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Shen J, Xu X, Fan J, Chen H, Zhao Y, Huang W, Liu W, Zhang Z, Cui Q, Li Q, Niu Z, Jiang D, Cao G. APOBEC3-related mutations in the spike protein-encoding region facilitate SARS-CoV-2 evolution. Heliyon 2024; 10:e32139. [PMID: 38868014 PMCID: PMC11168432 DOI: 10.1016/j.heliyon.2024.e32139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/14/2024] Open
Abstract
SARS-CoV-2 evolves gradually to cause COVID-19 epidemic. One of driving forces of SARS-CoV-2 evolution might be activation of apolipoprotein B mRNA editing catalytic subunit-like protein 3 (APOBEC3) by inflammatory factors. Here, we aimed to elucidate the effect of the APOBEC3-related viral mutations on the infectivity and immune evasion of SARS-CoV-2. The APOBEC3-related C > U mutations ranked as the second most common mutation types in the SARS-CoV-2 genome. mRNA expression of APOBEC3A (A3A), APOBEC3B (A3B), and APOBEC3G (A3G) in peripheral blood cells increased with disease severity. A3B, a critical member of the APOBEC3 family, was significantly upregulated in both severe and moderate COVID-19 patients and positively associated with neutrophil proportion and COVID-19 severity. We identified USP18 protein, a key molecule centralizing the protein-protein interaction network of key APOBEC3 proteins. Furthermore, mRNA expression of USP18 was significantly correlated to ACE2 and TMPRSS2 expression in the tissue of upper airways. Knockdown of USP18 mRNA significantly decreased A3B expression. Ectopic expression of A3B gene increased SARS-CoV-2 infectivity. C > U mutations at S371F, S373L, and S375F significantly conferred with the immune escape of SARS-CoV-2. Thus, APOBEC3, whose expression are upregulated by inflammatory factors, might promote SARS-CoV-2 evolution and spread via upregulating USP18 level and facilitating the immune escape. A3B and USP18 might be therapeutic targets for interfering with SARS-CoV-2 evolution.
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Affiliation(s)
- Jiaying Shen
- Tongji University School of Medicine, Tongji University, Shanghai 200120, China
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
| | - Xinxin Xu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Junyan Fan
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Hongsen Chen
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Yue Zhao
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Weijin Huang
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), WHO Collaborating Center for Standardization and Evaluation of Biologicals, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, 102629 Beijing, China
| | - Wenbin Liu
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Zihan Zhang
- Tongji University School of Medicine, Tongji University, Shanghai 200120, China
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
| | - Qianqian Cui
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), WHO Collaborating Center for Standardization and Evaluation of Biologicals, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, 102629 Beijing, China
| | - Qianqian Li
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), WHO Collaborating Center for Standardization and Evaluation of Biologicals, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, 102629 Beijing, China
| | - Zheyun Niu
- Tongji University School of Medicine, Tongji University, Shanghai 200120, China
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
| | - Dongming Jiang
- Tongji University School of Medicine, Tongji University, Shanghai 200120, China
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
| | - Guangwen Cao
- Tongji University School of Medicine, Tongji University, Shanghai 200120, China
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
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Kumar P, Park H, Yuk Y, Kim H, Jang J, Pagolu R, Park S, Yeo C, Choi KY. Developed and emerging 1,4-butanediol commercial production strategies: forecasting the current status and future possibility. Crit Rev Biotechnol 2024; 44:530-546. [PMID: 37286203 DOI: 10.1080/07388551.2023.2176740] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/26/2022] [Accepted: 01/17/2023] [Indexed: 06/09/2023]
Abstract
1,4-Butanediol (1,4-BDO) is a valuable industrial chemical that is primarily produced via several energy-intensive petrochemical processes based on fossil-based raw materials, leading to issues related to: non-renewability, environmental contamination, and high production costs. 1,4-BDO is used in many chemical reactions to develop a variety of useful, valuable products, such as: polyurethane, Spandex intermediates, and polyvinyl pyrrolidone (PVP), a water-soluble polymer with numerous personal care and pharmaceutical uses. In recent years, to satisfy the growing need for 1,4-BDO, there has been a major shift in focus to sustainable bioproduction via microorganisms using: recombinant strains, metabolic engineering, synthetic biology, enzyme engineering, bioinformatics, and artificial intelligence-guided algorithms. This article discusses the current status of the development of: various chemical and biological production techniques for 1,4-BDO, advances in biological pathways for 1,4-BDO biosynthesis, prospects for future production strategies, and the difficulties associated with environmentally friendly and bio-based commercial production strategies.
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Affiliation(s)
- Pradeep Kumar
- Institute of Environmental Engineering, Ajou University, Suwon, South Korea
| | - HyunA Park
- Department of Environmental Engineering, Ajou University, Suwon, South Korea
| | - Yong Yuk
- Institute of Environmental Engineering, Ajou University, Suwon, South Korea
| | - Hayan Kim
- Department of Life Science, Ajou University, Suwon, South Korea
| | - Jihwan Jang
- Institute of Environmental Engineering, Ajou University, Suwon, South Korea
| | - Raviteja Pagolu
- Institute of Environmental Engineering, Ajou University, Suwon, South Korea
| | - SeoA Park
- Department of Environmental Engineering, Ajou University, Suwon, South Korea
| | - Chanseo Yeo
- Department of Environmental and Safety Engineering, Ajou University, Suwon, South Korea
| | - Kwon-Young Choi
- Institute of Environmental Engineering, Ajou University, Suwon, South Korea
- Department of Environmental Engineering, Ajou University, Suwon, South Korea
- Department of Environmental and Safety Engineering, Ajou University, Suwon, South Korea
- Department of Energy Systems Research, Ajou University, Suwon, South Korea
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Tolksdorf B, Heinze J, Niemeyer D, Röhrs V, Berg J, Drosten C, Kurreck J. Development of a highly stable, active small interfering RNA with broad activity against SARS-CoV viruses. Antiviral Res 2024; 226:105879. [PMID: 38599550 DOI: 10.1016/j.antiviral.2024.105879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/22/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
Treatment options for COVID-19 remain limited. Here, we report the optimization of an siRNA targeting the highly conserved leader region of SARS-CoV-2. The siRNA was rendered nuclease resistant by the introduction of modified nucleotides without loss of activity. Importantly, the siRNA also retained its inhibitory activity against the emerged omicron sublineage variant BA.2, which occurred after the siRNA was designed and is resistant to other antiviral agents such as antibodies. In addition, we show that a second highly active siRNA designed against the viral 5'-UTR can be applied as a rescue molecule, to minimize the spread of escape mutations. We therefore consider our siRNA-based molecules to be promising broadly active candidates for the treatment of current and future SARS-CoV-2 variants.
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Affiliation(s)
- Beatrice Tolksdorf
- Chair of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Berlin, 10623, Germany
| | - Julian Heinze
- German Center for Infection Research (DZIF), Charitéplatz 1, 10117, Berlin, Germany; Institute of Virology, Charité-Universitätsmedizin Berlin, 10117, Germany
| | - Daniela Niemeyer
- German Center for Infection Research (DZIF), Charitéplatz 1, 10117, Berlin, Germany; Institute of Virology, Charité-Universitätsmedizin Berlin, 10117, Germany
| | - Viola Röhrs
- Chair of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Berlin, 10623, Germany
| | - Johanna Berg
- Chair of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Berlin, 10623, Germany
| | - Christian Drosten
- German Center for Infection Research (DZIF), Charitéplatz 1, 10117, Berlin, Germany; Institute of Virology, Charité-Universitätsmedizin Berlin, 10117, Germany
| | - Jens Kurreck
- Chair of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Berlin, 10623, Germany.
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Bes-Berlandier H, Coiffard B, Bermudez J, Demazes-Dufeu N, Coltey B, Boschi C, Colson P, Hraiech S, Reynaud-Gaubert M, Cassir N. Management of immunosuppression in lung transplant recipients and COVID-19 outcomes: an observational retrospective cohort-study. BMC Infect Dis 2024; 24:536. [PMID: 38807049 PMCID: PMC11134755 DOI: 10.1186/s12879-024-09269-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 03/28/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND The aim of this study was to assess the impact of immunosuppression management on coronavirus disease 2019 (COVID-19) outcomes. METHODS We performed a single-center retrospective study in a cohort of 358 lung transplant recipients (LTx) over the period from March 2020 to April 2022. All included symptomatic patients had at least one positive SARS-CoV-2 rt-PCR. We used a composite primary outcome for COVID-19 including increased need for oxygen since the hospital admission, ICU transfer, and in-hospital mortality. We assessed by univariate and multivariate analyses the risk factors for poor outcomes. RESULTS Overall, we included 91 LTx who contracted COVID-19. The COVID-19 in-hospital mortality rate reached 4.4%. By hierarchical clustering, we found a strong and independent association between the composite poor outcome and the discontinuation of at least one immunosuppressive molecule among tacrolimus, cyclosporine, mycophenolate mofetil, and everolimus. Obesity (OR = 16, 95%CI (1.96; 167), p = 0.01) and chronic renal failure (OR = 4.6, 95%CI (1.4; 18), p = 0.01) were also independently associated with the composite poor outcome. Conversely, full vaccination was protective (OR = 0.23, 95%CI (0.046; 0.89), p = 0.047). CONCLUSION The administration of immunosuppressive drugs such as tacrolimus, cyclocporine or everolimus can have a protective effect in LTx with COVID-19, probably related to their intrinsic antiviral capacity.
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Affiliation(s)
- Hugo Bes-Berlandier
- Department of Infectious Diseases, University Hospital Institute -Méditerranée Infection (IHU), Marseille, France
| | - Benjamin Coiffard
- Department of Respiratory Medicine and Lung Transplantation, Aix Marseille Univ, APHM, Hôpital Nord, Marseille, France
| | - Julien Bermudez
- Department of Respiratory Medicine and Lung Transplantation, Aix Marseille Univ, APHM, Hôpital Nord, Marseille, France
| | - Nadine Demazes-Dufeu
- Department of Respiratory Medicine and Lung Transplantation, Aix Marseille Univ, APHM, Hôpital Nord, Marseille, France
| | - Bérengère Coltey
- Department of Respiratory Medicine and Lung Transplantation, Aix Marseille Univ, APHM, Hôpital Nord, Marseille, France
| | - Céline Boschi
- Department of Infectious Diseases, University Hospital Institute -Méditerranée Infection (IHU), Marseille, France
- Microbes, Evolution, Phylogeny and Infection (MEΦI), Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Institut de Recherche Pour le Développement IRD, Assistance Publique, Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille, Cedex 05 13385, France
| | - Philippe Colson
- Department of Infectious Diseases, University Hospital Institute -Méditerranée Infection (IHU), Marseille, France
- Microbes, Evolution, Phylogeny and Infection (MEΦI), Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Institut de Recherche Pour le Développement IRD, Assistance Publique, Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille, Cedex 05 13385, France
| | - Sami Hraiech
- Service de Médecine Intensive - Réanimation, AP-HM, Hôpital Nord, Marseille, France
- Faculté de médecine, Centre d'Etudes et de Recherches sur les Services de Santé et qualité de vie EA 3279, Aix-Marseille Université, Marseille, 13005, France
| | - Martine Reynaud-Gaubert
- Department of Respiratory Medicine and Lung Transplantation, Aix Marseille Univ, APHM, Hôpital Nord, Marseille, France
- Microbes, Evolution, Phylogeny and Infection (MEΦI), Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Institut de Recherche Pour le Développement IRD, Assistance Publique, Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille, Cedex 05 13385, France
| | - Nadim Cassir
- Department of Infectious Diseases, University Hospital Institute -Méditerranée Infection (IHU), Marseille, France.
- Microbes, Evolution, Phylogeny and Infection (MEΦI), Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Institut de Recherche Pour le Développement IRD, Assistance Publique, Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille, Cedex 05 13385, France.
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Jung SB, Choi G, Kim HJ, Moon KS, Lee G, Na KH, Kwon YM, Moon J, Shin MY, Yu JY, Baek YB, Park JG, Park SI. A Noble Extract of Pseudomonas sp. M20A4R8 Efficiently Controlling the Influenza Virus-Induced Cell Death. Microorganisms 2024; 12:677. [PMID: 38674621 PMCID: PMC11051866 DOI: 10.3390/microorganisms12040677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Epidemic diseases that arise from infectious RNA viruses, particularly influenza viruses, pose a constant threat to the global economy and public health. Viral evolution has undermined the efficacy of acquired immunity from vaccines and the antiviral effects of FDA-approved drugs. As such, there is an urgent need to develop new antiviral lead agents. Natural compounds, owing to their historical validation of application and safety, have become a promising solution. In this light, a novel marine bacterium, Pseudomonas sp. M20A4R8, has been found to exhibit significant antiviral activity [half maximal inhibitory concentration (IC50) = 1.3 µg/mL, selectivity index (SI) = 919.4] against influenza virus A/Puerto Rico/8/34, surpassing the activity of chloroquine. The antiviral response via M20A4R8 extract was induced during post-entry stages of the influenza virus, indicating suitability for post-application after the establishment of viral infection. Furthermore, post-treatment with M20A4R8 extract protected the host from virus-induced apoptosis, suggesting its potential use in acute respiratory disease complexes resulting from immune effectors' overstimulation and autophagy-mediated self-apoptosis. The extract demonstrated an outstanding therapeutic index against influenza virus A/Wisconsin/15/2009 (IC50 = 8.1 µg/mL, SI = 146.2) and B/Florida/78/2015 Victoria lineage (IC50 = 3.5 µg/mL, SI = 343.8), indicating a broad anti-influenza virus activity with guaranteed safety and effectiveness. This study provides a new perspective on mechanisms for preventing a broad spectrum of viral infections through antiviral agents from novel and natural origins. Future studies on a single or combined compound from the extract hold promise, encouraging its use in preclinical challenge tests with various influenza virus strains.
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Affiliation(s)
- Su-Bin Jung
- Department of Veterinary Pathology, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, Republic of Korea; (S.-B.J.); (K.-S.M.); (G.L.); (K.-H.N.)
| | - Grace Choi
- Department of Biological Application and Technology, National Marine Biodiversity Institute of Korea, Seocheon 33662, Republic of Korea; (G.C.); (Y.M.K.)
| | - Hyo-Jin Kim
- Department of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju 61186, Republic of Korea; (H.-J.K.); (Y.-B.B.)
| | - Kyeong-Seo Moon
- Department of Veterinary Pathology, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, Republic of Korea; (S.-B.J.); (K.-S.M.); (G.L.); (K.-H.N.)
| | - Gun Lee
- Department of Veterinary Pathology, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, Republic of Korea; (S.-B.J.); (K.-S.M.); (G.L.); (K.-H.N.)
| | - Kyeong-Hak Na
- Department of Veterinary Pathology, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, Republic of Korea; (S.-B.J.); (K.-S.M.); (G.L.); (K.-H.N.)
| | - Yong Min Kwon
- Department of Biological Application and Technology, National Marine Biodiversity Institute of Korea, Seocheon 33662, Republic of Korea; (G.C.); (Y.M.K.)
| | - Jimin Moon
- College of Pharmacy, Yeungnam University, Gyeongsan 38541, Republic of Korea;
| | - Mi Yeong Shin
- Department of Health Research, Jeollanam-do Institute of Health and Environment, Muan 58568, Republic of Korea; (M.Y.S.); (J.-Y.Y.)
| | - Jae-Yeong Yu
- Department of Health Research, Jeollanam-do Institute of Health and Environment, Muan 58568, Republic of Korea; (M.Y.S.); (J.-Y.Y.)
| | - Yeong-Bin Baek
- Department of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju 61186, Republic of Korea; (H.-J.K.); (Y.-B.B.)
| | - Jun-Gyu Park
- Department of Veterinary Zoonotic Diseases, College of Veterinary Medicine, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sang-Ik Park
- Department of Veterinary Pathology, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, Republic of Korea; (S.-B.J.); (K.-S.M.); (G.L.); (K.-H.N.)
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Moore E, Wohlauer MV, Dorosh J, Kabeil M, Malgor RD, O'Banion LA, Lopez-Pena G, Gillette R, Colborn K, Cuff RF, Lucero L, Ali A, Koleilat I, Batarseh P, Talathi S, Rivera A, Humphries MD, Ly K, Harroun N, Smith BK, Darelli-Anderson AM, Choudhry A, Hammond E, Costanza M, Khetarpaul V, Cosentino A, Watson J, Afifi R, Mouawad NJ, Tan TW, Sharafuddin M, Quevedo JP, Nkansah R, Shibale P, Shalhub S, Lin JC. Impact of COVID-19 on patients undergoing scheduled procedures for chronic venous disease. Vascular 2024:17085381241240679. [PMID: 38520224 DOI: 10.1177/17085381241240679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
OBJECTIVE The COVID-19 pandemic has drastically altered the medical landscape. Various strategies have been employed to preserve hospital beds, personal protective equipment, and other resources to accommodate the surges of COVID-19 positive patients, hospital overcapacities, and staffing shortages. This has had a dramatic effect on vascular surgical practice. The objective of this study is to analyze the impact of the COVID-19 pandemic on surgical delays and adverse outcomes for patients with chronic venous disease scheduled to undergo elective operations. METHODS The Vascular Surgery COVID-19 Collaborative (VASCC) was founded in March 2020 to evaluate the outcomes of patients with vascular disease whose operations were delayed. Modules were developed by vascular surgeon working groups and tested before implementation. A data analysis of outcomes of patients with chronic venous disease whose surgeries were postponed during the COVID-19 pandemic from March 2020 through February 2021 was performed for this study. RESULTS A total of 150 patients from 12 institutions in the United States were included in the study. Indications for venous intervention were: 85.3% varicose veins, 10.7% varicose veins with venous ulceration, and 4.0% lipodermatosclerosis. One hundred two surgeries had successfully been completed at the time of data entry. The average length of the delay was 91 days, with a median of 78 days. Delays for venous ulceration procedures ranged from 38 to 208 days. No patients required an emergent intervention due to their venous disease, and no patients experienced major adverse events following their delayed surgeries. CONCLUSIONS Interventions may be safely delayed for patients with venous disease requiring elective surgical intervention during the COVID-19 pandemic. This finding supports the American College of Surgeons' recommendations for the management of elective vascular surgical procedures. Office-based labs may be safe locations for continued treatment when resources are limited. Although the interventions can be safely postponed, the negative impact on quality of life warrants further investigation.
