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van Raaij BFM, Noordam R, Smits RAL, van der Klei VMGTH, Jansen SWM, van der Linden CMJ, Polinder-Bos HA, Minnema J, Tap L, van der Bol JM, van de Glind EMM, Willems HC, van Deudekom FJA, Ruiter R, van Munster BC, Robben SHM, Schouten HJ, Barten DG, Lucke JA, Peeters G, Trompet S, Drewes YM, van den Bos F, Gussekloo J, Mooijaart SP. Preparing for future pandemics: frailty associates with mortality in hospitalised older people during the entire COVID-19 pandemic, a Dutch multicentre cohort study. Eur Geriatr Med 2024:10.1007/s41999-024-01001-1. [PMID: 38849648 DOI: 10.1007/s41999-024-01001-1] [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: 02/12/2024] [Accepted: 05/22/2024] [Indexed: 06/09/2024]
Abstract
PURPOSE Viral mutations and improved prevention or treatment options may have changed the association of frailty with mortality throughout the COVID-19 pandemic. We investigated how associations of frailty with in-hospital mortality changed throughout the pandemic in older people hospitalised for COVID-19. METHODS The COVID-OLD study included COVID-19 patients aged ≥ 70 years hospitalised during the first (early 2020), second (late 2020), third (late 2021) or fourth wave (early 2022). Based on the clinical frailty scale, patients were categorised as fit (1-3), pre-frail (4-5) or frail (6-9). Associations of frailty with in-hospital mortality were assessed with pairwise comparisons with fit as reference category and modelled using binary logistic regression adjusted for age and sex. RESULTS This study included 2362 patients (mean age 79.7 years, 60% men). In the first wave, in-hospital mortality was 46% in patients with frailty and 27% in fit patients. In-hospital mortality decreased in each subsequent wave to 25% in patients with frailty and 11% in fit patients in the fourth wave. After adjustments, an overall higher risk of in-hospital mortality was found in frail (OR 2.26, 95% CI: 1.66-3.07) and pre-frail (OR 1.73, 95% CI: 1.27-2.35) patients compared to fit patients, which did not change over time (p for interaction = 0.74). CONCLUSIONS Frailty remained associated with a higher risk of in-hospital mortality throughout the entire COVID-19 pandemic, although overall in-hospital mortality rates decreased. Frailty therefore remains a relevant risk factor in all stages of a pandemic and is important to consider in prevention and treatment guidelines for future pandemics.
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Affiliation(s)
- Bas F M van Raaij
- Department of Internal Medicine, Section of Geriatrics and Gerontology, Leiden University Medical Center, Albinusdreef 2, 2333ZA, Leiden, The Netherlands.
- LUMC Center of Medicine for Older People, Leiden University Medical Center, Leiden, The Netherlands.
| | - Raymond Noordam
- Department of Internal Medicine, Section of Geriatrics and Gerontology, Leiden University Medical Center, Albinusdreef 2, 2333ZA, Leiden, The Netherlands
| | - Rosalinde A L Smits
- Department of Internal Medicine, Section of Geriatrics and Gerontology, Leiden University Medical Center, Albinusdreef 2, 2333ZA, Leiden, The Netherlands
- LUMC Center of Medicine for Older People, Leiden University Medical Center, Leiden, The Netherlands
| | - Veerle M G T H van der Klei
- Department of Internal Medicine, Section of Geriatrics and Gerontology, Leiden University Medical Center, Albinusdreef 2, 2333ZA, Leiden, The Netherlands
- LUMC Center of Medicine for Older People, Leiden University Medical Center, Leiden, The Netherlands
| | - Steffy W M Jansen
- Department of Geriatric Medicine, Catharina Hospital, Eindhoven, The Netherlands
| | | | - Harmke A Polinder-Bos
- Division of Geriatric Medicine, Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Julia Minnema
- Division of Geriatric Medicine, Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Lisanne Tap
- Division of Geriatric Medicine, Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | | | - Hanna C Willems
- Department of Internal Medicine and Geriatrics, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | | | - Rikje Ruiter
- Department of Internal Medicine, Maasstad Hospital, Rotterdam, The Netherlands
| | - Barbara C van Munster
- Department of Geriatric Medicine, University Medical Center Groningen, Groningen, The Netherlands
| | - Sarah H M Robben
- Department of Geriatric Medicine, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands
| | - Henrike J Schouten
- Department of Geriatric Medicine, Gelre Hospital, Apeldoorn, Zutphen, The Netherlands
| | - Dennis G Barten
- Department of Emergency Medicine, VieCuri Medical Center, Venlo, The Netherlands
| | - Jacinta A Lucke
- Department of Emergency Medicine, Spaarne Gasthuis, Haarlem, the Netherlands
| | - Geeske Peeters
- Department of Geriatric Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Stella Trompet
- Department of Internal Medicine, Section of Geriatrics and Gerontology, Leiden University Medical Center, Albinusdreef 2, 2333ZA, Leiden, The Netherlands
- LUMC Center of Medicine for Older People, Leiden University Medical Center, Leiden, The Netherlands
| | - Yvonne M Drewes
- Department of Internal Medicine, Section of Geriatrics and Gerontology, Leiden University Medical Center, Albinusdreef 2, 2333ZA, Leiden, The Netherlands
- LUMC Center of Medicine for Older People, Leiden University Medical Center, Leiden, The Netherlands
| | - Frederiek van den Bos
- Department of Internal Medicine, Section of Geriatrics and Gerontology, Leiden University Medical Center, Albinusdreef 2, 2333ZA, Leiden, The Netherlands
- LUMC Center of Medicine for Older People, Leiden University Medical Center, Leiden, The Netherlands
| | - Jacobijn Gussekloo
- Department of Internal Medicine, Section of Geriatrics and Gerontology, Leiden University Medical Center, Albinusdreef 2, 2333ZA, Leiden, The Netherlands
- LUMC Center of Medicine for Older People, Leiden University Medical Center, Leiden, The Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, The Netherlands
| | - Simon P Mooijaart
- Department of Internal Medicine, Section of Geriatrics and Gerontology, Leiden University Medical Center, Albinusdreef 2, 2333ZA, Leiden, The Netherlands
- LUMC Center of Medicine for Older People, Leiden University Medical Center, Leiden, The Netherlands
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2
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Leacy EJ, Teh JW, O’Rourke AM, Brady G, Gargan S, Conlon N, Scott J, Dunne J, Phelan T, Griffin MD, Power J, Mooney A, Naughton A, Kiersey R, Gardiner M, O’Brien C, Mullan R, Flood R, Clarkson M, Townsend L, O’Shaughnessy M, Dyer AH, Moran B, Fletcher JM, Zgaga L, Little MA. Effect of Immunosuppression on the Immune Response to SARS-CoV-2 Infection and Vaccination. Int J Mol Sci 2024; 25:5239. [PMID: 38791279 PMCID: PMC11120762 DOI: 10.3390/ijms25105239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/30/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Immunosuppressive treatment in patients with rheumatic diseases can maintain disease remission but also increase risk of infection. Their response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination is frequently blunted. In this study we evaluated the effect of immunosuppression exposure on humoral and T cell immune responses to SARS-CoV-2 infection and vaccination in two distinct cohorts of patients; one during acute SARS-CoV-2 infection and 3 months later during convalescence, and another prior to SARS-CoV-2 vaccination, with follow up sampling 6 weeks after vaccination. Results were compared between rituximab-exposed (in previous 6 months), immunosuppression-exposed (in previous 3 months), and non-immunosuppressed groups. The immune cell phenotype was defined by flow cytometry and ELISA. Antigen specific T cell responses were estimated using a whole blood stimulation interferon-γ release assay. A focused post-vaccine assessment of rituximab-treated patients using high dimensional spectral cytometry was conducted. Acute SARS-CoV-2 infection was characterised by T cell lymphopenia, and a reduction in NK cells and naïve CD4 and CD8 cells, without any significant differences between immunosuppressed and non-immunosuppressed patient groups. Conversely, activated CD4 and CD8 cell counts increased in non-immunosuppressed patients with acute SARS-CoV-2 infection but this response was blunted in the presence of immunosuppression. In rituximab-treated patients, antigen-specific T cell responses were preserved in SARS-CoV-2 vaccination, but patients were unable to mount an appropriate humoral response.
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Affiliation(s)
- Emma J. Leacy
- Trinity Kidney Centre, Trinity Translational Medicine Institute, School of Medicine, Trinity College Dublin, D08 W9RT Dublin, Ireland (G.B.)
| | - Jia Wei Teh
- Department of Nephrology, Galway University Hospital, H91 YR71 Galway, Ireland
| | - Aoife M. O’Rourke
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 R590 Dublin, Ireland; (A.M.O.)
| | - Gareth Brady
- Trinity Kidney Centre, Trinity Translational Medicine Institute, School of Medicine, Trinity College Dublin, D08 W9RT Dublin, Ireland (G.B.)
| | - Siobhan Gargan
- Department of Clinical Medicine, School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
| | - Niall Conlon
- Department of Immunology, St. James’s Hospital, D08 NHY1 Dublin, Ireland (J.D.)
| | - Jennifer Scott
- Trinity Kidney Centre, Trinity Translational Medicine Institute, School of Medicine, Trinity College Dublin, D08 W9RT Dublin, Ireland (G.B.)
| | - Jean Dunne
- Department of Immunology, St. James’s Hospital, D08 NHY1 Dublin, Ireland (J.D.)
| | - Thomas Phelan
- Trinity Kidney Centre, Trinity Translational Medicine Institute, School of Medicine, Trinity College Dublin, D08 W9RT Dublin, Ireland (G.B.)
| | - Matthew D. Griffin
- Department of Nephrology, Galway University Hospital, H91 YR71 Galway, Ireland
- Regenerative Medicine Institute (REMEDI) at CÚRAM SFI Research Centre for Medical Devices, School of Medicine, University of Galway, H91 TK33 Galway, Ireland
| | - Julie Power
- Vasculitis Ireland Awareness, Belfast & Dublin, Ireland
| | - Aoife Mooney
- Department of Immunology, St. James’s Hospital, D08 NHY1 Dublin, Ireland (J.D.)
| | - Aifric Naughton
- Department of Immunology, St. James’s Hospital, D08 NHY1 Dublin, Ireland (J.D.)
| | - Rachel Kiersey
- Department of Immunology, St. James’s Hospital, D08 NHY1 Dublin, Ireland (J.D.)
| | - Mary Gardiner
- Department of Immunology, St. James’s Hospital, D08 NHY1 Dublin, Ireland (J.D.)
| | - Caroline O’Brien
- Department of Immunology, St. James’s Hospital, D08 NHY1 Dublin, Ireland (J.D.)
| | - Ronan Mullan
- Department of Clinical Medicine, School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
- Department of Rheumatology, Tallaght University Hospital, D24 NR0A Dublin, Ireland
| | - Rachael Flood
- Department of Clinical Medicine, School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
- Department of Rheumatology, Tallaght University Hospital, D24 NR0A Dublin, Ireland
| | - Michael Clarkson
- Department of Nephrology, Cork University Hospital, T12 DC4A Cork, Ireland
| | - Liam Townsend
- Department of Infectious Diseases, St. James’s Hospital, D08 NHY1 Dublin, Ireland
| | - Michelle O’Shaughnessy
- Department of Nephrology, Galway University Hospital, H91 YR71 Galway, Ireland
- Department of Nephrology, Cork University Hospital, T12 DC4A Cork, Ireland
| | - Adam H. Dyer
- Discipline of Medical Gerontology, School of Medicine, Trinity College Dublin, D08 W9RT Dublin, Ireland
| | - Barry Moran
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 R590 Dublin, Ireland; (A.M.O.)
| | - Jean M. Fletcher
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 R590 Dublin, Ireland; (A.M.O.)
| | - Lina Zgaga
- Department of Public Health and Primary Care, Institute of Population Health, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Mark A. Little
- Trinity Kidney Centre, Trinity Translational Medicine Institute, School of Medicine, Trinity College Dublin, D08 W9RT Dublin, Ireland (G.B.)
