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Lopes R, Pham K, Klaassen F, Chitwood MH, Hahn AM, Redmond S, Swartwood NA, Salomon JA, Menzies NA, Cohen T, Grubaugh ND. Combining genomic data and infection estimates to characterize the complex dynamics of SARS-CoV-2 Omicron variants in the US. Cell Rep 2024; 43:114451. [PMID: 38970788 DOI: 10.1016/j.celrep.2024.114451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 05/03/2024] [Accepted: 06/20/2024] [Indexed: 07/08/2024] Open
Abstract
Omicron surged as a variant of concern in late 2021. Several distinct Omicron variants appeared and overtook each other. We combined variant frequencies and infection estimates from a nowcasting model for each US state to estimate variant-specific infections, attack rates, and effective reproduction numbers (Rt). BA.1 rapidly emerged, and we estimate that it infected 47.7% of the US population before it was replaced by BA.2. We estimate that BA.5 infected 35.7% of the US population, persisting in circulation for nearly 6 months. Other variants-BA.2, BA.4, and XBB-together infected 30.7% of the US population. We found a positive correlation between the state-level BA.1 attack rate and social vulnerability and a negative correlation between the BA.1 and BA.2 attack rates. Our findings illustrate the complex interplay between viral evolution, population susceptibility, and social factors during the Omicron emergence in the US.
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Affiliation(s)
- Rafael Lopes
- Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA.
| | - Kien Pham
- Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA
| | - Fayette Klaassen
- Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Melanie H Chitwood
- Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA
| | - Seth Redmond
- Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA
| | - Nicole A Swartwood
- Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Joshua A Salomon
- Department of Health Policy, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicolas A Menzies
- Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA.
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
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Asplin P, Mancy R, Finnie T, Cumming F, Keeling MJ, Hill EM. Symptom propagation in respiratory pathogens of public health concern: a review of the evidence. J R Soc Interface 2024; 21:20240009. [PMID: 39045688 PMCID: PMC11267474 DOI: 10.1098/rsif.2024.0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 05/28/2024] [Indexed: 07/25/2024] Open
Abstract
Symptom propagation occurs when the symptom set an individual experiences is correlated with the symptom set of the individual who infected them. Symptom propagation may dramatically affect epidemiological outcomes, potentially causing clusters of severe disease. Conversely, it could result in chains of mild infection, generating widespread immunity with minimal cost to public health. Despite accumulating evidence that symptom propagation occurs for many respiratory pathogens, the underlying mechanisms are not well understood. Here, we conducted a scoping literature review for 14 respiratory pathogens to ascertain the extent of evidence for symptom propagation by two mechanisms: dose-severity relationships and route-severity relationships. We identify considerable heterogeneity between pathogens in the relative importance of the two mechanisms, highlighting the importance of pathogen-specific investigations. For almost all pathogens, including influenza and SARS-CoV-2, we found support for at least one of the two mechanisms. For some pathogens, including influenza, we found convincing evidence that both mechanisms contribute to symptom propagation. Furthermore, infectious disease models traditionally do not include symptom propagation. We summarize the present state of modelling advancements to address the methodological gap. We then investigate a simplified disease outbreak scenario, finding that under strong symptom propagation, isolating mildly infected individuals can have negative epidemiological implications.
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Affiliation(s)
- Phoebe Asplin
- EPSRC & MRC Centre for Doctoral Training in Mathematics for Real-World Systems, University of Warwick, Coventry, UK
- Mathematics Institute, University of Warwick, Coventry, UK
- The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, University of Warwick, Coventry, UK
| | - Rebecca Mancy
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
- MRC/CSO Social and Public Health Sciences Unit, University of Glasgow, Glasgow, UK
| | - Thomas Finnie
- Data, Analytics and Surveillance, UK Health Security Agency, London, UK
| | - Fergus Cumming
- Foreign, Commonwealth and Development Office, London, UK
| | - Matt J. Keeling
- Mathematics Institute, University of Warwick, Coventry, UK
- The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, University of Warwick, Coventry, UK
- School of Life Sciences, University of Glasgow, Glasgow, UK
| | - Edward M. Hill
- Mathematics Institute, University of Warwick, Coventry, UK
- The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, University of Warwick, Coventry, UK
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Biswas D, Mahalingam G, Subaschandrabose RK, Priya S, Ramachandran R, Suresh S, Mathivanan TV, Balu NV, Selvaraj K, Nellickal AJ, Christudoss P, Samuel P, Kt RD, Marepally S, Moorthy M. Role of prior immunity in binding to spike of "future" Omicron subvariants. Indian J Med Microbiol 2024; 50:100615. [PMID: 38782260 DOI: 10.1016/j.ijmmb.2024.100615] [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: 11/11/2023] [Revised: 04/18/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Throughout the COVID-19 pandemic, virus evolution and large-scale vaccination programs have caused multiple exposures to SARS CoV-2 spike protein, resulting in complex antibody profiles. The binding of these to spike protein of "future" variants in the context of such heterogeneous exposure has not been studied. METHODS We tested archival sera (Delta and Omicron period) stratified by anti-spike antibody (including IgG) levels for reactivity to Omicron-subvariants(BA.1, BA.2,BA.2.12.1, BA.2.75, BA.4/5 and BF.7) spike protein. Assessed antigenic distance between groups using Antigenic Cartography and performed hierarchical clustering of antibody data in a Euclidean distance framework. RESULTS Antibody (including IgG) antibody reactivity to Wild-type (CLIA) and subvariants (ELISA) spike protein were similar between periods (p > 0.05). Both 'High S' and 'Low S' of Delta and Omicron periods were closely related to "future" subvariants by Antigenic Cartography. Sera from different S groups clustered together with 'Low S' interspersed between 'High S' on hierarchical clustering, suggesting common binding sites. Further, anti-spike antibodies (including IgG) to Wild-type (S1/S2 and Trimeric S) clustered with Omicron-subvariant binding antibodies. CONCLUSIONS Hybrid immunity caused by cumulative virus exposure in Delta or Omicron periods resulted in equivalent binding to "future" variants, which might be due to binding to conserved regions of spike protein of future variants. A prominent finding is that the 'Low S' antibody demonstrates similar binding.