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Affiliation(s)
- Ethan Moore
- Department of Surgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - Max V Wohlauer
- Department of Surgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - James Dorosh
- Deparment of Surgery, McLaren Greater Lansing at Michigan State University, East Lansing, MI, USA
| | - Mahmood Kabeil
- Department of Surgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - Rafael D Malgor
- Department of Surgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - Leigh A O'Banion
- Department of Surgery, University of California San Francisco Fresno, Fresno, CA, USA
| | - Gabriel Lopez-Pena
- Department of Surgery, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Riley Gillette
- Department of Surgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - Kathryn Colborn
- Department of Surgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - Robert F Cuff
- Department of Surgery, Spectrum Health/Michigan State University, Grand Rapids, MI, USA
| | - Leah Lucero
- Department of Surgery, University of California San Francisco Fresno, Fresno, CA, USA
| | - Amna Ali
- Department of Surgery, University of California San Francisco Fresno, Fresno, CA, USA
| | - Issam Koleilat
- Department of Surgery, RWJ/Barnabas Health, Toms River, NJ, USA
| | - Paola Batarseh
- Department of Surgery, Jacobi Medical Center, Albert Einstein School of Medicine, Bronx, NY, USA
| | - Sonia Talathi
- Department of Surgery, Jacobi Medical Center, Albert Einstein School of Medicine, Bronx, NY, USA
| | - Aksim Rivera
- Department of Surgery, Jacobi Medical Center, Albert Einstein School of Medicine, Bronx, NY, USA
| | - Misty D Humphries
- Department of Surgery, University of California Davis Health, Sacramento, CA, USA
| | - Kevin Ly
- Department of Surgery, University of California Davis Health, Sacramento, CA, USA
| | - Nikolai Harroun
- Department of Surgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - Brigitte K Smith
- Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Asad Choudhry
- Department of Surgery, SUNY Upstate University Hospital, Syracuse, NY, USA
| | - Eric Hammond
- Department of Surgery, SUNY Upstate University Hospital, Syracuse, NY, USA
| | - Michael Costanza
- Department of Surgery, SUNY Upstate University Hospital, Syracuse, NY, USA
| | - Vipul Khetarpaul
- Department of Surgery, Barnes Jewish Hospital, Washington University School of Medicine, St. Louis, MO, USA
| | - Ashley Cosentino
- Department of Surgery, Barnes Jewish Hospital, Washington University School of Medicine, St. Louis, MO, USA
| | - Jacob Watson
- Department of Cardiothoracic and Vascular Surgery, McGovern Medical School at UTHealth, Houston, TX, USA
| | - Rana Afifi
- Department of Cardiothoracic and Vascular Surgery, McGovern Medical School at UTHealth, Houston, TX, USA
| | - Nicolas J Mouawad
- Department of Vascular and Endovascular Surgery, McLaren Center for Research and Innovation, Bay City, MI, USA
| | - Tze-Woei Tan
- Department of Surgery, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Mel Sharafuddin
- Department of Surgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Judith P Quevedo
- Department of Surgery, University of Washington, Seattle, WA, USA
| | - Reggie Nkansah
- Department of Surgery, University of Washington, Seattle, WA, USA
| | - Palcah Shibale
- Department of Surgery, University of Washington, Seattle, WA, USA
| | - Sherene Shalhub
- Department of Surgery, University of Washington, Seattle, WA, USA
| | - Judith C Lin
- Deparment of Surgery, McLaren Greater Lansing at Michigan State University, East Lansing, MI, USA
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Overton CE, Abbey R, Baird T, Christie R, Daniel O, Day J, Gittins M, Jones O, Paton R, Tang M, Ward T, Wilkinson J, Woodrow-Hill C, Aldridge T, Chen Y. Identifying employee, workplace and population characteristics associated with COVID-19 outbreaks in the workplace: a population-based study. Occup Environ Med 2024; 81:92-100. [PMID: 38191477 DOI: 10.1136/oemed-2023-109032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/15/2023] [Indexed: 01/10/2024]
Abstract
OBJECTIVES To identify risk factors that contribute to outbreaks of COVID-19 in the workplace and quantify their effect on outbreak risk. METHODS We identified outbreaks of COVID-19 cases in the workplace and investigated the characteristics of the individuals, the workplaces, the areas they work and the mode of commute to work, through data linkages based on Middle Layer Super Output Areas in England between 20 June 2021 and 20 February 2022. We estimated population-level associations between potential risk factors and workplace outbreaks, adjusting for plausible confounders identified using a directed acyclic graph. RESULTS For most industries, increased physical proximity in the workplace was associated with increased risk of COVID-19 outbreaks, while increased vaccination was associated with reduced risk. Employee demographic risk factors varied across industry, but for the majority of industries, a higher proportion of black/African/Caribbean ethnicities and living in deprived areas, was associated with increased outbreak risk. A higher proportion of employees in the 60-64 age group was associated with reduced outbreak risk. There were significant associations between gender, work commute modes and staff contract type with outbreak risk, but these were highly variable across industries. CONCLUSIONS This study has used novel national data linkages to identify potential risk factors of workplace COVID-19 outbreaks, including possible protective effects of vaccination and increased physical distance at work. The same methodological approach can be applied to wider occupational and environmental health research.
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Affiliation(s)
- Christopher E Overton
- UK Health Security Agency, London, UK
- Department of Mathematical Sciences, University of Liverpool, Liverpool, UK
| | | | - Tarrion Baird
- UK Health Security Agency, London, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | | | - Julie Day
- UK Health Security Agency, London, UK
| | - Matthew Gittins
- Centre for Biostatistics, The University of Manchester, Manchester, UK
| | | | | | | | - Tom Ward
- UK Health Security Agency, London, UK
| | - Jack Wilkinson
- Centre for Biostatistics, The University of Manchester, Manchester, UK
| | | | | | - Yiqun Chen
- Science Division, Health and Safety Executive, Buxton, UK
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Kim D, Kim M, Kim J, Baek K, Park H, Park S, Kang BM, Kim S, Kim MJ, Mostafa MN, Maharjan S, Shin HE, Lee MH, Il Kim J, Park MS, Kim YS, Choi EK, Lee Y, Kwon HJ. A mouse xenograft long-term replication yields a SARS-CoV-2 Delta mutant with increased lethality. J Med Virol 2024; 96:e29459. [PMID: 38345153 DOI: 10.1002/jmv.29459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/26/2023] [Accepted: 01/16/2024] [Indexed: 02/15/2024]
Abstract
We recently established a long-term SARS-CoV-2 infection model using lung-cancer xenograft mice and identified mutations that arose in the SARS-CoV-2 genome during long-term propagation. Here, we applied our model to the SARS-CoV-2 Delta variant, which has increased transmissibility and immune escape compared with ancestral SARS-CoV-2. We observed limited mutations in SARS-CoV-2 Delta during long-term propagation, including two predominant mutations: R682W in the spike protein and L330W in the nucleocapsid protein. We analyzed two representative isolates, Delta-10 and Delta-12, with both predominant mutations and some additional mutations. Delta-10 and Delta-12 showed lower replication capacity compared with SARS-CoV-2 Delta in cultured cells; however, Delta-12 was more lethal in K18-hACE2 mice compared with SARS-CoV-2 Delta and Delta-10. Mice infected with Delta-12 had higher viral titers, more severe histopathology in the lungs, higher chemokine expression, increased astrocyte and microglia activation, and extensive neutrophil infiltration in the brain. Brain tissue hemorrhage and mild vacuolation were also observed, suggesting that the high lethality of Delta-12 was associated with lung and brain pathology. Our long-term infection model can provide mutant viruses derived from SARS-CoV-2 Delta and knowledge about the possible contributions of emergent mutations to the properties of new variants.
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Affiliation(s)
- Dongbum Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Minyoung Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Jinsoo Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Kyeongbin Baek
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Heedo Park
- Department of Microbiology, Vaccine Innovation Center College of Medicine, Institute for Viral Diseases, Korea University, Seoul, Republic of Korea
| | - Sangkyu Park
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Bo Min Kang
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Suyeon Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Mo-Jong Kim
- Ilsong Institute of Life Science, Hallym University, Seoul, Republic of Korea
| | - Mohd Najib Mostafa
- Ilsong Institute of Life Science, Hallym University, Seoul, Republic of Korea
- Department of Biomedical Gerontology, Graduate School of Hallym University, Chuncheon, Republic of Korea
| | - Sony Maharjan
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Ha-Eun Shin
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Myeong-Heon Lee
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Jin Il Kim
- Department of Microbiology, Vaccine Innovation Center College of Medicine, Institute for Viral Diseases, Korea University, Seoul, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Vaccine Innovation Center College of Medicine, Institute for Viral Diseases, Korea University, Seoul, Republic of Korea
| | - Yong-Sun Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
- Ilsong Institute of Life Science, Hallym University, Seoul, Republic of Korea
| | - Eun-Kyoung Choi
- Ilsong Institute of Life Science, Hallym University, Seoul, Republic of Korea
- Department of Biomedical Gerontology, Graduate School of Hallym University, Chuncheon, Republic of Korea
| | - Younghee Lee
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Hyung-Joo Kwon
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
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9
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Tiwari S, Petrov AN, Golosov N, Devlin M, Welford M, DeGroote J, Degai T, Ksenofontov S. Regional geographies and public health lessons of the COVID-19 pandemic in the Arctic. Front Public Health 2024; 11:1324105. [PMID: 38259778 PMCID: PMC10801898 DOI: 10.3389/fpubh.2023.1324105] [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: 10/19/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
Objectives This study examines the COVID-19 pandemic's spatiotemporal dynamics in 52 sub-regions in eight Arctic states. This study further investigates the potential impact of early vaccination coverage on subsequent COVID-19 outcomes within these regions, potentially revealing public health insights of global significance. Methods We assessed the outcomes of the COVID-19 pandemic in Arctic sub-regions using three key epidemiological variables: confirmed cases, confirmed deaths, and case fatality ratio (CFR), along with vaccination rates to evaluate the effectiveness of the early vaccination campaign on the later dynamics of COVID-19 outcomes in these regions. Results From February 2020 to February 2023, the Arctic experienced five distinct waves of COVID-19 infections and fatalities. However, most Arctic regions consistently maintained Case Fatality Ratios (CFRs) below their respective national levels throughout these waves. Further, the regression analysis indicated that the impact of initial vaccination coverage on subsequent cumulative mortality rates and Case Fatality Ratio (CFR) was inverse and statistically significant. A common trend was the delayed onset of the pandemic in the Arctic due to its remoteness. A few regions, including Greenland, Iceland, the Faroe Islands, Northern Canada, Finland, and Norway, experienced isolated spikes in cases at the beginning of the pandemic with minimal or no fatalities. In contrast, Alaska, Northern Sweden, and Russia had generally high death rates, with surges in cases and fatalities. Conclusion Analyzing COVID-19 data from 52 Arctic subregions shows significant spatial and temporal variations in the pandemic's severity. Greenland, Iceland, the Faroe Islands, Northern Canada, Finland, and Norway exemplify successful pandemic management models characterized by low cases and deaths. These outcomes can be attributed to successful vaccination campaigns, and proactive public health initiatives along the delayed onset of the pandemic, which reduced the impact of COVID-19, given structural and population vulnerabilities. Thus, the Arctic experience of COVID-19 informs preparedness for future pandemic-like public health emergencies in remote regions and marginalized communities worldwide that share similar contexts.
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Affiliation(s)
- Sweta Tiwari
- ARCTICenter, University of Northern Iowa, Cedar Falls, IA, United States
- Department of Geography, University of Northern Iowa, Cedar Falls, IA, United States
| | - Andrey N. Petrov
- ARCTICenter, University of Northern Iowa, Cedar Falls, IA, United States
- Department of Geography, University of Northern Iowa, Cedar Falls, IA, United States
| | - Nikolay Golosov
- Department of Geography, Pennsylvania State University, University Park, PA, United States
| | - Michele Devlin
- United States Army War College, Carlisle, PA, United States
| | - Mark Welford
- Department of Geography, University of Northern Iowa, Cedar Falls, IA, United States
| | - John DeGroote
- Department of Geography, University of Northern Iowa, Cedar Falls, IA, United States
| | - Tatiana Degai
- ARCTICenter, University of Northern Iowa, Cedar Falls, IA, United States
- Department of Anthropology, University of Victoria, Victoria, BC, Canada
| | - Stanislav Ksenofontov
- ARCTICenter, University of Northern Iowa, Cedar Falls, IA, United States
- Department of Geography, University of Northern Iowa, Cedar Falls, IA, United States
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10
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Arabi-Jeshvaghani F, Javadi-Zarnaghi F, Löchel HF, Martin R, Heider D. LAMPPrimerBank, a manually curated database of experimentally validated loop-mediated isothermal amplification primers for detection of respiratory pathogens. Infection 2023; 51:1809-1818. [PMID: 37828369 DOI: 10.1007/s15010-023-02100-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/13/2023] [Indexed: 10/14/2023]
Abstract
PURPOSE AND METHODS The emergence of coronavirus disease 2019 (COVID-19) has once again affirmed the significant threat of respiratory infections to global public health and the utmost importance of prompt diagnosis in managing and mitigating any pandemic. The nucleic acid amplification test (NAAT) is the primary detection method for most pathogens. Loop-mediated isothermal amplification (LAMP) is a rapid, simple, sensitive, and specific epitome of isothermal NAAT performed using a set of four to six primers. Primer design is a fundamental step in LAMP assays, with several complexities and experimental screening requirements. To address this challenge, an online database is presented here. Its workflow comprises three steps: literature aggregation, data curation, and database and website implementation. RESULTS LAMPPrimerBank ( https://lampprimerbank.mathematik.uni-marburg.de ) is a manually curated database dedicated to experimentally validated LAMP primers, their peculiarities of assays, and accompanying literature, with a primary emphasis on respiratory pathogens. LAMPPrimerBank, with its user-friendly web interface and an open application programming interface, enables the accelerated and facile exploration, comparison, and exportation of LAMP primer sequences and their respective information from the massively scattered literature. LAMPPrimerBank currently comprises LAMP primers for diagnosing viral, bacterial, and fungal respiratory pathogens. Additionally, to address the challenge of false-positive results generated by nonspecific amplifications, LAMPPrimerBank computationally predicted and visualized the sizes of LAMP products for recorded primer sets in the database. CONCLUSION LAMPPrimerBank, as a pioneering database in the rapidly expanding field of isothermal NAAT, endeavors to confront the two challenges of the LAMP: primer design and discrimination of false-positive results.
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Affiliation(s)
- Fatemeh Arabi-Jeshvaghani
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Fatemeh Javadi-Zarnaghi
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Hannah Franziska Löchel
- Department of Data Science in Biomedicine, Faculty of Mathematics and Computer Science, University of Marburg, Marburg, Germany
| | - Roman Martin
- Department of Data Science in Biomedicine, Faculty of Mathematics and Computer Science, University of Marburg, Marburg, Germany
| | - Dominik Heider
- Department of Data Science in Biomedicine, Faculty of Mathematics and Computer Science, University of Marburg, Marburg, Germany
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11
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Singh M, Lo SH, Dubey R, Kumar S, Chaubey KK, Kumar S. Plant-Derived Natural Compounds as an Emerging Antiviral in Combating COVID-19. Indian J Microbiol 2023; 63:429-446. [PMID: 38031604 PMCID: PMC10682353 DOI: 10.1007/s12088-023-01121-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a human virus that burst at Wuhan in China and spread quickly over the world, leading to millions of deaths globally. The journey of this deadly virus to different mutant strains is still ongoing. The plethora of drugs and vaccines have been tested to cope up this pandemic. The herbal plants and different spices have received great attention during pandemic, because of their anti-inflammatory, and immunomodulatory properties in treating viruses and their symptoms. Also, it has been shown that nano-formulation of phytochemicals has potential therapeutic effect against COVID-19. Furthermore, the plant derived compound nano-formulation specifically increases its antiviral property by enhancing its bioavailability, solubility, and target-specific delivery system. This review highlights the potentiality of herbal plants and their phytochemical against SARS-CoV-2 utilizing different mechanisms such as blocking the ACE-2 receptors, inhibiting the main proteases, binding spike proteins and reducing the cytokine storms.