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Er AG, Ding DY, Er B, Uzun M, Cakmak M, Sadee C, Durhan G, Ozmen MN, Tanriover MD, Topeli A, Aydin Son Y, Tibshirani R, Unal S, Gevaert O. Multimodal data fusion using sparse canonical correlation analysis and cooperative learning: a COVID-19 cohort study. NPJ Digit Med 2024; 7:117. [PMID: 38714751 PMCID: PMC11076490 DOI: 10.1038/s41746-024-01128-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/25/2024] [Indexed: 05/10/2024] Open
Abstract
Through technological innovations, patient cohorts can be examined from multiple views with high-dimensional, multiscale biomedical data to classify clinical phenotypes and predict outcomes. Here, we aim to present our approach for analyzing multimodal data using unsupervised and supervised sparse linear methods in a COVID-19 patient cohort. This prospective cohort study of 149 adult patients was conducted in a tertiary care academic center. First, we used sparse canonical correlation analysis (CCA) to identify and quantify relationships across different data modalities, including viral genome sequencing, imaging, clinical data, and laboratory results. Then, we used cooperative learning to predict the clinical outcome of COVID-19 patients: Intensive care unit admission. We show that serum biomarkers representing severe disease and acute phase response correlate with original and wavelet radiomics features in the LLL frequency channel (cor(Xu1, Zv1) = 0.596, p value < 0.001). Among radiomics features, histogram-based first-order features reporting the skewness, kurtosis, and uniformity have the lowest negative, whereas entropy-related features have the highest positive coefficients. Moreover, unsupervised analysis of clinical data and laboratory results gives insights into distinct clinical phenotypes. Leveraging the availability of global viral genome databases, we demonstrate that the Word2Vec natural language processing model can be used for viral genome encoding. It not only separates major SARS-CoV-2 variants but also allows the preservation of phylogenetic relationships among them. Our quadruple model using Word2Vec encoding achieves better prediction results in the supervised task. The model yields area under the curve (AUC) and accuracy values of 0.87 and 0.77, respectively. Our study illustrates that sparse CCA analysis and cooperative learning are powerful techniques for handling high-dimensional, multimodal data to investigate multivariate associations in unsupervised and supervised tasks.
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Affiliation(s)
- Ahmet Gorkem Er
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine, Stanford University, Stanford, CA, 94305, USA.
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey.
- Department of Infectious Diseases and Clinical Microbiology, Hacettepe University Faculty of Medicine, 06230, Ankara, Turkey.
| | - Daisy Yi Ding
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Berrin Er
- Department of Internal Medicine, Division of Intensive Care Medicine, Hacettepe University Faculty of Medicine, 06230, Ankara, Turkey
| | - Mertcan Uzun
- Department of Infectious Diseases and Clinical Microbiology, Hacettepe University Faculty of Medicine, 06230, Ankara, Turkey
| | - Mehmet Cakmak
- Department of Internal Medicine, Hacettepe University Faculty of Medicine, 06230, Ankara, Turkey
| | - Christoph Sadee
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Gamze Durhan
- Department of Radiology, Hacettepe University Faculty of Medicine, 06230, Ankara, Turkey
| | - Mustafa Nasuh Ozmen
- Department of Radiology, Hacettepe University Faculty of Medicine, 06230, Ankara, Turkey
| | - Mine Durusu Tanriover
- Department of Internal Medicine, Hacettepe University Faculty of Medicine, 06230, Ankara, Turkey
| | - Arzu Topeli
- Department of Internal Medicine, Division of Intensive Care Medicine, Hacettepe University Faculty of Medicine, 06230, Ankara, Turkey
| | - Yesim Aydin Son
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey
| | - Robert Tibshirani
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
- Department of Statistics, Stanford University, Stanford, CA, 94305, USA
| | - Serhat Unal
- Department of Infectious Diseases and Clinical Microbiology, Hacettepe University Faculty of Medicine, 06230, Ankara, Turkey
| | - Olivier Gevaert
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine, Stanford University, Stanford, CA, 94305, USA.
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA.
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4
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Qian J, Zhang S, Wang F, Li J, Zhang J. What makes SARS-CoV-2 unique? Focusing on the spike protein. Cell Biol Int 2024; 48:404-430. [PMID: 38263600 DOI: 10.1002/cbin.12130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/25/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024]
Abstract
Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) seriously threatens public health and safety. Genetic variants determine the expression of SARS-CoV-2 structural proteins, which are associated with enhanced transmissibility, enhanced virulence, and immune escape. Vaccination is encouraged as a public health intervention, and different types of vaccines are used worldwide. However, new variants continue to emerge, especially the Omicron complex, and the neutralizing antibody responses are diminished significantly. In this review, we outlined the uniqueness of SARS-CoV-2 from three perspectives. First, we described the detailed structure of the spike (S) protein, which is highly susceptible to mutations and contributes to the distinct infection cycle of the virus. Second, we systematically summarized the immunoglobulin G epitopes of SARS-CoV-2 and highlighted the central role of the nonconserved regions of the S protein in adaptive immune escape. Third, we provided an overview of the vaccines targeting the S protein and discussed the impact of the nonconserved regions on vaccine effectiveness. The characterization and identification of the structure and genomic organization of SARS-CoV-2 will help elucidate its mechanisms of viral mutation and infection and provide a basis for the selection of optimal treatments. The leaps in advancements regarding improved diagnosis, targeted vaccines and therapeutic remedies provide sound evidence showing that scientific understanding, research, and technology evolved at the pace of the pandemic.
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Affiliation(s)
- Jingbo Qian
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Shichang Zhang
- Department of Clinical Laboratory Medicine, Shenzhen Hospital of Southern Medical University, Shenzhen, China
| | - Fang Wang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiexin Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
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5
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Majchrzak M, Madej Ł, Łysek-Gładysińska M, Zarębska-Michaluk D, Zegadło K, Dziuba A, Nogal-Nowak K, Kondziołka W, Sufin I, Myszona-Tarnowska M, Jaśkowski M, Kędzierski M, Maciukajć J, Matykiewicz J, Głuszek S, Adamus-Białek W. The RdRp genotyping of SARS-CoV-2 isolated from patients with different clinical spectrum of COVID-19. BMC Infect Dis 2024; 24:281. [PMID: 38439047 PMCID: PMC10913261 DOI: 10.1186/s12879-024-09146-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 02/16/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND The evolution of SARS-CoV-2 has been observed from the very beginning of the fight against COVID-19, some mutations are indicators of potentially dangerous variants of the virus. However, there is no clear association between the genetic variants of SARS-CoV-2 and the severity of COVID-19. We aimed to analyze the genetic variability of RdRp in correlation with different courses of COVID-19. RESULTS The prospective study included 77 samples of SARS-CoV-2 isolated from outpatients (1st degree of severity) and hospitalized patients (2nd, 3rd and 4th degree of severity). The retrospective analyses included 15,898,266 cases of SARS-CoV-2 genome sequences deposited in the GISAID repository. Single-nucleotide variants were identified based on the four sequenced amplified fragments of SARS-CoV-2. The analysis of the results was performed using appropriate statistical methods, with p < 0.05, considered statistically significant. Additionally, logistic regression analysis was performed to predict the strongest determinants of the observed relationships. The number of mutations was positively correlated with the severity of the COVID-19, and older male patients. We detected four mutations that significantly increased the risk of hospitalization of COVID-19 patients (14676C > T, 14697C > T, 15096 T > C, and 15279C > T), while the 15240C > T mutation was common among strains isolated from outpatients. The selected mutations were searched worldwide in the GISAID database, their presence was correlated with the severity of COVID-19. CONCLUSION Identified mutations have the potential to be used to assess the increased risk of hospitalization in COVID-19 positive patients. Experimental studies and extensive epidemiological data are needed to investigate the association between individual mutations and the severity of COVID-19.
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Affiliation(s)
- Michał Majchrzak
- Institute of Medical Sciences, Jan Kochanowski University, Kielce, Poland
| | - Łukasz Madej
- Institute of Medical Sciences, Jan Kochanowski University, Kielce, Poland
| | | | | | - Katarzyna Zegadło
- Institute of Medical Sciences, Jan Kochanowski University, Kielce, Poland
| | - Anna Dziuba
- Institute of Medical Sciences, Jan Kochanowski University, Kielce, Poland
| | | | | | | | | | | | | | | | | | - Stanisław Głuszek
- Institute of Medical Sciences, Jan Kochanowski University, Kielce, Poland
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6
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Balasubramaniam S, Raju BP, Perumpallipatty Kumarasamy S, Ramasubramanian S, Srinivasan AK, Gopinath I, Shanmugam K, Kumar AS, Visakan Sivasakthi V, Srinivasan S. Lung Involvement Patterns in COVID-19: CT Scan Insights and Prognostic Implications From a Tertiary Care Center in Southern India. Cureus 2024; 16:e53335. [PMID: 38435896 PMCID: PMC10907113 DOI: 10.7759/cureus.53335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2024] [Indexed: 03/05/2024] Open
Abstract
Background COVID-19, caused by the SARS-CoV-2 virus, has presented an unparalleled challenge and a profound learning curve globally. Among the myriad of investigative tools, CT scans of the chest have become instrumental in assessing the magnitude of lung involvement in the pathogenesis of this disease. Objectives This study aimed to evaluate the distribution and patterns of lung involvement depicted in the CT chest scans of COVID-19 patients admitted to a specialized tertiary care center located in a southern state of India. Methods With clearance secured from the Institutional Ethics Committee, an analytical cross-sectional study was conducted. It encompassed CT chest images from all symptomatic COVID-19 patients within the designated study center during the specified study timeline. Subsequent data analysis ensued. Results Among the 1066 COVID-19 patients evaluated, ground-glass opacities (GGO) were the predominant lung involvement pattern. Distinct patterns, such as GGOs combined with solid consolidation or atelectasis, were noted, with the highest mortality linked to GGOs paired with pneumomediastinum (PM). Data underscored a direct correlation between the extent of lung involvement and patient prognosis, with specific lung regions, namely the right apical, right posterior, right superior basal, left superior lingular, and left inferior lingular segments, showing frequent involvement. Conclusion Amidst the pandemic, our study emphasizes that ground-glass opacities on CT scans are robust indicators of COVID-19 in RT-PCR-positive patients. Early identification can enhance patient management, with findings highlighting a strong link between lung involvement and prognosis. This insight aids in refining patient triage, while further research is warranted to delve deeper into variations in lung involvement and guide treatment advancements.
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Affiliation(s)
| | - Bharathi Priya Raju
- Radiodiagnosis, Government Stanley Medical College and Hospital, Chennai, IND
| | | | | | | | - Ishwar Gopinath
- Radiodiagnosis, Government Medical College, Omandurar Government Estate, Chennai, IND
| | - Kamakshi Shanmugam
- Radiodiagnosis, Government Medical College, Omandurar Government Estate, Chennai, IND
| | - Aravind S Kumar
- Radiodiagnosis, Government Medical College, Omandurar Government Estate, Chennai, IND
| | - Varun Visakan Sivasakthi
- Orthopaedics, Kovai Medical Centre and Hospital Institute of Health Sciences and Research, Coimbatore, IND
| | - Srinidhi Srinivasan
- Radiodiagnosis, Alluri Sitarama Raju Academy of Medical Sciences College and Hospital, Eluru, IND
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7
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Diotallevi A, Buffi G, Barocci S, Ceccarelli M, Bencardino D, Andreoni F, Orlandi C, Ferri M, Vandini D, Menzo S, Carlotti E, Casabianca A, Magnani M, Galluzzi L. Rapid monitoring of SARS-CoV-2 variants of concern through high-resolution melt analysis. Sci Rep 2023; 13:21598. [PMID: 38062105 PMCID: PMC10703772 DOI: 10.1038/s41598-023-48929-1] [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: 02/26/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
The current global pandemic of COVID-19 is characterized by waves of infection due to the emergence of new SARS-CoV-2 variants carrying mutations on the Spike (S) protein gene. Since autumn 2020 many Variants of Concern (VOC) have been reported: Alpha/B.1.1.7, Beta/B.1.351, Gamma/P.1, Delta/B.1.617.2, Omicron/B.1.1.529, and sublineages. Surveillance of genomic variants is currently based on whole-genome sequencing (WGS) of viral genomes on a random fraction of samples positive to molecular tests. WGS involves high costs, extended analysis time, specialized staff, and expensive instruments compared to a PCR-based test. To rapidly identify the VOCs in positive samples, six assays based on real-time PCR and high-resolution melting (HRM) were designed on the S gene and applied to 120 oro/nasopharyngeal swab samples collected from October 2020 to June 2022 (106 positive and 14 negative samples). Overall, the assays showed 100% specificity and sensitivity compared with commercial PCR tests for COVID-19. Moreover, 104 samples out of 106 (98.1%) were correctly identified as follows: 8 Wuhan (wild type), 12 Alpha, 23 Delta, 46 Omicron BA.1/BA.1.1, 15 Omicron BA.2/BA.4/BA.5. With our lab equipment, about 10 samples can be processed every 3 h at the cost of less than € 10 ($ 10.60) per sample, including RNA extraction. The implementation of this approach could help local epidemiological surveillance and clinical decision-making.