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Affiliation(s)
- Deepayan Biswas
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| | - Gokulnath Mahalingam
- Centre for Stem Cell Research (CSCR) (a unit of InStem, Bengaluru), Christian Medical College, Vellore, Pin: 632002, Tamil Nadu, India.
| | | | - Sangeetha Priya
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| | - Rohini Ramachandran
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| | - Sevanthy Suresh
- Centre for Stem Cell Research (CSCR) (a unit of InStem, Bengaluru), Christian Medical College, Vellore, Pin: 632002, Tamil Nadu, India.
| | - Tamil Venthan Mathivanan
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| | - Nelson Vijaykumar Balu
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| | - Kavitha Selvaraj
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| | - Arun Jose Nellickal
- Department of Clinical Biochemistry, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| | - Pamela Christudoss
- Department of Clinical Biochemistry, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| | - Prasanna Samuel
- Department of Biostatistics, Christian Medical College, Vellore, Tamil Nadu, Pin: 632002, India.
| | - Ramya Devi Kt
- Department of Biotechnology, SRM Institute of Science and Technology, Kanchipuram, Tamil Nadu, Pin: 603203, India.
| | - Srujan Marepally
- Centre for Stem Cell Research (CSCR) (a unit of InStem, Bengaluru), Christian Medical College, Vellore, Pin: 632002, Tamil Nadu, India.
| | - Mahesh Moorthy
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
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Presume M, Gaudart J, Michel E, Marseille S, Altmann M. Geographical coverage of SARS-CoV-2 screening and care centers in Haiti: what do national surveillance data tell us? BMC Public Health 2024; 24:1732. [PMID: 38943127 PMCID: PMC11214257 DOI: 10.1186/s12889-024-19262-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 06/25/2024] [Indexed: 07/01/2024] Open
Abstract
BACKGROUND In Haiti, reported incidence and mortality rates for COVID-19 were lower than expected. We aimed to analyze factors at communal and individual level that might lead to an underestimation of the true burden of the COVID-19 epidemic in Haiti during its first two years. METHODS We analyzed national COVID-19 surveillance data from March 2020 to December 2021, to describe the epidemic using cluster detection, time series, and cartographic approach. We performed multivariate Quasi-Poisson regression models to determine socioeconomic factors associated with incidence and mortality. We performed a mixed-effect logistic regression model to determine individual factors associated with the infection. RESULTS Among the 140 communes of Haiti, 57 (40.7%) had a COVID-19 screening center, and the incidence was six times higher in these than in those without. Only 22 (15.7%) communes had a COVID-19 care center, and the mortality was five times higher in these than in those without. All the richest communes had a COVID-19 screening center while only 30.8% of the poorest had one. And 75% of the richest communes had a COVID-19 care center while only 15.4% of the poorest had one. Having more than three healthcare workers per 1000 population in the commune was positively associated with the incidence (SIR: 3.31; IC95%: 2.50, 3.93) and the mortality (SMR: 2.73; IC95%: 2.03, 3.66). At the individual level, male gender (adjusted OR: 1.11; IC95%: 1.01, 1.22), age with a progressive increase of the risk compared to youngers, and having Haitian nationality only (adjusted OR:2.07; IC95%: 1.53, 2.82) were associated with the infection. CONCLUSIONS This study highlights the weakness of SARS-CoV-2 screening and care system in Haiti, particularly in the poorest communes, suggesting that the number of COVID-19 cases and deaths were probably greatly underestimated.
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Affiliation(s)
- Marcmy Presume
- Directorate of Epidemiology Laboratories and Research (DELR), Ministry of Public Health and Population (MSPP), Research Institute for Sustainable Development (IRD), Bordeaux Population Health Research Centre, EMR 271, Bordeaux, France.