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Affiliation(s)
- Mansi Singh
- Department of Pharmacy, Institute of Pharmaceutical Research, GLA University, Mathura, UP 281406 India
| | - Shih-Hsiu Lo
- Department of Urology, Taipei Medical University Hospital, Taipei, Taiwan
| | - Rajni Dubey
- Division of Cardiology, Department of Internal Medicine, Taipei Medical University Hospital, No. 252, Wuxing Street, Taipei, 11031 Taiwan
| | - Sudhashekhar Kumar
- Department of Physiology, School of Medical Sciences and Research, Sharda University, Greater Noida, UP 201310 India
| | - Kundan Kumar Chaubey
- Division of Research and Innovation, School of Applied and Life Sciences, Uttaranchal University, Arcadia Grant, P.O. Chandanwari, Premnagar, Dehradun, Uttarakhand 248007 India
- School of Basic and Applied Sciences, Sanskriti University, Mathura, UP 281401 India
| | - Sanjay Kumar
- Biological and Bio-Computational Lab, Department of Life Science, Sharda School of Basic Sciences and Research, Sharda University, Greater Noida, UP 201310 India
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12
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Daily AM, Popat S, Koenig HG, Fuller TW, Lee UJ. Female pelvic medicine and reconstructive surgery fellows' case logs remained stable during the COVID-19 pandemic. Neurourol Urodyn 2023; 42:1789-1794. [PMID: 37545331 DOI: 10.1002/nau.25261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/12/2023] [Accepted: 07/27/2023] [Indexed: 08/08/2023]
Abstract
INTRODUCTION During the COVID-19 pandemic and subsequent staffing shortages there was concern about the case volume, and thus competency, of graduating trainees due to reduced surgical volumes. Elective procedures were particularly affected, which includes Female Pelvic Medicine and Reconstructive Surgery (FPMRS) cases. To understand whether FPMRS fellows were affected, we assessed their case logs for changes during the pandemic. METHODS The nationally aggregated case logs of graduating FPMRS fellows, both urology and obstetrics and gynecology (OBGYN), were obtained from the Accreditation Council for Graduate Medical Education. The available academic years (AYs) included 2018-2019, 2019-2020, and 2020-2021. Standard deviation for each index category was derived from the average and 90th percentile data. One-way analysis of variance was used to compare differences in case volumes for tracked index categories between AYs. RESULTS Graduating fellows logged an average of 517.4 (standard deviation [SD] 28.6) and 818.0 (SD 37.9) cases, for urology and OBGYN respectively, over their fellowship training during the examined period. No significant differences in total surgical procedures were found for either specialty between pre-COVID AY 2018-2019 and COVID-affected AYs 2019-2020 and 2020-2021. For urology fellows, gastrointestinal (GI) procedures was the only index case category with a significant difference, and it was a decrease between the two COVID-affected AYs: 2020-2021 compared to 2019-2020 (8.9 vs. 4.2, p = 0.04). For both urology and OBGYN fellows, there was a statistically significant decrease in graft/mesh augmentation procedures from COVID-affected AY 2019-2020 to AY 2020-2021. This may be attributed to the reclassification of mesh removal cases from graft/mesh augmentation procedures to genital procedures in 2020-2021. There was not a significant decrease in these procedures from pre-COVID AY 2018-2019 to the COVID-affected AYs. There were no other statistically significant differences between AYs for OBGYN fellows. CONCLUSIONS Surgical case volumes for FPMRS urology and OBGYN fellows who trained during the COVID-19 pandemic were comparable to those of their pre-pandemic peers. No significant differences between pre-COVID and COVID-affected years were found for either total surgical procedures or index case categories. Despite disruptions in health care nationwide, FPMRS trainee case volumes were largely unaffected.
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Affiliation(s)
- Adam M Daily
- Section of Urology and Renal Transplantation, Virginia Mason Franciscan Health, Seattle, Washington, USA
| | - Shreeya Popat
- Section of Urology and Renal Transplantation, Virginia Mason Franciscan Health, Seattle, Washington, USA
| | - Hannah G Koenig
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, Washington, USA
| | - Thomas W Fuller
- Section of Urology and Renal Transplantation, Virginia Mason Franciscan Health, Seattle, Washington, USA
| | - Una J Lee
- Section of Urology and Renal Transplantation, Virginia Mason Franciscan Health, Seattle, Washington, USA
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13
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Boix-Besora A, Gòdia F, Cervera L. Gag Virus-like Particles Functionalized with SARS-CoV-2 Variants: Generation, Characterization and Recognition by COVID-19 Convalescent Patients' Sera. Vaccines (Basel) 2023; 11:1641. [PMID: 38005972 PMCID: PMC10675557 DOI: 10.3390/vaccines11111641] [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: 09/12/2023] [Revised: 10/16/2023] [Accepted: 10/21/2023] [Indexed: 11/26/2023] Open
Abstract
The robustness, safety, versatility, and high immunogenicity of virus-like particles (VLPs) make them a promising approach for the generation of vaccines against a broad range of pathogens. VLPs are recombinant macromolecular structures that closely mimic the native conformation of viruses without carrying viral genetic material. Particularly, HIV-1 Gag-based VLPs are a suitable platform for the presentation of the SARS-CoV-2 Spike (S) protein on their surface. In this context, this work studies the effect of different rationally engineered mutations of the S protein to improve some of its characteristics. The studied variants harbored mutations such as proline substitutions for S stabilization, D614G from the early dominant pandemic form, the elimination of the S1/S2 furin cleavage site to improve S homogeneity, the suppression of a retention motif to favor its membrane localization, and cysteine substitutions to increase its immunogenicity and avoid potential undesired antibody-dependent enhancement (ADE) effects. The influence of the mutations on VLP expression was studied, as well as their immunogenic potential, by testing the recognition of the generated VLP variants by COVID-19 convalescent patients' sera. The results of this work are conceived to give insights on the selection of S protein candidates for their use as immunogens and to showcase the potential of VLPs as carriers for antigen presentation.
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Affiliation(s)
- Arnau Boix-Besora
- Grup d’Enginyeria de Bioprocessos i Biocatàlisi Aplicada ENG4BIO, Escola d’Enginyeria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Barcelona, Spain
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14
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Jones RP, Ponomarenko A. COVID-19-Related Age Profiles for SARS-CoV-2 Variants in England and Wales and States of the USA (2020 to 2022): Impact on All-Cause Mortality. Infect Dis Rep 2023; 15:600-634. [PMID: 37888139 PMCID: PMC10606787 DOI: 10.3390/idr15050058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 10/28/2023] Open
Abstract
Since 2020, COVID-19 has caused serious mortality around the world. Given the ambiguity in establishing COVID-19 as the direct cause of death, we first investigate the effects of age and sex on all-cause mortality during 2020 and 2021 in England and Wales. Since infectious agents have their own unique age profile for death, we use a 9-year time series and several different methods to adjust single-year-of-age deaths in England and Wales during 2019 (the pre-COVID-19 base year) to a pathogen-neutral single-year-of-age baseline. This adjusted base year is then used to confirm the widely reported higher deaths in males for most ages above 43 in both 2020 and 2021. During 2020 (+COVID-19 but no vaccination), both male and female population-adjusted deaths significantly increased above age 35. A significant reduction in all-cause mortality among both males and females aged 75+ could be demonstrated in 2021 during the widespread COVID-19 vaccination period; however, deaths below age 75 progressively increased. This finding arises from a mix of vaccination coverage and year-of-age profiles of deaths for the different SARS-CoV-2 variants. In addition, specific effects of age around puberty were demonstrated, where females had higher deaths than males. There is evidence that year-of-birth cohorts may also be involved, indicating that immune priming to specific pathogen outbreaks in the past may have led to lower deaths for some birth cohorts. To specifically identify the age profile for the COVID-19 variants from 2020 to 2023, we employ the proportion of total deaths at each age that are potentially due to or 'with' COVID-19. The original Wuhan strain and the Alpha variant show somewhat limited divergence in the age profile, with the Alpha variant shifting to a moderately higher proportion of deaths below age 84. The Delta variant specifically targeted individuals below age 65. The Omicron variants showed a significantly lower proportion of overall mortality, with a markedly higher relative proportion of deaths above age 65, steeply increasing with age to a maximum around 100 years of age. A similar age profile for the variants can be seen in the age-banded deaths in US states, although they are slightly obscured by using age bands rather than single years of age. However, the US data shows that higher male deaths are greatly dependent on age and the COVID variant. Deaths assessed to be 'due to' COVID-19 (as opposed to 'involving' COVID-19) in England and Wales were especially overestimated in 2021 relative to the change in all-cause mortality. This arose as a by-product of an increase in COVID-19 testing capacity in late 2020. Potential structure-function mechanisms for the age-specificity of SARS-CoV-2 variants are discussed, along with potential roles for small noncoding RNAs (miRNAs). Using data from England, it is possible to show that the unvaccinated do indeed have a unique age profile for death from each variant and that vaccination alters the shape of the age profile in a manner dependent on age, sex, and the variant. The question is posed as to whether vaccines based on different variants carry a specific age profile.
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Affiliation(s)
| | - Andrey Ponomarenko
- Department of Biophysics, Informatics and Medical Instrumentation, Odessa National Medical University, Valikhovsky Lane 2, 65082 Odessa, Ukraine
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15
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Shivgunde P, Thakare S, Sen S, Kanitkar M, Agrawal M, Vidyasagar M. COVID-19 Pandemic in Malegaon: SUTRA over the Three Waves. Indian J Microbiol 2023; 63:344-351. [PMID: 37781020 PMCID: PMC10533435 DOI: 10.1007/s12088-023-01096-3] [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: 11/22/2022] [Accepted: 08/13/2023] [Indexed: 10/03/2023] Open
Abstract
Over the past two years, the COVID-19 pandemic has seen multiple waves with high morbidity and mortality. Lockdowns and other prompt responses helped India's situation become less severe. Although Malegaon in the Indian state of Maharashtra has a high population density, poor hygienic standards, and oppositional local community views toward national pandemic addressing measures, it is nevertheless reasonably safe. To understand the possible reasons serosurvey was conducted to estimate the anti-SARS-CoV-2 neutralizing antibody levels in the Malegaon population. Also, we did SUTRA mathematical modeling to the Malegaon daily data on COVID-19 attributable events and compared it with the National and state level. The case fatality rate (CFR) in Malegaon city for the first, second, and third waves was 3.25%, 2.25%, and 0.39%, respectively. The crude death rate (CDR) for Maharashtra ranked first for the initial two waves and India for the third wave. Malegaon, meanwhile, finished second in the first two waves but fared best in the third. The Vaccination coverage for the first dose before the second wave was only 0.34% but had risen to 64.46% by 12 Oct 2022. By then, the second and booster dose coverage was 27.55% and 2.38%, respectively. Serosurvey did between 12 and 18 Jan 2022 showed a 93.93% anti-SARS-CoV-2 neutralizing antibody presence. SUTRA modeling elucidated the high levels of antibodies due to the pandemic-reach over 102% by the third wave. The serosurvey and the model explain why the pandemic severity in terms of duration and CFR during the subsequent waves, especially third wave, was milder compared to the first wave in spite of low vaccination rates. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-023-01096-3.
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Affiliation(s)
- Prashant Shivgunde
- Department of Pharmaceutical Medicine, Maharashtra University of Health Sciences, Nashik, MH 422004 India
| | - Sapana Thakare
- Malegaon Municipal Corporation, Malegaon, MH 423105 India
| | - Sourav Sen
- University Research Department, Maharashtra University of Health Sciences, Nashik, MH 422004 India
| | - Madhuri Kanitkar
- Maharashtra University of Health Sciences, Nashik, MH 422004 India
| | | | - Mathukumalli Vidyasagar
- Department of Artificial Intelligence, Indian Institute of Technology Hyderabad, Kandi, TS 502284 India
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16
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Asimakos AT, Vassiliou AG, Keskinidou C, Spetsioti S, Antonoglou A, Vrettou CS, Mourelatos P, Diamantopoulos A, Pratikaki M, Athanasiou N, Jahaj E, Gallos P, Kotanidou A, Dimopoulou I, Orfanos SE, Katsaounou P. Persistent Endothelial Lung Damage and Impaired Diffusion Capacity in Long COVID. J Pers Med 2023; 13:1351. [PMID: 37763119 PMCID: PMC10533128 DOI: 10.3390/jpm13091351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Since the beginning of the pandemic, both COVID-19-associated coagulopathy biomarkers and a plethora of endothelial biomarkers have been proposed and tested as prognostic tools of severity and mortality prediction. As the pandemic is gradually being controlled, attention is now focusing on the long-term sequelae of COVID-19. In the present study, we investigated the role of endothelial activation/dysfunction in long COVID syndrome. This observational study included 68 consecutive long COVID patients and a healthy age and sex-matched control group. In both groups, we measured 13 endothelial biomarkers. Moreover, in the long COVID patients, we evaluated fatigue and dyspnea severity, lung diffusion capacity (DLCO), and the 6-min walk (6MWT) test as measures of functional capacity. Our results showed that markers of endothelial activation/dysfunction were higher in long COVID patients, and that soluble intracellular adhesion molecule 1 (sICAM-1) and soluble vascular adhesion molecule 1 (sVCAM-1) negatively correlated with lung diffusion and functional capacity (sICAM-1 vs. DLCO, r = -0.306, p = 0.018; vs. 6MWT, r = -0.263, p = 0.044; and sVCAM-1 vs. DLCO, r= -0.346, p = 0.008; vs. 6MWT, r = -0.504, p < 0.0001). In conclusion, evaluating endothelial biomarkers alongside clinical tests might yield more specific insights into the pathophysiological mechanisms of long COVID manifestations.
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Affiliation(s)
- Andreas T. Asimakos
- First Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 106 76 Athens, Greece; (A.T.A.); (A.G.V.); (C.K.); (S.S.); (A.A.); (C.S.V.); (N.A.); (E.J.); (A.K.); (I.D.); (S.E.O.)
| | - Alice G. Vassiliou
- First Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 106 76 Athens, Greece; (A.T.A.); (A.G.V.); (C.K.); (S.S.); (A.A.); (C.S.V.); (N.A.); (E.J.); (A.K.); (I.D.); (S.E.O.)
| | - Chrysi Keskinidou
- First Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 106 76 Athens, Greece; (A.T.A.); (A.G.V.); (C.K.); (S.S.); (A.A.); (C.S.V.); (N.A.); (E.J.); (A.K.); (I.D.); (S.E.O.)
| | - Stavroula Spetsioti
- First Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 106 76 Athens, Greece; (A.T.A.); (A.G.V.); (C.K.); (S.S.); (A.A.); (C.S.V.); (N.A.); (E.J.); (A.K.); (I.D.); (S.E.O.)
| | - Archontoula Antonoglou
- First Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 106 76 Athens, Greece; (A.T.A.); (A.G.V.); (C.K.); (S.S.); (A.A.); (C.S.V.); (N.A.); (E.J.); (A.K.); (I.D.); (S.E.O.)
| | - Charikleia S. Vrettou
- First Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 106 76 Athens, Greece; (A.T.A.); (A.G.V.); (C.K.); (S.S.); (A.A.); (C.S.V.); (N.A.); (E.J.); (A.K.); (I.D.); (S.E.O.)
| | - Panagiotis Mourelatos
- Department of Endocrinology Diabetes and Metabolism, National Expertise Center for Rare Endocrine Diseases, Evangelismos Hospital, 106 76 Athens, Greece; (P.M.); (A.D.)
| | - Aristidis Diamantopoulos
- Department of Endocrinology Diabetes and Metabolism, National Expertise Center for Rare Endocrine Diseases, Evangelismos Hospital, 106 76 Athens, Greece; (P.M.); (A.D.)
| | - Maria Pratikaki
- Biochemical Department, Evangelismos Hospital, 106 76 Athens, Greece;
| | - Nikolaos Athanasiou
- First Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 106 76 Athens, Greece; (A.T.A.); (A.G.V.); (C.K.); (S.S.); (A.A.); (C.S.V.); (N.A.); (E.J.); (A.K.); (I.D.); (S.E.O.)
| | - Edison Jahaj
- First Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 106 76 Athens, Greece; (A.T.A.); (A.G.V.); (C.K.); (S.S.); (A.A.); (C.S.V.); (N.A.); (E.J.); (A.K.); (I.D.); (S.E.O.)
| | - Parisis Gallos
- Computational Biomedicine Laboratory, Department of Digital Systems, University of Piraeus, 185 34 Piraeus, Greece;
| | - Anastasia Kotanidou
- First Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 106 76 Athens, Greece; (A.T.A.); (A.G.V.); (C.K.); (S.S.); (A.A.); (C.S.V.); (N.A.); (E.J.); (A.K.); (I.D.); (S.E.O.)
| | - Ioanna Dimopoulou
- First Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 106 76 Athens, Greece; (A.T.A.); (A.G.V.); (C.K.); (S.S.); (A.A.); (C.S.V.); (N.A.); (E.J.); (A.K.); (I.D.); (S.E.O.)
| | - Stylianos E. Orfanos
- First Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 106 76 Athens, Greece; (A.T.A.); (A.G.V.); (C.K.); (S.S.); (A.A.); (C.S.V.); (N.A.); (E.J.); (A.K.); (I.D.); (S.E.O.)
| | - Paraskevi Katsaounou
- First Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 106 76 Athens, Greece; (A.T.A.); (A.G.V.); (C.K.); (S.S.); (A.A.); (C.S.V.); (N.A.); (E.J.); (A.K.); (I.D.); (S.E.O.)