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Affiliation(s)
- Aurora Diotallevi
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy.
| | - Gloria Buffi
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy
| | - Simone Barocci
- Department of Clinical Pathology, Azienda Sanitaria Territoriale (AST) Pesaro e Urbino, Marche, 61029, Urbino, PU, Italy
| | - Marcello Ceccarelli
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy
- Department of Clinical Pathology, Azienda Sanitaria Territoriale (AST) Pesaro e Urbino, Marche, 61029, Urbino, PU, Italy
| | - Daniela Bencardino
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy
| | - Francesca Andreoni
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy
- Department of Clinical Pathology, Azienda Sanitaria Territoriale (AST) Pesaro e Urbino, Marche, 61029, Urbino, PU, Italy
| | - Chiara Orlandi
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy
| | - Marilisa Ferri
- Department of Clinical Pathology, Azienda Sanitaria Territoriale (AST) Pesaro e Urbino, Marche, 61029, Urbino, PU, Italy
| | - Daniela Vandini
- Department of Clinical Pathology, Azienda Sanitaria Territoriale (AST) Pesaro e Urbino, Marche, 61029, Urbino, PU, Italy
| | - Stefano Menzo
- Virology Laboratory, Azienda Ospedaliero Universitaria delle Marche, 60126, Ancona, AN, Italy
| | - Eugenio Carlotti
- Department of Prevention, Azienda Sanitaria Territoriale (AST) Pesaro e Urbino Marche, 61029, Urbino, PU, Italy
| | - Anna Casabianca
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy
| | - Mauro Magnani
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy
| | - Luca Galluzzi
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy
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8
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Ealand CS, Gordhan BG, Machowski EE, Kana BD. Development of primer-probe sets to rapidly distinguish single nucleotide polymorphisms in SARS-CoV-2 lineages. Front Cell Infect Microbiol 2023; 13:1283328. [PMID: 38130775 PMCID: PMC10733533 DOI: 10.3389/fcimb.2023.1283328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/10/2023] [Indexed: 12/23/2023] Open
Abstract
Ongoing SARS-CoV-2 infections are driven by the emergence of various variants, with differential propensities to escape immune containment. Single nucleotide polymorphisms (SNPs) in the RNA genome result in altered protein structures and when these changes occur in the S-gene, encoding the spike protein, the ability of the virus to penetrate host cells to initiate an infection can be significantly altered. As a result, vaccine efficacy and prior immunity may be diminished, potentially leading to new waves of infection. Early detection of SARS-CoV-2 variants using a rapid and scalable approach will be paramount for continued monitoring of new infections. In this study, we developed minor groove-binding (MGB) probe-based qPCR assays targeted to specific SNPs in the S-gene, which are present in variants of concern (VOC), namely the E484K, N501Y, G446S and D405N mutations. A total of 95 archived SARS-CoV-2 positive clinical specimens collected in Johannesburg, South Africa between February 2021 and March 2022 were assessed using these qPCR assays. To independently confirm SNP detection, Sanger sequencing of the relevant region in the S-gene were performed. Where a PCR product could be generated and sequenced, qPCR assays were 100% concordant highlighting the robustness of the approach. These assays, and the approach described, offer the opportunity for easy detection and scaling of targeted detection of variant-defining SNPs in the clinical setting.
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Affiliation(s)
| | | | | | - Bavesh D. Kana
- Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical Tuberculosis (TB) Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and The National Health Laboratory Service, Johannesburg, South Africa
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9
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Caponnetto F, De Martino M, Stefanizzi D, Del Sal R, Manini I, Kharrat F, D'Aurizio F, Fabris M, Visentini D, Poz D, Sozio E, Tascini C, Cesselli D, Isola M, Beltrami AP, Curcio F. Extracellular vesicle features are associated with COVID-19 severity. J Cell Mol Med 2023; 27:4107-4117. [PMID: 37964734 PMCID: PMC10746943 DOI: 10.1111/jcmm.17996] [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: 06/07/2023] [Revised: 08/08/2023] [Accepted: 10/05/2023] [Indexed: 11/16/2023] Open
Abstract
COVID-19 is heterogeneous; therefore, it is crucial to identify early biomarkers for adverse outcomes. Extracellular vesicles (EV) are involved in the pathophysiology of COVID-19 and have both negative and positive effects. The objective of this study was to identify the potential role of EV in the prognostic stratification of COVID-19 patients. A total of 146 patients with severe or critical COVID-19 were enrolled. Demographic and comorbidity characteristics were collected, together with routine haematology, blood chemistry and lymphocyte subpopulation data. Flow cytometric characterization of the dimensional and antigenic properties of COVID-19 patients' plasma EVs was conducted. Elastic net logistic regression with cross-validation was employed to identify the best model for classifying critically ill patients. Features of smaller EVs (i.e. the fraction of EVs smaller than 200 nm expressing either cluster of differentiation [CD] 31, CD 140b or CD 42b), albuminemia and the percentage of monocytes expressing human leukocyte antigen DR (HLA-DR) were associated with a better outcome. Conversely, the proportion of larger EVs expressing N-cadherin, CD 34, CD 56, CD31 or CD 45, interleukin 6, red cell width distribution (RDW), N-terminal pro-brain natriuretic peptide (NT-proBNP), age, procalcitonin, Charlson Comorbidity Index and pro-adrenomedullin were associated with disease severity. Therefore, the simultaneous assessment of EV dimensions and their antigenic properties complements laboratory workup and helps in patient stratification.
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Affiliation(s)
| | | | | | | | - Ivana Manini
- Department of MedicineUniversity of UdineUdineItaly
| | | | | | - Martina Fabris
- Department of MedicineUniversity of UdineUdineItaly
- Azienda Sanitaria Universitaria Friuli CentraleUdineItaly
| | | | - Donatella Poz
- Azienda Sanitaria Universitaria Friuli CentraleUdineItaly
| | - Emanuela Sozio
- Azienda Sanitaria Universitaria Friuli CentraleUdineItaly
| | - Carlo Tascini
- Department of MedicineUniversity of UdineUdineItaly
- Azienda Sanitaria Universitaria Friuli CentraleUdineItaly
| | - Daniela Cesselli
- Department of MedicineUniversity of UdineUdineItaly
- Azienda Sanitaria Universitaria Friuli CentraleUdineItaly
| | - Miriam Isola
- Department of MedicineUniversity of UdineUdineItaly
| | - Antonio Paolo Beltrami
- Department of MedicineUniversity of UdineUdineItaly
- Azienda Sanitaria Universitaria Friuli CentraleUdineItaly
| | - Francesco Curcio
- Department of MedicineUniversity of UdineUdineItaly
- Azienda Sanitaria Universitaria Friuli CentraleUdineItaly
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10
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Ahmadi AS, Shafiei-Jandaghi NZ, Sadeghi K, Nejati A, Zadheidar S, Mokhtari-Azad T, Yavarian J. Comparison of Circulating Variants during the Beginning, Middle and the End of the 4th Wave of COVID-19 in Tehran Province, Iran in 2021. IRANIAN JOURNAL OF PUBLIC HEALTH 2023; 52:2621-2629. [PMID: 38435775 PMCID: PMC10903313 DOI: 10.18502/ijph.v52i12.14323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 08/11/2023] [Indexed: 03/05/2024]
Abstract
Background Whole viral genome sequencing with next generation sequencing (NGS) technique is useful tool for determining the diversity of variants and mutations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this study we have attempted to characterize the mutations and circulating variants of the SARSCoV-2 genome during the 4th wave of COVID-19 pandemic in Tehran, Iran in 2021. Methods We performed complete genome sequencing of 15 SARS-CoV-2 detected from 15 COVID-19 patients during the 4th wave of COVID-19 pandemic with NGS. Three groups of the patients at the beginning, middle and the end of the 4th wave were compared together. Results We detected alpha and delta variants during the 4th wave of the pandemic. The results illustrated a dominance of amino acid substitution D614G in spike, and the most frequent mutants were N-R203K, G204R, S235F, nsp12-P323L, nsp6-G106del, G107del and F108del. Conclusion The detection of the virus mutations is a useful procedure for identifying the virus behavior and its genetic evolution in order to improve the efficacy of the monitoring strategies and therapeutic measures.
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Affiliation(s)
- Akram Sadat Ahmadi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Kaveh Sadeghi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Nejati
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Sevrin Zadheidar
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Talat Mokhtari-Azad
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Jila Yavarian
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Antibiotic Stewardship and Antimicrobial Resistance, Tehran University of Medical Sciences, Tehran, Iran
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11
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Lu Y, Ye Z, Liu X, Zhou L, Ding X, Hou Y. Role of SARS‑CoV‑2 nucleocapsid protein in affecting immune cells and insights on its molecular mechanisms. Exp Ther Med 2023; 26:504. [PMID: 37822585 PMCID: PMC10562965 DOI: 10.3892/etm.2023.12203] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 08/07/2023] [Indexed: 10/13/2023] Open
Abstract
The present study aimed to explore the immune regulatory function of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid (N) protein and related mechanisms. In a series of protein activity experiments, SARS-CoV-2 N protein promoted proliferation of three immune cell lines: mouse Raw264.7, human Jurkat and human Raji in a dose-dependent manner. A total of 10 µg/ml N protein could significantly change cell cycle progression of the aforementioned three immune cell lines and could promote quick entry of Raw264.7 cells into G2/M phase from S phase to achieve rapid growth. Additionally, the N protein could also stimulate Raw264.7 cells to secrete a number of proinflammatory factors such as TNF-α, IL-6 and IL-10. RNA sequencing analysis indicated that the N protein changed the expression of certain genes involved in immune-related functions and four important signaling pathways, including JAK-STAT, TNF, NF-κB and MAPK signaling pathways, which suggested that the N protein may not only regulate the expression of genes involved in the process of resisting viral infection in macrophages of the immune system, but also change cellular signal processing.
