randomised, double-blind, placebo-controlled, multicentre, proof-of-concept, phase 2 trial. EClinicalMedicine 2023; 65:102237. [PMID: 38106555 PMCID: PMC10725048 DOI: 10.1016/j.eclinm.2023.102237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 12/19/2023] Open
Abstract
Background Zapnometinib is an oral, non-ATP-competitive, small-molecule inhibitor of MEK1/MEK2 with immunomodulatory and antiviral properties. We aimed to investigate the safety and efficacy of zapnometinib in patients with COVID-19. Methods In this randomised, double-blind, placebo-controlled, multicentre, proof-of-concept, phase 2 trial, we recruited hospitalised adults with moderate or severe COVID-19 from 18 hospitals in Germany, India, Romania, South Africa, and Spain. Those requiring ICU admission or ventilator support at screening or randomisation were excluded. Patients were randomly assigned (1:1) to receive oral zapnometinib (900 mg on Day 1; 600 mg on Days 2-6) or matching placebo, on top of standard of care. Randomisation, stratified by baseline clinical severity status (CSS 3 or 4, measured on a 7-point ordinal scale), was done using Interactive Response Technology. Patients, investigators, and the sponsor were masked to treatment allocation. The primary endpoint was CSS at Day 15 and was conducted on the full analysis set (FAS: all patients who were randomised to the study, received at least one dose of study medication and had at least one post-dose assessment of CSS, as randomised). Safety analyses were conducted on the safety analysis set (all study participants who received at least one dose of study medication, as treated). This study is registered at ClinicalTrials.gov (NCT04776044) and EudraCT (2020-004206-59). Findings The trial was terminated early as the emergence of the Omicron variant impacted recruitment. Between 12th April 2021 and 9th August 2022, 104 of the planned 220 patients were enrolled and randomly assigned, 103 were treated, and 101 were included in the FAS (zapnometinib: n = 50; placebo: n = 51). The primary outcome was not significantly different between the two groups, but patients on zapnometinib had higher odds of improved CSS versus placebo (odds ratio [OR] 1.54 [95% CI 0.72-3.33]; p = 0.26). Predefined subgroup analyses identified trends for improved CSS in patients with severe disease at baseline (OR 2.57 [0.76-8.88]; p = 0.13) and non-Omicron variants (OR 2.36 [0.85-6.71]; p = 0.10); the p value of the CSS subgroup by Treatment interaction term in the model was p = 0.28. The frequency and intensity of adverse events was low and similar between arms. Twenty (39.2%) patients treated with zapnometinib experienced adverse events compared with eighteen (34.6%) patients treated with placebo. One patient receiving zapnometinib and two patients receiving placebo died during the study. None of the deaths were considered related to study medication. Interpretation These results provide proof-of-concept for the innovative approach of targeting the Raf/MEK/ERK pathway in patients with hospitalised moderate/severe COVID-19. Further clinical studies will be required to evaluate the clinical benefit of zapnometinib in this and other indications. Funding Atriva Therapeutics GmbH and the Federal Ministry of Education and Research, Germany.
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Affiliation(s)
- Gernot Rohde
- Goethe University Frankfurt, University Hospital, Medical Clinic I, Department of Respiratory Medicine, Frankfurt/Main, Germany
| | | | - Hans Prozesky
- Division of Infectious Diseases, Department of Medicine, Stellenbosch University and TREAD Research, Tygerberg Hospital, Cape Town, South Africa
| | | | - Oana Sandulescu
- National Institute for Infectious Diseases “Prof. Dr. Matei Bals”, Bucharest, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | | | | | | | - Dennis Neuschwander
- Department of Biostatistics, GCP-Service International Ltd. & Co. KG, Bremen, Germany
| | | | - Antoni Torres
- Hospital Clinic i Provincial de Barcelona, Barcelona, Spain, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Catalan Institution for Research and Advanced Studies (ICREA), Biomedical Research Networking Centers in Respiratory Diseases (CIBERES), University of Barcelona, Barcelona, Spain
| | - Martin Witzenrath
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Berlin, Germany, German Center for Lung Research (DZL), Berlin, Germany
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Pingping Z, Yanyu Z, Xuri S, Qiming H, Yi W, Guoliang T. Comparison between original SARS-CoV-2 strain and omicron variant on thin-section chest CT imaging of COVID-19 pneumonia. RADIOLOGIE (HEIDELBERG, GERMANY) 2023; 63:55-63. [PMID: 37280418 PMCID: PMC10243278 DOI: 10.1007/s00117-023-01147-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/23/2023] [Indexed: 06/08/2023]
Abstract
OBJECTIVES We investigated different computed tomography (CT) features between Omicron-variant and original-strain SARS-CoV‑2 pneumonia to facilitate the clinical management. MATERIALS AND METHODS Medical records were retrospectively reviewed to select patients with original-strain SARS-CoV‑2 pneumonia from February 22 to April 22, 2020, or Omicron-variant SARS-CoV‑2 pneumonia from March 26 to May 31, 2022. Data on the demographics, comorbidities, symptoms, clinical types, and CT features were compared between the two groups. RESULTS There were 62 and 78 patients with original-strain or Omicron-variant SARS-CoV‑2 pneumonia, respectively. There were no differences between the two groups in terms of age, sex, clinical types, symptoms, and comorbidities. The main CT features differed between the two groups (p = 0.003). There were 37 (59.7%) and 20 (25.6%) patients with ground-glass opacities (GGO) in the original-strain and Omicron-variant pneumonia, respectively. A consolidation pattern was more frequently observed in the Omicron-variant than original-strain pneumonia (62.8% vs. 24.2%). There was no difference in crazy-paving pattern between the original-strain and Omicron-variant pneumonia (16.1% vs. 11.6%). Pleural effusion was observed more often in Omicron-variant pneumonia, while subpleural lesions were more common in the original-strain pneumonia. The CT score in the Omicron-variant group was higher than that in the original-strain group for critical-type (17.00, 16.00-18.00 vs. 16.00, 14.00-17.00, p = 0.031) and for severe-type (13.00, 12.00-14.00 vs 12.00, 10.75-13.00, p = 0.027) pneumonia. CONCLUSION The main CT finding of the Omicron-variant SARS-CoV‑2 pneumonia included consolidations and pleural effusion. By contrast, CT findings of original-strain SARS-CoV‑2 pneumonia showed frequent GGO and subpleural lesions, but without pleural effusion. The CT scores were also higher in the critical and severe types of Omicron-variant than original-strain pneumonia.
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Affiliation(s)
- Zeng Pingping
- Department ICU of the Second Affiliated Hospital, Fujian Medical University, No. 34, Zhongshan North Road, Licheng District, Quanzhou City, Fujian, China
| | - Zhou Yanyu
- Department ICU of the Second Affiliated Hospital, Fujian Medical University, No. 34, Zhongshan North Road, Licheng District, Quanzhou City, Fujian, China
| | - Sun Xuri
- Department ICU of the Second Affiliated Hospital, Fujian Medical University, No. 34, Zhongshan North Road, Licheng District, Quanzhou City, Fujian, China
| | - Huang Qiming
- Department of Medical Imaging of the Second Affiliated Hospital, Fujian Medical University, No. 34, Zhongshan North Road, Licheng District, Quanzhou City, Fujian, China
| | - Wang Yi
- Department of Medical Imaging of the Second Affiliated Hospital, Fujian Medical University, No. 34, Zhongshan North Road, Licheng District, Quanzhou City, Fujian, China
| | - Tan Guoliang
- Department ICU of the Second Affiliated Hospital, Fujian Medical University, No. 34, Zhongshan North Road, Licheng District, Quanzhou City, Fujian, China.
- Wuhan Jinyintan Hospital, Wuhan City, China.
- The Fourth People's Hospital of Shanghai, Shanghai City, China.
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Carmola LR, Roebling AD, Khosravi D, Langsjoen RM, Bombin A, Bixler B, Reid A, Chen C, Wang E, Lu Y, Zheng Z, Zhang R, Nguyen PV, Arthur RA, Fitts E, Gulick DA, Higginbotham D, Taz A, Ahmed A, Crumpler JH, Kraft C, Lam WA, Babiker A, Waggoner JJ, Openo KP, Johnson LM, Westbrook A, Piantadosi A. Viral and host factors associated with SARS-CoV-2 disease severity in Georgia, USA. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.25.23297530. [PMID: 37961729 PMCID: PMC10635197 DOI: 10.1101/2023.10.25.23297530] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
While SARS-CoV-2 vaccines have shown strong efficacy, their suboptimal uptake combined with the continued emergence of new viral variants raises concerns about the ongoing and future public health impact of COVID-19. We investigated viral and host factors, including vaccination status, that were associated with SARS-CoV-2 disease severity in a setting with low vaccination rates. We analyzed clinical and demographic data from 1,957 individuals in the state of Georgia, USA, coupled with viral genome sequencing from 1,185 samples. We found no difference in disease severity between individuals infected with Delta and Omicron variants among the participants in this study, after controlling for other factors, and we found no specific mutations associated with disease severity. Compared to those who were unvaccinated, vaccinated individuals experienced less severe SARS-CoV-2 disease, and the effect was similar for both variants. Vaccination within 270 days before infection was associated with decreased odds of moderate and severe outcomes, with the strongest association observed at 91-270 days post-vaccination. Older age and underlying health conditions, especially immunosuppression and renal disease, were associated with increased disease severity. Overall, this study provides insights into the impact of vaccination status, variants/mutations, and clinical factors on disease severity in SARS-CoV-2 infection when vaccination rates are low. Understanding these associations will help refine and reinforce messaging around the crucial importance of vaccination in mitigating the severity of SARS-CoV-2 disease.
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Affiliation(s)
- Ludy R. Carmola
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Allison Dorothy Roebling
- Georgia Emerging Infections Program; Georgia Department of Health; Atlanta, GA, 30303; USA
- Atlanta Veterans Affairs Medical Center; Decatur, GA, 30033; USA
- Division of Infectious Diseases; Department of Medicine, Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Dara Khosravi
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Rose M. Langsjoen
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Andrei Bombin
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
- Division of Infectious Diseases; Department of Medicine, Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Bri Bixler
- Graduate Program in Genetics and Molecular Biology, Emory University; Atlanta, GA, 30322; USA
| | - Alex Reid
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Cara Chen
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Ethan Wang
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Yang Lu
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Ziduo Zheng
- Department of Biostatistics and Bioinformatics; Rollins School of Public Health, Emory University; Atlanta, GA, 30322; USA
| | - Rebecca Zhang
- Department of Biostatistics and Bioinformatics; Rollins School of Public Health, Emory University; Atlanta, GA, 30322; USA
| | - Phuong-Vi Nguyen
- Division of Infectious Diseases; Department of Medicine, Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Robert A. Arthur
- Emory Integrated Computational Core; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Eric Fitts
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Dalia Arafat Gulick
- Georgia Clinical & Translational Science Alliance; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Dustin Higginbotham
- Georgia Clinical & Translational Science Alliance; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Azmain Taz
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Alaa Ahmed
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
- Emory Integrated Genomics Core; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - John Hunter Crumpler
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Colleen Kraft
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
- Division of Infectious Diseases; Department of Medicine, Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Wilbur A. Lam
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies; Atlanta, GA, 30322; USA
- Department of Pediatrics, Emory University School of Medicine; Atlanta, GA, 30322; USA
- Aflac Cancer and Blood Disorders Center at Children’s Healthcare of Atlanta; Atlanta, GA, 30322; USA
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
| | - Ahmed Babiker
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
- Division of Infectious Diseases; Department of Medicine, Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Jesse J. Waggoner
- Division of Infectious Diseases; Department of Medicine, Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Kyle P. Openo
- Georgia Emerging Infections Program; Georgia Department of Health; Atlanta, GA, 30303; USA
- Atlanta Veterans Affairs Medical Center; Decatur, GA, 30033; USA
- Division of Infectious Diseases; Department of Medicine, Emory University School of Medicine; Atlanta, GA, 30322; USA
| | - Laura M. Johnson
- Pediatric Biostatistics Core; Department of Pediatrics; School of Medicine; Emory University; Atlanta, GA, 30322; USA
| | - Adrianna Westbrook
- Pediatric Biostatistics Core; Department of Pediatrics; School of Medicine; Emory University; Atlanta, GA, 30322; USA
| | - Anne Piantadosi
- Department of Pathology and Laboratory Medicine; Emory University School of Medicine; Atlanta, GA, 30322; USA
- Division of Infectious Diseases; Department of Medicine, Emory University School of Medicine; Atlanta, GA, 30322; USA
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Aboul-Fotouh S, Mahmoud AN, Elnahas EM, Habib MZ, Abdelraouf SM. What are the current anti-COVID-19 drugs? From traditional to smart molecular mechanisms. Virol J 2023; 20:241. [PMID: 37875904 PMCID: PMC10594888 DOI: 10.1186/s12985-023-02210-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 10/13/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Coronavirus disease 19 (COVID-19) is the disease caused by SARS-CoV-2, a highly infectious member of the coronavirus family, which emerged in December 2019 in "Wuhan, China". It induces respiratory illness ranging from mild symptoms to severe disease. It was declared a "pandemic" by the World Health Organization (WHO) in March 2020. Since then, a vast number of clinical and experimental studies have been conducted to identify effective approaches for its prevention and treatment. MAIN BODY The pathophysiology of COVID-19 represents an unprecedented challenge; it triggers a strong immune response, which may be exacerbated by "a cytokine storm syndrome". It also induces thrombogenesis and may trigger multi-organ injury. Therefore, different drug classes have been proposed for its treatment and prevention, such as antivirals, anti-SARS-CoV-2 antibody agents (monoclonal antibodies, convalescent plasma, and immunoglobulins), anti-inflammatory drugs, immunomodulators, and anticoagulant drugs. To the best of our knowledge, this review is the first to present, discuss, and summarize the current knowledge about the different drug classes used for the treatment of COVID-19, with special emphasis on their targets, mechanisms of action, and important adverse effects and drug interactions. Additionally, we spotlight the latest "October 2023" important guidelines (NIH, IDSA, and NICE) and FDA approval or authorization regarding the use of these agents in the management of COVID-19. CONCLUSION Despite the wide array of therapeutic strategies introduced for the treatment of COVID-19, one of the most prominent therapeutic challenges is SARS-CoV-2 mutations and emerging new variants and subvariants. Currently, the anti-COVID-19 drug pipeline is continuously affording novel treatments to face this growing challenge.
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Affiliation(s)
- Sawsan Aboul-Fotouh
- Department of Clinical Pharmacology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
- Clinical Pharmacology Unit, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Ahmed Nageh Mahmoud
- Department of Clinical Pharmacology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Esraa M Elnahas
- Department of Clinical Pharmacology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Mohamed Z Habib
- Department of Clinical Pharmacology, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
| | - Sahar M Abdelraouf
- Department of Biochemistry, Faculty of Pharmacy, Misr International University, Cairo, Egypt
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Kline JA, Reed B, Frost A, Alanis N, Barshay M, Melzer A, Galbraith JW, Budd A, Winn A, Pun E, Camargo CA. Database derived from an electronic medical record-based surveillance network of US emergency department patients with acute respiratory illness. BMC Med Inform Decis Mak 2023; 23:224. [PMID: 37848896 PMCID: PMC10580574 DOI: 10.1186/s12911-023-02310-4] [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: 05/26/2023] [Accepted: 09/27/2023] [Indexed: 10/19/2023] Open
Abstract
BACKGROUND For surveillance of episodic illness, the emergency department (ED) represents one of the largest interfaces for generalizable data about segments of the US public experiencing a need for unscheduled care. This protocol manuscript describes the development and operation of a national network linking symptom, clinical, laboratory and disposition data that provides a public database dedicated to the surveillance of acute respiratory infections (ARIs) in EDs. METHODS The Respiratory Virus Laboratory Emergency Department Network Surveillance (RESP-LENS) network includes 26 academic investigators, from 24 sites, with 91 hospitals, and the Centers for Disease Control and Prevention (CDC) to survey viral infections. All data originate from electronic medical records (EMRs) accessed by structured query language (SQL) coding. Each Tuesday, data are imported into the standard data form for ARI visits that occurred the prior week (termed the index file); outcomes at 30 days and ED volume are also recorded. Up to 325 data fields can be populated for each case. Data are transferred from sites into an encrypted Google Cloud Platform, then programmatically checked for compliance, parsed, and aggregated into a central database housed on a second cloud platform prior to transfer to CDC. RESULTS As of August, 2023, the network has reported data on over 870,000 ARI cases selected from approximately 5.2 million ED encounters. Post-contracting challenges to network execution have included local shifts in testing policies and platforms, delays in ICD-10 coding to detect ARI cases, and site-level personnel turnover. The network is addressing these challenges and is poised to begin streaming weekly data for dissemination. CONCLUSIONS The RESP-LENS network provides a weekly updated database that is a public health resource to survey the epidemiology, viral causes, and outcomes of ED patients with acute respiratory infections.