| | - Jean Gaudart
- Aix Marseille Univ, INSERM, IRD, SESSTIM, ISSPAM, AP-HM, Hospital La Timone, BioSTIC Unit, Marseille, France
| | - Edwige Michel
- Directorate of Epidemiology Laboratories and Research (DELR), Ministry of Public Health and Population (MSPP), Port-Au-Prince, Haiti
| | - Samson Marseille
- Directorate of Epidemiology Laboratories and Research (DELR), Ministry of Public Health and Population (MSPP), Port-Au-Prince, Haiti
| | - Mathias Altmann
- University of Bordeaux, National Institute for Health and Medical Research (INSERM) UMR 1219, Research Institute for Sustainable Development (IRD) EMR 271, Bordeaux Population Health Research Centre, Bordeaux, France
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Mirska B, Zenczak M, Nowis K, Stolarek I, Podkowiński J, Rakoczy M, Marcinkowska-Swojak M, Koralewska N, Zmora P, Lenartowicz Onyekaa E, Osuch M, Łasińska K, Kuczma-Napierała J, Jaworska M, Madej Ł, Ciechomska M, Jamsheer A, Kurowski K, Figlerowicz M, Handschuh L. The landscape of the COVID-19 pandemic in Poland emerging from epidemiological and genomic data. Sci Rep 2024; 14:14416. [PMID: 38909091 PMCID: PMC11193717 DOI: 10.1038/s41598-024-65468-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 06/20/2024] [Indexed: 06/24/2024] Open
Abstract
The COVID-19 pandemic has profoundly affected all aspects of our lives. Through real-time monitoring and rapid vaccine implementation, we succeeded in suppressing the spread of the disease and mitigating its consequences. Finally, conclusions can be summarized and drawn. Here, we use the example of Poland, which was seriously affected by the pandemic. Compared to other countries, Poland has not achieved impressive results in either testing or vaccination, which may explain its high mortality (case fatality rate, CFR 1.94%). Through retrospective analysis of data collected by the COVID-19 Data Portal Poland, we found significant regional differences in the number of tests performed, number of cases detected, number of COVID-19-related deaths, and vaccination rates. The Masovian, Greater Poland, and Pomeranian voivodeships, the country's leaders in vaccination, reported high case numbers but low death rates. In contrast, the voivodeships in the eastern and southern parts of Poland (Subcarpathian, Podlaskie, Lublin, Opole), which documented low vaccination levels and low case numbers, had higher COVID-19-related mortality rates. The strong negative correlation between the CFR and the percentage of the population that was vaccinated in Poland supports the validity of vaccination. To gain insight into virus evolution, we sequenced more than 500 genomes and analyzed nearly 80 thousand SARS-CoV-2 genome sequences deposited in GISAID by Polish diagnostic centers. We showed that the SARS-CoV-2 variant distribution over time in Poland reflected that in Europe. Haplotype network analysis allowed us to follow the virus transmission routes and identify potential superspreaders in each pandemic wave.
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Affiliation(s)
- Barbara Mirska
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Michal Zenczak
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Katarzyna Nowis
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Ireneusz Stolarek
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Jan Podkowiński
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Magdalena Rakoczy
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | | | - Natalia Koralewska
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Paweł Zmora
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | | | - Marcin Osuch
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | | | | | | | - Łukasz Madej
- Regional Science and Technology Center, Podzamcze, Poland
| | - Marzena Ciechomska
- National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland
| | - Aleksander Jamsheer
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
- Centers for Medical Genetics GENESIS, Poznan, Poland
| | - Krzysztof Kurowski
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Luiza Handschuh
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland.
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Rurek M. Mitochondria in COVID-19: from cellular and molecular perspective. Front Physiol 2024; 15:1406635. [PMID: 38974521 PMCID: PMC11224649 DOI: 10.3389/fphys.2024.1406635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/27/2024] [Indexed: 07/09/2024] Open
Abstract
The rapid development of the COVID-19 pandemic resulted in a closer analysis of cell functioning during β-coronavirus infection. This review will describe evidence for COVID-19 as a syndrome with a strong, albeit still underestimated, mitochondrial component. Due to the sensitivity of host mitochondria to coronavirus infection, SARS-CoV-2 affects mitochondrial signaling, modulates the immune response, modifies cellular energy metabolism, induces apoptosis and ageing, worsening COVID-19 symptoms which can sometimes be fatal. Various aberrations across human systems and tissues and their relationships with mitochondria were reported. In this review, particular attention is given to characterization of multiple alterations in gene expression pattern and mitochondrial metabolism in COVID-19; the complexity of interactions between SARS-CoV-2 and mitochondrial proteins is presented. The participation of mitogenome fragments in cell signaling and the occurrence of SARS-CoV-2 subgenomic RNA within membranous compartments, including mitochondria is widely discussed. As SARS-CoV-2 severely affects the quality system of mitochondria, the cellular background for aberrations in mitochondrial dynamics in COVID-19 is additionally characterized. Finally, perspectives on the mitigation of COVID-19 symptoms by affecting mitochondrial biogenesis by numerous compounds and therapeutic treatments are briefly outlined.
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Affiliation(s)
- Michał Rurek
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
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7
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Cao Z, Sun F, Ding H, Tian Z, Cui Y, Yang W, Hu S, Shi L. A retrospective analysis of the influencing factors of nucleic acid CT value fluctuation in COVID-19 patients infected with Omicron variant virus in Changchun city. Front Public Health 2024; 12:1377135. [PMID: 38947348 PMCID: PMC11211536 DOI: 10.3389/fpubh.2024.1377135] [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: 01/31/2024] [Accepted: 06/03/2024] [Indexed: 07/02/2024] Open
Abstract
Objective This study aimed to determine the risk factors associated with fluctuations in nucleic acid CT values in patients infected with the Omicron variant during an outbreak at a hospital in Changchun city. Methods A retrospective analysis was conducted on general information, medical history, vaccination history, and laboratory test data of COVID-19 patients infected with the Omicron variant and admitted to the hospital in Changchun from March 2022 to April 2022. The study aimed to explore the factors influencing nucleic acid CT value fluctuations in COVID-19 patients infected with the Omicron variant in Changchun city. Results Fluctuations in nucleic acid CT values were significantly correlated with occupation composition (p = 0.030), hospital stay duration (p = 0.000), heart rate (p = 0.026), creatinine (p = 0.011), platelet count (p = 0.000), glutamic-pyruvic transaminase (p = 0.045), and glutamic oxaloacetic transaminase (p = 0.017). Binary logistic regression analysis revealed significant correlations between hospital stay duration (p = 0.000), platelet count (p = 0.019), heart rate (p = 0.036), and nucleic acid CT value fluctuations (p < 0.05), indicating that they were independent risk factors. Red blood cell count was identified as a factor influencing nucleic acid CT value fluctuations in Group A patients. Occupation composition, direct bilirubin, and platelet count were identified as factors influencing nucleic acid CT value fluctuations in Group B patients. Further binary logistic regression analysis indicated that occupational composition and direct bilirubin are significant independent factors for nucleic acid CT value fluctuations in Group B patients, positively correlated with occupational risk and negatively correlated with direct bilirubin. Conclusion Therefore, enhancing patients' immunity, increasing physical exercise to improve myocardial oxygen consumption, reducing the length of hospital stays, and closely monitoring liver function at the onset of hospitalization to prevent liver function abnormalities are effective measures to control fluctuations in nucleic acid CT values.