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Affiliation(s)
- Yan Lu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Sciences, China West Normal University, Nanchong, Sichuan 637009, P.R. China
| | - Ziyu Ye
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Sciences, China West Normal University, Nanchong, Sichuan 637009, P.R. China
| | - Xinlan Liu
- Key Laboratory of Nanchong City of Ecological Environment Protection and Pollution Prevention in Jialing River Basin, College of Environmental Science and Engineering, China West Normal University, Nanchong, Sichuan 637009, P.R. China
| | - Liqian Zhou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Sciences, China West Normal University, Nanchong, Sichuan 637009, P.R. China
| | - Xiang Ding
- Key Laboratory of Nanchong City of Ecological Environment Protection and Pollution Prevention in Jialing River Basin, College of Environmental Science and Engineering, China West Normal University, Nanchong, Sichuan 637009, P.R. China
| | - Yiling Hou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Sciences, China West Normal University, Nanchong, Sichuan 637009, P.R. China
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12
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Nakhaie M, Ghoreshi ZAS, Rukerd MRZ, Askarpour H, Arefinia N. Novel Mutations in the Non-Structure Protein 2 of SARS-CoV-2. Mediterr J Hematol Infect Dis 2023; 15:e2023059. [PMID: 38028396 PMCID: PMC10631707 DOI: 10.4084/mjhid.2023.059] [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: 06/10/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Mutation in the genome of SARS-CoV-2 may play a role in immune evasion, pathogenicity, and speed of its transmission. Our investigation aimed to evaluate the mutations that exist in the NSP2. Materials and Method RNA was extracted from nasopharyngeal swabs from 100 COVID-19 patients. RT-PCR was performed on all samples using NSP2-specific primers. Following gel electrophoresis, the bands were cut, purified, and sequenced using the Sanger method. After sequencing, 90 sequences could be used for further analysis. Bioinformatics analysis was conducted to investigate the effect of mutations on protein structure, stability, prediction of homology models, and phylogeny tree. Results The patients' mean age was 51.08. The results revealed that 8 of the 17 NSP2 mutations (R207C, T224I, G262V, T265I, K337D, N348S, G392D, and I431M) were missense. One deletion was also found in NSP2. Among NSP2 missense mutations studied, K337D and G392D increased structural stability while the others decreased it. The homology-designed models demonstrated that the homologies were comparable to the sequences of the Wuhan-HU-1 virus. Conclusion Our study suggested that the mutations K337D and G392D modulate the stability of NSP2, and tracking viral evolution should be implemented and vaccine development updated.
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Affiliation(s)
- Mohsen Nakhaie
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran
- Gastroenterology and Hepatology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Zohreh-al-sadat Ghoreshi
- School of Medicine, Jiroft University of Medical Sciences, Jiroft, Iran
- Student Research Committee Jiroft University of Medical Sciences, Jiroft, Iran
| | - Mohammad Rezaei Zadeh Rukerd
- Gastroenterology and Hepatology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
- Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Hedyeh Askarpour
- School of Medicine, Jiroft University of Medical Sciences, Jiroft, Iran
| | - Nasir Arefinia
- School of Medicine, Jiroft University of Medical Sciences, Jiroft, Iran
- Bio Environmental Health Hazard Research Center, Jiroft University of Medical Sciences, Jiroft, Iran
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13
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Kumthip K, Khamrin P, Yodmeeklin A, Ushijima H, Maneekarn N. Molecular detection and characterization of SARS-CoV-2 in wastewater in Thailand during 2020-2022. J Infect Public Health 2023; 16:1884-1890. [PMID: 37839311 DOI: 10.1016/j.jiph.2023.09.011] [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: 06/05/2023] [Revised: 09/13/2023] [Accepted: 09/21/2023] [Indexed: 10/17/2023] Open
Abstract
BACKGROUND SARS-CoV-2 has been detected in feces of infected individuals and in wastewater in many countries, which indicates that wastewater may be used to monitor contamination of the virus in community. However, information about the presence of SARS-CoV-2 in different types of environmental water and their genetic characterization are still limited. The purpose of this study was to investigate the presence of SARS-CoV-2 contaminating in environmental water in Thailand. METHODS We collected 600 water samples from 10 different sampling sites in Chiang Mai city, Thailand twice a month from July 2020 to December 2022. The SARS-CoV-2 RNA was detected by real-time RT-PCR and further amplified for ORF1a and S genes to investigate their genetic relationship to the reference strains by phylogenetic analysis. RESULTS SARS-CoV-2 was detected at 0.17% in the wastewater sample collected in the vicinity of fresh market where the outbreak of COVID-19 cases were simultaneously reported. The detected SARS-CoV-2 strain (W323/21) had nucleotide and amino acid sequences identical to SARS-CoV-2 Delta variant. Amino acid sequence alignment of spike protein revealed that the W323/21 strain carried a mutation of D950N as it was demonstrated in Delta variant reference strains. CONCLUSIONS The findings indicated that SARS-CoV-2 Delta variant was detected in wastewater in Chiang Mai, Thailand during the outbreak of COVID-19, suggesting a circulation of the virus in environmental water and in the community during the outbreak.
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Affiliation(s)
- Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Center of Excellence (Emerging and Re-emerging Diarrheal Viruses), Chiang Mai University, Chiang Mai, Thailand
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Center of Excellence (Emerging and Re-emerging Diarrheal Viruses), Chiang Mai University, Chiang Mai, Thailand
| | - Arpaporn Yodmeeklin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Center of Excellence (Emerging and Re-emerging Diarrheal Viruses), Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Center of Excellence (Emerging and Re-emerging Diarrheal Viruses), Chiang Mai University, Chiang Mai, Thailand.
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14
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Kim IH, No JS, Kim JA, Park AK, Lee H, Kim JM, Lee NJ, Kim CK, Lee CY, Woo S, Lee J, Rhee J, Kim EJ. Genomic epidemiology of SARS-CoV-2 variants in South Korea between January 2020 and February 2023. Virology 2023; 587:109869. [PMID: 37673001 DOI: 10.1016/j.virol.2023.109869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/10/2023] [Accepted: 08/15/2023] [Indexed: 09/08/2023]
Abstract
The Korea Disease Control and Prevention Agency (KDCA) has been conducting national genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2). To monitor and characterize circulating SARS-CoV-2 variants in South Korea, 102,873 oropharyngeal/nasopharyngeal swab samples collected from patients with confirmed COVID-19 were sequenced, assigned lineages, and phylogenetically analyzed. Each wave followed a pattern of variants emerging first abroad and then spreading domestically. In 2020, B.41 lineage led the first wave, and B.1.497 dominated the second and third waves. In 2021, the fourth wave was driven by Delta (AY.69 and AY.122.5). In 2022, the fifth to seventh waves were dominated by Omicron sub-lineages BA.1/BA.1.1 and BA.2/BA.2.3, BA.5/BA.5.2, and BN.1, sequentially. The KDCA detected and monitored increasing variants in advance prior to large-scale epidemics, but the repeated emergence of new variants could threaten public health again. Therefore, it is important to continue to monitor and characterize emerging and circulating variants through national genomic surveillance.
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Affiliation(s)
- Il-Hwan Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Jin Sun No
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Jeong-Ah Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Ae Kyung Park
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - HyeokJin Lee
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Jeong-Min Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Nam-Joo Lee
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Chi-Kyeong Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Chae Young Lee
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - SangHee Woo
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Jaehee Lee
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - JeeEun Rhee
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - Eun-Jin Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, South Korea.
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15
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Pondé RADA. Physicochemical effects of emerging exchanges on the spike protein's RBM of the SARS-CoV-2 Omicron subvariants BA.1-BA.5 and its influence on the biological properties and attributes developed by these subvariants. Virology 2023; 587:109850. [PMID: 37562286 DOI: 10.1016/j.virol.2023.109850] [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: 04/24/2023] [Revised: 06/13/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023]
Abstract
Emerging in South Africa, SARS-CoV-2 Omicron variant was marked by the expression of an exaggerated number of mutations throughout its genome and by the emergence of subvariants, whose attributes developed by them have been associated with amino acid exchanges that occur mainly in the RBM region of the spike protein. The RBM comprises a region within the RBD and is directly involved in the SARS-CoV-2 spike protein interaction with the host cell ACE2 receptor, during the infection mechanism and viral transmission. Defined as the region from aa 437 to aa 508, there are several residues in certain positions that interact directly with the human ACE-2 receptor during these processes. The occurrence of amino acid exchanges in these positions causes physicochemical alterations in the SARS-CoV-2 spike protein, which confer additional advantages and attributes to the agent. In addition, these exchanges serve as a basis for the characterization of new variants and subvariants of SARS-CoV-2. In this review, the amino acid exchanges that have occurred in the RBM of the subvariants BA.1 to BA.5 of SARS-CoV-2 that emerged from the Omicron are described. The physicochemical effects caused by them on spike protein are also described, as well as their influence on the biological properties and attributes developed by the subvariants BA.1, BA.2, BA.3, BA.4 and BA.5.
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Affiliation(s)
- Robério Amorim de Almeida Pondé
- Secretaria de Estado da Saúde -SES/Superintendência de Vigilância em Saúde-SUVISA/GO, Gerência de Vigilância Epidemiológica de Doenças Transmissíveis-GVEDT/Coordenação de Análises e Pesquisas-CAP, Goiânia, Goiás, Brazil; Laboratory of Human Virology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil.
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16
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Makowski JA, Kensinger AH, Cunningham CL, Frye CJ, Shine M, Lackey PE, Mihailescu MR, Evanseck JD. Delta SARS-CoV-2 s2m Structure, Dynamics, and Entropy: Consequences of the G15U Mutation. ACS PHYSICAL CHEMISTRY AU 2023; 3:434-443. [PMID: 37780540 PMCID: PMC10540284 DOI: 10.1021/acsphyschemau.3c00008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 10/03/2023]
Abstract
Bioinformatic analysis of the Delta SARS-CoV-2 genome reveals a single nucleotide mutation (G15U) in the stem-loop II motif (s2m) relative to ancestral SARS-CoV-2. Despite sequence similarity, unexpected differences between SARS-CoV-2 and Delta SARS-CoV-2 s2m homodimerization experiments require the discovery of unknown structural and thermodynamic changes necessary to rationalize the data. Using our reported SARS-CoV-2 s2m model, we induced the G15U substitution and performed 3.5 microseconds of unbiased molecular dynamics simulation at 283 and 310 K. The resultant Delta s2m adopted a secondary structure consistent with our reported NMR data, resulting in significant deviations in the tertiary structure and dynamics from our SARS-CoV-2 s2m model. First, we find differences in the overall three-dimensional structure, where the characteristic 90° L-shaped kink of the SARS-CoV-2 s2m did not form in the Delta s2m resulting in a "linear" hairpin with limited bending dynamics. Delta s2m helical parameters are calculated to align closely with A-form RNA, effectively eliminating a hinge point to form the L-shape kink by correcting an upper stem defect in SARS-CoV-2 induced by a noncanonical and dynamic G:A base pair. Ultimately, the shape difference rationalizes the migration differences in reported electrophoresis experiments. Second, increased fluctuation of the Delta s2m palindromic sequence, within the terminal loop, compared to SARS-CoV-2 s2m results in an estimated increase of entropy of 6.8 kcal/mol at 310 K relative to the SARS-CoV-2 s2m. The entropic difference offers a unique perspective on why the Delta s2m homodimerizes less spontaneously, forming fewer kissing dimers and extended duplexes compared to SARS-CoV-2. In this work, both the L-shape reduction and palindromic entropic penalty provides an explanation of our reported in vitro electrophoresis homodimerization results. Ultimately, the structural, dynamical, and entropic differences between the SARS-CoV-2 s2m and Delta s2m serve to establish a foundation for future studies of the s2m function in the viral lifecycle.