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17
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Mediavilla JR, Lozy T, Lee A, Kim J, Kan VW, Titova E, Amin A, Zody MC, Corvelo A, Oschwald DM, Baldwin A, Fennessey S, Zuckerman JM, Kirn T, Chen L, Zhao Y, Chow KF, Maniatis T, Perlin DS, Kreiswirth BN. Molecular and Clinical Epidemiology of SARS-CoV-2 Infection among Vaccinated and Unvaccinated Individuals in a Large Healthcare Organization from New Jersey. Viruses 2023; 15:1699. [PMID: 37632041 PMCID: PMC10457875 DOI: 10.3390/v15081699] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
New Jersey was among the first states impacted by the COVID-19 pandemic, with one of the highest overall death rates in the nation. Nevertheless, relatively few reports have been published focusing specifically on New Jersey. Here we report on molecular, clinical, and epidemiologic observations, from the largest healthcare network in the state, in a cohort of vaccinated and unvaccinated individuals with laboratory-confirmed SARS-CoV-2 infection. We conducted molecular surveillance of SARS-CoV-2-positive nasopharyngeal swabs collected in nine hospitals from December 2020 through June 2022, using both whole genome sequencing (WGS) and a real-time RT-PCR screening assay targeting spike protein mutations found in variants of concern (VOCs) within our region. De-identified clinical data were obtained retrospectively, including demographics, COVID-19 vaccination status, ICU admission, ventilator support, mortality, and medical history. Statistical analyses were performed to identify associations between SARS-CoV-2 variants, vaccination status, clinical outcomes, and medical risk factors. A total of 5007 SARS-CoV-2-positive nasopharyngeal swabs were successfully screened and/or sequenced. Variant screening identified three predominant VOCs, including Alpha (n = 714), Delta (n = 1877), and Omicron (n = 1802). Omicron isolates were further sub-typed as BA.1 (n = 899), BA.2 (n = 853), or BA.4/BA.5 (n = 50); the remaining 614 isolates were classified as "Other". Approximately 31.5% (1577/5007) of the samples were associated with vaccine breakthrough infections, which increased in frequency following the emergence of Delta and Omicron. Severe clinical outcomes included ICU admission (336/5007 = 6.7%), ventilator support (236/5007 = 4.7%), and mortality (430/5007 = 8.6%), with increasing age being the most significant contributor to each (p < 0.001). Unvaccinated individuals accounted for 79.7% (268/336) of ICU admissions, 78.3% (185/236) of ventilator cases, and 74.4% (320/430) of deaths. Highly significant (p < 0.001) increases in mortality were observed in individuals with cardiovascular disease, hypertension, cancer, diabetes, and hyperlipidemia, but not with obesity, thyroid disease, or respiratory disease. Significant differences (p < 0.001) in clinical outcomes were also noted between SARS-CoV-2 variants, including Delta, Omicron BA.1, and Omicron BA.2. Vaccination was associated with significantly improved clinical outcomes in our study, despite an increase in breakthrough infections associated with waning immunity, greater antigenic variability, or both. Underlying comorbidities contributed significantly to mortality in both vaccinated and unvaccinated individuals, with increasing risk based on the total number of comorbidities. Real-time RT-PCR-based screening facilitated timely identification of predominant variants using a minimal number of spike protein mutations, with faster turnaround time and reduced cost compared to WGS. Continued evolution of SARS-CoV-2 variants will likely require ongoing surveillance for new VOCs, with real-time assessment of clinical impact.
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Affiliation(s)
- José R. Mediavilla
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Tara Lozy
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
- Department of Pediatrics, Hackensack University Medical Center, Hackensack, NJ 07601, USA
| | - Annie Lee
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Justine Kim
- Hackensack Meridian Health Biorepository, Hackensack, NJ 07601, USA
| | - Veronica W. Kan
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Elizabeth Titova
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Ashish Amin
- Hackensack Meridian Health Biorepository, Hackensack, NJ 07601, USA
| | - Michael C. Zody
- New York Genome Center, New York, NY 10013, USA (S.F.); (T.M.)
| | - André Corvelo
- New York Genome Center, New York, NY 10013, USA (S.F.); (T.M.)
| | | | - Amy Baldwin
- New York Genome Center, New York, NY 10013, USA (S.F.); (T.M.)
| | | | - Jerry M. Zuckerman
- Department of Patient Safety and Quality, Hackensack Meridian Health, Edison, NJ 08837, USA
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
| | - Thomas Kirn
- Public Health and Environmental Laboratories, New Jersey Department of Health, Ewing, NJ 08628, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
| | - Yanan Zhao
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
| | - Kar Fai Chow
- Hackensack Meridian Health Biorepository, Hackensack, NJ 07601, USA
- Department of Pathology, Hackensack University Medical Center, Hackensack, NJ 07601, USA
| | - Tom Maniatis
- New York Genome Center, New York, NY 10013, USA (S.F.); (T.M.)
| | - David S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
| | - Barry N. Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
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18
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Garcia-Carretero R, Vazquez-Gomez O, Ordoñez-Garcia M, Garrido-Peño N, Gil-Prieto R, Gil-de-Miguel A. Differences in Trends in Admissions and Outcomes among Patients from a Secondary Hospital in Madrid during the COVID-19 Pandemic: A Hospital-Based Epidemiological Analysis (2020-2022). Viruses 2023; 15:1616. [PMID: 37515302 PMCID: PMC10384448 DOI: 10.3390/v15071616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Spain had some of Europe's highest incidence and mortality rates for coronavirus disease 2019 (COVID-19). This study highlights the impact of the COVID-19 pandemic on daily health care in terms of incidence, critical patients, and mortality. We describe the characteristics and clinical outcomes of patients, comparing variables over the different waves. We performed a descriptive, retrospective study using the historical records of patients hospitalized with COVID-19. We describe demographic characteristics, admissions, and occupancy. Time series allowed us to visualize and analyze trends and patterns, and identify several waves during the 27-month period. A total of 3315 patients had been hospitalized with confirmed COVID-19. One-third of these patients were hospitalized during the first weeks of the pandemic. We observed that 4.6% of all hospitalizations had been admitted to the intensive care unit, and we identified a mortality rate of 9.4% among hospitalized patients. Arithmetic- and semi-logarithmic-scale charts showed how admissions and deaths rose sharply during the first weeks, increasing by 10 every few days. We described a single hospital's response and experiences during the pandemic. This research highlights certain demographic profiles in a population and emphasizes the importance of identifying waves when performing research on COVID-19. Our results can extend the analysis of the impact of COVID-19 and can be applied in other contexts, and can be considered when further analyzing the clinical, epidemiological, or demographic characteristics of populations with COVID-19. Our findings suggest that the pandemic should be analyzed not as a whole but rather in different waves.
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Affiliation(s)
- Rafael Garcia-Carretero
- Department of Internal Medicine, Mostoles University Hospital, 28935 Móstoles, Madrid, Spain
| | - Oscar Vazquez-Gomez
- Department of Internal Medicine, Mostoles University Hospital, 28935 Móstoles, Madrid, Spain
| | - María Ordoñez-Garcia
- Department of Hematology, Mostoles University Hospital, 28935 Móstoles, Madrid, Spain
| | - Noelia Garrido-Peño
- Department of Pharmacy, Mostoles University Hospital, 28935 Móstoles, Madrid, Spain
| | - Ruth Gil-Prieto
- Department of Preventive Medicine and Public Health, Rey Juan Carlos University, 28922 Alcorcón, Madrid, Spain
| | - Angel Gil-de-Miguel
- Department of Preventive Medicine and Public Health, Rey Juan Carlos University, 28922 Alcorcón, Madrid, Spain
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19
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Garcia-Carretero R, Vazquez-Gomez O, Gil-Prieto R, Gil-de-Miguel A. Hospitalization burden and epidemiology of the COVID-19 pandemic in Spain (2020-2021). BMC Infect Dis 2023; 23:476. [PMID: 37464303 DOI: 10.1186/s12879-023-08454-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Spain had some of Europe's highest incidence and mortality rates for coronavirus disease 2019 (COVID-19). Here we describe the epidemiology and trends in hospitalizations, the number of critical patients, and deaths in Spain in 2020 and 2021. METHODS We performed a descriptive, retrospective, nationwide study using an administrative database, the Minimum Basic Data Set at Hospitalization, which includes 95-97% of discharge reports for patients hospitalized in Spain in 2020 and 2021. We analyzed the number of hospitalizations, admissions to intensive care units, and deaths and their geographic distribution across regions of Spain. RESULTS As of December 31, 2021, a total of 498,789 patients (1.04% of the entire Spanish population) had needed hospitalization. At least six waves of illness were identified. Men were more prone to hospitalization than women. The median age was 66. A total of 54,340 patients (10.9% of all hospitalizations) had been admitted to the intensive care unit. We identified 71,437 deaths (mortality rate of 14.3% among hospitalized patients). We also observed important differences among regions, with Madrid being the epicenter of hospitalizations and mortality. CONCLUSIONS We analyzed Spain's response to COVID-19 and describe here its experiences during the pandemic in terms of hospitalizations, critical illness, and deaths. This research highlights changes over several months and waves and the importance of factors such as vaccination, the predominant variant of the virus, and public health interventions in the rise and fall of the outbreaks.
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Affiliation(s)
- Rafael Garcia-Carretero
- Department of Internal Medicine, Mostoles University Hospital, Rey Juan Carlos University, Madrid, Spain.
| | - Oscar Vazquez-Gomez
- Department of Internal Medicine, Mostoles University Hospital, Rey Juan Carlos University, Madrid, Spain
| | - Ruth Gil-Prieto
- Department of Preventive Medicine and Public Health, Rey Juan Carlos University, Madrid, Spain
| | - Angel Gil-de-Miguel
- Department of Preventive Medicine and Public Health, Rey Juan Carlos University, Madrid, Spain
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20
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Machado RRG, Walker JL, Scharton D, Rafael GH, Mitchell BM, Reyna RA, de Souza WM, Liu J, Walker DH, Plante JA, Plante KS, Weaver SC. Immunogenicity and efficacy of vaccine boosters against SARS-CoV-2 Omicron subvariant BA.5 in male Syrian hamsters. Nat Commun 2023; 14:4260. [PMID: 37460536 DOI: 10.1038/s41467-023-40033-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
The SARS-CoV-2 Omicron subvariant BA.5 rapidly spread worldwide and replaced BA.1/BA.2 in many countries, becoming globally dominant. BA.5 has unique amino acid substitutions in the spike protein that both mediate immune escape from neutralizing antibodies produced by immunizations and increase ACE2 receptor binding affinity. In a comprehensive, long-term (up to 9 months post primary vaccination), experimental vaccination study using male Syrian hamsters, we evaluate neutralizing antibody responses and efficacy against BA.5 challenge after primary vaccination with Ad26.COV2.S (Janssen) or BNT162b2 (Pfizer/BioNTech) followed by a homologous or heterologous booster with mRNA-1273 (Moderna) or NVX-CoV2373 (Novavax). Notably, one high or low dose of Ad26.COV2.S provides more durable immunity than two primary doses of BNT162b2, and the NVX-CoV2373 booster provides the strongest augmentation of immunity, reduction in BA.5 viral replication, and disease. Our data demonstrate the immunogenicity and efficacy of different prime/boost vaccine regimens against BA.5 infection in an immune-competent model and provide new insights regarding COVID-19 vaccine strategies.
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Affiliation(s)
- Rafael R G Machado
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, SP, 05508000, Brazil
| | - Jordyn L Walker
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Dionna Scharton
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Grace H Rafael
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Brooke M Mitchell
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Rachel A Reyna
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - William M de Souza
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jianying Liu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - David H Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, 77555, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jessica A Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Kenneth S Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, 77555, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, 77555, USA.
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, 77555, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, 77555, USA.
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21
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Agarwal A, Rizwana, Tripathi AD, Kumar T, Sharma KP, Patel SKS. Nutritional and Functional New Perspectives and Potential Health Benefits of Quinoa and Chia Seeds. Antioxidants (Basel) 2023; 12:1413. [PMID: 37507952 PMCID: PMC10376479 DOI: 10.3390/antiox12071413] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Quinoa (Chenopodium quinoa Willd) and chia (Salvia hispanica) are essential traditional crops with excellent nutritional properties. Quinoa is known for its high and good quality protein content and nine essential amino acids vital for an individual's development and growth, whereas chia seeds contain high dietary fiber content, calories, lipids, minerals (calcium, magnesium, iron, phosphorus, and zinc), and vitamins (A and B complex). Chia seeds are also known for their presence of a high amount of omega-3 fatty acids. Both quinoa and chia seeds are gluten-free and provide medicinal properties due to bioactive compounds, which help combat various chronic diseases such as diabetes, obesity, cardiovascular diseases, and metabolic diseases such as cancer. Quinoa seeds possess phenolic compounds, particularly kaempferol, which can help prevent cancer. Many food products can be developed by fortifying quinoa and chia seeds in different concentrations to enhance their nutritional profile, such as extruded snacks, meat products, etc. Furthermore, it highlights the value-added products that can be developed by including quinoa and chia seeds, alone and in combination. This review focused on the recent development in quinoa and chia seeds nutritional, bioactive properties, and processing for potential human health and therapeutic applications.
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Affiliation(s)
- Aparna Agarwal
- Department of Food & Nutrition and Food Technology, Lady Irwin College, Sikandra Road, New Delhi 110001, India
| | - Rizwana
- Department of Food Technology, Bhaskaracharya College of Applied Sciences, Sector-2, Dwarka, New Delhi 110075, India
| | - Abhishek Dutt Tripathi
- Department of Dairy Science and Food Technology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Tarika Kumar
- Department of Environmental Studies, The Maharaja Sayajirao University of Baroda, Vadodara 390002, India
| | - Kanti Prakash Sharma
- Department of Nutrition Biology, Central University of Haryana, Mahendergarh 123031, India
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22
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Kumari M, Su SC, Liang KH, Lin HT, Lu YF, Chen KC, Chen WY, Wu HC. Bivalent mRNA vaccine effectiveness against SARS-CoV-2 variants of concern. J Biomed Sci 2023; 30:46. [PMID: 37380988 DOI: 10.1186/s12929-023-00936-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/02/2023] [Indexed: 06/30/2023] Open
Abstract
BACKGROUND Sequential infections with SARS-CoV-2 variants such as Alpha, Delta, Omicron and its sublineages may cause high morbidity, so it is necessary to develop vaccines that can protect against both wild-type (WT) virus and its variants. Mutations in SARS-CoV-2's spike protein can easily alter viral transmission and vaccination effectiveness. METHODS In this study, we designed full-length spike mRNAs for WT, Alpha, Delta, and BA.5 variants and integrated each into monovalent or bivalent mRNA-lipid nanoparticle vaccines. A pseudovirus neutralization assay was conducted on immunized mouse sera in order to examine the neutralizing potential of each vaccine. RESULTS Monovalent mRNA vaccines were only effective against the same type of virus. Interestingly, monovalent BA.5 vaccination could neutralize BF.7 and BQ.1.1. Moreover, WT, Alpha, Delta, BA.5, and BF.7 pseudoviruses were broadly neutralized by bivalent mRNA vaccinations, such as BA.5 + WT, BA.5 + Alpha, and BA.5 + Delta. In particular, BA.5 + WT exhibited high neutralization against most variants of concern (VOCs) in a pseudovirus neutralization assay. CONCLUSIONS Our results show that combining two mRNA sequences may be an effective way to develop a broadly protective SARS-CoV-2 vaccine against a wide range of variant types. Importantly, we provide the optimal combination regimen and propose a strategy that may prove useful in combating future VOCs.
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Affiliation(s)
- Monika Kumari
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Shih-Chieh Su
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Kang-Hao Liang
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan
| | - Hsiu-Ting Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Yu-Feng Lu
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Kai-Chi Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Wan-Yu Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Han-Chung Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan.
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan.
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23
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Lobaina Y, Chen R, Suzarte E, Ai P, Huerta V, Tan C, Alvarez-Lajonchere L, Liling Y, Musacchio A, Silva R, Guillén G, Zaixue J, Yang K, Perera Y, Hermida L. Broad humoral immunity generated in mice by a formulation composed of two antigens from the Delta variant of SARS-CoV-2. Arch Virol 2023; 168:190. [PMID: 37351679 DOI: 10.1007/s00705-023-05812-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/05/2023] [Indexed: 06/24/2023]
Abstract
Due to the rapid development of new variants of SARS-CoV-2 as well as the real threat of new coronavirus zoonosis events, the development of a preventive vaccine with a broader scope of functionality is highly desirable. Previously, we reported the functionality of a nasal formulation containing the nucleocapsid protein and the receptor-binding domain (RBD) of the spike protein of the Delta variant of SARS-CoV-2 combined with the ODN-39M adjuvant. This combination induced cross-reactive immunity in mucosal and systemic compartments at the sarbecovirus level. In the present study, we explored the magnitude of the immunity generated in BALB/c mice by the same formulation with alum added as an additional adjuvant, to enhance the humoral immunity against the two antigens. Animals were immunized with three doses of the bivalent formulation, administered by subcutaneous route. Humoral immunity was tested by ELISA, and the neutralizing capacity of the resulting antibodies (Abs) was evaluated using a surrogate test and a vesicular stomatitis virus (VSV) pseudovirus-based assay. Cell-mediated immunity was also investigated using an IFN-γ ELISpot assay. High levels of antibodies against both antigens (N and RBD) were obtained upon immunization. Anti-RBD Abs with neutralizing capacity reacted with the RBD of three SARS-CoV-2 variants tested, including Omicron. Abs recognizing the nucleocapsid proteins of SARS-CoV-1 and the SARS-CoV-2 Delta and Omicron variants were also detected. Taken together, these results suggest that this bivalent formulation could be an attractive component of a pancorona vaccine able to broaden the scope of humoral immunity against both antigens. This will be particularly important for the reinforcement of immunity in previously vaccinated and/or infected populations.