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Affiliation(s)
- Zhenghua Cao
- Changchun University of Traditional Chinese Medicine, Changchun, Jilin, China
| | - Feng Sun
- Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, Jilin, China
| | - Huan Ding
- Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, Jilin, China
| | - Zhiyu Tian
- Changchun University of Traditional Chinese Medicine, Changchun, Jilin, China
| | - Yingzi Cui
- Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, Jilin, China
| | - Wei Yang
- Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, Jilin, China
| | - Shaodan Hu
- Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, Jilin, China
| | - Li Shi
- Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, Jilin, China
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8
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de Rioja VL, Perramon-Malavez A, Alonso S, Andrés C, Antón A, Bordoy AE, Càmara J, Cardona PJ, Català M, López D, Martí S, Martró E, Saludes V, Prats C, Alvarez-Lacalle E. Mathematical modeling of SARS-CoV-2 variant substitutions in European countries: transmission dynamics and epidemiological insights. Front Public Health 2024; 12:1339267. [PMID: 38855458 PMCID: PMC11160439 DOI: 10.3389/fpubh.2024.1339267] [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: 11/15/2023] [Accepted: 04/08/2024] [Indexed: 06/11/2024] Open
Abstract
Background Countries across Europe have faced similar evolutions of SARS-CoV-2 variants of concern, including the Alpha, Delta, and Omicron variants. Materials and methods We used data from GISAID and applied a robust, automated mathematical substitution model to study the dynamics of COVID-19 variants in Europe over a period of more than 2 years, from late 2020 to early 2023. This model identifies variant substitution patterns and distinguishes between residual and dominant behavior. We used weekly sequencing data from 19 European countries to estimate the increase in transmissibility ( Δ β ) between consecutive SARS-CoV-2 variants. In addition, we focused on large countries with separate regional outbreaks and complex scenarios of multiple competing variants. Results Our model accurately reproduced the observed substitution patterns between the Alpha, Delta, and Omicron major variants. We estimated the daily variant prevalence and calculated Δ β between variants, revealing that: ( i ) Δ β increased progressively from the Alpha to the Omicron variant; ( i i ) Δ β showed a high degree of variability within Omicron variants; ( i i i ) a higher Δ β was associated with a later emergence of the variant within a country; ( i v ) a higher degree of immunization of the population against previous variants was associated with a higher Δ β for the Delta variant; ( v ) larger countries exhibited smaller Δ β , suggesting regionally diverse outbreaks within the same country; and finally ( v i ) the model reliably captures the dynamics of competing variants, even in complex scenarios. Conclusion The use of mathematical models allows for precise and reliable estimation of daily cases of each variant. By quantifying Δ β , we have tracked the spread of the different variants across Europe, highlighting a robust increase in transmissibility trend from Alpha to Omicron. Additionally, we have shown that the geographical characteristics of a country, as well as the timing of new variant entrances, can explain some of the observed differences in variant substitution dynamics across countries.