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Affiliation(s)
- Jeffrey A Kline
- Department of Emergency Medicine, Wayne State University, Detroit, MI, USA.
| | - Brian Reed
- Department of Emergency Medicine, Wayne State University, Detroit, MI, USA
| | | | - Naomi Alanis
- Department of Emergency Medicine, John Peter Smith Hospital, Ft. Worth, TX, USA
| | - Meylakh Barshay
- Department of Emergency Medicine, George Washington University School of Medicine, Washington, DC, USA
| | - Andrew Melzer
- Department of Emergency Medicine, George Washington University School of Medicine, Washington, DC, USA
| | - James W Galbraith
- Department of Emergency Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Alicia Budd
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, USA
| | - Amber Winn
- Coronavirus and Other Respiratory Viruses Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, USA
| | - Eugene Pun
- General Dynamics Contractor to the Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, USA
| | - Carlos A Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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Joshi K, Kahn R, Boyer C, Lipsitch M. Some principles for using epidemiologic study results to parameterize transmission models. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.03.23296455. [PMID: 37873220 PMCID: PMC10593029 DOI: 10.1101/2023.10.03.23296455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background Infectious disease models, including individual based models (IBMs), can be used to inform public health response. For these models to be effective, accurate estimates of key parameters describing the natural history of infection and disease are needed. However, obtaining these parameter estimates from epidemiological studies is not always straightforward. We aim to 1) outline challenges to parameter estimation that arise due to common biases found in epidemiologic studies and 2) describe the conditions under which careful consideration in the design and analysis of the study could allow us to obtain a causal estimate of the parameter of interest. In this discussion we do not focus on issues of generalizability and transportability. Methods Using examples from the COVID-19 pandemic, we first identify different ways of parameterizing IBMs and describe ideal study designs to estimate these parameters. Given real-world limitations, we describe challenges in parameter estimation due to confounding and conditioning on a post-exposure observation. We then describe ideal study designs that can lead to unbiased parameter estimates. We finally discuss additional challenges in estimating progression probabilities and the consequences of these challenges. Results Causal estimation can only occur if we are able to accurately measure and control for all confounding variables that create non-causal associations between the exposure and outcome of interest, which is sometimes challenging given the nature of the variables we need to measure. In the absence of perfect control, non-causal parameter estimates should still be used, as sometimes they are the best available information we have. Conclusions Identifying which estimates from epidemiologic studies correspond to the quantities needed to parameterize disease models, and determining whether these parameters have causal interpretations, can inform future study designs and improve inferences from infectious disease models. Understanding the way in which biases can arise in parameter estimation can inform sensitivity analyses or help with interpretation of results if the magnitude and direction of the bias is understood.
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Affiliation(s)
- Keya Joshi
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, 02115 Boston, Massachusetts
| | - Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, 02115 Boston, Massachusetts
| | - Christopher Boyer
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, 02115 Boston, Massachusetts
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, 02115 Boston, Massachusetts
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 02115 Boston, Massachusetts
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Liu LT, Chiou SS, Chen PC, Chen CH, Lin PC, Tsai CY, Chuang WL, Hwang SJ, Chong IW, Tsai JJ. Epidemiology and analysis of SARS-CoV-2 Omicron subvariants BA.1 and 2 in Taiwan. Sci Rep 2023; 13:16583. [PMID: 37789031 PMCID: PMC10547678 DOI: 10.1038/s41598-023-43357-7] [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: 08/02/2023] [Accepted: 09/22/2023] [Indexed: 10/05/2023] Open
Abstract
The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first detected in October 2021, possessed many mutations compared to previous variants. We aimed to identify and analyze SARS-CoV-2 Omicron subvariants among coronavirus disease 2019 (COVID-19) patients between January 2022 and September 2022 in Taiwan. The results revealed that BA.2.3.7, featuring K97E and G1251V in the spike protein compared with BA.2, emerged in March 2022 and persistently dominated between April 2022 and August 2022, resulting in the largest COVID-19 outbreak since 2020. The accumulation of amino acid (AA) variations, mainly AA substitution, in the spike protein was accompanied by increasing severity in Omicron-related COVID-19 between April 2022 and January 2023. Older patients were more likely to have severe COVID-19, and comorbidity was a risk factor for COVID-19-related mortality. The accumulated case fatality rate (CFR) dropped drastically after Omicron variants, mainly BA.2.3.7, entered Taiwan after April 2022, and the CFR was 0.16% in Taiwan, which was lower than that worldwide (0.31%) between April 2021 and January 2023. The relatively low CFR in Omicron-related COVID-19 patients can be attributed to adjustments to public health policies, promotion of vaccination programs, effective antiviral drugs, and the lower severity of the Omicron variant.
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Affiliation(s)
- Li-Teh Liu
- Department of Medical Laboratory Science and Biotechnology, College of Medical Technology, Chung Hwa University of Medical Technology, Tainan City, Taiwan
| | - Shyh-Shin Chiou
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan
- Center of Applied Genomics, Kaohsiung Medical University, Kaohsiung City, Taiwan
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
| | - Po-Chih Chen
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung City, Taiwan
| | - Chun-Hong Chen
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Ping-Chang Lin
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
| | - Ching-Yi Tsai
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
| | - Wan-Long Chuang
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
| | - Shang-Jyh Hwang
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan
- Division of Nephrology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
| | - Inn-Wen Chong
- Department of Internal Medicine and Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan
- Department of Pulmonary Medicine, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
| | - Jih-Jin Tsai
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan.
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan.
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, No. 100, Tzyou 1st Road, Kaohsiung City, 80756, Taiwan.
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Naik R, Avula S, Palleti SK, Gummadi J, Ramachandran R, Chandramohan D, Dhillon G, Gill AS, Paiwal K, Shaik B, Balachandran M, Patel B, Gurugubelli S, Mariswamy Arun Kumar AK, Nanjundappa A, Bellamkonda M, Rathi K, Sakhamuri PL, Nassar M, Bali A. From Emergence to Endemicity: A Comprehensive Review of COVID-19. Cureus 2023; 15:e48046. [PMID: 37916248 PMCID: PMC10617653 DOI: 10.7759/cureus.48046] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2023] [Indexed: 11/03/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), later renamed coronavirus disease 2019 (COVID-19), was first identified in Wuhan, China, in early December 2019. Initially, the China office of the World Health Organization was informed of numerous cases of pneumonia of unidentified etiology in Wuhan, Hubei Province at the end of 2019. This would subsequently result in a global pandemic with millions of confirmed cases of COVID-19 and millions of deaths reported to the WHO. We have analyzed most of the data published since the beginning of the pandemic to compile this comprehensive review of SARS-CoV-2. We looked at the core ideas, such as the etiology, epidemiology, pathogenesis, clinical symptoms, diagnostics, histopathologic findings, consequences, therapies, and vaccines. We have also included the long-term effects and myths associated with some therapeutics of COVID-19. This study presents a comprehensive assessment of the SARS-CoV-2 virology, vaccines, medicines, and significant variants identified during the course of the pandemic. Our review article is intended to provide medical practitioners with a better understanding of the fundamental sciences, clinical treatment, and prevention of COVID-19. As of May 2023, this paper contains the most recent data made accessible.
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Affiliation(s)
- Roopa Naik
- Medicine, Geisinger Commonwealth School of Medicine, Scranton, USA
- Internal Medicine/Hospital Medicine, Geisinger Health System, Wilkes Barre, USA
| | - Sreekant Avula
- Diabetes, Endocrinology, and Metabolism, University of Minnesota, Minneapolis, USA
| | - Sujith K Palleti
- Nephrology, Louisiana State University Health Sciences Center, Shreveport, USA
| | - Jyotsna Gummadi
- Internal Medicine, MedStar Franklin Square Medical Center, Baltimore, USA
| | | | | | - Gagandeep Dhillon
- Physician Executive MBA, University of Tennessee, Knoxville, USA
- Internal Medicine, University of Maryland Baltimore Washington Medical Center, Glen Burnie, USA
| | | | - Kapil Paiwal
- Oral & Maxillofacial Pathology, Daswani Dental College & Research Center, Kota, IND
| | - Bushra Shaik
- Internal Medicine, Onslow Memorial Hospital, Jacksonville, USA
| | | | - Bhumika Patel
- Oral Medicine and Radiology, Howard University, Washington, D.C., USA
| | | | | | | | - Mahita Bellamkonda
- Hospital Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, USA
| | - Kanika Rathi
- Internal Medicine, University of Florida, Gainesville, USA
| | | | - Mahmoud Nassar
- Endocrinology, Diabetes, and Metabolism, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - Atul Bali
- Internal Medicine/Nephrology, Geisinger Medical Center, Danville, USA
- Internal Medicine/Nephrology, Geisinger Health System, Wilkes-Barre, USA
- Medicine, Geisinger Commonwealth School of Medicine, Scranton, USA
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Cheng F, Xiang H, Gale RP, Chen S, Qu J, Guo H, Li Q, Zhang Y, Li W. SARS-CoV-2 Omicron BA.5.2-infection and COVID-19 in persons with chronic myeloid leukaemia. J Cancer Res Clin Oncol 2023; 149:11025-11030. [PMID: 37337067 DOI: 10.1007/s00432-023-04995-6] [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: 04/20/2023] [Accepted: 06/15/2023] [Indexed: 06/21/2023]
Abstract
OBJECTIVE A SARS-CoV-2 Omicron (BA.5.2) epidemic began in China in December, 2022 following stopping the zero COVID policy. METHODS We studied features of the epidemic in 1,121 persons with chronic myeloid leukaemia (CML). RESULTS 1103 (98%) were in chronic, 10 in accelerated and 8 in acute phases. 834 (74%) became infected almost all of whom met criteria for COVID-19. The most common symptoms were fever (91%), cough (90%) and fatigue (82%). 42 infected persons were asymptomatic. Most people quarantined at home and self-medicated. 22 were hospitalized for COVID-19. At admission 5 had mild, 14, moderate and 3, severe/critical disease according to World Health Organization (WHO) criteria. 5 received respiratory assistance, 3 were admitted to the intensive care unit (ICU) and 1 in accelerated phase died from COVID-19. Co-variates associated with a risk of COVID-19 in SARS-CoV-2-infected subjects include age ≥ 65 years, higher education level and imatinib therapy. CONCLUSION In conclusion, most SARS-CoV-2 Omicron BA.5.2 infections in persons with CML resulted in COVID-19 most of which cases are mild with only 1 death.
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Affiliation(s)
- Fang Cheng
- Department of Pharmacy, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan, 430022, China
| | - Hang Xiang
- Department of Hematology, The Ventral Hospital of Enshi Tujia and Miao Autonomous Prefecture, Yichang, 443000, China
| | - Robert Peter Gale
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College of Science, Technology and Medicine, London, UK
| | - Siyi Chen
- Department of Rheumatology and Immunology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jiao Qu
- Department of Hematology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Hao Guo
- Department of Hematology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, 450000, Henan, China
| | - Qiubai Li
- Department of Rheumatology and Immunology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Hubei Engineering Research Center for Application of Extracellular Vesicles, Hubei University of Science and Technology, Xianning, China.
| | - Yanli Zhang
- Department of Hematology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, 450000, Henan, China.
| | - Weiming Li
- Department of Hematology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology, Wuhan, 430022, China.
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Potter AL, Vaddaraju V, Venkateswaran S, Mansur A, Bajaj SS, Kiang MV, Jena AB, Yang CFJ. Deaths Due to COVID-19 in Patients With Cancer During Different Waves of the Pandemic in the US. JAMA Oncol 2023; 9:1417-1422. [PMID: 37651113 PMCID: PMC10472259 DOI: 10.1001/jamaoncol.2023.3066] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 06/02/2023] [Indexed: 09/01/2023]
Abstract
Importance With the ongoing relaxation of guidelines to prevent COVID-19 transmission, particularly in hospital settings, medically vulnerable groups, such as patients with cancer, may experience a disparate burden of COVID-19 mortality compared with the general population. Objective To evaluate COVID-19 mortality among US patients with cancer compared with the general US population during different waves of the pandemic. Design, Setting, and Participants This cross-sectional study used data from the Center for Disease Control and Prevention's Wide-Ranging Online Data for Epidemiologic Research database to examine COVID-19 mortality among US patients with cancer and the general population from March 1, 2020, to May 31, 2022. The number of deaths due to COVID-19 during the 2021 to 2022 winter Omicron surge was compared with deaths during the preceding year's COVID-19 winter surge (when the wild-type SARS-CoV-2 variant was predominant) using mortality ratios. Data were analyzed from July 21 through August 31, 2022. Exposures Pandemic wave during which the wild-type variant (December 2020 to February 2021), Delta variant (July 2021 to November 2021), or Omicron variant (December 2021 to February 2022) was predominant. Main Outcomes and Measures Number of COVID-19 deaths per month. Results The sample included 34 350 patients with cancer (14 498 females [42.2%] and 19 852 males [57.8%]) and 628 156 members of the general public (276 878 females [44.1%] and 351 278 males [55.9%]) who died from COVID-19 when the wild-type (December 2020-February 2021), Delta (July 2021-November 2021), and winter Omicron (December 2021-February 2022) variants were predominant. Among patients with cancer, the greatest number of COVID-19 deaths per month occurred during the winter Omicron period (n = 5958): at the peak of the winter Omicron period, there were 18% more deaths compared with the peak of the wild-type period. In contrast, among the general public, the greatest number of COVID-19 deaths per month occurred during the wild-type period (n = 105 327), and at the peak of the winter Omicron period, there were 21% fewer COVID-19 deaths compared with the peak of the wild-type period. In subgroup analyses by cancer site, COVID-19 mortality increased the most, by 38%, among patients with lymphoma during the winter Omicron period vs the wild-type period. Conclusions and Relevance Findings of this cross-sectional study suggest that patients with cancer had a disparate burden of COVID-19 mortality during the winter Omicron wave compared with the general US population. With the emergence of new, immune-evasive SARS-CoV-2 variants, many of which are anticipated to be resistant to monoclonal antibody treatments, strategies to prevent COVID-19 transmission should remain a high priority.
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Affiliation(s)
- Alexandra L. Potter
- Division of Thoracic Surgery, Department of Surgery, Massachusetts General Hospital, Boston
| | - Vedha Vaddaraju
- Division of Thoracic Surgery, Department of Surgery, Massachusetts General Hospital, Boston
| | - Shivaek Venkateswaran
- Division of Thoracic Surgery, Department of Surgery, Massachusetts General Hospital, Boston
| | - Arian Mansur
- Division of Thoracic Surgery, Department of Surgery, Massachusetts General Hospital, Boston
| | - Simar S. Bajaj
- Division of Thoracic Surgery, Department of Surgery, Massachusetts General Hospital, Boston
| | - Mathew V. Kiang
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, California
| | - Anupam B. Jena
- Department of Health Care Policy, Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Massachusetts General Hospital, Boston
- National Bureau of Economic Research, Cambridge, Massachusetts
| | - Chi-Fu Jeffrey Yang
- Division of Thoracic Surgery, Department of Surgery, Massachusetts General Hospital, Boston
- Mongan Institute Health Policy Research Center, Massachusetts General Hospital, Boston
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Coimbra MT, Francisco JATS, Freitas JC, Carvalho RV, Vilela SRB, Ribeiro CICD, Silvano JLCSL, Pedroso S, Almeida M, Martins LS, Malheiro J. Excess Mortality in Kidney and Kidney-Pancreas Transplant Recipients in the COVID-19 Pandemic in Portugal-A Cohort Study. Transpl Int 2023; 36:11655. [PMID: 37850156 PMCID: PMC10577594 DOI: 10.3389/ti.2023.11655] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/19/2023] [Indexed: 10/19/2023]
Abstract
The COVID-19 pandemic increased morbidity and mortality worldwide, particularly in the Kidney and Kidney-Pancreas Transplant Recipient (KTR/KPTR) population. Aiming at assessing the absolute and relative excess mortality (EM) in a Portuguese KTR/KPTR cohort, we conducted a retrospective observational study of two KTR/KPTRs cohorts: cohort 1 (P1; n = 2,179) between September/2012 and March/2020; cohort 2 (P2; n = 2067) between March/2020, and August/2022. A correlation between relative and absolute EM and age, sex, time from transplantation and cause of death was explored. A total of 145 and 84 deaths by all causes were observed in P1 and P2, respectively. The absolute EM in P2 versus P1 was 19.2 deaths (observed/expected mortality ratio 1.30, p = 0.006), and the relative EM was 1.47/1,000 person-months (95% CI 1.11-1.93, p = 0.006). Compared to the same period in the general population, the standardized mortality rate by age in P2 was 3.86 (95% CI 2.40-5.31), with a peak at 9.00 (95% CI 4.84-13.16) in P2C. The higher EM identified in this population was associated, mainly, with COVID-19 infection, with much higher values during the second seasonal COVID-19 peak when compared to the general population, despite generalized vaccination. These highlight the need for further preventive measures and improved therapies in these patients.
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Affiliation(s)
- Miguel T. Coimbra
- Department of Nephrology, Centro Hospitalar Universitário de Santo António, Porto, Portugal
- Department of Nephrology, Hospital Espírito Santo de Évora, Évora, Portugal
| | - José A. T. S. Francisco
- Department of Nephrology, Centro Hospitalar Universitário de Santo António, Porto, Portugal
- Department of Nephrology, Centro Hospitalar de Trás-os-Montes e Alto Douro, Vila Real, Portugal
| | - Joana C. Freitas
- Department of Nephrology, Centro Hospitalar Universitário de Santo António, Porto, Portugal
| | - Renata V. Carvalho
- Department of Nephrology, Centro Hospitalar Universitário de Santo António, Porto, Portugal
- Department of Nephrology, Hospital de Braga, Braga, Portugal
| | - Sara R. B. Vilela
- Department of Nephrology, Centro Hospitalar Universitário de Santo António, Porto, Portugal
- Department of Nephrology, Hospital Garcia de Orta, Almada, Portugal
| | | | | | - Sofia Pedroso
- Department of Nephrology, Centro Hospitalar Universitário de Santo António, Porto, Portugal
| | - Manuela Almeida
- Department of Nephrology, Centro Hospitalar Universitário de Santo António, Porto, Portugal
| | - La Salete Martins
- Department of Nephrology, Centro Hospitalar Universitário de Santo António, Porto, Portugal
| | - Jorge Malheiro
- Department of Nephrology, Centro Hospitalar Universitário de Santo António, Porto, Portugal
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Qi X, Yang Y, Gong B, Li Z, Liang D. Real-world effectiveness of azvudine for patients infected with the SARS-CoV-2 omicron subvariant BA.5 in an intensive care unit. J Thorac Dis 2023; 15:4925-4937. [PMID: 37868850 PMCID: PMC10586978 DOI: 10.21037/jtd-23-1093] [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: 07/15/2023] [Accepted: 09/13/2023] [Indexed: 10/24/2023]
Abstract
Background Azvudine (FNC) has been shown to be effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but data regarding the Omicron BA.5.1.3 subvariant are lacking. This retrospective analysis investigated the effectiveness and safety of FNC against the SARS-CoV-2 Omicron BA.5.1.3 subvariant in a real-world setting, utilizing data from a patient cohort at our institution. Methods Data were retrospectively collected from patients admitted to the intensive care unit (ICU) of Sanya Central Hospital during the Sanya outbreak (August 13 to September 7, 2022). The patients, all infected with the Omicron BA.5.1.3 subvariant, were selected based on predefined inclusion and exclusion criteria. The patients were classified as the FNC (azvudine 5 mg, qd + standard supportive treatment) and non-FNC (standard supportive treatment only) groups. Results The study comprised 13 patients, with 6 and 7 in the FNC and non-FNC groups, respectively. Baseline data, clinical features, and imaging manifestations were generally similar between the two groups. However, patients administered FNC demonstrated significantly lower levels of inflammatory indicators at baseline. Although there was no significant difference in the duration of ICU stay between the FNC and non-FNC groups, overall ICU stay appeared to be reduced in the FNC group. Conclusions FNC emerges as a feasible treatment against the Omicron BA.5.1.3 subvariant. It may reduce ICU stay and demonstrate a promising safety profile without major side effects or disruption to normal physiological parameters.