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Affiliation(s)
- Joseph A. Makowski
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Adam H. Kensinger
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Caylee L. Cunningham
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Caleb J. Frye
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Morgan Shine
- Department
of Biochemistry and Chemistry, Westminster
College, New Wilmington, Pennsylvania 16172, United States
| | - Patrick E. Lackey
- Department
of Biochemistry and Chemistry, Westminster
College, New Wilmington, Pennsylvania 16172, United States
| | - Mihaela Rita Mihailescu
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Jeffrey D. Evanseck
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
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17
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Abbasi H, Behrouzikhah M, Divbandi M, Tabaraei A, Khosravi A, Razavi Nikoo H. Genomic analysis of SARS-CoV-2 variants: diagnosis and vaccination challenges. J Biomol Struct Dyn 2023; 41:14939-14951. [PMID: 37676289 DOI: 10.1080/07391102.2023.2252069] [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: 06/20/2022] [Accepted: 02/18/2023] [Indexed: 09/08/2023]
Abstract
SARS-CoV-2 put a heavy financial burden on the healthcare system, with millions of laboratory-confirmed cases and deaths worldwide in the last 2 years. During the seventh wave of this pandemic, the continuously evolving nature of SARS-CoV-2 resulted in the emergence of new variants that harbor different mutations. Mutations are associated with changes in the virus behavior, including increased transmissibility, increased virulence, and evasion of neutralizing antibodies. Currently, we need detailed and comprehensive genomic information on all SARS-CoV-2 variants. One of the key points in this study was the genome survey of mutation profiles across variants as a genomic data source, to determine the efficiency of RT-qPCR assays. We also used the source to calculate the binding affinity changes of neutralizing antibodies-mutant receptor binding domain (RBD) complexes and determine vaccine efficacy. Our result revealed that the number of nucleotide mismatches is variable in the WHO-recommended primer-probe sets. Mismatches located at the 3' ends of the oligonucleotide, may lead to false-negative results. Only the primer-probe sets designed by the Ministry of Public Health of Thailand were exclusive and cannot detect the omicron variant reliably. Binding affinity changes showed that E484K was more deleterious than other mutations and decreased stability between the mutant RBD protein and neutralizing antibodies. The Omicrons show the highest change in binding affinity which may lead to immune escape and increase transmissibility. Additionally, the 7D6 monoclonal antibody in the 7eam complex could neutralize all variants of SARS-CoV-2. We strongly recommend creating and improving a matrix accuracy by processing a large number of SARS-CoV-2 sequences to update RT-qPCR assays and identified immunogenic residues among conserved RBD. Also, a detail computational analysis is needed to investigate distinctive amino acid substitution patterns which may be foundational in the vaccines. Finally, designing in-vitro studies can help confirm the present study and manage COVID-19 patients.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hamidreza Abbasi
- Department of Medical Biotechnology, Faculty of Advanced Medical Technologies, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mehdi Behrouzikhah
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Marzieh Divbandi
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Alijan Tabaraei
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ayyoob Khosravi
- Stem Cell Research Center, Golestan University of Medical Sciences, Gorgan, Iran
- Department of Molecular Medicine, Faculty of Advanced Medical Technologies, Golestan University of Medical Sciences, Gorgan, Iran
| | - Hadi Razavi Nikoo
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
- Infectious Disease Research Center, Golestan University of Medical Sciences, Gorgan, Iran
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18
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Gatti G, Brandolini M, Mancini A, Taddei F, Zannoli S, Dirani G, Manera M, Arfilli V, Denicolò A, Marzucco A, Montanari MS, Zaghi I, Guerra M, Tennina R, Marino MM, Grumiro L, Cricca M, Sambri V. Genomic and Temporal Analysis of Deletions Correlated to qRT-PCR Dropout in N Gene in Alpha, Delta and Omicron Variants. Viruses 2023; 15:1630. [PMID: 37631974 PMCID: PMC10458892 DOI: 10.3390/v15081630] [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: 07/05/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Since the first SARS-CoV-2 outbreak, mutations such as single nucleotide polymorphisms (SNPs) and insertion/deletions (INDELs) have changed and characterized the viral genome sequence, structure and protein folding leading to the onset of new variants. The presence of those alterations challenges not only the clinical field but also the diagnostic demand due to failures in gene detection or incompleteness of polymerase chain reaction (PCR) results. In particular, the analysis of understudied genes such as N and the investigation through whole-genome next generation sequencing (WG-NGS) of regions more prone to mutate can help in the identification of new or reacquired mutations, with the aim of designing robust and long-lasting primers. In 48 samples of SARS-CoV-2 (including Alpha, Delta and Omicron variants), a lack of N gene amplification was observed in the genomes analyzed through WG-NGS. Three gene regions were detected hosting the highest number of SNPs and INDELs. In several cases, the latter can interfere deeply with both the sensitivity of diagnostic methodologies and the final protein folding. The monitoring over time of the viral evolution and the reacquisition among different variants of the same mutations or different alterations within the same genomic positions can be relevant to avoid unnecessary consumption of resources.
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Affiliation(s)
- Giulia Gatti
- Department of Medical and Surgical Sciences (DIMEC)—Alma Mater Studiorum, University of Bologna, 40138 Bologna, Italy; (G.G.); (M.B.); (M.C.)
| | - Martina Brandolini
- Department of Medical and Surgical Sciences (DIMEC)—Alma Mater Studiorum, University of Bologna, 40138 Bologna, Italy; (G.G.); (M.B.); (M.C.)
| | - Andrea Mancini
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Francesca Taddei
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Silvia Zannoli
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Giorgio Dirani
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Martina Manera
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Valentina Arfilli
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Agnese Denicolò
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Anna Marzucco
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Maria Sofia Montanari
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Irene Zaghi
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Massimiliano Guerra
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Rita Tennina
- Unit of Laboratory Medicine—Local Health Authority 1 Complex Operative Unit, 67051 L’Aquila, Italy
| | - Maria Michela Marino
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Laura Grumiro
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Monica Cricca
- Department of Medical and Surgical Sciences (DIMEC)—Alma Mater Studiorum, University of Bologna, 40138 Bologna, Italy; (G.G.); (M.B.); (M.C.)
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Vittorio Sambri
- Department of Medical and Surgical Sciences (DIMEC)—Alma Mater Studiorum, University of Bologna, 40138 Bologna, Italy; (G.G.); (M.B.); (M.C.)
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
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19
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Kelch MA, Vera-Guapi A, Beder T, Oswald M, Hiemisch A, Beil N, Wajda P, Ciesek S, Erfle H, Toptan T, Koenig R. Machine learning on large scale perturbation screens for SARS-CoV-2 host factors identifies β-catenin/CBP inhibitor PRI-724 as a potent antiviral. Front Microbiol 2023; 14:1193320. [PMID: 37342561 PMCID: PMC10277617 DOI: 10.3389/fmicb.2023.1193320] [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: 03/24/2023] [Accepted: 05/16/2023] [Indexed: 06/23/2023] Open
Abstract
Expanding antiviral treatment options against SARS-CoV-2 remains crucial as the virus evolves under selection pressure which already led to the emergence of several drug resistant strains. Broad spectrum host-directed antivirals (HDA) are promising therapeutic options, however the robust identification of relevant host factors by CRISPR/Cas9 or RNA interference screens remains challenging due to low consistency in the resulting hits. To address this issue, we employed machine learning, based on experimental data from several knockout screens and a drug screen. We trained classifiers using genes essential for virus life cycle obtained from the knockout screens. The machines based their predictions on features describing cellular localization, protein domains, annotated gene sets from Gene Ontology, gene and protein sequences, and experimental data from proteomics, phospho-proteomics, protein interaction and transcriptomic profiles of SARS-CoV-2 infected cells. The models reached a remarkable performance suggesting patterns of intrinsic data consistency. The predicted HDF were enriched in sets of genes particularly encoding development, morphogenesis, and neural processes. Focusing on development and morphogenesis-associated gene sets, we found β-catenin to be central and selected PRI-724, a canonical β-catenin/CBP disruptor, as a potential HDA. PRI-724 limited infection with SARS-CoV-2 variants, SARS-CoV-1, MERS-CoV and IAV in different cell line models. We detected a concentration-dependent reduction in cytopathic effects, viral RNA replication, and infectious virus production in SARS-CoV-2 and SARS-CoV-1-infected cells. Independent of virus infection, PRI-724 treatment caused cell cycle deregulation which substantiates its potential as a broad spectrum antiviral. Our proposed machine learning concept supports focusing and accelerating the discovery of host dependency factors and identification of potential host-directed antivirals.
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Affiliation(s)
- Maximilian A. Kelch
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | | | - Thomas Beder
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Marcus Oswald
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Alicia Hiemisch
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Nina Beil
- Advanced Biological Screening Facility (ABSF), High-Content Analysis of the Cell (HiCell), BioQuant, Heidelberg University, Heidelberg, Germany
| | - Piotr Wajda
- Advanced Biological Screening Facility (ABSF), High-Content Analysis of the Cell (HiCell), BioQuant, Heidelberg University, Heidelberg, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
- German Centre for Infection Research (DZIF), External Partner Site Frankfurt, Frankfurt, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt, Germany
| | - Holger Erfle
- Advanced Biological Screening Facility (ABSF), High-Content Analysis of the Cell (HiCell), BioQuant, Heidelberg University, Heidelberg, Germany
| | - Tuna Toptan
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | - Rainer Koenig
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
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20
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Joshi D, Nyhoff LE, Zarnitsyna VI, Moreno A, Manning K, Linderman S, Burrell AR, Stephens K, Norwood C, Mantus G, Ahmed R, Anderson EJ, Staat MA, Suthar MS, Wrammert J. Infants and young children generate more durable antibody responses to SARS-CoV-2 infection than adults. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.10.23288360. [PMID: 37090559 PMCID: PMC10120804 DOI: 10.1101/2023.04.10.23288360] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Since the emergence of SARS-CoV-2, research has shown that adult patients mount broad and durable immune responses to infection. However, response to infection remains poorly studied in infants/young children. In this study, we evaluated humoral responses to SARS-CoV-2 in 23 infants/young children before and after infection. We found that antibody responses to SARS-CoV-2 spike antigens peaked approximately 30 days after infection and were maintained up to 500 days with little apparent decay. While the magnitude of humoral responses was similar to an adult cohort recovered from mild/moderate COVID-19, both binding and neutralization titers to WT SARS-CoV-2 were more durable in infants/young children, with Spike and RBD IgG antibody half-life nearly 4X as long as in adults. The functional breadth of adult and infant/young children SARS-CoV-2 responses were comparable, with similar reactivity against panel of recent and previously circulating viral variants. Notably, IgG subtype analysis revealed that while IgG1 formed the majority of both adults' and infants/young children's response, IgG3 was more common in adults and IgG2 in infants/young children. These findings raise important questions regarding differential regulation of humoral immunity in infants/young children and adults and could have broad implications for the timing of vaccination and booster strategies in this age group.
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21
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Rahman MS, Hoque MN, Chowdhury SR, Siddique MM, Islam OK, Galib SM, Islam MT, Hossain MA. Temporal dynamics and fatality of SARS-CoV-2 variants in Bangladesh. Health Sci Rep 2023; 6:e1209. [PMID: 37077184 PMCID: PMC10108430 DOI: 10.1002/hsr2.1209] [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: 01/11/2023] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 04/21/2023] Open
Abstract
Background and Aims Since the beginning of the SARS-CoV-2 pandemic, multiple new variants have emerged posing an increased risk to global public health. This study aimed to investigate SARS-CoV-2 variants, their temporal dynamics, infection rate (IFR) and case fatality rate (CFR) in Bangladesh by analyzing the published genomes. Methods We retrieved 6610 complete whole genome sequences of the SARS-CoV-2 from the GISAID (Global Initiative on Sharing all Influenza Data) platform from March 2020 to October 2022, and performed different in-silico bioinformatics analyses. The clade and Pango lineages were assigned by using Nextclade v2.8.1. SARS-CoV-2 infections and fatality data were collected from the Institute of Epidemiology Disease Control and Research (IEDCR), Bangladesh. The average IFR was calculated from the monthly COVID-19 cases and population size while average CFR was calculated from the number of monthly deaths and number of confirmed COVID-19 cases. Results SARS-CoV-2 first emerged in Bangladesh on March 3, 2020 and created three pandemic waves so far. The phylogenetic analysis revealed multiple introductions of SARS-CoV-2 variant(s) into Bangladesh with at least 22 Nextstrain clades and 107 Pangolin lineages with respect to the SARS-CoV-2 reference genome of Wuhan/Hu-1/2019. The Delta variant was detected as the most predominant (48.06%) variant followed by Omicron (27.88%), Beta (7.65%), Alpha (1.56%), Eta (0.33%) and Gamma (0.03%) variant. The overall IFR and CFR from circulating variants were 13.59% and 1.45%, respectively. A time-dependent monthly analysis showed significant variations in the IFR (p = 0.012, Kruskal-Wallis test) and CFR (p = 0.032, Kruskal-Wallis test) throughout the study period. We found the highest IFR (14.35%) in 2020 while Delta (20A) and Beta (20H) variants were circulating in Bangladesh. Remarkably, the highest CFR (1.91%) from SARS-CoV-2 variants was recorded in 2021. Conclusion Our findings highlight the importance of genomic surveillance for careful monitoring of variants of concern emergence to interpret correctly their relative IFR and CFR, and thus, for implementation of strengthened public health and social measures to control the spread of the virus. Furthermore, the results of the present study may provide important context for sequence-based inference in SARS-CoV-2 variant(s) evolution and clinical epidemiology beyond Bangladesh.