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Affiliation(s)
- Yadira Lobaina
- Research Department, China-Cuba Biotechnology Joint Innovation Center (CCBJIC), Lengshuitan District, Yongzhou, 425000, Hunan, China
- Research Department, Yongzhou Zhong Gu Biotechnology Co., Ltd, Yangjiaqiao Street, Lengshuitan District, Yongzhou, 425000, Hunan, China
| | - Rong Chen
- Research Department, China-Cuba Biotechnology Joint Innovation Center (CCBJIC), Lengshuitan District, Yongzhou, 425000, Hunan, China
- Yongzhou Development and Construction Investment Co. Ltd. (YDCI), Changfeng Industry Park, Yongzhou Economic and Technological Development Zone, No. 1 Liebao Road, Lengshuitan District, Yongzhou, Hunan, China
| | - Edith Suzarte
- Biomedical Research Department, Center for Genetic Engineering and Biotechnology (CIGB), 10600, Havana, Cuba
| | - Panchao Ai
- Research Department, China-Cuba Biotechnology Joint Innovation Center (CCBJIC), Lengshuitan District, Yongzhou, 425000, Hunan, China
- Yongzhou Development and Construction Investment Co. Ltd. (YDCI), Changfeng Industry Park, Yongzhou Economic and Technological Development Zone, No. 1 Liebao Road, Lengshuitan District, Yongzhou, Hunan, China
| | - Vivian Huerta
- Research Department, China-Cuba Biotechnology Joint Innovation Center (CCBJIC), Lengshuitan District, Yongzhou, 425000, Hunan, China
- Biomedical Research Department, Center for Genetic Engineering and Biotechnology (CIGB), 10600, Havana, Cuba
| | - Changyuan Tan
- Research Department, China-Cuba Biotechnology Joint Innovation Center (CCBJIC), Lengshuitan District, Yongzhou, 425000, Hunan, China
- Yongzhou Development and Construction Investment Co. Ltd. (YDCI), Changfeng Industry Park, Yongzhou Economic and Technological Development Zone, No. 1 Liebao Road, Lengshuitan District, Yongzhou, Hunan, China
| | - Liz Alvarez-Lajonchere
- Biomedical Research Department, Center for Genetic Engineering and Biotechnology (CIGB), 10600, Havana, Cuba
| | - Yang Liling
- Department of Laboratory Medicine, Dongguan Ninth People's Hospital, No. 88, Shaditang, Guancheng District, Dongguan, Guangdong, China
| | - Alexis Musacchio
- Research Department, China-Cuba Biotechnology Joint Innovation Center (CCBJIC), Lengshuitan District, Yongzhou, 425000, Hunan, China
- Biomedical Research Department, Center for Genetic Engineering and Biotechnology (CIGB), 10600, Havana, Cuba
| | - Ricardo Silva
- Research Department, China-Cuba Biotechnology Joint Innovation Center (CCBJIC), Lengshuitan District, Yongzhou, 425000, Hunan, China
- Scientific Department, Representative Office of BioCubaFarma in China, Jingtai Tower, No. 24 Jianguomen Wai Street, Chaoyang District, Beijing, 100022, China
| | - Gerardo Guillén
- Biomedical Research Department, Center for Genetic Engineering and Biotechnology (CIGB), 10600, Havana, Cuba
| | - Jiang Zaixue
- Guangdong Eighth People's Hospital, No. 68 South, Shilong Xihu 3rd Road, Shilong Town, Dongguan, Guangdong, China
| | - Ke Yang
- Research Department, China-Cuba Biotechnology Joint Innovation Center (CCBJIC), Lengshuitan District, Yongzhou, 425000, Hunan, China.
- Yongzhou Development and Construction Investment Co. Ltd. (YDCI), Changfeng Industry Park, Yongzhou Economic and Technological Development Zone, No. 1 Liebao Road, Lengshuitan District, Yongzhou, Hunan, China.
| | - Yasser Perera
- Research Department, China-Cuba Biotechnology Joint Innovation Center (CCBJIC), Lengshuitan District, Yongzhou, 425000, Hunan, China.
- Biomedical Research Department, Center for Genetic Engineering and Biotechnology (CIGB), 10600, Havana, Cuba.
- Research Department, Yongzhou Zhong Gu Biotechnology Co., Ltd, Yangjiaqiao Street, Lengshuitan District, Yongzhou, 425000, Hunan, China.
| | - Lisset Hermida
- Research Department, China-Cuba Biotechnology Joint Innovation Center (CCBJIC), Lengshuitan District, Yongzhou, 425000, Hunan, China.
- Scientific Department, Representative Office of BioCubaFarma in China, Jingtai Tower, No. 24 Jianguomen Wai Street, Chaoyang District, Beijing, 100022, China.
- Yongzhou Development and Construction Investment Co. Ltd. (YDCI), Changfeng Industry Park, Yongzhou Economic and Technological Development Zone, No. 1 Liebao Road, Lengshuitan District, Yongzhou, Hunan, China.
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Bernauer E, Alebrand F, Heurich M. Same but Different? Comparing the Epidemiology, Treatments and Outcomes of COVID-19 and Non-COVID-19 ARDS Cases in Germany Using a Sample of Claims Data from 2021 and 2019. Viruses 2023; 15:1324. [PMID: 37376623 DOI: 10.3390/v15061324] [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: 05/10/2023] [Revised: 05/30/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Acute respiratory distress syndrome (ARDS) is a severe lung condition that can be caused by a variety of underlying illnesses. Due to SARS-CoV-2, the number of cases with ARDS has increased worldwide, making it essential to compare this form of acute respiratory failure with classical causes of ARDS. While there have been several studies investigating the differences between COVID-19 and non-COVID-19 ARDS in early stages of the pandemic, little is known about the differences in later phases, especially in Germany. AIM The aim of this study is to characterize and compare the comorbidities, treatments, adverse events, and outcomes of COVID-19-associated ARDS and non-COVID-19 ARDS using a representative sample of German health claims data from the years 2019 and 2021. METHODS We compare percentages and median values of the quantities of interest from the COVID-19 and non-COVID-19 ARDS group, with p-values calculated after conducting Pearson's chi-squared test or the Wilcoxon rank sum test. We also run logistic regressions to access the effect of comorbidities on mortality for COVID-19 ARDS and non-COVID-19 ARDS. RESULTS Despite many similarities, we find that that there are some remarkable differences between COVID-19 and non-COVID-19 ARDS cases in Germany. Most importantly, COVID-19 ARDS cases display fewer comorbidities and adverse events, and are more often treated with non-invasive ventilation and nasal high-flow therapy. CONCLUSIONS This study highlights the importance of comprehending the contrasting epidemiological features and clinical outcomes of COVID-19 and non-COVID-19 ARDS. This understanding can aid in clinical decision making and guide future research initiatives aimed at enhancing the management of patients afflicted with this severe condition.
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Affiliation(s)
- Eva Bernauer
- BinDoc GmbH, Karlstraße 3, 72072 Tübingen, Germany
| | - Felix Alebrand
- BinDoc GmbH, Karlstraße 3, 72072 Tübingen, Germany
- Clinic for Cardiology and Pneumology, Georg-August-Universität Göttingen, 37075 Göttingen, Germany
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25
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Kumar L, Kumar S, Sandeep K, Patel SKS. Therapeutic Approaches in Pancreatic Cancer: Recent Updates. Biomedicines 2023; 11:1611. [PMID: 37371705 DOI: 10.3390/biomedicines11061611] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/25/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
Cancer is a significant challenge for effective treatment due to its complex mechanism, different progressing stages, and lack of adequate procedures for screening and identification. Pancreatic cancer is typically identified in its advanced progression phase with a low survival of ~5 years. Among cancers, pancreatic cancer is also considered a high mortality-causing casualty over other accidental or disease-based mortality, and it is ranked seventh among all mortality-associated cancers globally. Henceforth, developing diagnostic procedures for its early detection, understanding pancreatic cancer-linked mechanisms, and various therapeutic strategies are crucial. This review describes the recent development in pancreatic cancer progression, mechanisms, and therapeutic approaches, including molecular techniques and biomedicines for effectively treating cancer.
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Affiliation(s)
- Lokender Kumar
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, India
| | - Sanjay Kumar
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida 201310, India
| | - Kumar Sandeep
- Dr. B.R.A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi 110029, India
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26
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Bhardwaj P, Mishra SK, Behera SP, Zaman K, Kant R, Singh R. Genomic evolution of the SARS-CoV-2 Variants of Concern: COVID-19 pandemic waves in India. EXCLI JOURNAL 2023; 22:451-465. [PMID: 37534220 PMCID: PMC10390896 DOI: 10.17179/excli2023-6098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 05/30/2023] [Indexed: 08/04/2023]
Abstract
SARS-CoV-2 has mutated rapidly since its first case report in Wuhan, China, leading to the emergence of an indefinite number of variants. India has witnessed three waves of the COVID-19 pandemic. The country saw its first wave of SARS-CoV-2 illness from late January 2020 to February 2021. With a peak surge of cases in mid-September 2020, India recorded more than 11 million cases and a death toll of more than 0.165 million at this time. India faced a brutal second wave driven by the emergence of highly infectious SARS-CoV-2 variants B.1.617.2 (Delta variant) and the third wave with the leading cause of BA.2 (Omicron variant), which has led to an unprecedented rise in COVID-19 cases in the country. On September 14, 2022, India recorded a cumulative 44.51 million cases of COVID-19 with more than 0.528 million deaths. The discovery of common circulating mutants is facilitated by genome sequencing. The changes in the Spike surface glycoprotein recombinant binding domains served as the critical alterations, resulting in enhanced infectivity and transmissibility, with severe clinical effects. Further, the predominant mutation in the SARS-CoV-2 spike protein; the D614G strains served as a model for vaccine development. The mutation of the Wuhan strain to the Variant of Concern led to a significant increase in SARS-CoV-2 infections. In addition, there was a shift in the age group affected by SARS-CoV-2 variant infection. The current review summarized the COVID-19 pandemic's Variant of Concern and the advent of SARS-CoV-2 in India.
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Affiliation(s)
- Pooja Bhardwaj
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Shailendra Kumar Mishra
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Sthita Pragnya Behera
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Kamran Zaman
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Rajni Kant
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Rajeev Singh
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
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Napa W, Neelapaichit N, Kongsakon R, Chotivitayataragorn S, Udomsubpayakul U. Impacts of COVID-19 on family violence in Thailand: prevalence and influencing factors. BMC Womens Health 2023; 23:294. [PMID: 37264359 DOI: 10.1186/s12905-023-02440-x] [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: 09/30/2022] [Accepted: 05/16/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND The COVID-19 pandemic drastically affected societies globally, prompting rising unemployment, insufficient household incomes, and stress and undermining women's and children's health within families. This study examined family violence and identified influencing factors during the COVID-19 pandemic in Thailand. METHODS A mixed-method design was used, entailing a questionnaire followed by focus group interviews. A cross-sectional survey was administered to investigate family violence among 1285 female respondents aged 15 years and above who were recruited through stratified sampling. The Cronbach alpha and and inter-raters Kappa coefficient values for the questionnaire were 0.67 and 1.00, respectively. In addition, a descriptive qualitative instrument was employed to analyze the data sets from four focus group interviews held with 32 staff members from agencies that deal with family violence. The researchers jointly developed the focus group questions, which focused on the impacts of the COVID-19 pandemic on family violence. They independently analyzed data using content analysis. RESULTS The majority of the study participants were aged above 45 years (>50%), married (61.1%), lived in single-family settings (52.5%), had lost their jobs (64.4%), and had economic constraints that were moderate (37.8%) to severe (40.6%). The prevalence of family violence, which was primarily physical, was 42.2%. Family income, stress, and substance abuse were the main factors associated with family violence. These findings were correlated with those from the qualitative interviews. CONCLUSIONS The COVID-19 pandemic had indirect impacts through family violence. Women were subjected to family violence behaviors, which were associated with household income, economic status, stress, and substance abuse. These behaviors included psychological and physical violence, as well as sexual abuse. Future interventions should focus on financial support and stress reduction.
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Affiliation(s)
- Wilai Napa
- Ramathibodi School of Nursing Faculty of Medicine Ramathibodi Hospital, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Nareemarn Neelapaichit
- Ramathibodi School of Nursing Faculty of Medicine Ramathibodi Hospital, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
| | - Ronachai Kongsakon
- Department of Psychiatry, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | | | - Umaporn Udomsubpayakul
- Department of Clinical Epidemiology and Biostatistics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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Subramoney K, Mtileni N, Davis A, Giandhari J, Tegally H, Wilkinson E, Naidoo Y, Ramphal Y, Pillay S, Ramphal U, Simane A, Reddy B, Mashishi B, Mbenenge N, de Oliveira T, Fielding BC, Treurnicht FK. SARS-CoV-2 spike protein diversity at an intra-host level, among SARS-CoV-2 infected individuals in South Africa, 2020 to 2022. PLoS One 2023; 18:e0286373. [PMID: 37253027 PMCID: PMC10228762 DOI: 10.1371/journal.pone.0286373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/15/2023] [Indexed: 06/01/2023] Open
Abstract
Intra-host diversity studies are used to characterise the mutational heterogeneity of SARS-CoV-2 infections in order to understand the impact of virus-host adaptations. This study investigated the frequency and diversity of the spike (S) protein mutations within SARS-CoV-2 infected South African individuals. The study included SARS-CoV-2 respiratory samples, from individuals of all ages, received at the National Health Laboratory Service at Charlotte Maxeke Johannesburg Academic hospital, Gauteng, South Africa, from June 2020 to May 2022. Single nucleotide polymorphism (SNP) assays and whole genome sequencing were performed on a random selection of SARS-CoV-2 positive samples. The allele frequency (AF) was determined using TaqMan Genotyper software for SNP PCR analysis and galaxy.eu for analysis of FASTQ reads from sequencing. The SNP assays identified 5.3% (50/948) of Delta cases with heterogeneity at delY144 (4%; 2/50), E484Q (6%; 3/50), N501Y (2%; 1/50) and P681H (88%; 44/50), however only heterogeneity for E484Q and delY144 were confirmed by sequencing. From sequencing we identified 9% (210/2381) of cases with Beta, Delta, Omicron BA.1, BA.2.15, and BA.4 lineages that had heterogeneity in the S protein. Heterogeneity was primarily identified at positions 19 (1.4%) with T19IR (AF 0.2-0.7), 371 (92.3%) with S371FP (AF 0.1-1.0), and 484 (1.9%) with E484AK (0.2-0.7), E484AQ (AF 0.4-0.5) and E484KQ (AF 0.1-0.4). Mutations at heterozygous amino acid positions 19, 371 and 484 are known antibody escape mutations, however the impact of the combination of multiple substitutions identified at the same position is unknown. Therefore, we hypothesise that intra-host SARS-CoV-2 quasispecies with heterogeneity in the S protein facilitate competitive advantage of variants that can completely/partially evade host's natural and vaccine-induced immune responses.
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Affiliation(s)
- Kathleen Subramoney
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Nkhensani Mtileni
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Ashlyn Davis
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Yeshnee Naidoo
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Yajna Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Upasana Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Andiswa Simane
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Bhaveshan Reddy
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Bonolo Mashishi
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Nonhlanhla Mbenenge
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Burtram C. Fielding
- Molecular Biology and Virology Research Laboratory, Department of Medical BioSciences, University of the Western Cape, Cape Town, South Africa
| | - Florette K. Treurnicht
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
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Dahiya D. COVID-19 Disease Prediction Utilizing Dilated Convolution Neural Network Based Levy Flight Tunicate Swarm Optimization. WIRELESS PERSONAL COMMUNICATIONS 2023; 131:1-14. [PMID: 37360135 PMCID: PMC10224759 DOI: 10.1007/s11277-023-10505-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 05/12/2023] [Indexed: 06/28/2023]
Abstract
The worldwide pandemic of COVID-19 illness has wreaked havoc on the health and lives of countless individuals in more than 200 countries. More than 44 million individuals have been afflicted by October 2020, with over 1,000,000 fatalities reported. This disease, which is classified as a pandemic, is still being researched for diagnosis and therapy. It is critical to diagnose this condition early in order to save a person's life. Diagnostic investigations based on deep learning are speeding up this procedure. As a result, in order to contribute to this sector, our research proposes a deep learning-based technique that may be employed for illness early detection. Based on this insight, gaussian filter is applied to the collected CT images and the filtered images are subjected to the proposed tunicate dilated convolutional neural network, whereas covid and non-covid disease are categorized to improve the accuracy requirement. The hyperparameters involved in the proposed deep learning techniques are optimally tuned using the proposed levy flight based tunicate behaviour. To validate the proposed methodology, evaluation metrics are tested and shows superiority of the proposed approach during COVID-19 diagnostic studies.
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Affiliation(s)
- Deepak Dahiya
- Computer Science (Tenure Stream), School of Engineering and Computer Science, University of Pittsburgh, Johnstown US
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30
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Vassiliou AG, Vrettou CS, Keskinidou C, Dimopoulou I, Kotanidou A, Orfanos SE. Endotheliopathy in Acute COVID-19 and Long COVID. Int J Mol Sci 2023; 24:ijms24098237. [PMID: 37175942 PMCID: PMC10179170 DOI: 10.3390/ijms24098237] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/28/2023] [Accepted: 04/30/2023] [Indexed: 05/15/2023] Open
Abstract
The pulmonary endothelium is a highly regulated organ that performs a wide range of functions under physiological and pathological conditions. Since endothelial dysfunction has been demonstrated to play a direct role in sepsis and acute respiratory distress syndrome, its role in COVID-19 has also been extensively investigated. Indeed, apart from the COVID-19-associated coagulopathy biomarkers, new biomarkers were recognised early during the pandemic, including markers of endothelial cell activation or injury. We systematically searched the literature up to 10 March 2023 for studies examining the association between acute and long COVID-19 severity and outcomes and endothelial biomarkers.