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Affiliation(s)
- Xiuping Qi
- Department of Clinical Pharmacy, Sanya Central Hospital (The Third People’s Hospital of Hainan Province), Sanya, China
| | - Yun Yang
- Department of Intensive Care Medicine, Sanya Central Hospital (The Third People’s Hospital of Hainan Province), Sanya, China
| | - Baoqiang Gong
- Department of Intensive Care Medicine, Sanya Central Hospital (The Third People’s Hospital of Hainan Province), Sanya, China
| | - Zhiwei Li
- Department of Radiology, Sanya Central Hospital (The Third People’s Hospital of Hainan Province), Sanya, China
| | - Dong Liang
- Department of Respiratory and Critical Care Medicine, Sanya Central Hospital (The Third People’s Hospital of Hainan Province), Sanya, China
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Andre M, Lau LS, Pokharel MD, Ramelow J, Owens F, Souchak J, Akkaoui J, Ales E, Brown H, Shil R, Nazaire V, Manevski M, Paul NP, Esteban-Lopez M, Ceyhan Y, El-Hage N. From Alpha to Omicron: How Different Variants of Concern of the SARS-Coronavirus-2 Impacted the World. BIOLOGY 2023; 12:1267. [PMID: 37759666 PMCID: PMC10525159 DOI: 10.3390/biology12091267] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/07/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023]
Abstract
SARS-CoV-2, the virus that causes COVID-19, is prone to mutations and the generation of genetic variants. Since its first outbreak in 2019, SARS-CoV-2 has continually evolved, resulting in the emergence of several lineages and variants of concern (VOC) that have gained more efficient transmission, severity, and immune evasion properties. The World Health Organization has given these variants names according to the letters of the Greek Alphabet, starting with the Alpha (B.1.1.7) variant, which emerged in 2020, followed by the Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529) variants. This review explores the genetic variation among different VOCs of SARS-CoV-2 and how the emergence of variants made a global impact on the pandemic.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Nazira El-Hage
- Herbert Wertheim College of Medicine, Biomedical Sciences Program Florida International University, Miami, FL 33199, USA; (M.A.); (L.-S.L.); (M.D.P.); (J.R.); (F.O.); (J.S.); (J.A.); (E.A.); (H.B.); (R.S.); (V.N.); (M.M.); (N.P.P.); (M.E.-L.); (Y.C.)
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Zahradka I, Petr V, Jakubov K, Modos I, Hruby F, Viklicky O. Early referring saved lives in kidney transplant recipients with COVID-19: a beneficial role of telemedicine. Front Med (Lausanne) 2023; 10:1252822. [PMID: 37795416 PMCID: PMC10546052 DOI: 10.3389/fmed.2023.1252822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/07/2023] [Indexed: 10/06/2023] Open
Abstract
Introduction There is a strong impetus for the use of telemedicine for boosting early detection rates and enabling early treatment and remote monitoring of COVID-19 cases, particularly in chronically ill patients such as kidney transplant recipients (KTRs). However, data regarding the effectiveness of this practice are lacking. Methods In this retrospective, observational study with prospective data gathering we analyzed the outcomes of all confirmed COVID-19 cases (n = 955) in KTRs followed at our center between March 1, 2020, and April 30, 2022. Risk factors of COVID-19 related mortality were analyzed with focus on the role of early referral to the transplant center, which enabled early initiation of treatment and remote outpatient management. This proactive approach was dependent on the establishment and use of a telemedicine system, which facilitated patient-physician communication and expedited diagnostics and treatment. The main exposure evaluated was early referral of KTRs to the transplantation center after confirmed or suspected COVID-19 infection. The primary outcome was the association of early referral to the transplantation center with the risk of death within 30 days following a COVID-19 diagnosis, evaluated by logistic regression. Results We found that KTRs who referred their illness to the transplant center late had a higher 30-day mortality (4.5 vs. 13.6%, p < 0.001). Thirty days mortality after the diagnosis of COVID-19 was independently associated with late referral to the transplant center (OR 2.08, 95% CI 1.08-3.98, p = 0.027), higher age (OR 1.09, 95% CI 1.05-1.13, p < 0.001), higher body mass index (OR 1.06, 95% CI 1.01-1.12, p = 0.03), and lower eGFR (OR 0.96, 95% CI 0.94-0.98, p < 0.001) in multivariable logistic regression. Furthermore, KTRs who contacted the transplant center late were older, had longer time from transplantation, lived farther from the center and presented with higher Charlson comorbidity index. Discussion A well-organized telemedicine program can help to protect KTRs during an infectious disease outbreak by facilitating pro-active management and close surveillance. Furthermore, these results can be likely extrapolated to other vulnerable populations, such as patients with chronic kidney disease, diabetes or autoimmune diseases requiring the use of immunosuppression.
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Affiliation(s)
- Ivan Zahradka
- Department of Nephrology, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Vojtech Petr
- Department of Nephrology, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Katarina Jakubov
- Department of Nephrology, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Istvan Modos
- Department of Information Technology, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Filip Hruby
- Department of Information Technology, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Ondrej Viklicky
- Department of Nephrology, Institute for Clinical and Experimental Medicine, Prague, Czechia
- Transplant Laboratory, Institute for Clinical and Experimental Medicine, Prague, Czechia
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Ko JY, Pham H, Anglin O, Chai SJ, Alden NB, Meek J, Anderson EJ, Weigel A, Kohrman A, Lynfield R, Rudin D, Barney G, Bennett NM, Billing LM, Sutton M, Talbot HK, Swain A, Havers FP, Taylor CA. Vaccination Status and Trends in Adult Coronavirus Disease 2019-Associated Hospitalizations by Race and Ethnicity: March 2020-August 2022. Clin Infect Dis 2023; 77:827-838. [PMID: 37132204 PMCID: PMC11019819 DOI: 10.1093/cid/ciad266] [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: 12/14/2022] [Revised: 04/14/2023] [Accepted: 04/28/2023] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND We sought to determine whether race/ethnicity disparities in severe coronavirus disease 2019 (COVID-19) outcomes persist in the era of vaccination. METHODS Population-based age-adjusted monthly rate ratios (RRs) of laboratory-confirmed COVID-19-associated hospitalizations were calculated among adult patients from the COVID-19-Associated Hospitalization Surveillance Network, March 2020 - August 2022 by race/ethnicity. Among randomly sampled patients July 2021 - August 2022, RRs for hospitalization, intensive care unit (ICU) admission, and in-hospital mortality were calculated for Hispanic, Black, American Indian/Alaskan Native (AI/AN), and Asian/Pacific Islander (API) persons vs White persons. RESULTS Based on data from 353 807 patients, hospitalization rates were higher among Hispanic, Black, and AI/AN vs White persons March 2020 - August 2022, yet the magnitude declined over time (for Hispanic persons, RR = 6.7; 95% confidence interval [CI], 6.5-7.1 in June 2020 vs RR < 2.0 after July 2021; for AI/AN persons, RR = 8.4; 95% CI, 8.2-8.7 in May 2020 vs RR < 2.0 after March 2022; and for Black persons RR = 5.3; 95% CI, 4.6-4.9 in July 2020 vs RR < 2.0 after February 2022; all P ≤ .001). Among 8706 sampled patients July 2021 - August 2022, hospitalization and ICU admission RRs were higher for Hispanic, Black, and AI/AN patients (range for both, 1.4-2.4) and lower for API (range for both, 0.6-0.9) vs White patients. All other race and ethnicity groups had higher in-hospital mortality rates vs White persons (RR range, 1.4-2.9). CONCLUSIONS Race/ethnicity disparities in COVID-19-associated hospitalizations declined but persist in the era of vaccination. Developing strategies to ensure equitable access to vaccination and treatment remains important.
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Affiliation(s)
- Jean Y Ko
- Centers for Disease Control and Prevention COVID-19 Response, Atlanta, Georgia, USA
- US Public Health Service Commissioned Corps, Rockville, Maryland, USA
| | - Huong Pham
- Centers for Disease Control and Prevention COVID-19 Response, Atlanta, Georgia, USA
| | - Onika Anglin
- Centers for Disease Control and Prevention COVID-19 Response, Atlanta, Georgia, USA
| | - Shua J Chai
- California Emerging Infections Program, Oakland, California, USA
- Career Epidemiology Field Officer Program, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Nisha B Alden
- Colorado Department of Public Health and Environment, Denver, Colorado, USA
| | - James Meek
- Connecticut Emerging Infections Program, Yale School of Public Health, New Haven, Connecticut, USA
| | - Evan J Anderson
- Emory University School of Medicine, Atlanta, Georgia, USA
- Georgia Department of Public Health, Georgia Emerging Infections Program, Atlanta, Georgia, USA
- Atlanta Veterans Affairs Medical Center, Atlanta, Georgia, USA
| | - Andy Weigel
- Iowa Department of Public Health, Des Moines, Iowa, USA
| | - Alexander Kohrman
- Michigan Department of Health and Human Services, Lansing, Michigan, USA
| | - Ruth Lynfield
- Minnesota Department of Health, St. Paul, Minnesota, USA
| | - Dominic Rudin
- New Mexico Emerging Infections Program, Albuquerque, New Mexico, USA
| | - Grant Barney
- New York State Department of Health, Albany, New York, USA
| | - Nancy M Bennett
- University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | | | - Melissa Sutton
- Public Health Division, Oregon Health Authority, Portland, Oregon, USA
| | - H Keipp Talbot
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Ashley Swain
- Salt Lake County Health Department, Salt Lake City, Utah, USA
| | - Fiona P Havers
- Centers for Disease Control and Prevention COVID-19 Response, Atlanta, Georgia, USA
- US Public Health Service Commissioned Corps, Rockville, Maryland, USA
| | - Christopher A Taylor
- Centers for Disease Control and Prevention COVID-19 Response, Atlanta, Georgia, USA
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Yin C, Hu B, Li K, Liu X, Wang S, He R, Ding H, Jin M, Chen C. Clinical characteristics and prognostic nomograms of 12555 non-severe COVID-19 cases with Omicron infection in Shanghai. BMC Infect Dis 2023; 23:606. [PMID: 37716953 PMCID: PMC10504722 DOI: 10.1186/s12879-023-08582-5] [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: 05/02/2023] [Accepted: 09/04/2023] [Indexed: 09/18/2023] Open
Abstract
BACKGROUND Omicron variant of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has rapidly become a global threat to public health. Numerous asymptomatic and mild cases had been admitted in shelter hospitals to quickly win the fight against Omicron pandemic in Shanghai. However, little is known about influencing factors for deterioration and length of stay (LOS) in hospitals among these non-severe cases. METHODS This study included 12,555 non-severe cases with COVID-19 in largest shelter hospital of Shanghai, aiming to explore prognostic factors and build effective models for prediction of LOS. RESULTS Data showed that 75.0% of participants were initially asymptomatic. In addition, 94.6% were discharged within 10 days, only 0.3% with deterioration in hospitals. The multivariate analysis indicated that less comorbidities (OR = 1.792, P = 0.012) and booster vaccination (OR = 0.255, P = 0.015) was associated with the decreased risk of deterioration. Moreover, age (HR = 0.991, P < 0.001), number of symptoms (HR = 0.969, P = 0.005), time from diagnosis to admission (HR = 1.013, P = 0.001) and Cycle threshold (CT) values of N gene (HR = 1.081, P < 0.001) were significant factors associated with LOS. Based on these factors, a concise nomogram model for predicting patients discharged within 3 days or more than 10 days was built in the development cohort. In validation cohort, 0.75 and 0.73 of Areas under the curve (AUC) in nomograms, similar with AUC in models of simple machine learning, showed good performance in estimating LOS. CONCLUSION Collectively, this study not only provides important evidence to deeply understand clinical characteristics and risk factors of short-term prognosis in Shanghai Omicron outbreaks, but also offers a concise and effective nomogram model to predict LOS. Our findings will play critical roles in screening high-risk groups, providing advice on duration of quarantine and helping decision-makers with better preparation in outbreak of COVID-19.
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Affiliation(s)
- Chun Yin
- Department of Cardiology, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Department of Cardiology, the 902Nd Hospital of PLA Joint Service Support Force, Bengbu, China
| | - Bo Hu
- Department of Radiology, Air Force Hospital of Eastern Theater Command, Malujie Road, Nanjing, China
| | - Kunyan Li
- Department of Cardiology, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xian Liu
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, China
| | - Shuili Wang
- Department of Cardiology, the 902Nd Hospital of PLA Joint Service Support Force, Bengbu, China
| | - Rulin He
- Department of Cardiology, the 902Nd Hospital of PLA Joint Service Support Force, Bengbu, China
| | - Haibing Ding
- Department of Cardiology, the 902Nd Hospital of PLA Joint Service Support Force, Bengbu, China
| | - Mingpeng Jin
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Cheng Chen
- The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.
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Garg N, Kunamneni AS, Garg P, Sharma S, Sharma D, Kunamneni A. Antiviral Drugs and Vaccines for Omicron Variant: A Focused Review. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2023; 2023:6695533. [PMID: 37719798 PMCID: PMC10504046 DOI: 10.1155/2023/6695533] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/14/2023] [Accepted: 08/31/2023] [Indexed: 09/19/2023]
Abstract
The Omicron variant of concern (VOC) replaced the delta variant rapidly and became the predominant strain due to more mutations in spike protein and receptor-binding domain (RBD) enhancing its infectivity and binding affinity. The severity of the illness is less than that of the delta variant. Omicron is nonsusceptible to REGEN-COV™ and bamlanivimab with etesevimab. Drugs that are effective against the Omicron variant are oral antiviral drugs such as Paxlovid (nirmatrelvir/ritonavir), remdesivir, sotrovimab, and molnupiravir. The potency of sotrovimab is reduced to 3-fold against Omicron, and 8-fold reduction in potency with sotrovimab is found in a particular variant of Omicron with a R346K substitution in spike protein. There are neither clinical trials comparing the efficacy of these 4 therapies with each other nor any data on a combination of two or more therapies. The current recommendation for mild-moderate, nonhospitalized patients who are at a high risk of disease progression is to use Paxlovid as the first-line option. If Paxlovid is not available or cannot be administered due to drug interactions, then the next best choice is sotrovimab. The third choice is remdesivir if sotrovimab is also not available and molnupiravir is to be given if the other three options are not available or cannot be administered. For prevention, 2130 (cilgavimab) in combination with COV2-2196 (tixagevimab) has been effective against BA.2 only. LY-CoV1404 (bebtelovimab) is recently authorized as it is effective against all sublineages of the Omicron variant. Regarding vaccine efficacy (VE), the 3-dose VE with mRNA vaccines at 14-60 days was found to be 71.6%, and after 60 days, it is 47.4%. There is a 34-38-fold reduction of neutralizing activity with prebooster sera and a 19-fold reduction with booster sera for the Omicron variant. This probably explains the reason for worldwide breakthrough infections with the Omicron variant with waning immunity. The neutralizing antibody response against Omicron elicited by the bivalent vaccine is superior to that of the ancestral Wuhan strain, without any safety concerns. For future advances, the ribosome display technology can be applied for the generation of human single-chain fragment variable (scFv) antibodies from B cells of recovered patients against Omicron and other Coronavirus variants as they are easier and faster to produce and have high affinity and high specificity.