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Affiliation(s)
- M. Shaminur Rahman
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive HealthBangabandhu Sheikh Mujibur Rahman Agricultural UniversityGazipurBangladesh
| | - Susmita Roy Chowdhury
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - Md. Moradul Siddique
- Department of Computer Science and EngineeringJashore University of Science and TechnologyJashoreBangladesh
| | - Ovinu Kibria Islam
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - Syed Md. Galib
- Department of Computer Science and EngineeringJashore University of Science and TechnologyJashoreBangladesh
| | - Md. Tanvir Islam
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - M. Anwar Hossain
- Department of MicrobiologyUniversity of DhakaDhakaBangladesh
- Jashore University of Science and TechnologyJashoreBangladesh
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22
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Wussow F, Kha M, Kim T, Ly M, Yll-Pico M, Kar S, Lewis MG, Chiuppesi F, Diamond DJ. Synthetic multiantigen MVA vaccine COH04S1 and variant-specific derivatives protect Syrian hamsters from SARS-CoV-2 Omicron subvariants. NPJ Vaccines 2023; 8:41. [PMID: 36928589 PMCID: PMC10018591 DOI: 10.1038/s41541-023-00640-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
Emerging SARS-CoV-2 Omicron subvariants continue to disrupt COVID-19 vaccine efficacy through multiple immune mechanisms including neutralizing antibody evasion. We developed COH04S1, a synthetic modified vaccinia Ankara vector that co-expresses Wuhan-Hu-1-based spike and nucleocapsid antigens. COH04S1 demonstrated efficacy against ancestral virus and Beta and Delta variants in animal models and was safe and immunogenic in a Phase 1 clinical trial. Here, we report efficacy of COH04S1 and analogous Omicron BA.1- and Beta-specific vaccines to protect Syrian hamsters from Omicron subvariants. Despite eliciting strain-specific antibody responses, all three vaccines protect hamsters from weight loss, lower respiratory tract infection, and lung pathology following challenge with Omicron BA.1 or BA.2.12.1. While the BA.1-specifc vaccine affords consistently improved efficacy compared to COH04S1 to protect against homologous challenge with BA.1, all three vaccines confer similar protection against heterologous challenge with BA.2.12.1. These results demonstrate efficacy of COH04S1 and variant-specific derivatives to confer cross-protective immunity against SARS-CoV-2 Omicron subvariants.
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Affiliation(s)
- Felix Wussow
- Department of Hematology and Transplant Center, City of Hope National Medical Center, Duarte, CA, 91010, USA.
| | - Mindy Kha
- Department of Hematology and Transplant Center, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Taehyun Kim
- Department of Hematology and Transplant Center, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Minh Ly
- Department of Hematology and Transplant Center, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Marcal Yll-Pico
- Department of Hematology and Transplant Center, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | | | | | - Flavia Chiuppesi
- Department of Hematology and Transplant Center, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Don J Diamond
- Department of Hematology and Transplant Center, City of Hope National Medical Center, Duarte, CA, 91010, USA.
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23
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Development of Next Generation Vaccines against SARS-CoV-2 and Variants of Concern. Viruses 2023; 15:v15030624. [PMID: 36992333 PMCID: PMC10057551 DOI: 10.3390/v15030624] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/20/2023] [Accepted: 02/20/2023] [Indexed: 03/02/2023] Open
Abstract
SARS-CoV-2 has caused the COVID-19 pandemic, with over 673 million infections and 6.85 million deaths globally. Novel mRNA and viral-vectored vaccines were developed and licensed for global immunizations under emergency approval. They have demonstrated good safety and high protective efficacy against the SARS-CoV-2 Wuhan strain. However, the emergence of highly infectious and transmissible variants of concern (VOCs) such as Omicron was associated with considerable reductions in the protective efficacy of the current vaccines. The development of next-generation vaccines that could confer broad protection against both the SARS-CoV-2 Wuhan strain and VOCs is urgently needed. A bivalent mRNA vaccine encoding the Spike proteins of both the SARS-CoV-2 Wuhan strain and the Omicron variant has been constructed and approved by the US FDA. However, mRNA vaccines are associated with instability and require an extremely low temperature (−80 °C) for storage and transportation. They also require complex synthesis and multiple chromatographic purifications. Peptide-based next-generation vaccines could be developed by relying on in silico predictions to identify peptides specifying highly conserved B, CD4+ and CD8+ T cell epitopes to elicit broad and long-lasting immune protection. These epitopes were validated in animal models and in early phase clinical trials to demonstrate immunogenicity and safety. Next-generation peptide vaccine formulations could be developed to incorporate only naked peptides, but they are costly to synthesize and production would generate extensive chemical waste. Continual production of recombinant peptides specifying immunogenic B and T cell epitopes could be achieved in hosts such as E. coli or yeast. However, recombinant protein/peptide vaccines require purification before administration. The DNA vaccine might serve as the most effective next-generation vaccine for low-income countries, since it does not require an extremely low temperature for storage or need extensive chromatographic purification. The construction of recombinant plasmids carrying genes specifying highly conserved B and T cell epitopes meant that vaccine candidates representing highly conserved antigenic regions could be rapidly developed. Poor immunogenicity of DNA vaccines could be overcome by the incorporation of chemical or molecular adjuvants and the development of nanoparticles for effective delivery.
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24
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Jesmani Y, Bozorgomid A, Shadmani FK, Dehbani A, Sayad B. Demographic and clinical characteristics and outcomes of COVID-19 patients admitted to a university hospital in the west of Iran: a retrospective study in the third wave. VACUNAS 2023; 24:S1576-9887(23)00007-9. [PMID: 36817340 PMCID: PMC9922569 DOI: 10.1016/j.vacun.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/27/2023] [Indexed: 02/15/2023]
Abstract
COVID-19 is a disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The characteristics of this infectious disease vary from a country to another and from one peak to the next. The aim of the present study was to describe the COVID-19 patients hospitalized in Kermanshah, a city in the west of Iran, in the third peak of the disease and to identify in-hospital mortality determinants in this disease. Methods: In this retrospective study, the clinical and demographic characteristics, laboratory findings, prescribed treatments and outcome of all COVID-19 patients (definitive, suspected, and probable) were collected from the medical records department of Farabi Hospital affiliated with Kermanshah University of Medical Sciences, Kermanshah, Iran from 22 October to 20 November 2020. Results: In total, 665 COVID-19 patients (265 females and 400 males, mean age: 58.7 years) were enrolled, including 479 confirmed, 15 probable, and 30 suspected cases. About 84% of the patients presented with low oxygen saturation levels. The most common comorbidities were hypertension (15%), diabetes (10%), and cardiovascular disease (3%). The median (IQR) length of hospital stay was 6 (Nojomi et al., 2021; Flores-Vega et al., 2022; Fattahi et al., 2021; Cusinato et al., 2022; Avatef Fazeli et al., 2021 (4., 5., 6., 7., 8.)) and 7 (Javadi Mamaghani et al., 2021; Abdolahnejad et al., 2022; Nojomi et al., 2021; Flores-Vega et al., 2022; Fattahi et al., 2021; Cusinato et al., 2022; Avatef Fazeli et al., 2021; Sayad et al., 2021; Hesni et al., 2022; Buttenschøn et al., 2022; Smits et al., 2022; Rosenberger et al., 2021; Shi et al., 2022 (2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12., 13., 14.)) day in discharged and deceased patients, respectively. Eighty-two out of 655 patients admitted to the hospital and 39of the 60 patients admitted to the ICU died. In total, in-hospital mortality rate was 12.33%. Regarding lab variables, in the adjusted model, no significant difference was observed between discharged and deceased patients.The results of multivariable logistic regression showed that each one-unit increase in oxygen saturation (SPO2) increased the odds of survival by 0.88 times (aOR 0.88, 95% CI 0.78-0.99, p = 0.043). Moreover, each one-day increase in the length of ICU stay reduced the odds of mortality by 0.49 times (aOR 0.82, 95% CI 0.26-0.95, p = 0.035). Conclusion: Hospitalized COVID-19 patients were generally more ill during the third peak so that about 85% of the patients had SPO2 ≤ 93%. The in-hospital mortality rate was also high. Demographic and paraclinical variables (except SPO2 level) were not suitable predictors of mortality.
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Affiliation(s)
- Younes Jesmani
- Infectious Diseases Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Clinical Research Development Center, Imam Reza Hospital, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Arezoo Bozorgomid
- Infectious Diseases Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Fatemeh Khosravi Shadmani
- Research Center for Environmental Determinants of Health, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ali Dehbani
- Infectious Diseases Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Clinical Research Development Center, Imam Reza Hospital, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Babak Sayad
- Infectious Diseases Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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Chung HY, Jian M, Chang CK, Chen CS, Li SY, Lin JC, Yeh KM, Yang YS, Chen CW, Hsieh SS, Tang SH, Perng CL, Hung KS, Chang FY, Shang HS. The application of a novel 5-in-1 multiplex reverse transcriptase-polymerase chain reaction assay for rapid detection of SARS-CoV-2 and differentiation between variants of concern. Int J Infect Dis 2023; 127:56-62. [PMID: 36455809 PMCID: PMC9703862 DOI: 10.1016/j.ijid.2022.11.027] [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: 06/05/2022] [Revised: 10/24/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES We have established a novel 5-in-1 VOC assay to rapidly detect SARS-CoV-2 and immediately distinguish whether positive samples represent variants of concern (VOCs). METHODS This assay could distinguish among five VOCs: Alpha, Beta, Gamma, Delta, and Omicron, in a single reaction tube. The five variants exhibit different single nucleotide polymorphisms (SNPs) in their viral genome, which can be used to distinguish them. We selected target SNPs in the spike gene, including N501Y, P681R, K417N, and deletion H69/V70 for the assay. RESULTS The limit of detection of each gene locus was 80 copies per polymerase chain reaction. We observed a high consistency among the results when comparing the performance of our 5-in-1 VOC assay, whole gene sequencing, and the Roche VirSNiP SARS-CoV-2 test in retrospectively analyzing 150 clinical SARS-CoV-2 variant positive samples. The 5-in-1 VOC assay offers an alternative and rapid high-throughput test for most diagnostic laboratories in a flexible sample-to-result platform. CONCLUSION The assay can also be applied in a commercial platform with the completion of the SARS-CoV-2 confirmation test and identification of its variant within 2.5 hours.
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Affiliation(s)
- Hsing-Yi Chung
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan,Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
| | - Ming Jian
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chih-Kai Chang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chi-Sheng Chen
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Shih-Yi Li
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Jung-Chung Lin
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Kuo-Ming Yeh
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Ya-Sung Yang
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chien-Wen Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Shan-Shan Hsieh
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Sheng-Hui Tang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Cherng-Lih Perng
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Kuo-Sheng Hung
- Center for Precision Medicine and Genomics, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Feng-Yee Chang
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Hung-Sheng Shang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan,Corresponding author
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Chrysostomou AC, Aristokleous A, Rodosthenous JH, Christodoulou C, Stathi G, Kostrikis LG. Detection of Circulating SARS-CoV-2 Variants of Concern (VOCs) Using a Multiallelic Spectral Genotyping Assay. Life (Basel) 2023; 13:life13020304. [PMID: 36836661 PMCID: PMC9960118 DOI: 10.3390/life13020304] [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: 12/19/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
Throughout the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously evolved, resulting in new variants, some of which possess increased infectivity, immune evasion, and virulence. Such variants have been denoted by the World Health Organization as variants of concern (VOC) because they have resulted in an increased number of cases, posing a strong risk to public health. Thus far, five VOCs have been designated, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529), including their sublineages. Next-generation sequencing (NGS) can produce a significant amount of information facilitating the study of variants; however, NGS is time-consuming and costly and not efficient during outbreaks, when rapid identification of VOCs is urgently needed. In such periods, there is a need for fast and accurate methods, such as real-time reverse transcription PCR in combination with probes, which can be used for monitoring and screening of the population for these variants. Thus, we developed a molecular beacon-based real-time RT-PCR assay according to the principles of spectral genotyping. This assay employs five molecular beacons that target ORF1a:ΔS3675/G3676/F3677, S:ΔH69/V70, S:ΔE156/F157, S:ΔΝ211, S:ins214EPE, and S:ΔL242/A243/L244, deletions and an insertion found in SARS-CoV-2 VOCs. This assay targets deletions/insertions because they inherently provide higher discrimination capacity. Here, the design process of the molecular beacon-based real-time RT-PCR assay for detection and discrimination of SARS-CoV-2 is presented, and experimental testing using SARS-CoV-2 VOC samples from reference strains (cultured virus) and clinical patient samples (nasopharyngeal samples), which have been previously classified using NGS, were evaluated. Based on the results, it was shown that all molecular beacons can be used under the same real-time RT-PCR conditions, consequently improving the time and cost efficiency of the assay. Furthermore, this assay was able to confirm the genotype of each of the tested samples from various VOCs, thereby constituting an accurate and reliable method for VOC detection and discrimination. Overall, this assay is a valuable tool that can be used for screening and monitoring the population for VOCs or other emerging variants, contributing to limiting their spread and protecting public health.