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Affiliation(s)
- Víctor López de Rioja
- Computational Biology and Complex Systems Group, Department of Physics, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Aida Perramon-Malavez
- Computational Biology and Complex Systems Group, Department of Physics, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Sergio Alonso
- Computational Biology and Complex Systems Group, Department of Physics, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Cristina Andrés
- Microbiology Department, Vall D’Hebron Hospital Universitari, Vall D’Hebron Institut de Recerca, Vall D’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Biomedical Research Networking Center in Infectious Diseases, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Andrés Antón
- Microbiology Department, Vall D’Hebron Hospital Universitari, Vall D’Hebron Institut de Recerca, Vall D’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Biomedical Research Networking Center in Infectious Diseases, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Antoni E. Bordoy
- Microbiology Department, Northern Metropolitan Clinical Laboratory, Germans Trias i Pujol University Hospital and Research Institute, Badalona, Spain
| | - Jordi Càmara
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, L’Hospitalet de Llobregat, Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Pere-Joan Cardona
- Microbiology Department, Northern Metropolitan Clinical Laboratory, Germans Trias i Pujol University Hospital and Research Institute, Badalona, Spain
- Research Network for Respiratory Diseases (CIBERES), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Martí Català
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Daniel López
- Computational Biology and Complex Systems Group, Department of Physics, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Sara Martí
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, L’Hospitalet de Llobregat, Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Elisa Martró
- Microbiology Department, Northern Metropolitan Clinical Laboratory, Germans Trias i Pujol University Hospital and Research Institute, Badalona, Spain
- Biomedical Research Center Network for Epidemiology and Public Health, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Verónica Saludes
- Microbiology Department, Northern Metropolitan Clinical Laboratory, Germans Trias i Pujol University Hospital and Research Institute, Badalona, Spain
- Biomedical Research Center Network for Epidemiology and Public Health, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Clara Prats
- Computational Biology and Complex Systems Group, Department of Physics, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Enrique Alvarez-Lacalle
- Computational Biology and Complex Systems Group, Department of Physics, Universitat Politècnica de Catalunya, Barcelona, Spain
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9
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Zhao Z, Bashiri S, Ziora ZM, Toth I, Skwarczynski M. COVID-19 Variants and Vaccine Development. Viruses 2024; 16:757. [PMID: 38793638 PMCID: PMC11125726 DOI: 10.3390/v16050757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/08/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), the global pandemic caused by severe acute respiratory syndrome 2 virus (SARS-CoV-2) infection, has caused millions of infections and fatalities worldwide. Extensive SARS-CoV-2 research has been conducted to develop therapeutic drugs and prophylactic vaccines, and even though some drugs have been approved to treat SARS-CoV-2 infection, treatment efficacy remains limited. Therefore, preventive vaccination has been implemented on a global scale and represents the primary approach to combat the COVID-19 pandemic. Approved vaccines vary in composition, although vaccine design has been based on either the key viral structural (spike) protein or viral components carrying this protein. Therefore, mutations of the virus, particularly mutations in the S protein, severely compromise the effectiveness of current vaccines and the ability to control COVID-19 infection. This review begins by describing the SARS-CoV-2 viral composition, the mechanism of infection, the role of angiotensin-converting enzyme 2, the host defence responses against infection and the most common vaccine designs. Next, this review summarizes the common mutations of SARS-CoV-2 and how these mutations change viral properties, confer immune escape and influence vaccine efficacy. Finally, this review discusses global strategies that have been employed to mitigate the decreases in vaccine efficacy encountered against new variants.
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Affiliation(s)
- Ziyao Zhao
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
| | - Sahra Bashiri
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
| | - Zyta M. Ziora
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Istvan Toth
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia;
- School of Pharmacy, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Mariusz Skwarczynski
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
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10
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Rodriguez Velásquez S, Biru LE, Hakiza SM, Al-Gobari M, Triulzi I, Dalal J, Varela CBG, Botero Mesa S, Keiser O. Long-term levels of protection of different types of immunity against the Omicron variant: a rapid literature review. Swiss Med Wkly 2024; 154:3732. [PMID: 38749028 DOI: 10.57187/s.3732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024] Open
Abstract
INTRODUCTION With the emergence of newer SARS-CoV-2 variants and their substantial effects on the levels and duration of protection against infection, an understanding of these characteristics of the protection conferred by humoral and cellular immunity can aid in the proper development and implementation of vaccine and safety guidelines. METHODS We conducted a rapid literature review and searched five electronic databases weekly from 1 November 2021 to 30 September 2022. Studies that assessed the humoral or cellular immunity conferred by infection, vaccination or a hybrid (combination of both) in adults and risk groups (immunocompromised and older populations) were identified. Studies were eligible when they reported data on immunological assays of COVID-19 (related to vaccination and/or infection) or the effectiveness of protection (related to the effectiveness of vaccination and/or infection). RESULTS We screened 5103 studies and included 205 studies, of which 70 provided data on the duration of protection against SARS-CoV-2 infection. The duration of protection of adaptive immunity was greatly impacted by Omicron and its subvariants: levels of protection were low by 3-6 months from exposure to infection/vaccination. Although more durable, cellular immunity also showed signs of waning by 6 months. First and second mRNA vaccine booster doses increased the levels of protection against infection and severe disease from Omicron and its subvariants but continued to demonstrate a high degree of waning over time. CONCLUSION All humoral immunities (infection-acquired, vaccine-acquired and hybrid) waned by 3-6 months. Cellular immunity was more durable but showed signs of waning by 6 months. Hybrid immunity had the highest magnitude of protection against SARS-CoV-2 infection. Boosting may be recommended as early as 3-4 months after the last dose, especially in risk groups.
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Affiliation(s)
- Sabina Rodriguez Velásquez
- Institute of Global Health, University of Geneva, Geneva, Switzerland
- The GRAPH Network, Geneva, Switzerland
| | - Loza Estifanos Biru
- Institute of Global Health, University of Geneva, Geneva, Switzerland
- The GRAPH Network, Geneva, Switzerland
| | - Sandrine Marie Hakiza
- Institute of Global Health, University of Geneva, Geneva, Switzerland
- The GRAPH Network, Geneva, Switzerland
| | - Muaamar Al-Gobari
- The GRAPH Network, Geneva, Switzerland
- HIV/AIDS Unit Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Isotta Triulzi
- The GRAPH Network, Geneva, Switzerland
- Scuola Superiore Sant'Anna, Pisa, Italy
| | | | | | - Sara Botero Mesa
- Institute of Global Health, University of Geneva, Geneva, Switzerland
- The GRAPH Network, Geneva, Switzerland
| | - Olivia Keiser
- Institute of Global Health, University of Geneva, Geneva, Switzerland
- The GRAPH Network, Geneva, Switzerland
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11
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Kumar DS, Prasanth K, Bhandari A, Kumar Jha V, Naveen A, Prasanna M. Innovations and Challenges in the Development of COVID-19 Vaccines for a Safer Tomorrow. Cureus 2024; 16:e60015. [PMID: 38854201 PMCID: PMC11162516 DOI: 10.7759/cureus.60015] [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: 05/09/2024] [Indexed: 06/11/2024] Open
Abstract
Vaccination, a historically effective public health intervention, has shielded millions from various diseases. Lessons from severe acute respiratory syndrome coronavirus (SARS-CoV) have improved COVID-19 vaccine development. Despite mRNA vaccines' efficacy, emerging variants pose challenges, exhibiting increased transmissibility, infectivity, and severity. Developing COVID-19 vaccines has faced hurdles due to urgency, limited virus understanding, and the need for safe solutions. Genetic variability necessitates continuous vaccine adjustments and production challenges demand scaling up manufacturing with stringent quality control. This review explores SARS-CoV-2's evolution, upcoming mutations that challenge vaccines, and strategies such as structure-based, T cell-based, respiratory mucosal-based, and nanotechnology approaches for vaccine development. This review insight provides a roadmap for navigating virus evolution and improving vaccine development.