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Affiliation(s)
- Nidhi Garg
- Division of Infectious Diseases, Department of Internal Medicine, Mayo Clinic, Jacksonville, Florida, USA
| | | | - Pankaj Garg
- Department of Chemistry, GLA University, Mathura, India
| | - Sandeep Sharma
- Department of Medical Laboratory Science, Lovely Professional University, Phagwara, Punjab 144411, India
| | - Divakar Sharma
- Department of Microbiology, Lady Hardinge Medical College, New Delhi 110001, India
| | - Adinarayana Kunamneni
- Division of Infectious Diseases, Department of Internal Medicine, Mayo Clinic, Jacksonville, Florida, USA
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70
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Wong MS, Frochen S, Steers WN, Washington DL. Hospital Catchment Areas Characteristics and Geographic Regions Associated With Higher COVID-19 Veterans Health Administration Hospitalization During the Omicron Surge. JOURNAL OF PUBLIC HEALTH MANAGEMENT AND PRACTICE 2023; 29:E198-E207. [PMID: 37104066 PMCID: PMC10363212 DOI: 10.1097/phh.0000000000001745] [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] [Indexed: 04/28/2023]
Abstract
CONTEXT Surges in the ongoing coronavirus-19 (COVID-19) pandemic and accompanying increases in hospitalizations continue to strain hospital systems. Identifying hospital-level characteristics associated with COVID-19 hospitalization rates and clusters of hospitalization "hot spots" can help with hospital system planning and resource allocation. OBJECTIVE To identify (1) hospital catchment area-level characteristics associated with higher COVID-19 hospitalization rates and (2) geographic regions with high and low COVID-19 hospitalization rates across catchment areas during COVID-19 Omicron surge (December 20, 2021-April 3, 2022). DESIGN This observational study used Veterans Health Administration (VHA), US Health Resource & Services Administration's Area Health Resources File, and US Census data. We used multivariate regression to identified hospital catchment area-level characteristics associated with COVID-19 hospitalization rates. We used ESRI ArcMap's Getis-Ord Gi* statistic to identify catchment area clusters of hospitalization hot and cold spots. SETTING AND PARTICIPANTS VHA hospital catchment areas in the United States (n = 143). MAIN OUTCOME MEASURES Hospitalization rate. RESULTS Greater COVID-19 hospitalization was associated with serving more high hospitalization risk patients (34.2 hospitalizations/10 000 patients per 10-percentage point increase in high hospitalization risk patients; 95% confidence intervals [CI]: 29.4, 39.0), fewer patients new to VHA during the pandemic (-3.9, 95% CI: -6.2, -1.6), and fewer COVID vaccine-boosted patients (-5.2; 95% CI: -7.9, -2.5).We identified 2 hospitalization cold spots located in the Pacific Northwest and in the Great Lakes regions, and 2 hot spots in the Great Plains and Southeastern US regions. CONCLUSIONS Within VHA's nationally integrated health care system, catchment areas serving a larger high hospitalization risk patient population were associated with more Omicron-related hospitalizations, while serving more patients fully vaccinated and boosted for COVID-19 and new VHA users were associated with lower hospitalization. Hospital and health care system efforts to vaccinate patients, particularly high-risk patients, can potentially safeguard against pandemic surges.Hospitalization hot spots within VHA include states with a high burden of chronic disease in the Great Plains and Southeastern United States.
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Affiliation(s)
- Michelle S Wong
- VA HSR&D Center for the Study of Healthcare
Innovation, Implementation & Policy (CSHIIP), VA Greater Los Angeles Healthcare
System, Los Angeles, CA
| | - Stephen Frochen
- VA HSR&D Center for the Study of Healthcare
Innovation, Implementation & Policy (CSHIIP), VA Greater Los Angeles Healthcare
System, Los Angeles, CA
| | - W. Neil Steers
- VA HSR&D Center for the Study of Healthcare
Innovation, Implementation & Policy (CSHIIP), VA Greater Los Angeles Healthcare
System, Los Angeles, CA
| | - Donna L Washington
- VA HSR&D Center for the Study of Healthcare
Innovation, Implementation & Policy (CSHIIP), VA Greater Los Angeles Healthcare
System, Los Angeles, CA
- Division of General Internal Medicine and Health Services
Research, Department of Medicine, University of California Los Angeles Geffen School
of Medicine, Los Angeles, CA
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Ramasamy R. Overview of immunological & virological factors driving the evolution & global spread of SARS-CoV-2 variants. Indian J Med Res 2023; 158:257-268. [PMID: 37815068 PMCID: PMC10720969 DOI: 10.4103/ijmr.ijmr_2591_22] [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: 12/21/2022] [Indexed: 10/11/2023] Open
Abstract
The SARS-CoV-2, a highly infectious positive strand RNA virus first identified in December 2019, has produced multiple genetic variants that have rapidly and sequentially spread worldwide during the coronavirus disease 2019 (COVID-19) pandemic. Genetic changes in SARS-CoV-2 for greater infectivity, replication and transmission were selected during the early stages of the pandemic. More recently, after widespread infection and vaccination, SARS-CoV-2 variants that evade antigen-specific adaptive immunity, have begun to be selected. This article provides an overview of the molecular immunological and virological factors underlying the origin and global spread of important SARS-CoV-2 variant lineages.
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72
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Nyberg T, Bager P, Svalgaard IB, Bejko D, Bundle N, Evans J, Krause TG, McMenamin J, Mossong J, Mutch H, Omokanye A, Peralta-Santos A, Pinto-Leite P, Starrfelt J, Thelwall S, Veneti L, Whittaker R, Wood J, Pebody R, Presanis AM. A standardised protocol for relative SARS-CoV-2 variant severity assessment, applied to Omicron BA.1 and Delta in six European countries, October 2021 to February 2022. Euro Surveill 2023; 28:2300048. [PMID: 37676146 PMCID: PMC10486193 DOI: 10.2807/1560-7917.es.2023.28.36.2300048] [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: 01/19/2023] [Accepted: 05/21/2023] [Indexed: 09/08/2023] Open
Abstract
Several SARS-CoV-2 variants that evolved during the COVID-19 pandemic have appeared to differ in severity, based on analyses of single-country datasets. With decreased testing and sequencing, international collaborative studies will become increasingly important for timely assessment of the severity of new variants. Therefore, a joint WHO Regional Office for Europe and ECDC working group was formed to produce and pilot a standardised study protocol to estimate relative case-severity of SARS-CoV-2 variants during periods when two variants were co-circulating. The study protocol and its associated statistical analysis code was applied by investigators in Denmark, England, Luxembourg, Norway, Portugal and Scotland to assess the severity of cases with the Omicron BA.1 virus variant relative to Delta. After pooling estimates using meta-analysis methods (random effects estimates), the risk of hospital admission (adjusted hazard ratio (aHR) = 0.41; 95% confidence interval (CI): 0.31-0.54), admission to intensive care unit (aHR = 0.12; 95% CI: 0.05-0.27) and death (aHR = 0.31; 95% CI: 0.28-0.35) was lower for Omicron BA.1 compared with Delta cases. The aHRs varied by age group and vaccination status. In conclusion, this study demonstrates the feasibility of conducting variant severity analyses in a multinational collaborative framework and adds evidence for the reduced severity of the Omicron BA.1 variant.
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Affiliation(s)
- Tommy Nyberg
- MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom
| | | | | | | | - Nick Bundle
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Josie Evans
- Public Health Scotland, Glasgow, Scotland, United Kingdom
| | | | - Jim McMenamin
- Public Health Scotland, Glasgow, Scotland, United Kingdom
| | | | - Heather Mutch
- Public Health Scotland, Glasgow, Scotland, United Kingdom
| | - Ajibola Omokanye
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | | | | | | | - Simon Thelwall
- COVID-19 Vaccines and Epidemiology Division, UK Health Security Agency, London, United Kingdom
| | | | | | - John Wood
- Public Health Scotland, Glasgow, Scotland, United Kingdom
| | - Richard Pebody
- These authors contributed equally to this work and share last authorship
- World Health Organization Regional Office for Europe, Copenhagen, Denmark
| | - Anne M Presanis
- MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom
- These authors contributed equally to this work and share last authorship
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Shuai H, Chan JFW, Hu B, Chai Y, Yoon C, Liu H, Liu Y, Shi J, Zhu T, Hu JC, Hu YF, Hou Y, Huang X, Yuen TTT, Wang Y, Zhang J, Xia Y, Chen LL, Cai JP, Zhang AJ, Yuan S, Zhou J, Zhang BZ, Huang JD, Yuen KY, To KKW, Chu H. The viral fitness and intrinsic pathogenicity of dominant SARS-CoV-2 Omicron sublineages BA.1, BA.2, and BA.5. EBioMedicine 2023; 95:104753. [PMID: 37579626 PMCID: PMC10448076 DOI: 10.1016/j.ebiom.2023.104753] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Among the Omicron sublineages that have emerged, BA.1, BA.2, BA.5, and their related sublineages have resulted in the largest number of infections. While recent studies demonstrated that all Omicron sublineages robustly escape neutralizing antibody response, it remains unclear on whether these Omicron sublineages share any pattern of evolutionary trajectory on their replication efficiency and intrinsic pathogenicity along the respiratory tract. METHODS We compared the virological features, replication capacity of dominant Omicron sublineages BA.1, BA.2 and BA.5 in the human nasal epithelium, and characterized their pathogenicity in K18-hACE2, A129, young C57BL/6, and aged C57BL/6 mice. FINDINGS We found that BA.5 replicated most robustly, followed by BA.2 and BA.1, in the differentiated human nasal epithelium. Consistently, BA.5 infection resulted in higher viral gene copies, infectious viral titres and more abundant viral antigen expression in the nasal turbinates of the infected K18-hACE2 transgenic mice. In contrast, the Omicron sublineages are continuously attenuated in lungs of infected K18-hACE2 and C57BL/6 mice, leading to decreased pathogenicity. Nevertheless, lung manifestations remain severe in Omicron sublineages-infected A129 and aged C57BL/6 mice. INTERPRETATION Our results suggested that the Omicron sublineages might be gaining intrinsic replication fitness in the upper respiratory tract, therefore highlighting the importance of global surveillance of the emergence of hyper-transmissive Omicron sublineages. On the contrary, replication and intrinsic pathogenicity of Omicron is suggested to be further attenuated in the lower respiratory tract. Effective vaccination and other precautions should be in place to prevent severe infections in the immunocompromised populations at risk. FUNDING A full list of funding bodies that contributed to this study can be found in the Acknowledgements section.
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Affiliation(s)
- Huiping Shuai
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, China; and The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China; Guangzhou Laboratory, Guangdong Province, China
| | - Bingjie Hu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yue Chai
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Chaemin Yoon
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Huan Liu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yuanchen Liu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jialu Shi
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Tianrenzheng Zhu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jing-Chu Hu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Ye-Fan Hu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yuxin Hou
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Xiner Huang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Terrence Tsz-Tai Yuen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yang Wang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jinjin Zhang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yao Xia
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Lin-Lei Chen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jian-Piao Cai
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Anna Jinxia Zhang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Jie Zhou
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Bao-Zhong Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong Province, China
| | - Jian-Dong Huang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, China; and The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China; Guangzhou Laboratory, Guangdong Province, China
| | - Kelvin Kai-Wang To
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China; Guangzhou Laboratory, Guangdong Province, China
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China.
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Feng S, O'Brien A, Chen DY, Saeed M, Baker SC. SARS-CoV-2 nonstructural protein 6 from Alpha to Omicron: evolution of a transmembrane protein. mBio 2023; 14:e0068823. [PMID: 37477426 PMCID: PMC10470488 DOI: 10.1128/mbio.00688-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/10/2023] [Indexed: 07/22/2023] Open
Abstract
We recently reported that mutations in both the spike glycoprotein and nonstructural protein 6 (nsp6) were associated with attenuation of the SARS-CoV-2 Omicron BA.1 variant. While mutations in spike allow evasion of neutralizing antibodies and promote specific modes of viral entry, the role of nsp6 mutations in pathogenesis is less clear. Nsp6 is essential for modifying the endoplasmic reticulum and generating double-membrane vesicles, the site of viral RNA replication. To investigate the evolution of nsp6, we evaluated 91,596 high-confidence human SARS-CoV-2 whole-genome sequences across 19 variants and lineages. While nsp6 of early variants of concern, such as Alpha, Beta, and Gamma, carried a triple amino acid deletion (106-108, termed ΔSGF), the Delta, Epsilon, and Mu lineages retained the ancestral nsp6 sequence. For nsp6 in the emerging Omicron variants, we report a transition from an amino acid 105-107 ΔLSG deletion in BA.1 to increased dominance of the ΔSGF in BA.2 and subsequent lineages. Our findings indicate that deletion within nsp6 was independently selected in multiple lineages of SARS-CoV-2, both early and late in the pandemic. Analysis of SARS-CoV-2-related coronaviruses in bats and pangolins revealed nsp6 sequences similar to the ancestral SARS-CoV-2 virus, indicating that the deletion in nsp6 may be an adaptation to replication in humans. Analysis of nsp6 sequences from multiple coronaviruses predicts a multipass transmembrane protein with a conserved C-terminal domain. Monitoring and evaluating changes in nsp6 and other nonstructural proteins will contribute to our understanding of factors associated with the attenuation of pandemic coronaviruses. IMPORTANCE There is an ongoing need to evaluate genetic changes in SARS-CoV-2 for effects on transmission and pathogenesis. We recently reported an unexpected role for replicase component nsp6, in addition to changes in spike, in the attenuation of Omicron BA.1. In this commentary, we document a triple-amino-acid deletion in a predicted lumenal domain of nsp6 that was found in multiple, independent variants of SARS-CoV-2, including all recent Omicron lineages. Furthermore, we modeled the predicted structure of nsp6, implicating a multipass transmembrane architecture as conserved in members of the Coronaviridae family. This information can guide future studies investigating the role of nsp6 in the pathogenesis of existing and emerging coronaviruses.
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Affiliation(s)
- Shuchen Feng
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Chicago, Illinois, USA
| | - Amornrat O'Brien
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Chicago, Illinois, USA
| | - Da-Yuan Chen
- Department of Biochemistry and Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston, Massachusetts, USA
| | - Mohsan Saeed
- Department of Biochemistry and Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston, Massachusetts, USA
| | - Susan C. Baker
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Chicago, Illinois, USA
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75
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Vishwakarma N, Goud RB, Tirupattur MP, Katwa LC. The Eye of the Storm: Investigating the Long-Term Cardiovascular Effects of COVID-19 and Variants. Cells 2023; 12:2154. [PMID: 37681886 PMCID: PMC10486388 DOI: 10.3390/cells12172154] [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: 07/26/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023] Open
Abstract
COVID-19 had stormed through the world in early March of 2019, and on 5 May 2023, SARS-CoV-2 was officially declared to no longer be a global health emergency. The rise of new COVID-19 variants XBB.1.5 and XBB.1.16, a product of recombinant variants and sub-strains, has fueled a need for continued surveillance of the pandemic as they have been deemed increasingly infectious. Regardless of the severity of the variant, this has caused an increase in hospitalizations, a strain in resources, and a rise of concern for public health. In addition, there is a growing population of patients experiencing cardiovascular complications as a result of post-acute sequelae of COVID-19. This review aims to focus on what was known about SARS-CoV-2 and its past variants (Alpha, Delta, Omicron) and how the knowledge has grown today with new emerging variants, with an emphasis on cardiovascular complexities. We focus on the possible mechanisms that cause the observations of chronic cardiac conditions seen even after patients have recovered from the infection. Further understanding of these mechanisms will help to close the gap in knowledge on post-acute sequelae of COVID-19 and the differences between the effects of variants.
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Affiliation(s)
| | | | | | - Laxmansa C. Katwa
- Department of Physiology, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA; (N.V.); (R.B.G.); (M.P.T.)
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76
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Flisiak R, Zarębska-Michaluk D, Dobrowolska K, Rorat M, Rogalska M, Kryńska JA, Moniuszko-Malinowska A, Czupryna P, Kozielewicz D, Jaroszewicz J, Sikorska K, Bednarska A, Piekarska A, Rzymski P. Change in the Clinical Picture of Hospitalized Patients with COVID-19 between the Early and Late Period of Dominance of the Omicron SARS-CoV-2 Variant. J Clin Med 2023; 12:5572. [PMID: 37685639 PMCID: PMC10488127 DOI: 10.3390/jcm12175572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
This study aimed to compare the clinical picture of COVID-19 in the initial and later period of Omicron dominance and to identify populations still at risk. A retrospective comparison of the clinical data of 965 patients hospitalized during the early period of Omicron's dominance (EO, January-June 2022) with 897 patients from a later period (LO, July 2022-April 2023) from the SARSTer database was performed. Patients hospitalized during LO, compared to EO, were older, had a better clinical condition on admission, had a lower need for oxygen and mechanical ventilation, had less frequent lung involvement in imaging, and showed much faster clinical improvement. Moreover, the overall mortality during EO was 14%, higher than that in LO-9%. Despite the milder course of the disease, mortality exceeding 15% was similar in both groups among patients with lung involvement. The accumulation of risk factors such as an age of 60+, comorbidities, lung involvement, and oxygen saturation <90% resulted in a constant need for oxygen in 98% of patients, an 8% risk of mechanical ventilation, and a 30% mortality rate in the LO period. Multiple logistic regression revealed lower odds of death during the LO phase. Despite the milder course of infections caused by the currently dominant subvariants, COVID-19 prophylaxis is necessary in people over 60 years of age, especially those with comorbidities, and in the case of pneumonia and respiratory failure.