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Affiliation(s)
- Alice G Vassiliou
- First Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 106 76 Athens, Greece
| | - Charikleia S Vrettou
- First Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 106 76 Athens, Greece
| | - Chrysi Keskinidou
- First Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 106 76 Athens, Greece
| | - Ioanna Dimopoulou
- First Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 106 76 Athens, Greece
| | - Anastasia Kotanidou
- First Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 106 76 Athens, Greece
| | - Stylianos E Orfanos
- First Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 106 76 Athens, Greece
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31
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Swami A, Mohanty A, Jamwal A, Turbadkar D, Baveja S, Shastri J, Chitalia V. A comparative analysis of the second and third wave of the Covid-19 pandemic: an experience from a tertiary care hospital in Western India. J Med Microbiol 2023; 72. [PMID: 37171852 DOI: 10.1099/jmm.0.001685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
Introduction. As the world was still recovering from the 2020 pandemic, the devastating impact of Covid-19 driven by the Delta variant shook the world in 2021. As the second wave was declining, there was an unusual surge in Covid-19 positive cases by the end of 2021 which led to global concern about the change in virus characteristics.Hypothesis/gap statement. Whole genome sequencing is critical for understanding a rapidly progressing pandemic.Aim. To provide an insight into the major differences encountered in the changing characteristics between the second and third waves of the pandemic at a tertiary care hospital in India.Methods. A retrospective observational cohort analysis was conducted on Covid-positive patients during the second wave of the Covid-19 pandemic (from March 2021 to April 2021) and the third wave of the Covid-19 pandemic (from December 2021 to January 2022).Results. Out of 303 Covid-19 positive cases, 52 samples were tested by whole genome sequencing during the second wave and 108 during the third wave. A decline of 18.5 % was observed in the case fatality rate from the second wave to the third wave. There was a 5 % decline in the number of patients admitted with ARDS and a 16.3 % decline in the number of patients with co-morbidities.In total, 51.9 percent of cases were due to the Delta variant during the second wave and 95 percent due to the Omicron variant during the third wave. We found that 36.5 % of Covid-positive patients during the second wave had been vaccinated compared to 40 % in the third wave.Conclusion. Whole genome sequencing of clinical samples from a wide range of individuals during a viral epidemic will enable us to develop a more rapid public health response to new variants and identify the required vaccine modifications more quickly.
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Affiliation(s)
- Anjali Swami
- Department of Microbiology, Lokmanya Tilak Municipal Medical College and General Hospital, Sion, Mumbai, Maharashtra, India
| | - Ankita Mohanty
- Department of Microbiology, Lokmanya Tilak Municipal Medical College and General Hospital, Sion, Mumbai, Maharashtra, India
| | - Ashima Jamwal
- Department of Microbiology, Lokmanya Tilak Municipal Medical College and General Hospital, Sion, Mumbai, Maharashtra, India
| | - Dilip Turbadkar
- Department of Microbiology, Lokmanya Tilak Municipal Medical College and General Hospital, Sion, Mumbai, Maharashtra, India
| | - Sujata Baveja
- Department of Microbiology, Lokmanya Tilak Municipal Medical College and General Hospital, Sion, Mumbai, Maharashtra, India
| | - Jayanthi Shastri
- Department of Microbiology, T.N.Medical college and B.Y.L Nair Charitable Hospital and Lab Director, Molecular Lab, Kasturba Hospital for Infectious Diseases, Mumbai, Maharashtra, India
| | - Vidushi Chitalia
- Molecular Lab, Kasturba Hospital for Infectious Diseases, Mumbai, Maharashtra, India
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32
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Silva JDP, Lima ABD, Alvim LB, Malta FSV, Mendonça CPTB, Carvalho AHBD, Rios JSH, Fonseca PLC, Queiroz DC, Santos LCGDAE, Ferreira ACDS, Souza RPD, Aguiar RSD, Zauli DAG. Epidemiological Surveillance Reveals the Rise and Establishment of the Omicron SARS-CoV-2 Variant in Brazil. Viruses 2023; 15:v15041017. [PMID: 37112997 PMCID: PMC10145299 DOI: 10.3390/v15041017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
The introduction of SARS-CoV-2 variants of concern (VOCs) in Brazil has been associated with major impacts on the epidemiological and public health scenario. In this study, 291,571 samples were investigated for SARS-CoV-2 variants from August 2021 to March 2022 (the highest peak of positive cases) in four geographical regions of Brazil. To identify the frequency, introduction, and dispersion of SARS-CoV-2 variants in 12 Brazilian capitals, VOCs defining spike mutations were identified in 35,735 samples through genotyping and viral genome sequencing. Omicron VOC was detected in late November 2021 and replaced the Delta VOC in approximately 3.5 weeks. We estimated viral load differences between SARS-CoV-2 Delta and Omicron through the evaluation of the RT-qPCR cycle threshold (Ct) score in 77,262 samples. The analysis demonstrated that the Omicron VOC has a lower viral load in infected patients than the Delta VOC. Analyses of clinical outcomes in 17,586 patients across the country indicated that individuals infected with Omicron were less likely to need ventilatory support. The results of our study reinforce the importance of surveillance programs at the national level and showed the introduction and faster dispersion of Omicron over Delta VOC in Brazil without increasing the numbers of severe cases of COVID-19.
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Affiliation(s)
- Joice do Prado Silva
- Departamento de Pesquisa & Desenvolvimento, Instituto Hermes Pardini, Belo Horizonte 31270-901, Brazil
| | - Aline Brito de Lima
- Departamento de Pesquisa & Desenvolvimento, Instituto Hermes Pardini, Belo Horizonte 31270-901, Brazil
| | - Luige Biciati Alvim
- Departamento de Produtos e Inovação, Instituto Hermes Pardini, Belo Horizonte 31270-901, Brazil
| | | | | | | | | | - Paula Luize Camargos Fonseca
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Daniel Costa Queiroz
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Luíza Campos Guerra de Araújo E Santos
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | | | - Renan Pedra de Souza
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Renato Santana de Aguiar
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
- Instituto D'Or de Pesquisa e Ensino (IDOR), Rio de Janeiro 22281-100, Brazil
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da Silva Santos Y, Gamon THM, de Azevedo MSP, Telezynski BL, de Souza EE, de Oliveira DBL, Dombrowski JG, Rosa-Fernandes L, Palmisano G, de Moura Carvalho LJ, Luvizotto MCR, Wrenger C, Covas DT, Curi R, Marinho CRF, Durigon EL, Epiphanio S. Virulence Profiles of Wild-Type, P.1 and Delta SARS-CoV-2 Variants in K18-hACE2 Transgenic Mice. Viruses 2023; 15:v15040999. [PMID: 37112979 PMCID: PMC10146242 DOI: 10.3390/v15040999] [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: 02/21/2023] [Revised: 03/30/2023] [Accepted: 04/01/2023] [Indexed: 04/29/2023] Open
Abstract
Since December 2019, the world has been experiencing the COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and we now face the emergence of several variants. We aimed to assess the differences between the wild-type (Wt) (Wuhan) strain and the P.1 (Gamma) and Delta variants using infected K18-hACE2 mice. The clinical manifestations, behavior, virus load, pulmonary capacity, and histopathological alterations were analyzed. The P.1-infected mice showed weight loss and more severe clinical manifestations of COVID-19 than the Wt and Delta-infected mice. The respiratory capacity was reduced in the P.1-infected mice compared to the other groups. Pulmonary histological findings demonstrated that a more aggressive disease was generated by the P.1 and Delta variants compared to the Wt strain of the virus. The quantification of the SARS-CoV-2 viral copies varied greatly among the infected mice although it was higher in P.1-infected mice on the day of death. Our data revealed that K18-hACE2 mice infected with the P.1 variant develop a more severe infectious disease than those infected with the other variants, despite the significant heterogeneity among the mice.
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Affiliation(s)
- Yasmin da Silva Santos
- Laboratory of Cellular and Molecular Immunopathology of Malaria, Department of Clinical and Toxicological Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
- Laboratory of Malaria Research, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil
| | - Thais Helena Martins Gamon
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Marcela Santiago Pacheco de Azevedo
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Bruna Larotonda Telezynski
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Edmarcia Elisa de Souza
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Danielle Bruna Leal de Oliveira
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
- Hospital Israelita Albert Einstein, São Paulo 05652-900, Brazil
| | - Jamille Gregório Dombrowski
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Livia Rosa-Fernandes
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
- School of Natural Sciences, Macquarie University, Sydney 2109, Australia
| | | | | | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Dimas Tadeu Covas
- Butantan Institute, São Paulo 05508-040, Brazil
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil
| | - Rui Curi
- Interdisciplinary Program of Health Sciences, Cruzeiro do Sul University, São Paulo 08060-070, Brazil
- Immunobiological Production Section, Bioindustrial Center, Butantan Institute, São Paulo 05503-900, Brazil
| | - Claudio Romero Farias Marinho
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Edison Luiz Durigon
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
- Scientific Plataform Pasteur/USP, University of São Paulo, São Paulo 05508-020, Brazil
| | - Sabrina Epiphanio
- Laboratory of Cellular and Molecular Immunopathology of Malaria, Department of Clinical and Toxicological Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
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Lenguiya LH, Fritz M, De Fonclare DDR, Corbet S, Becquart P, Mbou C, Nguie RJ, Mouellet WS, Demboux JEL, Issamou Mayengue P, Koukouikila-Koussounda F, Ar Gouilh M, Leroy EM, Niama FR. Whole-Genome Characterization of SARS-CoV-2 Reveals Simultaneous Circulation of Three Variants and a Putative Recombination (20B/20H) in Pets, Brazzaville, Republic of the Congo. Viruses 2023; 15:v15040933. [PMID: 37112914 PMCID: PMC10142050 DOI: 10.3390/v15040933] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Following the emergence of SARS-CoV-2, cases of pets infected with variants circulating among humans were reported. In order to evaluate the occurrence of SARS-CoV-2 circulation among pets in the Republic of the Congo, we conducted a ten-month study of dogs and cats living in COVID-19-positive households in Brazzaville and neighboring localities. Real-time PCR and the Luminex platform were used to detect SARS-CoV-2 RNA and antibodies to SARS-CoV-2 RBD and S proteins, respectively. Our results show for the first time the simultaneous circulation of several variants of SARS-CoV-2, including viruses from clades 20A and 20H and a putative recombinant variant between viruses from clades 20B and 20H. We found a high seroprevalence of 38.6%, with 14% of tested pets positive for SARS-CoV-2 RNA. Thirty-four percent of infected pets developed mild clinical signs, including respiratory and digestive signs, and shed the virus for about one day to two weeks. These results highlight the potential risk of SARS-CoV-2 interspecies transmission and the benefits of a "One Health" approach that includes SARS-CoV-2 diagnosis and surveillance of viral diversity in pets. This approach aims to prevent transmission to surrounding wildlife as well as spillback to humans.
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Affiliation(s)
| | - Matthieu Fritz
- Institut de Recherche pour le Développement, Unité Mixte de Recherche Mivegec, BP34090 Montpellier, France
| | - Daphné de Riols De Fonclare
- UNICAEN, Department of Viroloy, University of Rouen Normandie, Inserm Dynamicure UMR 1311, BP14000 Caen, France
| | - Sandrine Corbet
- UNICAEN, Department of Viroloy, University of Rouen Normandie, Inserm Dynamicure UMR 1311, BP14000 Caen, France
| | - Pierre Becquart
- Institut de Recherche pour le Développement, Unité Mixte de Recherche Mivegec, BP34090 Montpellier, France
| | | | | | | | | | - Pembe Issamou Mayengue
- Faculté des Sciences et Techniques, Université Marien Ngouabi, Brazzaville BP69, Congo
- Laboratoire National de Santé Publique, Brazzaville BP120, Congo
| | - Félix Koukouikila-Koussounda
- Faculté des Sciences et Techniques, Université Marien Ngouabi, Brazzaville BP69, Congo
- Laboratoire National de Santé Publique, Brazzaville BP120, Congo
| | - Meriadeg Ar Gouilh
- UNICAEN, Department of Viroloy, University of Rouen Normandie, Inserm Dynamicure UMR 1311, BP14000 Caen, France
| | - Eric M Leroy
- Institut de Recherche pour le Développement, Unité Mixte de Recherche Mivegec, BP34090 Montpellier, France
| | - Fabien Roch Niama
- Faculté des Sciences et Techniques, Université Marien Ngouabi, Brazzaville BP69, Congo
- Laboratoire National de Santé Publique, Brazzaville BP120, Congo
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35
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Verkhivker G, Alshahrani M, Gupta G. Coarse-Grained Molecular Simulations and Ensemble-Based Mutational Profiling of Protein Stability in the Different Functional Forms of the SARS-CoV-2 Spike Trimers: Balancing Stability and Adaptability in BA.1, BA.2 and BA.2.75 Variants. Int J Mol Sci 2023; 24:ijms24076642. [PMID: 37047615 PMCID: PMC10094791 DOI: 10.3390/ijms24076642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Abstract
Evolutionary and functional studies have suggested that the emergence of Omicron variants can be determined by multiple fitness tradeoffs including immune escape, binding affinity, conformational plasticity, protein stability, and allosteric modulation. In this study, we embarked on a systematic comparative analysis of the conformational dynamics, electrostatics, protein stability, and allostery in the different functional states of spike trimers for BA.1, BA.2, and BA.2.75 variants. Using efficient and accurate coarse-grained simulations and atomistic reconstruction of the ensembles, we examined the conformational dynamics of the spike trimers that agree with the recent functional studies, suggesting that BA.2.75 trimers are the most stable among these variants. A systematic mutational scanning of the inter-protomer interfaces in the spike trimers revealed a group of conserved structural stability hotspots that play a key role in the modulation of functional dynamics and are also involved in the inter-protomer couplings through local contacts and interaction networks with the Omicron mutational sites. The results of mutational scanning provided evidence that BA.2.75 trimers are more stable than BA.2 and comparable in stability to the BA.1 variant. Using dynamic network modeling of the S Omicron BA.1, BA.2, and BA.2.75 trimers, we showed that the key network mediators of allosteric interactions are associated with the major stability hotspots that are interconnected along potential communication pathways. The network analysis of the BA.1, BA.2, and BA.2.75 trimers suggested that the increased thermodynamic stability of the BA.2.75 variant may be linked with the organization and modularity of the residue interaction network that allows for allosteric communications between structural stability hotspots and Omicron mutational sites. This study provided a plausible rationale for a mechanism in which Omicron mutations may evolve by targeting vulnerable sites of conformational adaptability to elicit immune escape while maintaining their control on balancing protein stability and functional fitness through robust allosteric communications with the stability hotspots.
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Affiliation(s)
- Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
| | - Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
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36
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Kalyoncu S, Yilmaz S, Kuyucu AZ, Sayili D, Mert O, Soyturk H, Gullu S, Akinturk H, Citak E, Arslan M, Taskinarda MG, Tarman IO, Altun GY, Ozer C, Orkut R, Demirtas A, Tilmensagir I, Keles U, Ulker C, Aralan G, Mercan Y, Ozkan M, Caglar HO, Arik G, Ucar MC, Yildirim M, Yildirim TC, Karadag D, Bal E, Erdogan A, Senturk S, Uzar S, Enul H, Adiay C, Sarac F, Ekiz AT, Abaci I, Aksoy O, Polat HU, Tekin S, Dimitrov S, Ozkul A, Wingender G, Gursel I, Ozturk M, Inan M. Process development for an effective COVID-19 vaccine candidate harboring recombinant SARS-CoV-2 delta plus receptor binding domain produced by Pichia pastoris. Sci Rep 2023; 13:5224. [PMID: 36997624 PMCID: PMC10062263 DOI: 10.1038/s41598-023-32021-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/21/2023] [Indexed: 04/01/2023] Open
Abstract
Recombinant protein-based SARS-CoV-2 vaccines are needed to fill the vaccine equity gap. Because protein-subunit based vaccines are easier and cheaper to produce and do not require special storage/transportation conditions, they are suitable for low-/middle-income countries. Here, we report our vaccine development studies with the receptor binding domain of the SARS-CoV-2 Delta Plus strain (RBD-DP) which caused increased hospitalizations compared to other variants. First, we expressed RBD-DP in the Pichia pastoris yeast system and upscaled it to a 5-L fermenter for production. After three-step purification, we obtained RBD-DP with > 95% purity from a protein yield of > 1 g/L of supernatant. Several biophysical and biochemical characterizations were performed to confirm its identity, stability, and functionality. Then, it was formulated in different contents with Alum and CpG for mice immunization. After three doses of immunization, IgG titers from sera reached to > 106 and most importantly it showed high T-cell responses which are required for an effective vaccine to prevent severe COVID-19 disease. A live neutralization test was performed with both the Wuhan strain (B.1.1.7) and Delta strain (B.1.617.2) and it showed high neutralization antibody content for both strains. A challenge study with SARS-CoV-2 infected K18-hACE2 transgenic mice showed good immunoprotective activity with no viruses in the lungs and no lung inflammation for all immunized mice.
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Affiliation(s)
| | - Semiramis Yilmaz
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- VIB-UGent Center for Medical Biotechnology, Gent, Belgium
| | | | - Dogu Sayili
- Izmir Biomedicine and Genome Center, Izmir, Turkey
| | - Olcay Mert
- Izmir Biomedicine and Genome Center, Izmir, Turkey
| | | | - Seyda Gullu
- Izmir Biomedicine and Genome Center, Izmir, Turkey
| | | | - Erhan Citak
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- VIB-UGent Center for Medical Biotechnology, Gent, Belgium
| | - Merve Arslan
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | | | | | | | - Ceren Ozer
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Ridvan Orkut
- Izmir Biomedicine and Genome Center, Izmir, Turkey
| | | | | | - Umur Keles
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Lund University, Lund, Sweden
| | - Ceren Ulker
- Izmir Biomedicine and Genome Center, Izmir, Turkey
| | - Gizem Aralan
- Izmir Biomedicine and Genome Center, Izmir, Turkey
| | - Yavuz Mercan
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Muge Ozkan
- Izmir Biomedicine and Genome Center, Izmir, Turkey
| | - Hasan Onur Caglar
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Erzurum Technical University, Erzurum, Turkey
| | - Gizem Arik
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Ankara Medipol University, Ankara, Turkey
| | - Mehmet Can Ucar
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Imperial College London, London, UK
| | | | | | | | - Erhan Bal
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir Tinaztepe University, Izmir, Turkey
| | - Aybike Erdogan
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Serif Senturk
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Serdar Uzar
- Pendik Veterinary Research and Control Institute, Istanbul, Turkey
| | - Hakan Enul
- Pendik Veterinary Research and Control Institute, Istanbul, Turkey
| | - Cumhur Adiay
- Pendik Veterinary Research and Control Institute, Istanbul, Turkey
| | - Fahriye Sarac
- Pendik Veterinary Research and Control Institute, Istanbul, Turkey
| | | | - Irem Abaci
- Marmara Research Center, TUBITAK, Kocaeli, Turkey
| | - Ozge Aksoy
- Marmara Research Center, TUBITAK, Kocaeli, Turkey
| | | | - Saban Tekin
- Marmara Research Center, TUBITAK, Kocaeli, Turkey
- University of Health Sciences, Istanbul, Turkey
| | | | | | | | - Ihsan Gursel
- Izmir Biomedicine and Genome Center, Izmir, Turkey
| | - Mehmet Ozturk
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir Tinaztepe University, Izmir, Turkey
| | - Mehmet Inan
- Izmir Biomedicine and Genome Center, Izmir, Turkey.