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Affiliation(s)
| | - Antonia Aristokleous
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
| | | | | | - Georgia Stathi
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
| | - Leondios G. Kostrikis
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
- Cyprus Academy of Sciences, Letters, and Arts, 60-68 Phaneromenis Street, 1011 Nicosia, Cyprus
- Correspondence: ; Tel.: +35-72-289-2885
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COVID-19, SARS-CoV-2 Vaccination, and Human Herpesviruses Infections. Vaccines (Basel) 2023; 11:vaccines11020232. [PMID: 36851110 PMCID: PMC9963083 DOI: 10.3390/vaccines11020232] [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: 12/25/2022] [Revised: 01/10/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023] Open
Abstract
There are several human herpesviruses. A common characteristic of infection by these viruses is latency, by which the virus assumes a non-replicative state, subverting the attentions of the host's immune response. In immunocompetent hosts, herpesviruses are immunologically controlled, although periodic virus shedding can occur. In situations where immunological control is lost, herpesviruses can reactivate and produce clinically apparent disease. It is now becoming apparent that COVID-19 or exposure to COVID-19 vaccines can exert several effects on the immune system. The pandemic of COVID-19 shows no sign of abating, with new severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants continuing to evolve. Several COVID-19 vaccines have been developed, and much of the world's population has either experienced COVID-19 or been vaccinated against it. There are an increasing number of reports of associations between herpesvirus infections or reactivations and COVID-19 or COVID-19 vaccination. For instance, a positive cytomegalovirus serostatus may indicate a greater likelihood of severe COVID-19, and herpes simplex virus reactivation may be linked to increased mortality. Epstein-Barr virus reactivation appears to be associated with post-acute sequelae of COVID-19. Finally, herpes zoster has been reported to be associated with COVID-19 vaccination. This brief narrative review will provide several insights into associations between herpesvirus infections or reactivations and COVID-19 or SARS-CoV-2 vaccination.
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Gonçalves R, Couto J, Ferreirinha P, Costa JM, Silvério D, Silva ML, Fernandes AI, Madureira P, Alves NL, Lamas S, Saraiva M. SARS-CoV-2 variants induce distinct disease and impact in the bone marrow and thymus of mice. iScience 2023; 26:105972. [PMID: 36687317 PMCID: PMC9838028 DOI: 10.1016/j.isci.2023.105972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/05/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved to variants associated with milder disease. We employed the k18-hACE2 mouse model to study how differences in the course of infection by SARS-CoV-2 variants alpha, delta, and omicron relate to tissue pathology and the immune response triggered. We documented a variant-specific pattern of infection severity, inducing discrete lung and blood immune responses and differentially impacting primary lymphoid organs. Infections with variants alpha and delta promoted bone marrow (BM) emergency myelopoiesis, with blood and lung neutrophilia. The defects in the BM hematopoietic compartment extended to the thymus, with the infection by the alpha variant provoking a marked thymic atrophy. Importantly, the changes in the immune responses correlated with the severity of infection. Our study provides a comprehensive platform to investigate the modulation of disease by SARS-CoV-2 variants and underscores the impact of this infection on the function of primary lymphoid organs.
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Affiliation(s)
- Rute Gonçalves
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Joana Couto
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Pedro Ferreirinha
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal,IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - José Maria Costa
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal,FEUP—Faculdade de Engenharia, Universidade do Porto, 4200-465 Porto, Portugal
| | - Diogo Silvério
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal,ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Marta L. Silva
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal,ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Ana Isabel Fernandes
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal,ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Pedro Madureira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal,Immunethep, Biocant Park, 3060-197 Cantanhede, Portugal
| | - Nuno L. Alves
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal,IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Sofia Lamas
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal,IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Margarida Saraiva
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal,IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal,Corresponding author
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Peña Rodríguez M, Hernández Bello J, Vega Magaña N, Viera Segura O, García Chagollán M, Ceja Gálvez HR, Mora Mora JC, Rentería Flores FI, García González OP, Muñoz Valle JF. Prevalence of symptoms, comorbidities, and reinfections in individuals infected with Wild-Type SARS-CoV-2, Delta, or Omicron variants: a comparative study in western Mexico. Front Public Health 2023; 11:1149795. [PMID: 37181688 PMCID: PMC10174068 DOI: 10.3389/fpubh.2023.1149795] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/04/2023] [Indexed: 05/16/2023] Open
Abstract
Introduction The variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been classified into variants of interest (VOIs) or concern (VOCs) to prioritize global monitoring and research on variants with potential risks to public health. The SARS-CoV-2 high-rate mutation can directly impact the clinical disease progression, epidemiological behavior, immune evasion, vaccine efficacy, and transmission rates. Therefore, epidemiological surveillance is crucial for controlling the COVID-19 pandemic. In the present study, we aimed to describe the prevalence of wild-type (WT) SARS-CoV-2 and Delta and Omicron variants in Jalisco State, Mexico, from 2021 to 2022, and evaluate the possible association of these variants with clinical manifestations of COVID-19. Methods Four thousand and ninety-eight patients diagnosed with COVID-19 by real-time PCR (COVIFLU, Genes2Life, Mexico) from nasopharyngeal samples from January 2021 to January 2022 were included. Variant identification was performed by the RT-qPCR Master Mut Kit (Genes2Life, Mexico). A study population follow-up was performed to identify patients who had experienced reinfection after being vaccinated. Results and Discussion Samples were grouped into variants according to the identified mutations: 46.3% were Omicron, 27.9% were Delta, and 25.8% were WT. The proportions of dry cough, fatigue, headache, muscle pain, conjunctivitis, fast breathing, diarrhea, anosmia, and dysgeusia were significantly different among the abovementioned groups (p < 0.001). Anosmia and dysgeusia were mainly found in WT-infected patients, while rhinorrhea and sore throat were more prevalent in patients infected with the Omicron variant. For the reinfection follow-up, 836 patients answered, from which 85 cases of reinfection were identified (9.6%); Omicron was the VOC that caused all reported reinfection cases. In this study, we demonstrate that the Omicron variant caused the biggest outbreak in Jalisco during the pandemic from late December 2021 to mid-February 2022 but with a less severe form than the one demonstrated by Delta and WT. The co-analysis of mutations and clinical outcomes is a public health strategy with the potential to infer mutations or variants that could increase disease severity and even be an indicator of long-term sequelae of COVID-19.
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Affiliation(s)
- Marcela Peña Rodríguez
- Laboratorio de Enfermedades Emergentes y Reemergentes, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Jorge Hernández Bello
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Natali Vega Magaña
- Laboratorio de Enfermedades Emergentes y Reemergentes, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Oliver Viera Segura
- Laboratorio de Enfermedades Emergentes y Reemergentes, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Mariel García Chagollán
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Hazael Ramiro Ceja Gálvez
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Doctorado en Ciencias en Biología Molecular en Medicina, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Jesús Carlos Mora Mora
- Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Francisco Israel Rentería Flores
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Doctorado en Ciencias en Biología Molecular en Medicina, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | | | - José Francisco Muñoz Valle
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- *Correspondence: José Francisco Muñoz Valle,
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Zhang Y, Li X, Yu W. Comparison of the incidence of adverse reactions between herbal decoction and Chinese patent medicine combined with western medicine in treatment of COVID-19: A protocol for systematic review and meta-analysis. Medicine (Baltimore) 2022; 101:e32255. [PMID: 36626476 PMCID: PMC9750564 DOI: 10.1097/md.0000000000032255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
INTRODUCTION Coronavirus disease 2019 (COVID-19) is an acute respiratory infectious disease that has led to millions of confirmed cases and deaths worldwide. Traditional Chinese Medicine plays an irreplaceable role in the treatment and prevention of epidemics in China. Western medicine improves clinical symptoms as well as bringing many adverse reactions. The combination of Chinese and western medicine can significantly improve the clinical symptoms and efficacy of patients. Currently, there is a lack of systematic reviews on the comparison of the incidence of adverse reactions between the difference treatments. We conducted this study to evaluate the comparison of the incidence of adverse reactions between herbal decoction and Chinese patent medicine combined with western medicine in treatment of COVID-19. METHODS AND ANALYSIS Randomized controlled trials in 9 databases from December 2019 to September 2022, will be included, without language restrictions. Two independent researchers will screen and select studies, extract data, and evaluate the study quality. The Cochrane risk-of-bias tool for randomized controlled trials will be used to assess the risk of bias in the included studies. Statistical analyses will be conducted using Review Manager. RESULTS Our findings will compare the incidence of adverse reactions between herbal decoction and Chinese patent medicine combined with western medicine in treatment of COVID-19, which will be disseminated in a relevant conference and published in a peer-reviewed publication. ETHICS AND DISSEMINATION This study will not include personal information. Ethical approval is not required for this study. PROSPERO REGISTRATION NUMBER CRD42022371001.
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Affiliation(s)
- Yunliang Zhang
- Department of Pain, Zibo Central Hospital, Zibo, People’s Republic of China
| | - Xuhao Li
- School of Acupuncture-Moxibustion and Tuina, Shandong University of Traditional Chinese Medicine, Jinan, People’s Republic of China
| | - Wenyan Yu
- School of Acupuncture-Moxibustion and Tuina, Shandong University of Traditional Chinese Medicine, Jinan, People’s Republic of China
- *Correspondence: Wenyan Yu, School of Acupuncture-Moxibustion and Tuina, Shandong University of Traditional Chinese Medicine, No. 4655 The University Road, Jinan, Shandong Province 250355, People’s Republic of China (e-mail: )
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Caputo E, Mandrich L. SARS-CoV-2: Searching for the Missing Variants. Viruses 2022; 14:v14112364. [PMID: 36366461 PMCID: PMC9697249 DOI: 10.3390/v14112364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/21/2022] [Accepted: 10/25/2022] [Indexed: 01/31/2023] Open
Abstract
Structural and phylogenetic analysis of the spike glycoprotein highlighted that the last variants, annotated as omicron, have about 30 mutations compared to the initial version reported in China, while the delta variant, supposed to be the omicron ancestor, shows only 7 mutations. Moreover, the five omicron variants were isolated between November 2021 and January 2022, and the last variant BA.2.75, unofficially named centaurus, was isolated in May 2022. It appears that, since the isolation of the delta variant (October 2020) to the omicron BA.1 (November 2021), there was an interval of one year, whereas the five omicron variants were isolated in three months, and after a successive four months period, the BA.2.75 variant was isolated. So, what is the temporal and phylogenetic correlation among all these variants? The analysis of common mutations among delta and the omicron variants revealed: (i) a phylogenetic correlation among these variants; (ii) the existence of BA.1 and BA.2 omicron variants a few months before being isolated; (iii) at least three possible intermediate variants during the evolution of omicron; (iv) the evolution of the BA.2.12.1, BA.4 and BA.5 variants from omicron BA.2; (v) the centaurus variant evolution from omicron BA.2.12.1.