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Affiliation(s)
- Robert Flisiak
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, 15-540 Białystok, Poland; (R.F.); (M.R.); (J.A.K.)
| | - Dorota Zarębska-Michaluk
- Department of Infectious Diseases and Allergology, Jan Kochanowski University, 25-317 Kielce, Poland;
| | | | - Marta Rorat
- Department of Infectious Diseases and Hepatology, Wrocław Medical University, 51-149 Wrocław, Poland;
- Department of Forensic Medicine, Wrocław Medical University, 50-367 Wrocław, Poland
| | - Magdalena Rogalska
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, 15-540 Białystok, Poland; (R.F.); (M.R.); (J.A.K.)
| | - Justyna Anna Kryńska
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, 15-540 Białystok, Poland; (R.F.); (M.R.); (J.A.K.)
| | - Anna Moniuszko-Malinowska
- Department of Infectious Diseases and Neuroinfections, Medical University of Białystok, 15-809 Białystok, Poland; (A.M.-M.); (P.C.)
| | - Piotr Czupryna
- Department of Infectious Diseases and Neuroinfections, Medical University of Białystok, 15-809 Białystok, Poland; (A.M.-M.); (P.C.)
| | - Dorota Kozielewicz
- Department of Infectious Diseases and Hepatology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Toruń, Poland;
| | - Jerzy Jaroszewicz
- Department of Infectious Diseases and Hepatology, Medical University of Silesia in Katowice, 41-902 Bytom, Poland;
| | - Katarzyna Sikorska
- Division of Tropical and Parasitic Diseases, Faculty of Health Sciences, Medical University of Gdańsk, 80-210 Gdańsk, Poland;
| | - Agnieszka Bednarska
- Department of Adult’s Infectious Diseases, Medical University of Warsaw, Hospital for Infectious Diseases, 02-091 Warsaw, Poland;
| | - Anna Piekarska
- Department of Infectious Diseases and Hepatology, Medical University of Łódź, 90-419 Łódź, Poland;
| | - Piotr Rzymski
- Department of Environmental Medicine, Poznań University of Medical Sciences, 60-806 Poznań, Poland;
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Yang F, Tran TNA, Howerton E, Boni MF, Servadio JL. Benefits of near-universal vaccination and treatment access to manage COVID-19 burden in the United States. BMC Med 2023; 21:321. [PMID: 37620926 PMCID: PMC10463609 DOI: 10.1186/s12916-023-03025-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/08/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND As we continue the fourth year of the COVID-19 epidemic, SARS-CoV-2 infections still cause high morbidity and mortality in the United States. During 2020-2022, COVID-19 was one of the leading causes of death in the United States and by far the leading cause among infectious diseases. Vaccination uptake remains low despite this being an effective burden reducing intervention. The development of COVID-19 therapeutics provides hope for mitigating severe clinical outcomes. This modeling study examines combined strategies of vaccination and treatment to reduce the burden of COVID-19 epidemics over the next decade. METHODS We use a validated mathematical model to evaluate the reduction of incident cases, hospitalized cases, and deaths in the United States through 2033 under various levels of vaccination and treatment coverage. We assume that future seasonal transmission patterns for COVID-19 will be similar to those of influenza virus and account for the waning of infection-induced immunity and vaccine-induced immunity in a future with stable COVID-19 dynamics. Due to uncertainty in the duration of immunity following vaccination or infection, we consider three exponentially distributed waning rates, with means of 365 days (1 year), 548 days (1.5 years), and 730 days (2 years). We also consider treatment failure, including rebound frequency, as a possible treatment outcome. RESULTS As expected, universal vaccination is projected to eliminate transmission and mortality. Under current treatment coverage (13.7%) and vaccination coverage (49%), averages of 81,000-164,600 annual reported deaths, depending on duration of immunity, are expected by the end of this decade. Annual mortality in the United States can be reduced below 50,000 per year with 52-80% annual vaccination coverage and below 10,000 annual deaths with 59-83% annual vaccination coverage, depending on duration of immunity. Universal treatment reduces hospitalizations by 88.6% and deaths by 93.1% under current vaccination coverage. A reduction in vaccination coverage requires a comparatively larger increase in treatment coverage in order for hospitalization and mortality levels to remain unchanged. CONCLUSIONS Adopting universal vaccination and universal treatment goals in the United States will likely lead to a COVID-19 mortality burden below 50,000 deaths per year, a burden comparable to that of influenza virus.
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Affiliation(s)
- Fuhan Yang
- Department of Biology and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Thu Nguyen-Anh Tran
- Department of Biology and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Emily Howerton
- Department of Biology and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Maciej F Boni
- Department of Biology and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Joseph L Servadio
- Department of Biology and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA.
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Kojima N, Adams K, Self WH, Gaglani M, McNeal T, Ghamande S, Steingrub JS, Shapiro NI, Duggal A, Busse LW, Prekker ME, Peltan ID, Brown SM, Hager DN, Ali H, Gong MN, Mohamed A, Exline MC, Khan A, Wilson JG, Qadir N, Chang SY, Ginde AA, Withers CA, Mohr NM, Mallow C, Martin ET, Lauring AS, Johnson NJ, Casey JD, Stubblefield WB, Gibbs KW, Kwon JH, Baughman A, Chappell JD, Hart KW, Jones ID, Rhoads JP, Swan SA, Womack KN, Zhu Y, Surie D, McMorrow ML, Patel MM, Tenforde MW. Changing Severity and Epidemiology of Adults Hospitalized With Coronavirus Disease 2019 (COVID-19) in the United States After Introduction of COVID-19 Vaccines, March 2021-August 2022. Clin Infect Dis 2023; 77:547-557. [PMID: 37255285 PMCID: PMC10526883 DOI: 10.1093/cid/ciad276] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Indexed: 06/01/2023] Open
Abstract
INTRODUCTION Understanding the changing epidemiology of adults hospitalized with coronavirus disease 2019 (COVID-19) informs research priorities and public health policies. METHODS Among adults (≥18 years) hospitalized with laboratory-confirmed, acute COVID-19 between 11 March 2021, and 31 August 2022 at 21 hospitals in 18 states, those hospitalized during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron-predominant period (BA.1, BA.2, BA.4/BA.5) were compared to those from earlier Alpha- and Delta-predominant periods. Demographic characteristics, biomarkers within 24 hours of admission, and outcomes, including oxygen support and death, were assessed. RESULTS Among 9825 patients, median (interquartile range [IQR]) age was 60 years (47-72), 47% were women, and 21% non-Hispanic Black. From the Alpha-predominant period (Mar-Jul 2021; N = 1312) to the Omicron BA.4/BA.5 sublineage-predominant period (Jun-Aug 2022; N = 1307): the percentage of patients who had ≥4 categories of underlying medical conditions increased from 11% to 21%; those vaccinated with at least a primary COVID-19 vaccine series increased from 7% to 67%; those ≥75 years old increased from 11% to 33%; those who did not receive any supplemental oxygen increased from 18% to 42%. Median (IQR) highest C-reactive protein and D-dimer concentration decreased from 42.0 mg/L (9.9-122.0) to 11.5 mg/L (2.7-42.8) and 3.1 mcg/mL (0.8-640.0) to 1.0 mcg/mL (0.5-2.2), respectively. In-hospital death peaked at 12% in the Delta-predominant period and declined to 4% during the BA.4/BA.5-predominant period. CONCLUSIONS Compared to adults hospitalized during early COVID-19 variant periods, those hospitalized during Omicron-variant COVID-19 were older, had multiple co-morbidities, were more likely to be vaccinated, and less likely to experience severe respiratory disease, systemic inflammation, coagulopathy, and death.
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Affiliation(s)
- Noah Kojima
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Katherine Adams
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Wesley H Self
- Department of Emergency Medicine and Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Manjusha Gaglani
- Department of Pediatrics, Baylor Scott & White Health and Texas A&M University College of Medicine, Temple and Dallas, Texas, USA
| | - Tresa McNeal
- Department of Medical Education, Baylor Scott & White Health, Texas A&M University College of Medicine, Temple, Texas, USA
| | - Shekhar Ghamande
- Department of Medical Education, Baylor Scott & White Health, Texas A&M University College of Medicine, Temple, Texas, USA
| | - Jay S Steingrub
- Department of Medicine, Baystate Medical Center, Springfield, Massachusetts, USA
| | - Nathan I Shapiro
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Abhijit Duggal
- Department of Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | | | - Matthew E Prekker
- Department of Emergency Medicine and Medicine, Hennepin County Medical Center, Minneapolis, Minnesota, USA
| | - Ithan D Peltan
- Department of Medicine, Intermountain Medical Center, Murray, Utah and University of Utah, Salt Lake City, Utah, USA
| | - Samuel M Brown
- Department of Medicine, Intermountain Medical Center, Murray, Utah and University of Utah, Salt Lake City, Utah, USA
| | - David N Hager
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Harith Ali
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michelle N Gong
- Department of Medicine, Montefiore Health System, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Amira Mohamed
- Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Matthew C Exline
- Department of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Akram Khan
- Department of Medicine, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Jennifer G Wilson
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Nida Qadir
- Department of Medicine, University of California-Los Angeles, Los Angeles, California, USA
| | - Steven Y Chang
- Department of Medicine, University of California-Los Angeles, Los Angeles, California, USA
| | - Adit A Ginde
- Department of Emergency Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Cori A Withers
- Department of Emergency Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Nicholas M Mohr
- Department of Emergency Medicine, University of Iowa, Iowa City, Iowa, USA
| | | | - Emily T Martin
- School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Adam S Lauring
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Nicholas J Johnson
- Department of Emergency Medicine and Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, Washington, USA
| | - Jonathan D Casey
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - William B Stubblefield
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kevin W Gibbs
- Department of Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jennie H Kwon
- Department of Medicine, Washington University, St. Louis, Missouri, USA
| | - Adrienne Baughman
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - James D Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kimberly W Hart
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Ian D Jones
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jillian P Rhoads
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Sydney A Swan
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kelsey N Womack
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Yuwei Zhu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Diya Surie
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Meredith L McMorrow
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Manish M Patel
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mark W Tenforde
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Loguercio S, Calverley BC, Wang C, Shak D, Zhao P, Sun S, Budinger GS, Balch WE. Understanding the host-pathogen evolutionary balance through Gaussian process modeling of SARS-CoV-2. PATTERNS (NEW YORK, N.Y.) 2023; 4:100800. [PMID: 37602209 PMCID: PMC10436005 DOI: 10.1016/j.patter.2023.100800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/22/2023] [Accepted: 06/22/2023] [Indexed: 08/22/2023]
Abstract
We have developed a machine learning (ML) approach using Gaussian process (GP)-based spatial covariance (SCV) to track the impact of spatial-temporal mutational events driving host-pathogen balance in biology. We show how SCV can be applied to understanding the response of evolving covariant relationships linking the variant pattern of virus spread to pathology for the entire SARS-CoV-2 genome on a daily basis. We show that GP-based SCV relationships in conjunction with genome-wide co-occurrence analysis provides an early warning anomaly detection (EWAD) system for the emergence of variants of concern (VOCs). EWAD can anticipate changes in the pattern of performance of spread and pathology weeks in advance, identifying signatures destined to become VOCs. GP-based analyses of variation across entire viral genomes can be used to monitor micro and macro features responsible for host-pathogen balance. The versatility of GP-based SCV defines starting point for understanding nature's evolutionary path to complexity through natural selection.
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Affiliation(s)
| | - Ben C. Calverley
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | - Chao Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | - Daniel Shak
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | - Pei Zhao
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | - Shuhong Sun
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | - G.R. Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, IL, USA
| | - William E. Balch
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
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80
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Nunes SLP, de França CA, Rocha GD, Oliveira SADS, Freitas MR, da Silva EO, Coutinho KS, Jerônimo AS, de Lima GB, de Lima RE, Bezerra MF, Dezordi FZ, Paiva MHS, Wallau GDL, de Souza CDF, Armstrong ADC, do Carmo RF. Assessment of clinical characteristics and viral load in individuals infected by Delta and Omicron variants of SARS-CoV-2. Heliyon 2023; 9:e18994. [PMID: 37600420 PMCID: PMC10432967 DOI: 10.1016/j.heliyon.2023.e18994] [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: 02/09/2023] [Revised: 07/26/2023] [Accepted: 08/04/2023] [Indexed: 08/22/2023] Open
Abstract
In late 2021, a new variant of SARS-CoV-2 called Omicron emerged, replacing Delta worldwide. Although it has been associated with a lower risk of hospitalization and severe forms of COVID-19, there is little evidence of its relationship with specific symptoms and viral load. The aim of this study was to verify the relationship between Delta and Omicron variants of concern, viral load, and the occurrence of symptoms in individuals with COVID-19. Nasopharyngeal swab samples were collected and sequenced from patients with COVID-19 from the Northeast Region of Brazil between August 2021 and March 2022. The results showed a gradual replacement of the Delta variant by the Omicron variant during the study period. A total of 316 samples (157 Delta and 159 Omicron) were included. There was a higher prevalence of symptoms in Delta-infected individuals, such as coryza, olfactory and taste disturbances, headache, and myalgia. There was no association between viral load and the variants analyzed. The results reported here contribute to the understanding of the symptoms associated with the Delta and Omicron variants in individuals affected by COVID-19.
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Affiliation(s)
- Sávio Luiz Pereira Nunes
- Postgraduate Program in Applied Cellular and Molecular Biology, University of Pernambuco (UPE), Recife, Pernambuco, Brazil
| | - Chirles Araújo de França
- Multi-User Research Laboratory (LAMUPE), Dr. Washington Antônio de Barros Hospital – EBSERH/UNIVASF, Petrolina, Pernambuco, Brazil
| | - Gabriela Dias Rocha
- Postgraduate Program in Applied Cellular and Molecular Biology, University of Pernambuco (UPE), Recife, Pernambuco, Brazil
- Multi-User Research Laboratory (LAMUPE), Dr. Washington Antônio de Barros Hospital – EBSERH/UNIVASF, Petrolina, Pernambuco, Brazil
| | - Samily Aquino de Sá Oliveira
- Multi-User Research Laboratory (LAMUPE), Dr. Washington Antônio de Barros Hospital – EBSERH/UNIVASF, Petrolina, Pernambuco, Brazil
| | - Mariana Ramos Freitas
- Multi-User Research Laboratory (LAMUPE), Dr. Washington Antônio de Barros Hospital – EBSERH/UNIVASF, Petrolina, Pernambuco, Brazil
| | - Eliane Oliveira da Silva
- VIII Regional Health Management, State Health Secretariat of Pernambuco, Petrolina, Pernambuco, Brazil
| | - Katia Sampaio Coutinho
- VIII Regional Health Management, State Health Secretariat of Pernambuco, Petrolina, Pernambuco, Brazil
| | - Aline Silva Jerônimo
- VIII Regional Health Management, State Health Secretariat of Pernambuco, Petrolina, Pernambuco, Brazil
| | - Gustavo Barbosa de Lima
- Technology Platforms Center (NPT), Aggeu Magalhães Institute (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Raul Emídio de Lima
- Technology Platforms Center (NPT), Aggeu Magalhães Institute (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Matheus Filgueira Bezerra
- Departament of Microbiology, Aggeu Magalhães Institute (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Filipe Zimmer Dezordi
- Departament of Entomology, Aggeu Magalhães Institute (IAM)- FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
- Bioinformatics Center (NBI), Aggeu Magalhães Institute (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Marcelo Henrique Santos Paiva
- Departament of Entomology, Aggeu Magalhães Institute (IAM)- FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
- Life Sciences Center, Federal University of Pernambuco (UFPE), Caruaru, Pernambuco, Brazil
| | - Gabriel da Luz Wallau
- Departament of Entomology, Aggeu Magalhães Institute (IAM)- FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
- Bioinformatics Center (NBI), Aggeu Magalhães Institute (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases, Hamburg, Germany
| | | | - Anderson da Costa Armstrong
- Collegiate of Medicine, Federal University of the São Francisco Valley – UNIVASF, Petrolina, Pernambuco, Brazil
| | - Rodrigo Feliciano do Carmo
- Postgraduate Program in Applied Cellular and Molecular Biology, University of Pernambuco (UPE), Recife, Pernambuco, Brazil
- Collegiate of Pharmaceutical Sciences, Federal University of the São Francisco Valley – UNIVASF, Petrolina, Pernambuco, Brazil
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81
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Yao Y, Cui Y, Gao X, Qian Y, Hu B. Contamination of personal protective equipment and environmental surfaces in Fangcang shelter hospitals. Am J Infect Control 2023; 51:926-930. [PMID: 36435405 PMCID: PMC9683851 DOI: 10.1016/j.ajic.2022.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Fangcang shelter hospitals emerged as a new public health concept after COVID-19. Data regarding contamination of Fangcang shelter environments remains scarce. This study aims to investigate the extent of SARS-CoV-2 contamination on personal protective equipment and surfaces in Fangcang hospitals. METHODS Between March and May 2022, during wave of omicron variant, a prospective study was conducted in 2 Fangcang hospitals in Shanghai, China. Swabs of personal protective equipment worn and environmental surfaces of contaminated areas, doffing rooms, and potentially contaminated areas were collected. SARS-CoV-2 RNA was detected by reverse transcription quantitative polymerase chain reaction. If viral RNA was detected, sampling was repeated after cleaning and disinfection. RESULTS A total of 602 samples were collected. 13.3% of the personal protective equipment were contaminated. Positive rate was higher in the contaminated areas (48.4%) than in the doffing rooms (11.7%) and the potentially contaminated areas (0; P<.05). Contamination was highest in patient occupied areas (67.5%). After cleaning, samples taken at previously contaminated surfaces are all negative. CONCLUSIONS SARS-CoV-2 RNA contamination is prevalent in Fangcang hospitals and healthcare workers are under risk of infection. Potentially contaminated areas and surfaces after cleaning and disinfection are negative, underlying the importance of infection control policy.
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Affiliation(s)
- Yumeng Yao
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yangwen Cui
- Department of Infection Control and Management, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaodong Gao
- Department of Infection Control and Management, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yiyi Qian
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Bijie Hu
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China; Department of Infection Control and Management, Zhongshan Hospital, Fudan University, Shanghai, China.