- Akdeniz University, Antalya, Turkey.
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37
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Kumar R, Srivastava Y, Muthuramalingam P, Singh SK, Verma G, Tiwari S, Tandel N, Beura SK, Panigrahi AR, Maji S, Sharma P, Rai PK, Prajapati DK, Shin H, Tyagi RK. Understanding Mutations in Human SARS-CoV-2 Spike Glycoprotein: A Systematic Review & Meta-Analysis. Viruses 2023; 15:856. [PMID: 37112836 PMCID: PMC10142771 DOI: 10.3390/v15040856] [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: 03/07/2023] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Genetic variant(s) of concern (VoC) of SARS-CoV-2 have been emerging worldwide due to mutations in the gene encoding spike glycoprotein. We performed comprehensive analyses of spike protein mutations in the significant variant clade of SARS-CoV-2, using the data available on the Nextstrain server. We selected various mutations, namely, A222V, N439K, N501Y, L452R, Y453F, E484K, K417N, T478K, L981F, L212I, N856K, T547K, G496S, and Y369C for this study. These mutations were chosen based on their global entropic score, emergence, spread, transmission, and their location in the spike receptor binding domain (RBD). The relative abundance of these mutations was mapped with global mutation D614G as a reference. Our analyses suggest the rapid emergence of newer global mutations alongside D614G, as reported during the recent waves of COVID-19 in various parts of the world. These mutations could be instrumentally imperative for the transmission, infectivity, virulence, and host immune system's evasion of SARS-CoV-2. The probable impact of these mutations on vaccine effectiveness, antigenic diversity, antibody interactions, protein stability, RBD flexibility, and accessibility to human cell receptor ACE2 was studied in silico. Overall, the present study can help researchers to design the next generation of vaccines and biotherapeutics to combat COVID-19 infection.
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Affiliation(s)
- Reetesh Kumar
- Faculty of Agricultural Sciences, Institute of Applied Sciences & Humanities, GLA University, Mathura 281406, India
- Department of Biotherapeutics, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160036, India
| | - Yogesh Srivastava
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pandiyan Muthuramalingam
- Division of Horticultural Science, Gyeongsang National University, Jinju 52725, Republic of Korea
| | - Sunil Kumar Singh
- Department of Zoology, School of Biological Sciences, Central University of Punjab, Ghudda, Bathinda 151401, India
| | - Geetika Verma
- Department of Biotherapeutics, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160036, India
| | - Savitri Tiwari
- Division of Life Sciences, Department of Biosciences, School of Basic and Applied Sciences, Galgotias University, Gautam Buddha Nagar, Greater Noida 201310, India
| | - Nikunj Tandel
- Institute of Science, Nirma University, SG Highway, Gujarat 382481, India
| | - Samir Kumar Beura
- Department of Zoology, School of Biological Sciences, Central University of Punjab, Ghudda, Bathinda 151401, India
| | | | - Somnath Maji
- Department of Radiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Prakriti Sharma
- Biomedical Parasitology and Translational-Immunology Lab, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160036, India
| | - Pankaj Kumar Rai
- Department of Biotechnology, IIET, Invertis University, Bareilly 243001, India
| | | | - Hyunsuk Shin
- Division of Horticultural Science, Gyeongsang National University, Jinju 52725, Republic of Korea
| | - Rajeev K. Tyagi
- Biomedical Parasitology and Translational-Immunology Lab, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160036, India
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38
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Cassari L, Pavan A, Zoia G, Chinellato M, Zeni E, Grinzato A, Rothenberger S, Cendron L, Dettin M, Pasquato A. SARS-CoV-2 S Mutations: A Lesson from the Viral World to Understand How Human Furin Works. Int J Mol Sci 2023; 24:4791. [PMID: 36902222 PMCID: PMC10003014 DOI: 10.3390/ijms24054791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the etiological agent responsible for the worldwide pandemic and has now claimed millions of lives. The virus combines several unusual characteristics and an extraordinary ability to spread among humans. In particular, the dependence of the maturation of the envelope glycoprotein S from Furin enables the invasion and replication of the virus virtually within the entire body, since this cellular protease is ubiquitously expressed. Here, we analyzed the naturally occurring variation of the amino acids sequence around the cleavage site of S. We found that the virus grossly mutates preferentially at P positions, resulting in single residue replacements that associate with gain-of-function phenotypes in specific conditions. Interestingly, some combinations of amino acids are absent, despite the evidence supporting some cleavability of the respective synthetic surrogates. In any case, the polybasic signature is maintained and, as a consequence, Furin dependence is preserved. Thus, no escape variants to Furin are observed in the population. Overall, the SARS-CoV-2 system per se represents an outstanding example of the evolution of substrate-enzyme interaction, demonstrating a fast-tracked optimization of a protein stretch towards the Furin catalytic pocket. Ultimately, these data disclose important information for the development of drugs targeting Furin and Furin-dependent pathogens.
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Affiliation(s)
- Leonardo Cassari
- Department of Industrial Engineering, University of Padova, Via Marzolo 9, 35131 Padova, Italy
| | - Angela Pavan
- Department of Biology, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy
| | - Giulia Zoia
- Department of Biology, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy
| | - Monica Chinellato
- Department of Biology, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy
| | - Elena Zeni
- Department of Industrial Engineering, University of Padova, Via Marzolo 9, 35131 Padova, Italy
| | - Alessandro Grinzato
- European Synchrotron Radiation Facility, 71, Avenue des Martyrs, 38000 Grenoble, France
| | - Sylvia Rothenberger
- Institute of Microbiology, University Hospital Center and University of Lausanne, Rue du Bugnon 48, 1011 Lausanne, Switzerland
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, 3700 Spiez, Switzerland
| | - Laura Cendron
- Department of Biology, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy
| | - Monica Dettin
- Department of Industrial Engineering, University of Padova, Via Marzolo 9, 35131 Padova, Italy
| | - Antonella Pasquato
- Department of Industrial Engineering, University of Padova, Via Marzolo 9, 35131 Padova, Italy
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39
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Klivleyeva N, Lukmanova G, Glebova T, Shamenova M, Ongarbayeva N, Saktaganov N, Baimukhametova A, Baiseiit S, Ismagulova D, Kassymova G, Rachimbayeva A, Murzagaliyeva A, Xetayeva G, Isabayeva R, Sagatova M. Spread of Pathogens Causing Respiratory Viral Diseases Before and During CoVID-19 Pandemic in Kazakhstan. Indian J Microbiol 2023; 63:129-138. [PMID: 37168842 PMCID: PMC9972336 DOI: 10.1007/s12088-023-01064-x] [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: 09/22/2022] [Accepted: 02/11/2023] [Indexed: 03/06/2023] Open
Abstract
Analyze clinical samples collected and determine the etiology of viral pathogens and the dynamics of their spread. Acute respiratory viral infections remain one of the key health problems worldwide. They constitute etiologically independent diseases, with similar clinical infection manifestations and a single mechanism for the transmission of pathogens. 4712 nasopharyngeal swabs were collected from people before and during the COVID-19 pandemic with acute respiratory infections that tested negative for COVID-19 and were examined in this study. The collected samples were screened by a real-time polymerase chain reaction on a Rotor-Gene Q6 plex instrument. Statistical processing of the results, tabular, and graphical data were analyzed in the MS Excel. The largest number of the nasopharyngeal swabs were collected from children under 17 years of age (60.75%). In 702 samples (9.85%) pathogens of respiratory infections of non-influenza etiology were detected, including adenovirus, bocavirus, coronavirus, metapneumovirus, paramyxovirus types I–IV, respiratory syncytial virus, and rhinovirus. At the same time, both before and during the COVID-19 pandemic, different influenza virus variants co-circulation (A/H1N1, A/H3N2, and type B) were discovered, with a predominance of viruses with the antigenic formula A/H1N1. The results of the study indicate the need for continuous monitoring of the viral pathogens spread, which will expand the existing knowledge of the viral etiology of respiratory diseases and highlight the importance of viruses in the respiratory infections occurrence.
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Affiliation(s)
- Nailya Klivleyeva
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | - Galina Lukmanova
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | - Tatyana Glebova
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | - Mira Shamenova
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | - Nuray Ongarbayeva
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | - Nurbol Saktaganov
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | - Assem Baimukhametova
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | - Sagadat Baiseiit
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | - Dariya Ismagulova
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | | | - Almagul Rachimbayeva
- The Almaty Branch of National Center for Expertise, 3 Zhibek Zholy Avenue, Almaty, Kazakhstan
| | - Ardak Murzagaliyeva
- The West Kazakhstan Marat Ospanov Medical University, 68 Maresyev Street, Aktobe, Kazakhstan
| | - Gulzakira Xetayeva
- The Children’s City Clinical Infectious Diseases Hospital, SOPE On REM, ChCCIDH, 299a Baizakova Street, Almaty, Kazakhstan
| | - Rauna Isabayeva
- The Communal State Enterprise Regional Region Clinical Hospital (CSE RCH) of Karaganda Regional Health Department, 41/43 Erubaev Street, Karaganda, Kazakhstan
| | - Madisha Sagatova
- The East Kazakhstan Regional Branch of National Center for Expertise, 17 Independence Avenue, Ust-Kamenogorsk, Kazakhstan
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Takahata N, Sugawara H. Role of error catastrophe in transmission ability of virus. Genes Genet Syst 2023; 97:237-246. [PMID: 36709980 DOI: 10.1266/ggs.22-00096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The role played by error catastrophe is explicitly taken into account in a mathematical formulation to analyze COVID-19 data. The idea is to combine the mathematical genetics formalism of the error catastrophe of mutations in virus gene loci with the standard model of epidemics, which lacks the explicit incorporation of the effect of mutation on the spreading of viruses. We apply this formalism to the case of SARS-CoV-2 virus. We assume the universality of the error catastrophe in the process of analyzing the data. This means that some basic parameter to describe the error catastrophe is independent of which group (country or city) we deal with. Concretely, we analyze Omicron variant data from South Africa and then analyze cases from Japan using the same value of the basic parameter derived in the South Africa analysis. The excellent fit between the two sets of data, one from South Africa and the other from Japan, using the common values of genetic parameters, justifies our assumption of the universality of these parameters.
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Seroprevalence of COVID-19 infection in a densely populated district in the eastern Democratic Republic of Congo. Epidemiol Infect 2023; 151:e24. [PMID: 36775822 PMCID: PMC9947032 DOI: 10.1017/s0950268823000158] [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] [Indexed: 02/04/2023] Open
Abstract
Data on coronavirus disease 2019 (COVID-19) prevalence in the Democratic Republic of Congo are scarce. We conducted a cross-sectional study to determine the seroprevalence of antibodies against anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the slum of Kadutu, city of Bukavu, between June and September 2021. The survey participants were all unvaccinated against SARS-CoV-2. The crude seroprevalence rate was adjusted to the known characteristics of the assay. Participants aged 15-49 years old made up 80% of the population enrolled in the study (n = 507; 319 women and 188 men). The overall crude and adjusted seroprevalence rates of antibodies for COVID-19 were 59.7% (95% CI 55.4-63.9%) and 84.0% (95% CI 76.2-92.4%), respectively. This seroprevalence rate indicates widespread dissemination of SARS-CoV-2 in these communities. COVID-19 symptoms were either absent or mild in more than half of the participants with antibodies for COVID-19 and none of the participants with antibodies for COVID-19 required hospitalisation. These results suggest that SARS-CoV-2 spread did not appear to be associated with severe symptoms in the population of these settlements and that many cases went unreported in these densely populated locations. The relevance of vaccination in these communities should be thoroughly investigated.
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Houston A, Tovey C, Rogers-Smith K, Thompson K, Ladlow P, Barker-Davies R, Bahadur S, Goodall D, Gough M, Norman J, Phillip R, Turner P, Cranley M, O'Sullivan O. Changing characteristics of post-COVID-19 syndrome: Cross-sectional findings from 458 consultations using the Stanford Hall remote rehabilitation assessment tool. BMJ Mil Health 2023:e002248. [PMID: 36702521 DOI: 10.1136/military-2022-002248] [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: 09/05/2022] [Accepted: 12/17/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND In the UK, there have been multiple waves of COVID-19, with a five-tier alert system created to describe the transmission rate and appropriate restrictions. While acute mortality decreased, there continued to be a significant morbidity, with individuals suffering from persistent, life-restricting symptoms for months to years afterwards. A remote rehabilitation tool was created at the Defence Medical Rehabilitation Centre (DMRC) Stanford Hall to assess post-COVID-19 symptoms and their impact on the UK military.This study aims to understand changes in post-COVID-19 syndrome between wave 1 and wave 2, identify interactions between alert level and symptoms and investigate any predictive nature of acute symptoms for postacute symptomology in a young, physically active population. METHODS Cross-sectional study of 458 consecutive remote rehabilitation assessments performed at DMRC Stanford Hall between 2 April 2020 and 29 July 2021. Consultations were coded, anonymised, and statistical analysis was performed to determine associations between acute and postacute symptoms, and between symptoms, alert levels and waves. RESULTS 435 assessments were eligible; 174 in wave 1 and 261 in wave 2. Post-COVID-19 syndrome prevalence reduced from 43% to 2% between the waves. Acutely, widespread pain was more prevalent in wave 2 (p<0.001). Postacutely, there was increased anxiety (p=0.10) in wave 1 and increased sleep disturbance (p<0.001), memory/concentration issues (p<0.001) and shortness of breath/cough (p=0.017) in wave 2. Increasing alert level was associated with increased postacute symptom prevalence (p=0.046), with sleep disturbance increasing at higher alert level (p=0.016). Acute symptoms, including fatigue, sleep disturbance and myalgia, were associated with multiple postacute symptoms. CONCLUSIONS This study reports the overall prevalence and symptom burden in the UK military in the first two waves of COVID-19. By reporting differences in COVID-19 in different waves and alert level, this study highlights the importance of careful assessment and contextual understanding of acute and postacute illnesses for individual management plans.
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Affiliation(s)
- Andrew Houston
- Academic Department of Military Rehabilitation, Defence Medical Rehabilitation Centre (DMRC) Stanford Hall, Loughborough, UK
| | - C Tovey
- Defence Medical Rehabilitation Centre Stanford Hall, Loughborough, UK
| | - K Rogers-Smith
- Defence Medical Rehabilitation Centre Stanford Hall, Loughborough, UK
| | - K Thompson
- Headquarters Army Medical Services (HQ AMS), Camberley, UK
| | - P Ladlow
- Academic Department of Military Rehabilitation, Defence Medical Rehabilitation Centre (DMRC) Stanford Hall, Loughborough, UK
| | - R Barker-Davies
- Academic Department of Military Rehabilitation, Defence Medical Rehabilitation Centre (DMRC) Stanford Hall, Loughborough, UK
- Loughborough University, Loughborough, UK
| | - S Bahadur
- Defence Medical Rehabilitation Centre Stanford Hall, Loughborough, UK
| | - D Goodall
- Defence Medical Rehabilitation Centre Stanford Hall, Loughborough, UK
| | - M Gough
- Defence Medical Rehabilitation Centre Stanford Hall, Loughborough, UK
| | - J Norman
- Defence Medical Rehabilitation Centre Stanford Hall, Loughborough, UK
| | - R Phillip
- Defence Medical Rehabilitation Centre Stanford Hall, Loughborough, UK
| | - P Turner
- Defence Medical Rehabilitation Centre Stanford Hall, Loughborough, UK
| | - M Cranley
- Defence Medical Rehabilitation Centre Stanford Hall, Loughborough, UK
| | - O O'Sullivan
- Academic Department of Military Rehabilitation, Defence Medical Rehabilitation Centre (DMRC) Stanford Hall, Loughborough, UK
- Academic Unit of Injury, Recovery and Inflammation Sciences, University of Nottingham, Nottingham, UK
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Targeting the Variants of COVID-19 via the Unlimited Approach. Indian J Microbiol 2023; 63:152-154. [PMID: 36714462 PMCID: PMC9854402 DOI: 10.1007/s12088-023-01057-w] [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: 11/18/2022] [Accepted: 01/14/2023] [Indexed: 01/21/2023] Open
Abstract
Coronavirus has continued to evolve and has thus caused unprecedented challenges for human society. Multiple nations have fully or partially relied on the limited approach against the COVID-19 variants, which includes not wearing face masks, vaccine hesitancy, and political conflicts. For effective pandemic management, all nations still need to adhere to the unlimited approach, which includes wearing face masks, vaccination, and risk-oriented strategies. Despite many people's resistance to these relatively restrictive measures, the society could not only reduce physical impacts but also social impacts of COVID-19 variants in time, in particular without flexibly relying on the unlimited approach.