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Affiliation(s)
- Devika S Kumar
- Research, Panimalar Medical College Hospital and Research Institute, Chennai, IND
| | - Krishna Prasanth
- Department of Community Medicine, Sree Balaji Medical College and Hospital, Chennai, IND
| | - Ashni Bhandari
- Department of Community Medicine, Sree Balaji Medical College and Hospital, Chennai, IND
| | - Vivek Kumar Jha
- Department of Audiology and Speech Language Pathology, Shree Guru Gobind Singh Tricentenary (SGT) University, Haryana, IND
| | - Avula Naveen
- Pharmacology and Therapeutics, All India Institute Of Medical Science Bilaspur, Bilaspur, IND
| | - Muthu Prasanna
- Pharmaceutics, Pharmaceutical Biotechnology, Surya School of Pharmacy, Surya Group of Institutions, Villupuram, IND
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12
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Zhang Z, Tang L, Guo Y, Guo X, Pan Z, Ji X, Gao C. Development of Biomarkers and Prognosis Model of Mortality Risk in Patients with COVID-19. J Inflamm Res 2024; 17:2445-2457. [PMID: 38681069 PMCID: PMC11048291 DOI: 10.2147/jir.s449497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 04/04/2024] [Indexed: 05/01/2024] Open
Abstract
Background As of 30 April 2023, the COVID-19 pandemic has resulted in over 6.9 million deaths worldwide. The virus continues to spread and mutate, leading to continuously evolving pathological and physiological processes. It is imperative to reevaluate predictive factors for identifying the risk of early disease progression. Methods A retrospective study was conducted on a cohort of 1379 COVID-19 patients who were discharged from Xin Hua Hospital affiliated with Shanghai Jiao Tong University School of Medicine between 15 December 2022 and 15 February 2023. Patient symptoms, comorbidities, demographics, vital signs, and laboratory test results were systematically documented. The dataset was split into testing and training sets, and 15 different machine learning algorithms were employed to construct prediction models. These models were assessed for accuracy and area under the receiver operating characteristic curve (AUROC), and the best-performing model was selected for further analysis. Results AUROC for models generated by 15 machine learning algorithms all exceeded 90%, and the accuracy of 10 of them also surpassed 90%. Light Gradient Boosting model emerged as the optimal choice, with accuracy of 0.928 ± 0.0006 and an AUROC of 0.976 ± 0.0028. Notably, the factors with the greatest impact on in-hospital mortality were growth stimulation expressed gene 2 (ST2,19.3%), interleukin-8 (IL-8,17.2%), interleukin-6 (IL-6,6.4%), age (6.1%), NT-proBNP (5.1%), interleukin-2 receptor (IL-2R, 5%), troponin I (TNI,4.6%), congestive heart failure (3.3%) in Light Gradient Boosting model. Conclusion ST-2, IL-8, IL-6, NT-proBNP, IL-2R, TNI, age and congestive heart failure were significant predictors of in-hospital mortality among COVID-19 patients.
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Affiliation(s)
- Zhishuo Zhang
- Department of Emergency, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Lujia Tang
- Department of Emergency, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Yiran Guo
- Department of Emergency, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Xin Guo
- School of Information Science and Technology, Sanda University, Shanghai, Pudong District, 201209, China
| | - Zhiying Pan
- School of Information Science and Technology, Sanda University, Shanghai, Pudong District, 201209, China
| | - Xiaojing Ji
- Department of Emergency, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Chengjin Gao
- Department of Emergency, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
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13
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Salamango DJ. Finally neutralizing the threat? A novel SARS-CoV-2 vaccine platform that elicits enhanced neutralizing antibody responses. mBio 2024; 15:e0006724. [PMID: 38407097 PMCID: PMC11005347 DOI: 10.1128/mbio.00067-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) outbreak took the world by storm due to its rapid global spread and unpredictable disease outcomes. The extraordinary ascension of SARS-CoV-2 to pandemic status motivated a world-wide effort to rapidly develop vaccines that could effectively suppress virus spread and mitigate severe disease. These efforts culminated in the development and deployment of several highly effective vaccines that were heralded as the beginning-of-the-end of the pandemic. However, these successes were short lived due to the unexpected and continuous emergence of more transmissible and immune-evasive SARS-CoV-2 variants. Thus, attention has shifted toward developing novel vaccine platforms that elicit more robust and sustained neutralizing antibody responses. Recent findings by Muñoz-Alía and colleagues address this by combining a live recombinant measles vaccine platform with novel biochemical approaches to generate vaccine candidates that bolster the potency of neutralizing antibody responses against diverse SARS-CoV-2 spike proteins (M. Á. Muñoz-Alía, R. A. Nace, B. Balakrishnan, L. Zhang, et al., mBio 9:e02928-23, 2024, https://doi.org/10.1128/mbio.02928-23).