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82
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Pascall DJ, Vink E, Blacow R, Bulteel N, Campbell A, Campbell R, Clifford S, Davis C, da Silva Filipe A, El Sakka N, Fjodorova L, Forrest R, Goldstein E, Gunson R, Haughney J, Holden MTG, Honour P, Hughes J, James E, Lewis T, MacLean O, McHugh M, Mollett G, Nyberg T, Onishi Y, Parcell B, Ray S, Robertson DL, Seaman SR, Shabaan S, Shepherd JG, Smollett K, Templeton K, Wastnedge E, Wilkie C, Williams T, Thomson EC. Directions of change in intrinsic case severity across successive SARS-CoV-2 variant waves have been inconsistent. J Infect 2023; 87:128-135. [PMID: 37270070 PMCID: PMC10234362 DOI: 10.1016/j.jinf.2023.05.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 03/27/2023] [Accepted: 05/24/2023] [Indexed: 06/05/2023]
Abstract
OBJECTIVES To determine how the intrinsic severity of successively dominant SARS-CoV-2 variants changed over the course of the pandemic. METHODS A retrospective cohort analysis in the NHS Greater Glasgow and Clyde (NHS GGC) Health Board. All sequenced non-nosocomial adult COVID-19 cases in NHS GGC with relevant SARS-CoV-2 lineages (B.1.177/Alpha, Alpha/Delta, AY.4.2 Delta/non-AY.4.2 Delta, non-AY.4.2 Delta/Omicron, and BA.1 Omicron/BA.2 Omicron) during analysis periods were included. Outcome measures were hospital admission, ICU admission, or death within 28 days of positive COVID-19 test. We report the cumulative odds ratio; the ratio of the odds that an individual experiences a severity event of a given level vs all lower severity levels for the resident and the replacement variant after adjustment. RESULTS After adjustment for covariates, the cumulative odds ratio was 1.51 (95% CI: 1.08-2.11) for Alpha versus B.1.177, 2.09 (95% CI: 1.42-3.08) for Delta versus Alpha, 0.99 (95% CI: 0.76-1.27) for AY.4.2 Delta versus non-AY.4.2 Delta, 0.49 (95% CI: 0.22-1.06) for Omicron versus non-AY.4.2 Delta, and 0.86 (95% CI: 0.68-1.09) for BA.2 Omicron versus BA.1 Omicron. CONCLUSIONS The direction of change in intrinsic severity between successively emerging SARS-CoV-2 variants was inconsistent, reminding us that the intrinsic severity of future SARS-CoV-2 variants remains uncertain.
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Affiliation(s)
- David J Pascall
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, United Kingdom; Joint Universities Pandemic and Epidemiological Research (JUNIPER) Consortium, United Kingdom.
| | - Elen Vink
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom; NHS Lothian, Edinburgh EH1 3EG, United Kingdom.
| | - Rachel Blacow
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom; NHS Greater Glasgow and Clyde, Glasgow G12 0XH, United Kingdom.
| | | | | | | | | | - Chris Davis
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | | | | | | | - Emily Goldstein
- NHS Greater Glasgow and Clyde, Glasgow G12 0XH, United Kingdom.
| | - Rory Gunson
- NHS Greater Glasgow and Clyde, Glasgow G12 0XH, United Kingdom.
| | - John Haughney
- NHS Greater Glasgow and Clyde, Glasgow G12 0XH, United Kingdom.
| | - Matthew T G Holden
- Public Health Scotland, Edinburgh EH12 9EB, United Kingdom; School of Medicine, University of St Andrews, St Andrews KY16 9TF, United Kingdom.
| | | | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | | | - Tim Lewis
- NHS Lothian, Edinburgh EH1 3EG, United Kingdom.
| | - Oscar MacLean
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | | | - Guy Mollett
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom; NHS Greater Glasgow and Clyde, Glasgow G12 0XH, United Kingdom.
| | - Tommy Nyberg
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, United Kingdom.
| | | | - Ben Parcell
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.
| | - Surajit Ray
- School of Mathematics and Statistics, University of Glasgow, Glasgow G12 8TA, United Kingdom.
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | - Shaun R Seaman
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, United Kingdom.
| | - Sharif Shabaan
- Public Health Scotland, Edinburgh EH12 9EB, United Kingdom.
| | - James G Shepherd
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | - Katherine Smollett
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | | | | | - Craig Wilkie
- School of Mathematics and Statistics, University of Glasgow, Glasgow G12 8TA, United Kingdom.
| | - Thomas Williams
- NHS Lothian, Edinburgh EH1 3EG, United Kingdom; Royal Hospital for Children and Young People, University of Edinburgh, Edinburgh EH16 4TJ, United Kingdom.
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom; NHS Greater Glasgow and Clyde, Glasgow G12 0XH, United Kingdom; London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom.
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83
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Zhang Y, Huang Z, Zhuang S, Wu J, Lan M, Guo H, Chen J, Ou S, Zhang Y, Yuan Q. Effectiveness of first and second boost COVID-19 vaccination in healthy adults during BA.5.2/BF.7 surge in China. Hum Vaccin Immunother 2023; 19:2246483. [PMID: 37674298 PMCID: PMC10486280 DOI: 10.1080/21645515.2023.2246483] [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: 06/19/2023] [Revised: 07/26/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023] Open
Abstract
With the development of the SARS-CoV-2 pandemic, there have been doubts about the necessity of vaccine boosters for healthy adults. However, due to the lack of relevant evidence, current research is unable to provide reliable medical advice for COVID-19 boost in healthy adults. We conducted a retrospective observational study to evaluate the effectiveness of different COVID-19 vaccination regimens by investigating the SARS-CoV-2 infection status of healthy donors in Southeast China. From December 2022 to February 2023, 737 healthy adult blood donors were analyzed. Results showed that any COVID-19 vaccine boosts reduced the risk of Omicron BA.5.2/BF.7 infection compared to only receiving prime vaccination (rVE = 16%, 95%CI = 4, 27%). The second boost further enhanced vaccine effectiveness compared to the received first booster (rVE = 39%, 95%CI = 16, 55%). Through retrospective observation of healthy adults during the BA.5.2/BF.7 surge in China, we found that boost vaccinations significantly reduce the risk of SARS-CoV-2 infection and disease. Findings show healthy adults benefit from boost vaccinations, even if not at high-risk for severe COVID-19.
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Affiliation(s)
- Yongchang Zhang
- Molecular Biology Research Laboratory, Xiamen Blood Service, Xiamen, Fujian, P.R. China
| | - Zehong Huang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen, Fujian, P.R. China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University, Xiamen, Fujian, P.R. China
| | - Shucheng Zhuang
- Molecular Biology Research Laboratory, Xiamen Blood Service, Xiamen, Fujian, P.R. China
| | - Jiahuang Wu
- Molecular Biology Research Laboratory, Xiamen Blood Service, Xiamen, Fujian, P.R. China
| | - Miaolin Lan
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen, Fujian, P.R. China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University, Xiamen, Fujian, P.R. China
| | - Huilin Guo
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen, Fujian, P.R. China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University, Xiamen, Fujian, P.R. China
| | - Jijin Chen
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen, Fujian, P.R. China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University, Xiamen, Fujian, P.R. China
| | - Shanhai Ou
- Molecular Biology Research Laboratory, Xiamen Blood Service, Xiamen, Fujian, P.R. China
| | - Yali Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen, Fujian, P.R. China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University, Xiamen, Fujian, P.R. China
| | - Quan Yuan
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen, Fujian, P.R. China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University, Xiamen, Fujian, P.R. China
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84
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Li X, Liu H, Gao L, Sherchan SP, Zhou T, Khan SJ, van Loosdrecht MCM, Wang Q. Wastewater-based epidemiology predicts COVID-19-induced weekly new hospital admissions in over 150 USA counties. Nat Commun 2023; 14:4548. [PMID: 37507407 PMCID: PMC10382499 DOI: 10.1038/s41467-023-40305-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Although the coronavirus disease (COVID-19) emergency status is easing, the COVID-19 pandemic continues to affect healthcare systems globally. It is crucial to have a reliable and population-wide prediction tool for estimating COVID-19-induced hospital admissions. We evaluated the feasibility of using wastewater-based epidemiology (WBE) to predict COVID-19-induced weekly new hospitalizations in 159 counties across 45 states in the United States of America (USA), covering a population of nearly 100 million. Using county-level weekly wastewater surveillance data (over 20 months), WBE-based models were established through the random forest algorithm. WBE-based models accurately predicted the county-level weekly new admissions, allowing a preparation window of 1-4 weeks. In real applications, periodically updated WBE-based models showed good accuracy and transferability, with mean absolute error within 4-6 patients/100k population for upcoming weekly new hospitalization numbers. Our study demonstrated the potential of using WBE as an effective method to provide early warnings for healthcare systems.
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Affiliation(s)
- Xuan Li
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Huan Liu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Li Gao
- South East Water, 101 Wells Street, Frankston, VIC, 3199, Australia
| | - Samendra P Sherchan
- Department of Biology, Morgan State University, Baltimore, MD, USA
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Ting Zhou
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Stuart J Khan
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, the Netherlands
| | - Qilin Wang
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
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85
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Wolff ASB, Hansen L, Grytaas MA, Oftedal BE, Breivik L, Zhou F, Hufthammer KO, Sjøgren T, Olofsson JS, Trieu MC, Meager A, Jørgensen AP, Lima K, Greve-Isdahl Mohn K, Langeland N, Cox RJ, Husebye ES. Vaccination prevents severe COVID-19 outcome in patients with neutralizing type 1 interferon autoantibodies. iScience 2023; 26:107084. [PMID: 37346050 PMCID: PMC10251722 DOI: 10.1016/j.isci.2023.107084] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/05/2023] [Accepted: 06/06/2023] [Indexed: 06/23/2023] Open
Abstract
A hallmark of patients with autoimmune polyendocrine syndrome type 1 (APS-1) is serological neutralizing autoantibodies against type 1 interferons (IFN-I). The presence of these antibodies has been associated with severe course of COVID-19. The aims of this study were to investigate SARS-CoV-2 vaccine tolerability and immune responses in a large cohort of patients with APS-1 (N = 33) and how these vaccinated patients coped with subsequent infections. We report that adult patients with APS-1 were able to mount adequate SARS-CoV-2 spike-specific antibody responses after vaccination and observed no signs of decreased tolerability. Compared with age- and gender-matched healthy controls, patients with APS-1 had considerably lower peak antibody responses resembling elderly persons, but antibody decline was more rapid in the elderly. We demonstrate that vaccination protected patients with APS-1 from severe illness when infected with SARS-CoV-2 virus, overriding the systemic danger of IFN-I autoantibodies observed in previous studies.
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Affiliation(s)
- Anette S B Wolff
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Lena Hansen
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Influenza Centre, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | | | - Bergithe E Oftedal
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Lars Breivik
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Fan Zhou
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Influenza Centre, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Karl Ove Hufthammer
- Centre for Clinical Research, Haukeland University Hospital, 5021 Bergen, Norway
| | - Thea Sjøgren
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Jan Stefan Olofsson
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Influenza Centre, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Mai Chi Trieu
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Influenza Centre, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Anthony Meager
- Biotherapeutics Group, The National Institute for Biological Standards and Control, South Mimms, Potters Bar EN6 3QG, UK
| | - Anders P Jørgensen
- Department of Endocrinology, Oslo University Hospital, 0372 Oslo, Norway
| | - Kari Lima
- Department of Paediatric Medicine, Oslo University Hospital, 0372 Oslo, Norway
- Department of Endocrinology, Akershus University Hospital, 1478 Lørenskog, Norway
| | - Kristin Greve-Isdahl Mohn
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
- Influenza Centre, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Nina Langeland
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Rebecca Jane Cox
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Influenza Centre, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Eystein S Husebye
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
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Wei YY, Wang RR, Zhang DW, Chen SH, Tan YY, Zhang WT, Han MF, Fei GH. Differential Characteristics of Patients for Hospitalized Severe COVID-19 Infected by the Omicron Variants and Wild Type of SARS-CoV-2 in China. J Inflamm Res 2023; 16:3063-3078. [PMID: 37497065 PMCID: PMC10368135 DOI: 10.2147/jir.s420721] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/12/2023] [Indexed: 07/28/2023] Open
Abstract
Background As multiple mutations of SARS-Cov-2 exist, there are now many viral variants with regional differences in distribution. The clinical characteristics of patients hospitalized with the virus also vary significantly, with those of the Omicron variants being strikingly different from those of the earliest wild-type variant. However, comprehensive data on this subject is lacking. It is therefore crucial to explore these differences to develop better clinical strategies for the management of COVID-19. Methods A total of 554 confirmed COVID-19 cases in China were clinically classified as mild, moderate, severe, and critical according to their diagnoses and treatment plans. We compared the demographics and clinical characteristics of patients infected with the Omicron vs wild-type strains, between severe and non-severe cases. Bacterial co-infections with SARS-CoV-2 and correlation between inflammatory factors and T cells were analyzed. Results Compared to the wild-type cases, the severe Omicron cases were older (median age 48.36 vs 73.24), and had more upper-respiratory symptoms and comorbidities. Decreased leukocyte counts were less pronounced, although more instances of significantly decreased CD4+ and CD8+ T-cell counts, elevated infection-related biomarkers (eg procalcitonin and C-reactive protein), and abnormal coagulation factors (including increased D-dimer and fibrinogen levels) were detected in the severe Omicron cases. The mean length of hospital stay was significantly shorter in the severe Omicron cases. CD4+ and CD8+ T cell numbers were negatively correlated with neutrophil-to-lymphocyte ratios, as well as serum interleukin-6, procalcitonin, and C-reactive protein levels. Conclusion There were significant clinical differences between patients hospitalized with severe cases of Omicron- variant COVID-19 vs wild-type. The Omicron cases tended to be older and had more upper respiratory tract symptoms, comorbidities and bacterial co-infections. Elevated levels of inflammatory cytokines with T-cell depletion correlated with poor disease progression and prognosis. We hope these data provide a theoretical basis for future integrated prevention and control plans for COVID-19.
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Affiliation(s)
- Yuan-Yuan Wei
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, Anhui, 230022, People’s Republic of China
| | - Rui-Rui Wang
- Department of Respiratory and Critical Care Medicine, the Second People’s Hospital of Fuyang City, Fuyang, Anhui, 236015, People’s Republic of China
| | - Da-Wei Zhang
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, Anhui, 230022, People’s Republic of China
| | - Su-Hong Chen
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, Anhui, 230022, People’s Republic of China
- Department of Integrated Traditional Chinese and Western Medicine, Anhui Medical University, Hefei, Anhui, 230022, People’s Republic of China
| | - Yuan-Yuan Tan
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, Anhui, 230022, People’s Republic of China
- Department of Emergency Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, People’s Republic of China
| | - Wen-Ting Zhang
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, Anhui, 230022, People’s Republic of China
| | - Ming-Feng Han
- Department of Respiratory and Critical Care Medicine, the Second People’s Hospital of Fuyang City, Fuyang, Anhui, 236015, People’s Republic of China
| | - Guang-He Fei
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, Anhui, 230022, People’s Republic of China
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Müller TR, Sekine T, Trubach D, Niessl J, Chen P, Bergman P, Blennow O, Hansson L, Mielke S, Nowak P, Vesterbacka J, Akber M, Olofsson A, Amaya Hernandez SP, Gao Y, Cai C, Söderdahl G, Smith CIE, Österborg A, Loré K, Sällberg Chen M, Ljungman P, Ljunggren HG, Karlsson AC, Saini SK, Aleman S, Buggert M. Additive effects of booster mRNA vaccination and SARS-CoV-2 Omicron infection on T cell immunity across immunocompromised states. Sci Transl Med 2023; 15:eadg9452. [PMID: 37437015 PMCID: PMC7615622 DOI: 10.1126/scitranslmed.adg9452] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/23/2023] [Indexed: 07/14/2023]
Abstract
Suboptimal immunity to SARS-CoV-2 mRNA vaccination has frequently been observed in individuals with various immunodeficiencies. Given the increased antibody evasion properties of emerging SARS-CoV-2 subvariants, it is necessary to assess whether other components of adaptive immunity generate resilient and protective responses against infection. We assessed T cell responses in 279 individuals, covering five different immunodeficiencies and healthy controls, before and after booster mRNA vaccination, as well as after Omicron infection in a subset of patients. We observed robust and persistent Omicron-reactive T cell responses that increased markedly upon booster vaccination and correlated directly with antibody titers across all patient groups. Poor vaccination responsiveness in immunocompromised or elderly individuals was effectively counteracted by the administration of additional vaccine doses. Functionally, Omicron-reactive T cell responses exhibited a pronounced cytotoxic profile and signs of longevity, characterized by CD45RA+ effector memory subpopulations with stem cell-like properties and increased proliferative capacity. Regardless of underlying immunodeficiency, booster-vaccinated and Omicron-infected individuals appeared protected against severe disease and exhibited enhanced and diversified T cell responses against conserved and Omicron-specific epitopes. Our findings indicate that T cells retain the ability to generate highly functional responses against newly emerging variants, even after repeated antigen exposure and a robust immunological imprint from ancestral SARS-CoV-2 mRNA vaccination.