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Ali AM, Tofiq AM, Rostam HM, Ali KM, Tawfeeq HM. Reply to Letter to the Editor on disease severity and efficacy of homologous vaccination among patients infected with SARS-CoV-2 Delta or Omicron VOCs, compared to unvaccinated using main biomarkers. J Med Virol 2023; 95:e28313. [PMID: 36380449 DOI: 10.1002/jmv.28313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/08/2022] [Accepted: 11/12/2022] [Indexed: 11/17/2022]
Affiliation(s)
- Ayad M Ali
- Department of Chemistry, University of Garmian, Kalar, Kurdistan Region, Iraq
| | - Ahmed M Tofiq
- Department of Biology, College of Education, Head of International Academic Relations (IRO), University of Garmian, Kalar, Kurdistan Region, Iraq
| | - Hassan M Rostam
- Immunology and Immuno Bioengineering Group, Infections, Immunity and Microbes Division, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK.,Department of Medicine, College of Medicine, University of Garmian, Kalar, Kurdistan Region, Iraq
| | - Kameran M Ali
- Medical Lab Technology Department, Kalar Technical College, Sulaimani Polytechnic University, Kalar, Kurdistan Region, Iraq
| | - Hassan M Tawfeeq
- Medical Lab Technology Department, Kalar Technical College, Sulaimani Polytechnic University, Kalar, Kurdistan Region, Iraq
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Chrysostomou AC, Vrancken B, Haralambous C, Alexandrou M, Aristokleous A, Christodoulou C, Gregoriou I, Ioannides M, Kalakouta O, Karagiannis C, Koumbaris G, Loizides C, Mendris M, Papastergiou P, Patsalis PC, Pieridou D, Richter J, Schmitt M, Shammas C, Stylianou DC, Themistokleous G, Lemey P, Kostrikis LG. Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus from November 2020 to October 2021: The Passage of Waves of Alpha and Delta Variants of Concern. Viruses 2022; 15:108. [PMID: 36680148 PMCID: PMC9862594 DOI: 10.3390/v15010108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019 resulted in the coronavirus disease 2019 (COVID-19) pandemic, which has had devastating repercussions for public health. Over the course of this pandemic, the virus has continuously been evolving, resulting in new, more infectious variants that have frequently led to surges of new SARS-CoV-2 infections. In the present study, we performed detailed genetic, phylogenetic, phylodynamic and phylogeographic analyses to examine the SARS-CoV-2 epidemic in Cyprus using 2352 SARS-CoV-2 sequences from infected individuals in Cyprus during November 2020 to October 2021. During this period, a total of 61 different lineages and sublineages were identified, with most falling into three groups: B.1.258 & sublineages, Alpha (B.1.1.7 & Q. sublineages), and Delta (B.1.617.2 & AY. sublineages), each encompassing a set of S gene mutations that primarily confer increased transmissibility as well as immune evasion. Specifically, these lineages were coupled with surges of new infections in Cyprus, resulting in the following: the second wave of SARS-CoV-2 infections in Cyprus, comprising B.1.258 & sublineages, during late autumn 2020/beginning of winter 2021; the third wave, comprising Alpha (B.1.1.7 & Q. sublineages), during spring 2021; and the fourth wave, comprising Delta (B.1.617.2 & AY. sublineages) during summer 2021. Additionally, it was identified that these lineages were primarily imported from and exported to the UK, Greece, and Sweden; many other migration links were also identified, including Switzerland, Denmark, Russia, and Germany. Taken together, the results of this study indicate that the SARS-CoV-2 epidemic in Cyprus was characterized by successive introduction of new lineages from a plethora of countries, resulting in the generation of waves of infection. Overall, this study highlights the importance of investigating the spatiotemporal evolution of the SARS-CoV-2 epidemic in the context of Cyprus, as well as the impact of protective measures placed to mitigate transmission of the virus, providing necessary information to safeguard public health.
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Affiliation(s)
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Christos Haralambous
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, Nicosia 1148, Cyprus
| | - Maria Alexandrou
- Microbiology Department, Larnaca General Hospital, Larnaca 6301, Cyprus
| | - Antonia Aristokleous
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus
| | - Christina Christodoulou
- Department of Molecular Virology, Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Ioanna Gregoriou
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, Nicosia 1148, Cyprus
| | | | - Olga Kalakouta
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, Nicosia 1148, Cyprus
| | | | | | | | - Michail Mendris
- Microbiology Department, Limassol General Hospital, Limassol 4131, Cyprus
| | | | - Philippos C. Patsalis
- NIPD Genetics, Nicosia 2409, Cyprus
- Medical School, University of Nicosia, Nicosia 2417, Cyprus
| | - Despo Pieridou
- Microbiology Department, Nicosia General Hospital, Nicosia 2029, Cyprus
| | - Jan Richter
- Department of Molecular Virology, Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Markus Schmitt
- Eurofins Genomics Sequencing Europe, 85560 Ebersberg, Germany
| | - Christos Shammas
- S.C.I.N.A Bioanalysis Sciomedical Centre Ltd., Limassol 4040, Cyprus
| | - Dora C. Stylianou
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus
| | | | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Leondios G. Kostrikis
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus
- Cyprus Academy of Sciences, Letters, and Arts, 60-68 Phaneromenis Street, Nicosia 1011, Cyprus
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Horne BD, Bunker T. Pathogenic Mechanisms of the Severe Acute Respiratory Syndrome Coronavirus 2 and Potential Direct and Indirect Counteractions by Intermittent Fasting. Nutrients 2022; 15:20. [PMID: 36615679 PMCID: PMC9823718 DOI: 10.3390/nu15010020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic created an unprecedented burden on human health and on the function and interaction of societies across the globe. Public health preventive measures, vaccines, and antivirals were key components of the world-wide response to the health emergency. Due to the uncoordinated and variably successful response to COVID-19 and the ability of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to rapidly mutate, SARS-CoV-2 continues to create considerable difficulty for humanity today. Additional preventive or therapeutic modalities are needed to help people to achieve the best possible health outcomes in the context of the evolving COVID-19 threat. Intermittent fasting is a potential complementary therapy that not only impacts chronic disease risk but also has good evidence of an impact on infectious diseases. While the data regarding fasting and COVID-19 outcomes are very limited, the conceptual connection of fasting to better outcomes includes a variety of mechanisms in human biology. This paper reviews the known mechanisms of disease impacted by SARS-CoV-2 infection and the potential or likely direct or indirect counteractions that fasting may provide that may reduce the severity of COVID-19 and help to realize the best possible health outcomes. Furthermore, fasting adds no financial cost to a care plan and, when practiced safely, is available to most adults without limitation. Further research is needed on the impact of intermittent fasting on human health in the fight against infectious diseases including COVID-19.
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Affiliation(s)
- Benjamin D. Horne
- Intermountain Medical Center Heart Institute, Salt Lake City, UT 84107, USA
- Division of Cardiovascular Medicine, Stanford University, Stanford, CA 94305, USA
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Śliż D, Wiecha S, Gąsior JS, Kasiak PS, Ulaszewska K, Postuła M, Małek ŁA, Mamcarz A. The Influence of Nutrition and Physical Activity on Exercise Performance after Mild COVID-19 Infection in Endurance Athletes-CESAR Study. Nutrients 2022; 14:nu14245381. [PMID: 36558540 PMCID: PMC9788030 DOI: 10.3390/nu14245381] [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: 11/30/2022] [Revised: 12/11/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
COVID-19 and imposed restrictions are linked with numerous health consequences, especially among endurance athletes (EA). Unfavorable changes in physical activity and nutrition may affect later sports and competition performance. The aims of this study were: (1) to assess the impact of COVID-19 infection and pandemic restrictions on the nutrition and physical activity of EAs and (2) to compare them with the results of cardiopulmonary exercise testing (CPET). In total, 49 EAs (nmale = 43, nfemale = 6, mean age = 39.9 ± 7.8 year., height = 178.4 ± 6.8 cm, weight = 76.3 ± 10.4 kg; BMI = 24.0 ± 2.6 kg·m−2) underwent pre- and post-COVID-19 CPET and fulfilled the dietary and physical activity survey. COVID-19 infection significantly deteriorated CPET performance. There was a reduction in oxygen uptake and in heart rate post-COVID-19 (both p < 0.001). Consuming processed meat and replacing meat with plant-based protein affected blood lactate concentration (p = 0.035). Fat-free mass was linked with consuming unsaturated fatty acids (p = 0.031). Adding salt to meals influenced maximal speed/power (p = 0.024) and breathing frequency (p = 0.033). Dietary and Fitness Practitioners and Medical Professionals should be aware of possible COVID-19 infection and pandemic consequences among EA. The results of this study are a helpful guideline to properly adjust the treatment, nutrition, and training of EA.
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Affiliation(s)
- Daniel Śliż
- 3rd Department of Internal Medicine and Cardiology, Medical University of Warsaw, 04-749 Warsaw, Poland
- School of Public Health, Postgraduate Medical Education Center, 01-813 Warsaw, Poland
- Correspondence: (D.Ś.); (S.W.)
| | - Szczepan Wiecha
- Department of Physical Education and Health, Faculty in Biala Podlaska, Jozef Pilsudski University of Physical Education in Warsaw, 21-500 Biala Podlaska, Poland
- Correspondence: (D.Ś.); (S.W.)
| | - Jakub S. Gąsior
- Department of Pediatric Cardiology and General Pediatrics, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Przemysław Seweryn Kasiak
- Students’ Scientific Group of Lifestyle Medicine, 3rd Department of Internal Medicine and Cardiology, Medical University of Warsaw, 04-749 Warsaw, Poland
| | - Katarzyna Ulaszewska
- Students’ Scientific Group of Lifestyle Medicine, 3rd Department of Internal Medicine and Cardiology, Medical University of Warsaw, 04-749 Warsaw, Poland
| | - Marek Postuła
- Center for Preclinical Research and Technology CEPT, Department of Experimental and Clinical Pharmacology, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Łukasz A. Małek
- Department of Epidemiology, Cardiovascular Disease Prevention and Health Promotion, National Institute of Cardiology, 04-635 Warsaw, Poland
| | - Artur Mamcarz
- 3rd Department of Internal Medicine and Cardiology, Medical University of Warsaw, 04-749 Warsaw, Poland
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Stanhope BJ, Peterson B, Knight B, Decadiz RN, Pan R, Davis P, Fraser A, Nuth M, vanWestrienen J, Wendlandt E, Goodwin B, Myers C, Stone J, Sozhamannan S. Development, testing and validation of a SARS-CoV-2 multiplex panel for detection of the five major variants of concern on a portable PCR platform. Front Public Health 2022; 10:1042647. [PMID: 36590003 PMCID: PMC9798920 DOI: 10.3389/fpubh.2022.1042647] [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: 09/12/2022] [Accepted: 11/11/2022] [Indexed: 12/16/2022] Open
Abstract
Many SARS-CoV-2 variants have emerged during the course of the COVID-19 pandemic. These variants have acquired mutations conferring phenotypes such as increased transmissibility or virulence, or causing diagnostic, therapeutic, or immune escape. Detection of Alpha and the majority of Omicron sublineages by PCR relied on the so-called S gene target failure due to the deletion of six nucleotides coding for amino acids 69-70 in the spike (S) protein. Detection of hallmark mutations in other variants present in samples relied on whole genome sequencing. However, whole genome sequencing as a diagnostic tool is still in its infancy due to geographic inequities in sequencing capabilities, higher cost compared to other molecular assays, longer turnaround time from sample to result, and technical challenges associated with producing complete genome sequences from samples that have low viral load and/or high background. Hence, there is a need for rapid genotyping assays. In order to rapidly generate information on the presence of a variant in a given sample, we have created a panel of four triplex RT-qPCR assays targeting 12 mutations to detect and differentiate all five variants of concern: Alpha, Beta, Gamma, Delta, and Omicron. We also developed an expanded pentaplex assay that can reliably distinguish among the major sublineages (BA.1-BA.5) of Omicron. In silico, analytical and clinical testing of the variant panel indicate that the assays exhibit high sensitivity and specificity. This panel can help fulfill the need for rapid identification of variants in samples, leading to quick decision making with respect to public health measures, as well as treatment options for individuals. Compared to sequencing, these genotyping PCR assays allow much faster turn-around time from sample to results-just a couple hours instead of days or weeks.
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Affiliation(s)
| | | | | | | | - Roger Pan
- Naval Health Research Center (NHRC), San Diego, CA, United States
| | | | - Anne Fraser
- Naval Health Research Center (NHRC), San Diego, CA, United States
| | | | | | - Erik Wendlandt
- Integrated DNA Technologies, Coralville, IA, United States
| | - Bruce Goodwin
- Defense Biological Product Assurance Office (DBPAO), Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), Enabling Biotechnologies, Frederick, MD, United States
| | | | - Jennifer Stone
- MRIGlobal, Kansas City, MO, United States,*Correspondence: Jennifer Stone
| | - Shanmuga Sozhamannan
- Defense Biological Product Assurance Office (DBPAO), Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), Enabling Biotechnologies, Frederick, MD, United States,Logistics Management Institute, Tysons, VA, United States,Shanmuga Sozhamannan
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Muacevic A, Adler JR, Singh AK, Mohapatra PR, Gupta K, Patro BK, Sahu DP, Kar P, Purushotham P, Saha S, Das S, Mamidi P, Panda S, Mandal MC, Bhuniya S. Comparison of Clinical Presentation and Vaccine Effectiveness Among Omicron and Non-omicron SARS Coronavirus-2 Patients. Cureus 2022; 14:e32354. [PMID: 36628021 PMCID: PMC9826697 DOI: 10.7759/cureus.32354] [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: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Introduction The rapidly mutating Omicron SARS-CoV-2 variant has replaced the previous dominant SARS-CoV-2 variants like alpha, and delta resulting in the amplification of coronavirus disease 2019 (COVID-19) cases. The present study was conducted to compare the clinical profile and vaccination status in patients infected with Omicron and non-Omicron SARS-CoV-2 variants. Methods All patients who tested positive for coronavirus disease 2019 (COVID-19) during the study period (January 2022 to February 2022) were further tested for detection of SARS-CoV-2 Omicron variant by using Omisure kit (TATA MD CHECK RT-PCR, TATA MEDICAL AND DIAGNOSTICS LIMITED, Tamil Nadu, INDIA). Clinico-demographic factors and vaccination status were compared between both Omicron and non-Omicron groups. Results A total of 1,722 patients who tested positive for COVID-19 were included in the study, of which 656 (38.1%) were Omicron and 1,066 (61.9%) were non-Omicron SARS-CoV-2 variants. Blood group and vaccination status were the major predictors for Omicron. The proportion of male patients was 58.4% in the Omicron group and 57.9% in the non-Omicron group. Maximum cases (86.2%) belonged to >18-60 years age group, 7.3% to >60 years age group, and least to 0-18 years (6.5%). The average age of the study participants was 35.4 ± 14.5 years. Vaccinated participants had less chance of having Omicron than the unvaccinated participants (p-value - 0.003). Fever and loss of smell were found to be significantly associated with the non-Omicron SARS-CoV-2 variant. (p-value < 0.05). Conclusion The present study reflects that the clinical course of the disease is milder in Omicron as compared to the non-Omicron variant. However rapid rise in cases can badly affect the healthcare system demanding good preparedness to tackle all the predicaments. Good Vaccination coverage should be of utmost priority irrespective of the variant type.
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Kar J, Ramrao DP, Zomuansangi R, Lalbiaktluangi C, Singh SM, Joshi NC, Kumar A, Kaushalendra, Mehta S, Yadav MK, Singh PK. Revisiting the role of cyanobacteria-derived metabolites as antimicrobial agent: A 21st century perspective. Front Microbiol 2022; 13:1034471. [PMID: 36466636 PMCID: PMC9717611 DOI: 10.3389/fmicb.2022.1034471] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/18/2022] [Indexed: 11/23/2023] Open
Abstract
Cyanobacterial species are ancient photodiazotrophs prevalent in freshwater bodies and a natural reservoir of many metabolites (low to high molecular weight) such as non-ribosomal peptides, polyketides, ribosomal peptides, alkaloids, cyanotoxins, and isoprenoids with a well-established bioactivity potential. These metabolites enable cyanobacterial survival in extreme environments such as high salinity, heavy metals, cold, UV-B, etc. Recently, these metabolites are gaining the attention of researchers across the globe because of their tremendous applications as antimicrobial agents. Many reports claim the antimicrobial nature of these metabolites; unfortunately, the mode of action of such metabolites is not well understood and/or known limited. Henceforth, this review focuses on the properties and potential application, also critically highlighting the possible mechanism of action of these metabolites to offer further translational research. The review also aims to provide a comprehensive insight into current gaps in research on cyanobacterial biology as antimicrobials and hopes to shed light on the importance of continuing research on cyanobacteria metabolites in the search for novel antimicrobials.
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Affiliation(s)
- Joyeeta Kar
- Department of Biotechnology, Mizoram University (A Central University), Pachhunga University College Campus, Aizawl, Mizoram, India
| | - Devde Pandurang Ramrao
- Department of Biotechnology, Mizoram University (A Central University), Pachhunga University College Campus, Aizawl, Mizoram, India
| | - Ruth Zomuansangi
- Department of Biotechnology, Mizoram University (A Central University), Pachhunga University College Campus, Aizawl, Mizoram, India
| | - C. Lalbiaktluangi
- Department of Biotechnology, Mizoram University (A Central University), Pachhunga University College Campus, Aizawl, Mizoram, India
| | - Shiv Mohan Singh
- Centre of Advanced Studies in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Naveen Chandra Joshi
- Amity Institute of Microbial Technology (AIMT), Amity University, Noida, Uttar Pradesh, India
| | - Ajay Kumar
- Agriculture Research Organization (ARO) - The Volcani Center, Rishon LeZion, Israel
| | - Kaushalendra
- Department of Zoology, Mizoram University (A Central University), Pachhunga University College Campus, Aizawl, Mizoram, India
| | | | - Mukesh Kumar Yadav
- Department of Biotechnology, Mizoram University (A Central University), Pachhunga University College Campus, Aizawl, Mizoram, India
| | - Prashant Kumar Singh
- Department of Biotechnology, Mizoram University (A Central University), Pachhunga University College Campus, Aizawl, Mizoram, India
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