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Affiliation(s)
- Daniel J. Salamango
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health Science Center, San Antonio, Texas, USA
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14
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Ahmadi Badi S, Kariman A, Bereimipour A, Shojaie S, Aghsadeghi M, Khatami S, Masotti A. Association Between Altered Microbiota Composition and Immune System-Related Genes in COVID-19 Infection. Mol Biotechnol 2024:10.1007/s12033-024-01096-8. [PMID: 38456962 DOI: 10.1007/s12033-024-01096-8] [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: 09/23/2023] [Accepted: 01/18/2024] [Indexed: 03/09/2024]
Abstract
Microbiota and immunity affect the host's susceptibility to SARS-CoV-2 infection and the severity of COVID-19. This study aimed to identify significant alterations in the microbiota composition, immune signaling pathways, their potential association, and candidate microRNA in COVID-19 patients using an in silico study model. Enrichment online databases and Python programming were utilized to analyze GSE164805, GSE180594, and GSE182279, as well as NGS data of microbiota composition (PRJNA650244 and PRJNA660302) associated with COVID-19, employing amplicon-based/marker gene sequencing methods. C1, TNF, C2, IL1, and CFH genes were found to have a significant impact on immune signaling pathways. Additionally, we observed a notable decrease in Bacteroides spp. and Faecalibacterium sp., while Escherichia coli, Streptococcus spp., and Akkermansia muciniphila showed increased abundance in COVID-19. Notably, A. muciniphila demonstrated an association with immunity through C1 and TNF, while Faecalibacterium sp. was linked to C2 and IL1. The correlation between E. coli and CFH, as well as IL1 and Streptococcus spp. with C2, was identified. hsa-let-7b-5p was identified as a potential candidate that may be involved in the interaction between the microbiota composition, immune response, and COVID-19. In conclusion, integrative in silico analysis shows that these microbiota members are potentially crucial in the immune responses against COVID-19.
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Affiliation(s)
- Sara Ahmadi Badi
- Biochemistry Department, Pasteur Institute of Iran, Tehran, Iran.
- Pediatric Gastroenterology and Hepatology Research Center, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Science, Tehran, Iran.
| | - Arian Kariman
- Pediatric Gastroenterology and Hepatology Research Center, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Science, Tehran, Iran
| | - Ahmad Bereimipour
- Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Shima Shojaie
- Pediatric Gastroenterology and Hepatology Research Center, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Science, Tehran, Iran
| | | | - Shohreh Khatami
- Biochemistry Department, Pasteur Institute of Iran, Tehran, Iran
| | - Andrea Masotti
- Research Laboratories, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
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15
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McQuaid C, Montagne A. SARS-CoV-2 and vascular dysfunction: a growing role for pericytes. Cardiovasc Res 2023; 119:2591-2593. [PMID: 36063106 PMCID: PMC9494379 DOI: 10.1093/cvr/cvac143] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 08/17/2022] [Indexed: 12/03/2022] Open
Affiliation(s)
- Conor McQuaid
- Centre for Clinical Brain Sciences, UK Dementia Research Institute at the University of Edinburgh, Edinburgh Medical School, Chancellor’s Building, Edinburgh EH16 4SB, UK
| | - Axel Montagne
- Centre for Clinical Brain Sciences, UK Dementia Research Institute at the University of Edinburgh, Edinburgh Medical School, Chancellor’s Building, Edinburgh EH16 4SB, UK
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y Castro TR, Piccoli BC, Vieira AA, Casarin BC, Tessele LF, Salvato RS, Gregianini TS, Martins LG, Resende PC, Pereira EC, Moreira FRR, de Jesus JG, Seerig AP, Lobato MAO, de Campos MMA, Goularte JS, da Silva MS, Demoliner M, Filippi M, Pereira VMAG, Schwarzbold AV, Spilki FR, Trindade PA. Introduction, Dispersal, and Predominance of SARS-CoV-2 Delta Variant in Rio Grande do Sul, Brazil: A Retrospective Analysis. Microorganisms 2023; 11:2938. [PMID: 38138081 PMCID: PMC10745878 DOI: 10.3390/microorganisms11122938] [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: 09/28/2023] [Revised: 11/14/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Mutations in the SARS-CoV-2 genome can alter the virus' fitness, leading to the emergence of variants of concern (VOC). In Brazil, the Gamma variant dominated the pandemic in the first half of 2021, and from June onwards, the first cases of Delta infection were documented. Here, we investigate the introduction and dispersal of the Delta variant in the RS state by sequencing 1077 SARS-CoV-2-positive samples from June to October 2021. Of these samples, 34.7% were identified as Gamma and 65.3% as Delta. Notably, 99.2% of Delta sequences were clustered within the 21J lineage, forming a significant Brazilian clade. The estimated clock rate was 5.97 × 10-4 substitutions per site per year. The Delta variant was first reported on 17 June in the Vinhedos Basalto microregion and rapidly spread, accounting for over 70% of cases within nine weeks. Despite this, the number of cases and deaths remained stable, possibly due to vaccination, prior infections, and the continued mandatory mask use. In conclusion, our study provides insights into the Delta variant circulating in the RS state, highlighting the importance of genomic surveillance for monitoring viral evolution, even when the impact of new variants may be less severe in a given region.