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Affiliation(s)
- Thomas R. Müller
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Takuya Sekine
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Darya Trubach
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Julia Niessl
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Puran Chen
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Peter Bergman
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Clinical Immunology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Ola Blennow
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Transplantation, Karolinska University Hospital, Stockholm, Sweden
- Department of Medicine Huddinge, Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
| | - Lotta Hansson
- Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Stephan Mielke
- Department of Laboratory Medicine, Biomolecular and Cellular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Cellular Therapy and Allogeneic Stem Cell Transplantation (CAST), Karolinska Comprehensive Cancer Center, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Piotr Nowak
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Medicine Huddinge, Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
- Laboratory for Molecular Infection Medicine Sweden MIMS, Umeå University, Sweden
| | - Jan Vesterbacka
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Medicine Huddinge, Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
| | - Mira Akber
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna Olofsson
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Susana Patricia Amaya Hernandez
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Yu Gao
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Curtis Cai
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Gunnar Söderdahl
- Department of Transplantation, Karolinska University Hospital, Stockholm, Sweden
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - C. I. Edvard Smith
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Biomolecular and Cellular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Cellular Therapy and Allogeneic Stem Cell Transplantation (CAST), Karolinska Comprehensive Cancer Center, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Anders Österborg
- Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Karin Loré
- Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | | | - Per Ljungman
- Department of Cellular Therapy and Allogeneic Stem Cell Transplantation (CAST), Karolinska Comprehensive Cancer Center, Karolinska University Hospital Huddinge, Stockholm, Sweden
- Department of Medicine Huddinge, Hematology, Karolinska Institutet, Stockholm
| | - Hans-Gustaf Ljunggren
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Annika C. Karlsson
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Karolinska University Laboratory, Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Sunil Kumar Saini
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Soo Aleman
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Medicine Huddinge, Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
| | - Marcus Buggert
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
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Howerton E, Contamin L, Mullany LC, Qin M, Reich NG, Bents S, Borchering RK, Jung SM, Loo SL, Smith CP, Levander J, Kerr J, Espino J, van Panhuis WG, Hochheiser H, Galanti M, Yamana T, Pei S, Shaman J, Rainwater-Lovett K, Kinsey M, Tallaksen K, Wilson S, Shin L, Lemaitre JC, Kaminsky J, Hulse JD, Lee EC, McKee C, Hill A, Karlen D, Chinazzi M, Davis JT, Mu K, Xiong X, Piontti APY, Vespignani A, Rosenstrom ET, Ivy JS, Mayorga ME, Swann JL, España G, Cavany S, Moore S, Perkins A, Hladish T, Pillai A, Toh KB, Longini I, Chen S, Paul R, Janies D, Thill JC, Bouchnita A, Bi K, Lachmann M, Fox S, Meyers LA, Srivastava A, Porebski P, Venkatramanan S, Adiga A, Lewis B, Klahn B, Outten J, Hurt B, Chen J, Mortveit H, Wilson A, Marathe M, Hoops S, Bhattacharya P, Machi D, Cadwell BL, Healy JM, Slayton RB, Johansson MA, Biggerstaff M, Truelove S, Runge MC, Shea K, Viboud C, Lessler J. Informing pandemic response in the face of uncertainty. An evaluation of the U.S. COVID-19 Scenario Modeling Hub. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.28.23291998. [PMID: 37461674 PMCID: PMC10350156 DOI: 10.1101/2023.06.28.23291998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
Our ability to forecast epidemics more than a few weeks into the future is constrained by the complexity of disease systems, our limited ability to measure the current state of an epidemic, and uncertainties in how human action will affect transmission. Realistic longer-term projections (spanning more than a few weeks) may, however, be possible under defined scenarios that specify the future state of critical epidemic drivers, with the additional benefit that such scenarios can be used to anticipate the comparative effect of control measures. Since December 2020, the U.S. COVID-19 Scenario Modeling Hub (SMH) has convened multiple modeling teams to make 6-month ahead projections of the number of SARS-CoV-2 cases, hospitalizations and deaths. The SMH released nearly 1.8 million national and state-level projections between February 2021 and November 2022. SMH performance varied widely as a function of both scenario validity and model calibration. Scenario assumptions were periodically invalidated by the arrival of unanticipated SARS-CoV-2 variants, but SMH still provided projections on average 22 weeks before changes in assumptions (such as virus transmissibility) invalidated scenarios and their corresponding projections. During these periods, before emergence of a novel variant, a linear opinion pool ensemble of contributed models was consistently more reliable than any single model, and projection interval coverage was near target levels for the most plausible scenarios (e.g., 79% coverage for 95% projection interval). SMH projections were used operationally to guide planning and policy at different stages of the pandemic, illustrating the value of the hub approach for long-term scenario projections.
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Affiliation(s)
| | | | | | | | | | - Samantha Bents
- National Institutes of Health Fogarty International Center (NIH)
| | | | | | - Sara L Loo
- Johns Hopkins University Infectious Disease Dynamics (JHU-IDD)
| | - Claire P Smith
- Johns Hopkins University Infectious Disease Dynamics (JHU-IDD)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Shi Chen
- University of North Carolina at Charlotte (UNCC)
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89
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Relan P, Motaze NV, Kothari K, Askie L, Le Polain O, Van Kerkhove MD, Diaz J, Tirupakuzhi Vijayaraghavan BK. Severity and outcomes of Omicron variant of SARS-CoV-2 compared to Delta variant and severity of Omicron sublineages: a systematic review and metanalysis. BMJ Glob Health 2023; 8:e012328. [PMID: 37419502 PMCID: PMC10347449 DOI: 10.1136/bmjgh-2023-012328] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/16/2023] [Indexed: 07/09/2023] Open
Abstract
OBJECTIVES To compare severity and clinical outcomes from Omicron as compared with the Delta variant and to compare outcomes between Omicron sublineages. METHODS We searched the WHO COVID-19 Research database for studies that compared clinical outcomes for patients with Omicron variant and the Delta variant, and separately Omicron sublineages BA.1 and BA.2. A random-effects meta-analysis was used to pool estimates of relative risk (RR) between variants and sublineages. Heterogeneity between studies was assessed using the I2 index. Risk of bias was assessed using the tool developed by the Clinical Advances through Research and Information Translation team. RESULTS Our search identified 1494 studies and 42 met the inclusion criteria. Eleven studies were published as preprints. Of the 42 studies, 29 adjusted for vaccination status; 12 had no adjustment; and for 1, the adjustment was unclear. Three of the included studies compared the sublineages of Omicron BA.1 versus BA.2. As compared with Delta, individuals infected with Omicron had 61% lower risk of death (RR 0.39, 95% CI 0.33 to 0.46) and 56% lower risk of hospitalisation (RR 0.44, 95% CI 0.34 to 0.56). Omicron was similarly associated with lower risk of intensive care unit (ICU) admission, oxygen therapy, and non-invasive and invasive ventilation. The pooled risk ratio for the outcome of hospitalisation when comparing sublineages BA.1 versus BA.2 was 0.55 (95% 0.23 to 1.30). DISCUSSION Omicron variant was associated with lower risk of hospitalisation, ICU admission, oxygen therapy, ventilation and death as compared with Delta. There was no difference in the risk of hospitalisation between Omicron sublineages BA.1 and BA.2. PROSPERO REGISTRATION NUMBER CRD42022310880.
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Affiliation(s)
- Pryanka Relan
- Health Emergencies Programme, WHO, Geneva, Switzerland
| | - Nkengafac Villyen Motaze
- Health Emergencies Programme, WHO, Geneva, Switzerland
- Medicine Usage in South Africa, School of Pharmacy, Faculty of Health Sciences, North-West University, Potchefstroom, South Africa
| | - Kavita Kothari
- Library and Digital Information Networks, World Health Organization, Kobe, Japan
| | - Lisa Askie
- Methods and Standards Unit, Science Division, World Health Organization, Geneva, Switzerland
| | - Olivier Le Polain
- Acute Response Coordination Department, World Health Organization, Geneva, Switzerland
| | - Maria D Van Kerkhove
- COVID-19 Health Operations, World Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Janet Diaz
- Health Emergencies Programme, WHO, Geneva, Switzerland
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90
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Wang RC, Gottlieb M, Montoy JCC, Rodriguez RM, Yu H, Spatz ES, Chandler CW, Elmore JG, Hannikainen PA, Chang AM, Hill M, Huebinger RM, Idris AH, Koo K, Li SX, McDonald S, Nichol G, O’Laughlin KN, Plumb ID, Santangelo M, Saydah S, Stephens KA, Venkatesh AK, Weinstein RA. Association Between SARS-CoV-2 Variants and Frequency of Acute Symptoms: Analysis of a Multi-institutional Prospective Cohort Study-December 20, 2020-June 20, 2022. Open Forum Infect Dis 2023; 10:ofad275. [PMID: 37426947 PMCID: PMC10327880 DOI: 10.1093/ofid/ofad275] [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: 04/05/2023] [Accepted: 05/22/2023] [Indexed: 07/11/2023] Open
Abstract
Background While prior work examining severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern focused on hospitalization and death, less is known about differences in clinical presentation. We compared the prevalence of acute symptoms across pre-Delta, Delta, and Omicron. Methods We conducted an analysis of the Innovative Support for Patients with SARS-CoV-2 Infections Registry (INSPIRE), a cohort study enrolling symptomatic SARS-CoV-2-positive participants. We determined the association between the pre-Delta, Delta, and Omicron time periods and the prevalence of 21 coronavirus disease 2019 (COVID-19) acute symptoms. Results We enrolled 4113 participants from December 2020 to June 2022. Pre-Delta vs Delta vs Omicron participants had increasing sore throat (40.9%, 54.6%, 70.6%; P < .001), cough (50.9%, 63.3%, 66.7%; P < .001), and runny noses (48.9%, 71.3%, 72.9%; P < .001). We observed reductions during Omicron in chest pain (31.1%, 24.2%, 20.9%; P < .001), shortness of breath (42.7%, 29.5%, 27.5%; P < .001), loss of taste (47.1%, 61.8%, 19.2%; P < .001), and loss of smell (47.5%, 55.6%, 20.0%; P < .001). After adjustment, those infected during Omicron had significantly higher odds of sore throat vs pre-Delta (odds ratio [OR], 2.76; 95% CI, 2.26-3.35) and Delta (OR, 1.96; 95% CI, 1.69-2.28). Conclusions Participants infected during Omicron were more likely to report symptoms of common respiratory viruses, such as sore throat, and less likely to report loss of smell and taste. Trial registration NCT04610515.
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Affiliation(s)
- Ralph C Wang
- Department of Emergency Medicine, University of California San Francisco, San Francisco, California, USA
| | - Michael Gottlieb
- Department of Emergency Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Juan Carlos C Montoy
- Department of Emergency Medicine, University of California San Francisco, San Francisco, California, USA
| | - Robert M Rodriguez
- Department of Emergency Medicine, University of California San Francisco, San Francisco, California, USA
| | - Huihui Yu
- Center for Outcomes Research and Evaluation, Section of Cardiovascular Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Erica S Spatz
- Center for Outcomes Research and Evaluation, Section of Cardiovascular Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Christopher W Chandler
- Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Joann G Elmore
- Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
- Department of Health Policy and Management, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California, USA
| | - Paavali A Hannikainen
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Anna Marie Chang
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Mandy Hill
- Department of Emergency Medicine, UTHealth Houston, Houston, Texas, USA
| | - Ryan M Huebinger
- Department of Emergency Medicine, UTHealth Houston, Houston, Texas, USA
| | - Ahamed H Idris
- Department of Emergency Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Katherine Koo
- Department of Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois, USA
| | - Shu-Xia Li
- Center for Outcomes Research and Evaluation, Section of Cardiovascular Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Samuel McDonald
- Department of Emergency Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Graham Nichol
- Departments of Medicine and Emergency Medicine, University of Washington, Seattle, Washington, USA
| | - Kelli N O’Laughlin
- Departments of Emergency Medicine and Global Health, University of Washington, Seattle, Washington, USA
| | - Ian D Plumb
- Centers for Disease Control and Prevention, National Center for Immunizations and Respiratory Diseases, Atlanta, Georgia, USA
| | - Michelle Santangelo
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Sharon Saydah
- Centers for Disease Control and Prevention, National Center for Immunizations and Respiratory Diseases, Atlanta, Georgia, USA
| | - Kari A Stephens
- Departments of Family Medicine and Biomedical Informatics & Medical Education, University of Washington, Seattle, Washington, USA
| | - Arjun K Venkatesh
- Center for Outcomes Research and Evaluation, Section of Cardiovascular Medicine, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Emergency Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Robert A Weinstein
- Department of Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois, USA
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Lewnard JA, McLaughlin JM, Malden D, Hong V, Puzniak L, Ackerson BK, Lewin BJ, Kim JS, Shaw SF, Takhar H, Jodar L, Tartof SY. Effectiveness of nirmatrelvir-ritonavir in preventing hospital admissions and deaths in people with COVID-19: a cohort study in a large US health-care system. THE LANCET. INFECTIOUS DISEASES 2023; 23:806-815. [PMID: 36933565 PMCID: PMC10081864 DOI: 10.1016/s1473-3099(23)00118-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/29/2023] [Accepted: 02/14/2023] [Indexed: 03/17/2023]
Abstract
BACKGROUND In the USA, oral nirmatrelvir-ritonavir is authorised for use in patients aged 12 years or older with mild-to-moderate COVID-19 who are at risk of progression to severe disease and hospitalisation. We aimed to establish the effectiveness of nirmatrelvir-ritonavir in preventing hospital admissions and death in people with COVID-19 in an outpatient prescribing context in the USA. METHODS In this matched observational outpatient cohort study in the Kaiser Permanente Southern California (CA, USA) health-care system, data were extracted from electronic health records of non-hospitalised patients aged 12 years or older who received a positive SARS-CoV-2 PCR test result (their index test) between April 8 and Oct 7, 2022, and had not received another positive test result within the preceding 90 days. We compared outcomes between people who received nirmatrelvir-ritonavir and those who did not receive nirmatrelvir-ritonavir by matching cases by date, age, sex, clinical status (including care received, the presence or absence of acute COVID-19 symptoms at testing, and time from symptom onset to testing), vaccination history, comorbidities, health-care seeking during the previous year, and BMI. Our primary endpoint was the estimated effectiveness of nirmatrelvir-ritonavir in preventing hospital admissions or death within 30 days of a positive test for SARS-CoV-2. FINDINGS 7274 nirmatrelvir-ritonavir recipients and 126 152 non-recipients with positive SARS-CoV-2 tests were included in our study. 5472 (75·2%) treatment recipients and 84 657 (67·1%) non-recipients were tested within 5 days of symptom onset. Nirmatrelvir-ritonavir had an overall estimated effectiveness of 53·6% (95% CI 6·6-77·0) in preventing hospital admission or death within 30 days of a positive test for SARS-CoV-2, which increased to 79·6% (33·9-93·8) when nirmatrelvir-ritonavir was dispensed within 5 days of symptom onset. Within the subgroup of patients tested within 5 days of symptom onset and whose treatment was dispensed on the day of their test, the estimated effectiveness of nirmatrelvir-ritonavir was 89·6% (50·2-97·8). INTERPRETATION In a setting with high levels of COVID-19 vaccine uptake, nirmatrelvir-ritonavir effectively reduced the risk of hospital admission or death within 30 days of a positive outpatient SARS-CoV-2 test. FUNDING US Centers for Disease Control and Prevention and US National Institutes of Health.
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Affiliation(s)
- Joseph A Lewnard
- Division of Epidemiology and Division of Infectious Diseases and Vaccinology, School of Public Health, and Center for Computational Biology, College of Engineering, University of California, Berkeley, Berkeley, CA, USA.
| | | | - Debbie Malden
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Vennis Hong
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | | | - Bradley K Ackerson
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Bruno J Lewin
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Jeniffer S Kim
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Sally F Shaw
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Harpreet Takhar
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | | | - Sara Y Tartof
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA; Department of Health Systems Science, Kaiser Permanente Bernard J Tyson School of Medicine, Pasadena, CA, USA
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92
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Lewnard JA, Hong V, Kim JS, Shaw SF, Lewin B, Takhar H, Lipsitch M, Tartof SY. Increased vaccine sensitivity of an emerging SARS-CoV-2 variant. Nat Commun 2023; 14:3854. [PMID: 37386005 PMCID: PMC10310822 DOI: 10.1038/s41467-023-39567-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/16/2023] [Indexed: 07/01/2023] Open
Abstract
Host immune responses are a key source of selective pressure driving pathogen evolution. Emergence of many SARS-CoV-2 lineages has been associated with enhancements in their ability to evade population immunity resulting from both vaccination and infection. Here we show diverging trends of escape from vaccine-derived and infection-derived immunity for the emerging XBB/XBB.1.5 Omicron lineage. Among 31,739 patients tested in ambulatory settings in Southern California from December, 2022 to February, 2023, adjusted odds of prior receipt of 2, 3, 4, and ≥5 COVID-19 vaccine doses were 10% (95% confidence interval: 1-18%), 11% (3-19%), 13% (3-21%), and 25% (15-34%) lower, respectively, among cases infected with XBB/XBB.1.5 than among cases infected with other co-circulating lineages. Similarly, prior vaccination was associated with greater point estimates of protection against progression to hospitalization among cases with XBB/XBB.1.5 than among non-XBB/XBB.1.5 cases (70% [30-87%] and 48% [7-71%], respectively, for recipients of ≥4 doses). In contrast, cases infected with XBB/XBB.1.5 had 17% (11-24%) and 40% (19-65%) higher adjusted odds of having experienced 1 and ≥2 prior documented infections, respectively, including with pre-Omicron variants. As immunity acquired from SARS-CoV-2 infection becomes increasingly widespread, fitness costs associated with enhanced vaccine sensitivity in XBB/XBB.1.5 may be offset by increased ability to evade infection-derived host responses.
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Affiliation(s)
- Joseph A Lewnard
- Division of Epidemiology, School of Public Health, , University of California, Berkeley, Berkeley, CA, 94720, USA.
- Division of Infectious Diseases & Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720, USA.
- Center for Computational Biology, College of Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA.
| | - Vennis Hong
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, 91101, USA
| | - Jeniffer S Kim
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, 91101, USA
| | - Sally F Shaw
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, 91101, USA
| | - Bruno Lewin
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, 91101, USA
- Department of Clinical Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA, 91101, USA
| | - Harpreet Takhar
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, 91101, USA
| | - Marc Lipsitch
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Sara Y Tartof
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, 91101, USA.
- Department of Health Systems Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA, 91101, USA.