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Affiliation(s)
- Emilia Caputo
- Institute of Genetics and Biophysics-IGB-CNR, “A. Buzzati-Traverso”, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Luigi Mandrich
- Research Institute on Terrestrial Ecosystems-IRET-CNR, Via Pietro Castellino 111, 80131 Naples, Italy
- Correspondence:
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Roeder AJ, Koehler MA, Jasbi P, McKechnie D, Vanderhoof J, Edwards BA, Gonzalez-Moa MJ, Seit-Nebi A, Svarovsky SA, Lake DF. Longitudinal Comparison of Neutralizing Antibody Responses to COVID-19 mRNA Vaccines after Second and Third Doses. Vaccines (Basel) 2022; 10:vaccines10091459. [PMID: 36146537 PMCID: PMC9504054 DOI: 10.3390/vaccines10091459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/26/2022] [Accepted: 08/31/2022] [Indexed: 12/23/2022] Open
Abstract
COVID-19 mRNA vaccines protect against severe disease and hospitalization. Neutralizing antibodies (NAbs) are a first-line defense mechanism, but protective NAb responses are variable. Currently, NAb testing is not widely available. This study employed a lateral flow assay for monitoring NAb levels postvaccination and natural infection, using a finger-stick drop of blood. We report longitudinal NAb data from BNT162b2 (Pfizer) and mRNA-1273 (Moderna) recipients after second and third doses. Results demonstrate a third dose of mRNA vaccine elicits higher and more durable NAb titers than the second dose, independent of manufacturer, sex, and age. Our analyses also revealed that vaccinated individuals could be categorized as strong, moderate, and poorly neutralizing responders. After the second dose, 34% of subjects were classified as strong responders, compared to 79% after the third dose. The final months of this study coincided with the emergence of the SARS-CoV-2 Omicron variant and symptomatic breakthrough infections within our study population. Lastly, we show that NAb levels sufficient for protection from symptomatic infection with early SARS-CoV-2 variants were not protective against Omicron infection and disease. This work highlights the need for accessible vaccine response monitoring for use in healthcare, such that individuals, particularly those in vulnerable populations, can make informed vaccination decisions.
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Affiliation(s)
- Alexa J. Roeder
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Megan A. Koehler
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Paniz Jasbi
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Davis McKechnie
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - John Vanderhoof
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Baylee A. Edwards
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | | | | | | | - Douglas F. Lake
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- Correspondence:
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Sonaglioni A, Lombardo M, Albini A, Noonan DM, Re M, Cassandro R, Elia D, Caminati A, Nicolosi GL, Harari S. Charlson comorbidity index, neutrophil-to-lymphocyte ratio and undertreatment with renin-angiotensin-aldosterone system inhibitors predict in-hospital mortality of hospitalized COVID-19 patients during the omicron dominant period. Front Immunol 2022; 13:958418. [PMID: 36090992 PMCID: PMC9453812 DOI: 10.3389/fimmu.2022.958418] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/04/2022] [Indexed: 11/24/2022] Open
Abstract
Purpose To investigate the clinical predictors of in-hospital mortality in hospitalized patients with Coronavirus disease 2019 (COVID-19) infection during the Omicron period. Methods All consecutive hospitalized laboratory‐confirmed COVID-19 patients between January and May 2022 were retrospectively analyzed. All patients underwent accurate physical, laboratory, radiographic and echocardiographic examination. Primary endpoint was in-hospital mortality. Results 74 consecutive COVID-19 patients (80.0 ± 12.6 yrs, 45.9% males) were included. Patients who died during hospitalization (27%) and those who were discharged alive (73%) were separately analyzed. Compared to patients discharged alive, those who died were significantly older, with higher comorbidity burden and greater prevalence of laboratory, radiographic and echographic signs of pulmonary and systemic congestion. Charlson comorbidity index (CCI) (OR 1.76, 95%CI 1.07-2.92), neutrophil-to-lymphocyte ratio (NLR) (OR 1.24, 95%CI 1.10-1.39) and absence of angiotensin-converting enzyme inhibitors (ACEI)/angiotensin II receptor blockers (ARBs) therapy (OR 0.01, 95%CI 0.00-0.22) independently predicted the primary endpoint. CCI ≥7 and NLR ≥9 were the best cut-off values for predicting mortality. The mortality risk for patients with CCI ≥7, NLR ≥9 and not in ACEI/ARBs therapy was high (86%); for patients with CCI <7, NLR ≥9, with (16.6%) or without (25%) ACEI/ARBs therapy was intermediate; for patients with CCI <7, NLR <9 and in ACEI/ARBs therapy was of 0%. Conclusions High comorbidity burden, high levels of NLR and the undertreatment with ACEI/ARBs were the main prognostic indicators of in-hospital mortality. The risk stratification of COVID-19 patients at hospital admission would help the clinicians to take care of the high-risk patients and reduce the mortality.
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Affiliation(s)
- Andrea Sonaglioni
- Division of Cardiology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) MultiMedica, Milan, Italy
| | - Michele Lombardo
- Division of Cardiology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) MultiMedica, Milan, Italy
| | - Adriana Albini
- European Institute of Oncology (IEO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
- *Correspondence: Adriana Albini,
| | - Douglas M. Noonan
- Immunology and General Pathology Laboratory, Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- Unit of Molecular Pathology, Immunology and Biochemistry, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) MultiMedica, Milan, Italy
| | - Margherita Re
- Division of Internal Medicine, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) MultiMedica, Milan, Italy
| | - Roberto Cassandro
- Division of Pneumology, Semi Intensive Care Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) MultiMedica, Milan, Italy
| | - Davide Elia
- Division of Pneumology, Semi Intensive Care Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) MultiMedica, Milan, Italy
| | - Antonella Caminati
- Division of Pneumology, Semi Intensive Care Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) MultiMedica, Milan, Italy
| | | | - Sergio Harari
- Division of Pneumology, Semi Intensive Care Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) MultiMedica, Milan, Italy
- Department of Clinical Sciences and Community Health, Università Di Milano, Milan, Italy
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Fiaschi L, Dragoni F, Schiaroli E, Bergna A, Rossetti B, Giammarino F, Biba C, Gidari A, Lai A, Nencioni C, Francisci D, Zazzi M, Vicenti I. Efficacy of Licensed Monoclonal Antibodies and Antiviral Agents against the SARS-CoV-2 Omicron Sublineages BA.1 and BA.2. Viruses 2022; 14:v14071374. [PMID: 35891355 PMCID: PMC9321742 DOI: 10.3390/v14071374] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 12/10/2022] Open
Abstract
Newly emerging SARS-CoV-2 variants may escape monoclonal antibodies (mAbs) and antiviral drugs. By using live virus assays, we assessed the ex vivo inhibition of the B.1 wild-type (WT), delta and omicron BA.1 and BA.2 lineages by post-infusion sera from 40 individuals treated with bamlanivimab/etesevimab (BAM/ETE), casirivimab/imdevimab (CAS/IMD), and sotrovimab (SOT) as well as the activity of remdesivir, nirmatrelvir and molnupiravir. mAbs and drug activity were defined as the serum dilution (ID50) and drug concentration (IC50), respectively, showing 50% protection of virus-induced cytopathic effect. All pre-infusion sera were negative for SARS-CoV-2 neutralizing activity. BAM/ETE, CAS/IMD, and SOT showed activity against the WT (ID50 6295 (4355–8075) for BAM/ETE; 18,214 (16,248–21,365) for CAS/IMD; and 456 (265–592) for SOT) and the delta (14,780 (ID50 10,905–21,020) for BAM/ETE; 63,937 (47,211–79,971) for CAS/IMD; and 1103 (843–1334) for SOT). Notably, only SOT was active against BA.1 (ID50 200 (37–233)), whereas BA.2 was neutralized by CAS/IMD (ID50 174 (134–209) ID50) and SOT (ID50 20 (9–31) ID50), but not by BAM/ETE. No significant inter-variant IC50 differences were observed for molnupiravir (1.5 ± 0.1/1.5 ± 0.7/1.0 ± 0.5/0.8 ± 0.01 μM for WT/delta/BA.1/BA.2, respectively), nirmatrelvir (0.05 ± 0.02/0.06 ± 0.01/0.04 ± 0.02/0.04 ± 0.01 μM) or remdesivir (0.08 ± 0.04/0.11 ± 0.08/0.05 ± 0.04/0.08 ± 0.01 μM). Continued evolution of SARS-CoV-2 requires updating the mAbs arsenal, although antivirals have so far remained unaffected.
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Affiliation(s)
- Lia Fiaschi
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (L.F.); (F.D.); (F.G.); (C.B.); (M.Z.)
| | - Filippo Dragoni
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (L.F.); (F.D.); (F.G.); (C.B.); (M.Z.)
| | - Elisabetta Schiaroli
- Department of Medicine and Surgery, Clinic of Infectious Diseases, University of Perugia, 06129 Perugia, Italy; (E.S.); (A.G.); (D.F.)
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, 20157 Milan, Italy; (A.B.); (A.L.)
| | - Barbara Rossetti
- Infectious Disease Department, USL SUDEST, Toscana, Misericordia Hospital, 58100 Grosseto, Italy; (B.R.); (C.N.)
| | - Federica Giammarino
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (L.F.); (F.D.); (F.G.); (C.B.); (M.Z.)
| | - Camilla Biba
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (L.F.); (F.D.); (F.G.); (C.B.); (M.Z.)
| | - Anna Gidari
- Department of Medicine and Surgery, Clinic of Infectious Diseases, University of Perugia, 06129 Perugia, Italy; (E.S.); (A.G.); (D.F.)
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, 20157 Milan, Italy; (A.B.); (A.L.)
| | - Cesira Nencioni
- Infectious Disease Department, USL SUDEST, Toscana, Misericordia Hospital, 58100 Grosseto, Italy; (B.R.); (C.N.)
| | - Daniela Francisci
- Department of Medicine and Surgery, Clinic of Infectious Diseases, University of Perugia, 06129 Perugia, Italy; (E.S.); (A.G.); (D.F.)
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (L.F.); (F.D.); (F.G.); (C.B.); (M.Z.)
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (L.F.); (F.D.); (F.G.); (C.B.); (M.Z.)
- Correspondence: ; Tel.: +39-057-7233-855
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Rakhmatullin A, Kutlubaev M. An analysis of clinical and laboratory characteristics of patients with ischemic stroke and COVID-19. Zh Nevrol Psikhiatr Im S S Korsakova 2022; 122:34-37. [DOI: 10.17116/jnevro202212211234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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36
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Roggero PF, Calistri A, Palù G. On the intrinsic nature of viral pathogenesis: The assumption of a Darwinian paradigm to describe COVID-19 pandemic. Comput Struct Biotechnol J 2022; 20:5870-5872. [PMID: 36320938 PMCID: PMC9613777 DOI: 10.1016/j.csbj.2022.10.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 10/17/2022] [Accepted: 10/23/2022] [Indexed: 11/30/2022] Open
Abstract
Our hypothesis about evolution of the COVID-19 pandemic foresees an inverse relation between infectivity (R0) and lethality (L) of SARS-CoV-2. The above parameters are driven by a continuing mutation process granting the virus a clear survival advantage over virulence. For interpreting this relation we adopted a simple equation, R0 × L ≈ k, by which R0 and L depend upon a constant k, that corresponds to an intrinsic property of the viral species involved. The hypothesis was verified by following changes of the R0 and L terms of the formula in the different variants of SARS-CoV-2 that progressively appeared. A further validation came when the equation was applied to pandemic and epidemic influenza type A viruses, Ebola virus and measles virus. We believe this equation that considers virus biology in Darwinian terms could be extremely useful to better face infectious viral threats and validate virus-host molecular interactions relevant to viral pathogenesis.
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Affiliation(s)
- Pier Francesco Roggero
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Arianna Calistri
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy,Italian Medicines Agency, Via del Tritone 181, 00187 Rome, Italy,Corresponding author at: Department of Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy; Italian Medicines Agency, Via del Tritone 181, 00187, Rome, Italy
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