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93
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Arabi M, Al-Najjar Y, Sharma O, Kamal I, Javed A, Gohil HS, Paul P, Al-Khalifa AM, Laws S, Zakaria D. Role of previous infection with SARS-CoV-2 in protecting against omicron reinfections and severe complications of COVID-19 compared to pre-omicron variants: a systematic review. BMC Infect Dis 2023; 23:432. [PMID: 37365490 DOI: 10.1186/s12879-023-08328-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/13/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND The SARS-CoV-2 virus elicited a major public concern worldwide since December 2019 due to the high number of infections and deaths caused by COVID-19. The Omicron variant was detected in October 2021 which evolved from the wild-type SARS-CoV-2 and was found to possess many mutations. Omicron exhibited high transmissibility and immune evasion as well as reduced severity when compared to the earlier variants. Although vaccinated individuals were largely protected against infections in previous waves, the high prevalence of both reinfections and breakthrough infections with Omicron was observed. The aim of this review is to understand the effectiveness of previous infection on subsequent reinfection, given its significance in driving public health policy, including vaccination prioritization and lockdown requirements. METHODS A comprehensive literature search was conducted using several databases to target studies reporting data related to the effectiveness of the previous infection with SARS-CoV-2 in protecting against the Omicron variant. Screening of the studies, quality assessment and data extraction were conducted by two reviewers for each study. RESULTS Only 27 studies met our inclusion criteria. It was observed that previous infection was less effective in preventing reinfections with the Omicron variant compared to the Delta variant irrespective of vaccination status. Furthermore, being fully vaccinated with a booster dose provided additional protection from the Omicron variant. Additionally, most infections caused by Omicron were asymptomatic or mild and rarely resulted in hospitalizations or death in comparison to the Delta wave. CONCLUSION A majority of the studies reached a consensus that although previous infection provides some degree of immunity against Omicron reinfection, it is much lower in comparison to Delta. Full vaccination with two doses was more protective against Delta than Omicron. Receiving a booster dose provided additional protection against Omicron. It is therefore clear that neither vaccination nor previous infection alone provide optimal protection; hybrid immunity has shown the best results in terms of protecting against either Omicron or Delta variants. However, additional research is needed to quantify how long immunity from vaccination versus previous infection lasts and whether individuals will benefit from variant-specific vaccinations to enhance protection from infection.
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Affiliation(s)
- Maryam Arabi
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Yousef Al-Najjar
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Omna Sharma
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Ibtihal Kamal
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Aimen Javed
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Harsh S Gohil
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Pradipta Paul
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Aljazi M Al-Khalifa
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Sa'ad Laws
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Dalia Zakaria
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar.
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Cheng Q, Hao X, Wu D, Wang Q, Spear RC, Wei S. Feasible intervention combinations for achieving a safe exit of the Zero-COVID policy in China and its determinants: an individual-based model study. BMC Infect Dis 2023; 23:390. [PMID: 37308872 PMCID: PMC10258473 DOI: 10.1186/s12879-023-08382-x] [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: 02/20/2023] [Accepted: 06/07/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Although several pathways have been proposed as the prerequisite for a safe phase-out in China, it is not clear which of them are the most important for keeping the mortality rate low, what thresholds should be achieved for these most important interventions, and how the thresholds change with the assumed key epidemiological parameters and population characteristics. METHODS We developed an individual-based model (IBM) to simulate the transmission of the Omicron variant in the synthetic population, accounting for the age-dependent probabilities of severe clinical outcomes, waning vaccine-induced immunity, increased mortality rates when hospitals are overburdened, and reduced transmission when self-isolated at home after testing positive. We applied machine learning algorithms on the simulation outputs to examine the importance of each intervention parameter and the feasible intervention parameter combinations for safe exits, which is defined as having mortality rates lower than that of influenza in China (14.3 per 100, 000 persons). RESULTS We identified vaccine coverage in those above 70 years old, number of ICU beds per capita, and the availability of antiviral treatment as the most important interventions for safe exits across all studied locations, although the thresholds required for safe exits vary remarkably with the assumed vaccine effectiveness, as well as the age structure, age-specific vaccine coverage, community healthcare capacity of the studied locations. CONCLUSIONS The analytical framework developed here can provide the basis for further policy decisions that incorporate considerations about economic costs and societal impacts. Achieving safe exits from the Zero-COVID policy is possible, but challenging for China's cities. When planning for safe exits, local realities such as the age structure and current age-specific vaccine coverage must be taken into consideration.
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Affiliation(s)
- Qu Cheng
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Xingjie Hao
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Degang Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Departments of Epidemiology and Biostatistics, School of Public Health, Guangzhou Medical University, Guangzhou, China
| | - Qi Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Robert C Spear
- Division of Environmental Health, of Public Health, University of California, Berkeley, CA, USA
| | - Sheng Wei
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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95
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Luan N, Cao H, Wang Y, Lin K, Hu J, Liu C. Comparison of Immune Responses between Inactivated and mRNA SARS-CoV-2 Vaccines Used for a Booster Dose in Mice. Viruses 2023; 15:1351. [PMID: 37376650 DOI: 10.3390/v15061351] [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: 05/16/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
A large amount of real-world data suggests that the emergence of variants of concern (VOCs) has brought new challenges to the fight against SARS-CoV-2 because the immune protection elicited by the existing coronavirus disease 2019 (COVID-19) vaccines was weakened. In response to the VOCs, it is necessary to advocate for the administration of booster vaccine doses to extend the effectiveness of vaccines and enhance neutralization titers. In this study, the immune effects of mRNA vaccines based on the WT (prototypic strain) and omicron (B1.1.529) strains for use as booster vaccines were investigated in mice. It was determined that with two-dose inactivated vaccine priming, boosting with mRNA vaccines could elevate IgG titers, enhance cell-mediated immunity, and provide immune protection against the corresponding variants, but cross-protection against distinct strains was inferior. This study comprehensively describes the differences in the mice boosted with mRNA vaccines based on the WT strain and the omicron strain, a harmful VOC that has resulted in a sharp rise in the number of infections, and reveals the most efficacious vaccination strategy against omicron and future SARS-CoV-2 variants.
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Affiliation(s)
- Ning Luan
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Han Cao
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Yunfei Wang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Kangyang Lin
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Jingping Hu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Cunbao Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
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96
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Ren H, Ling Y, Cao R, Wang Z, Li Y, Huang T. Early warning of emerging infectious diseases based on multimodal data. BIOSAFETY AND HEALTH 2023; 5:S2590-0536(23)00074-5. [PMID: 37362865 PMCID: PMC10245235 DOI: 10.1016/j.bsheal.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/18/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has dramatically increased the awareness of emerging infectious diseases. The advancement of multiomics analysis technology has resulted in the development of several databases containing virus information. Several scientists have integrated existing data on viruses to construct phylogenetic trees and predict virus mutation and transmission in different ways, providing prospective technical support for epidemic prevention and control. This review summarized the databases of known emerging infectious viruses and techniques focusing on virus variant forecasting and early warning. It focuses on the multi-dimensional information integration and database construction of emerging infectious viruses, virus mutation spectrum construction and variant forecast model, analysis of the affinity between mutation antigen and the receptor, propagation model of virus dynamic evolution, and monitoring and early warning for variants. As people have suffered from COVID-19 and repeated flu outbreaks, we focused on the research results of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses. This review comprehensively viewed the latest virus research and provided a reference for future virus prevention and control research.
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Affiliation(s)
- Haotian Ren
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yunchao Ling
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ruifang Cao
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhen Wang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yixue Li
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024 China
- Guangzhou Laboratory, Guangzhou 510005, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200433, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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97
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Sabbatucci M, Vitiello A, Clemente S, Zovi A, Boccellino M, Ferrara F, Cimmino C, Langella R, Ponzo A, Stefanelli P, Rezza G. Omicron variant evolution on vaccines and monoclonal antibodies. Inflammopharmacology 2023:10.1007/s10787-023-01253-6. [PMID: 37204696 DOI: 10.1007/s10787-023-01253-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 05/09/2023] [Indexed: 05/20/2023]
Abstract
The severe acute respiratory syndrome coronavirus (SARS-CoV)-2 responsible for the global COVID-19 pandemic has caused almost 760 million confirmed cases and 7 million deaths worldwide, as of end-February 2023. Since the beginning of the first COVID-19 case, several virus variants have emerged: Alpha (B1.1.7), Beta (B135.1), Gamma (P.1), Delta (B.1.617.2) and then Omicron (B.1.1.529) and its sublineages. All variants have diversified in transmissibility, virulence, and pathogenicity. All the newly emerging SARS-CoV-2 variants appear to contain some similar mutations associated with greater "evasiveness" of the virus to immune defences. From early 2022 onward, several Omicron subvariants named BA.1, BA.2, BA.3, BA.4, and BA.5, with comparable mutation forms, have followed. After the wave of contagions caused by Omicron BA.5, a new Indian variant named Centaurus BA.2.75 and its new subvariant BA.2.75.2, a second-generation evolution of the Omicron variant BA.2, have recently been identified. From early evidence, it appears that this new variant has higher affinity for the cell entry receptor ACE-2, making it potentially able to spread very fast. According to the latest studies, the BA.2.75.2 variant may be able to evade more antibodies in the bloodstream generated by vaccination or previous infection, and it may be more resistant to antiviral and monoclonal antibody drug treatments. In this manuscript, the authors highlight and describe the latest evidences and critical issues have emerged on the new SARS-CoV-2 variants.
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Affiliation(s)
- Michela Sabbatucci
- Ministry of Health, Directorate-General for Health Prevention, Viale Giorgio Ribotta 5, 00144, Rome, Italy
- Department Infectious Diseases, Italian National Institute of Health, Viale Regina Elena 299, 00161, Rome, Italy
| | - Antonio Vitiello
- Ministry of Health, Directorate-General for Health Prevention, Viale Giorgio Ribotta 5, 00144, Rome, Italy
| | - Salvatore Clemente
- Ministry of Health, Directorate-General for Health Prevention, Viale Giorgio Ribotta 5, 00144, Rome, Italy
| | - Andrea Zovi
- Ministry of Health, Directorate General of Hygiene, Food Safety and Nutrition, Viale Giorgio Ribotta 5, 00144, Rome, Italy.
| | | | - Francesco Ferrara
- Pharmaceutical Department, Local Health Unit Napoli 3 Sud, Dell'amicizia Street 22, 80035, Nola, Italy
| | - Carla Cimmino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Roberto Langella
- Department of Pharmaceutics, Agency for Health Protection of the Metropolitan Area of Milan, Milan, Italy
| | | | - Paola Stefanelli
- Department Infectious Diseases, Italian National Institute of Health, Viale Regina Elena 299, 00161, Rome, Italy
| | - Giovanni Rezza
- Ministry of Health, Directorate-General for Health Prevention, Viale Giorgio Ribotta 5, 00144, Rome, Italy
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98
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Groza C, Totschnig D, Wenisch C, Atamaniuk J, Zoufaly A. A retrospective analysis of clinical features of patients hospitalized with SARS-CoV-2 Omicron variants BA.1 and BA.2. Sci Rep 2023; 13:7896. [PMID: 37193727 DOI: 10.1038/s41598-023-34712-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 05/05/2023] [Indexed: 05/18/2023] Open
Abstract
The causative agent of the ongoing Corona virus disease 2019 (COVID-19) pandemic, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has acquired a considerable amount of mutations, leading to changes in clinical manifestations and increased transmission. Recent studies based on animal disease models and data from the general population were reporting a higher pathogenicity of the BA.2 sublineage compared to BA.1. The aim of this study was to provide real world data on patients with the SARS-CoV-2 Omicron BA.1 and BA.2 subvariants treated at our center, highlighting similarities and differences in the clinical disease course. We retrospectively collected and analyzed the data of adult patients admitted with confirmed SARS-CoV-2 infection at the Department for Infectious Diseases and Tropical Medicine, Klinik Favoriten, Vienna, Austria. Patient characteristics including age, underlying diseases, vaccination status and outcome were compared between patients with the BA.1 and BA.2 subvariants. Between January 2022 and May 2022 we included 168 patients infected with Omicron BA.1 and 100 patients with BA.2. Patients admitted with BA.2 were significantly older, more often fully immunized and required less dexamethasone than patients with BA.1. No substantial differences were identified between patients infected with BA.1 and BA.2 regarding BMI, laboratory findings, need for supplemental oxygen, mortality and other evaluated comorbidities excepting active malignancies. The significantly larger percentage of fully immunized patients admitted with BA.2 is pointing to an increased transmissibility of this subvariant, while the comparable outcome of a somewhat older and sicker patient population might be indicative of reduced virulence.
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Affiliation(s)
- Cristina Groza
- Department of Medicine IV, Klinik Favoriten, Vienna Healthcare Group, Kundratstraße 3, 1100, Vienna, Austria.
- Faculty of Medicine, Sigmund Freud University, Vienna, Austria.
| | - David Totschnig
- Department of Medicine IV, Klinik Favoriten, Vienna Healthcare Group, Kundratstraße 3, 1100, Vienna, Austria
| | - Christoph Wenisch
- Department of Medicine IV, Klinik Favoriten, Vienna Healthcare Group, Kundratstraße 3, 1100, Vienna, Austria
| | - Johanna Atamaniuk
- Faculty of Medicine, Sigmund Freud University, Vienna, Austria
- Department of Laboratory Medicine, Klinik Favoriten, Vienna Healthcare Group, Kundratstraße 3, 1100, Vienna, Austria
| | - Alexander Zoufaly
- Department of Medicine IV, Klinik Favoriten, Vienna Healthcare Group, Kundratstraße 3, 1100, Vienna, Austria
- Faculty of Medicine, Sigmund Freud University, Vienna, Austria
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99
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Robinson ML, Morris CP, Betz JF, Zhang Y, Bollinger R, Wang N, Thiemann DR, Fall A, Eldesouki RE, Norton JM, Gaston DC, Forman M, Luo CH, Zeger SL, Gupta A, Garibaldi BT, Mostafa HH. Impact of Severe Acute Respiratory Syndrome Coronavirus 2 Variants on Inpatient Clinical Outcome. Clin Infect Dis 2023; 76:1539-1549. [PMID: 36528815 PMCID: PMC10411930 DOI: 10.1093/cid/ciac957] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/21/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Prior observation has shown differences in COVID-19 hospitalization risk between SARS-CoV-2 variants, but limited information describes hospitalization outcomes. METHODS Inpatients with COVID-19 at 5 hospitals in the eastern United States were included if they had hypoxia, tachypnea, tachycardia, or fever, and SARS-CoV-2 variant data, determined from whole-genome sequencing or local surveillance inference. Analyses were stratified by history of SARS-CoV-2 vaccination or infection. The average effect of SARS-CoV-2 variant on 28-day risk of severe disease, defined by advanced respiratory support needs, or death was evaluated using models weighted on propensity scores derived from baseline clinical features. RESULTS Severe disease or death within 28 days occurred for 977 (29%) of 3369 unvaccinated patients and 269 (22%) of 1230 patients with history of vaccination or prior SARS-CoV-2 infection. Among unvaccinated patients, the relative risk of severe disease or death for Delta variant compared with ancestral lineages was 1.30 (95% confidence interval [CI]: 1.11-1.49). Compared with Delta, the risk for Omicron patients was .72 (95% CI: .59-.88) and compared with ancestral lineages was .94 (.78-1.1). Among Omicron and Delta infections, patients with history of vaccination or prior SARS-CoV-2 infection had half the risk of severe disease or death (adjusted hazard ratio: .40; 95% CI: .30-.54), but no significant outcome difference by variant. CONCLUSIONS Although risk of severe disease or death for unvaccinated inpatients with Omicron was lower than with Delta, it was similar to ancestral lineages. Severe outcomes were less common in vaccinated inpatients, with no difference between Delta and Omicron infections.
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Affiliation(s)
- Matthew L Robinson
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - C Paul Morris
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Joshua F Betz
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Yifan Zhang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Robert Bollinger
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Natalie Wang
- Krieger School of Arts & Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - David R Thiemann
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Amary Fall
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Raghda E Eldesouki
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Julie M Norton
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David C Gaston
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael Forman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chun Huai Luo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Scott L Zeger
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Amita Gupta
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Brian T Garibaldi
- Division of Pulmonary and Critical Care, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Heba H Mostafa
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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100
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Ruis C, Peacock TP, Polo LM, Masone D, Alvarez MS, Hinrichs AS, Turakhia Y, Cheng Y, McBroome J, Corbett-Detig R, Parkhill J, Floto RA. A lung-specific mutational signature enables inference of viral and bacterial respiratory niche. Microb Genom 2023; 9. [PMID: 37185044 DOI: 10.1099/mgen.0.001018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Exposure to different mutagens leaves distinct mutational patterns that can allow inference of pathogen replication niches. We therefore investigated whether SARS-CoV-2 mutational spectra might show lineage-specific differences, dependent on the dominant site(s) of replication and onwards transmission, and could therefore rapidly infer virulence of emergent variants of concern (VOCs). Through mutational spectrum analysis, we found a significant reduction in G>T mutations in the Omicron variant, which replicates in the upper respiratory tract (URT), compared to other lineages, which replicate in both the URT and lower respiratory tract (LRT). Mutational analysis of other viruses and bacteria indicates a robust, generalizable association of high G>T mutations with replication within the LRT. Monitoring G>T mutation rates over time, we found early separation of Omicron from Beta, Gamma and Delta, while mutational patterns in Alpha varied consistent with changes in transmission source as social restrictions were lifted. Mutational spectra may be a powerful tool to infer niches of established and emergent pathogens.
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Affiliation(s)
- Christopher Ruis
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | - Luis M Polo
- Instituto de Histología y Embriología de Mendoza - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Diego Masone
- Instituto de Histología y Embriología de Mendoza - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo, Mendoza, Argentina
- Facultad de Ingeniería, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Maria Soledad Alvarez
- Instituto de Medicina y Biología Experimental de Cuyo (IMBECU), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina
| | - Angie S Hinrichs
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California San Diego, San Diego, CA, USA
| | - Ye Cheng
- Department of Electrical and Computer Engineering, University of California San Diego, San Diego, CA, USA
| | - Jakob McBroome
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - R Andres Floto
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for Lung Infection, Papworth Hospital, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
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