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Affiliation(s)
- Thaís Regina y Castro
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Bruna C. Piccoli
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Andressa A. Vieira
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Bruna C. Casarin
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Luíza F. Tessele
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Richard S. Salvato
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (CEVS/SES-RS), Porto Alegre 90610-000, Brazil
| | - Tatiana S. Gregianini
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (CEVS/SES-RS), Porto Alegre 90610-000, Brazil
| | - Leticia G. Martins
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (CEVS/SES-RS), Porto Alegre 90610-000, Brazil
| | - Paola Cristina Resende
- Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz Institute, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-360, Brazil
| | - Elisa C. Pereira
- Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz Institute, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-360, Brazil
| | - Filipe R. R. Moreira
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-853, Brazil
| | - Jaqueline G. de Jesus
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05508-220, Brazil
| | - Ana Paula Seerig
- Vigilância em Saúde, Secretaria Municipal da Saúde de Santa Maria, Santa Maria 97060-001, Brazil
| | - Marcos Antonio O. Lobato
- Departamento de Saúde Coletiva, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Marli M. A. de Campos
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Juliana S. Goularte
- Laboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo 93510-235, Brazil
| | - Mariana S. da Silva
- Laboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo 93510-235, Brazil
| | - Meriane Demoliner
- Laboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo 93510-235, Brazil
| | - Micheli Filippi
- Laboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo 93510-235, Brazil
| | | | - Alexandre V. Schwarzbold
- Departamento de Clínica Médica, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Fernando R. Spilki
- Laboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo 93510-235, Brazil
| | - Priscila A. Trindade
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
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de Souza AS, de Souza RF, Guzzo CR. Cooperative and structural relationships of the trimeric Spike with infectivity and antibody escape of the strains Delta (B.1.617.2) and Omicron (BA.2, BA.5, and BQ.1). J Comput Aided Mol Des 2023; 37:585-606. [PMID: 37792106 DOI: 10.1007/s10822-023-00534-0] [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: 03/22/2023] [Accepted: 09/11/2023] [Indexed: 10/05/2023]
Abstract
Herein, we conducted simulations of trimeric Spike from several SARS-CoV-2 variants of concern (Delta and Omicron sub-variants BA.2, BA.5, and BQ.1) and investigated the mechanisms by which specific mutations confer resistance to neutralizing antibodies. We observed that the mutations primarily affect the cooperation between protein domains within and between protomers. The substitutions K417N and L452R expand hydrogen bonding interactions, reducing their interaction with neutralizing antibodies. By interacting with nearby residues, the K444T and N460K mutations in the SpikeBQ.1 variant potentially reduces solvent exposure, thereby promoting resistance to antibodies. We also examined the impact of D614G, P681R, and P681H substitutions on Spike protein structure that may be related to infectivity. The D614G substitution influences communication between a glycine residue and neighboring domains, affecting the transition between up- and -down RBD states. The P681R mutation, found in the Delta variant, enhances correlations between protein subunits, while the P681H mutation in Omicron sub-variants weakens long-range interactions that may be associated with reduced fusogenicity. Using a multiple linear regression model, we established a connection between inter-protomer communication and loss of sensitivity to neutralizing antibodies. Our findings underscore the importance of structural communication between protein domains and provide insights into potential mechanisms of immune evasion by SARS-CoV-2. Overall, this study deepens our understanding of how specific mutations impact SARS-CoV-2 infectivity and shed light on how the virus evades the immune system.
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Affiliation(s)
- Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, Cidade Universitária, Sao Paulo, SP, 5508-900, Brazil.
| | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, Cidade Universitária, Sao Paulo, SP, 5508-900, Brazil
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, Cidade Universitária, Sao Paulo, SP, 5508-900, Brazil.
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18
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Mohammadian Erdi A, Zakavi M, Amani M, Fooladi S, Abedi A. Clinical manifestations of pain in patients suffering from COVID-19 infected with Delta variant of SARS-Cov-2. FRONTIERS IN PAIN RESEARCH 2023; 4:1282527. [PMID: 38034880 PMCID: PMC10684905 DOI: 10.3389/fpain.2023.1282527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Background Although respiratory presentations of COVID-19 predominate, the extra pulmonary involvement such as muscle pain, joint pain, headache, back pain, abdominal pain, and sore throat are usually included in the clinical picture of the disease and it can be considered as an early symptom in COVID-19 patients. The objective of the present study was to determine the frequency, localization, and intensity of pain in COVID-19 patients hospitalized in Imam Khomeini hospital of Ardabil, Iran. Methods and materials A prospective study was conducted on 388 COVID-19 patients who were admitted to Ardabil, Iran's Imam Khomeini Central Hospital between March and June 2020. Demographic characteristics of patients and general clinical manifestations of pain at the first admission to the hospital, localization, severity, and continuity of pain were evaluated by using a questionnaire and the Visual Analog Scale (VAS). Findings For the 388 (51.3% female, age 47.25 + 15.55 and 48.7% male, age 50.12 + 15.26 years old) Delta COVID-19 patients, the median duration from illness onset to hospitalization was 5 days. Patients' complaints included 89.7% fatigue, 85.56% cough, 67.8% fever, 64.17% loss of taste, 63.91% loss of smell, 37.9% diarrhea, and 11.85% skin lesions, respectively. Pain including muscle, joint, bone and low back pain was the chief complaint in both sexes. Pain complaints had started on average 5 days before admission. The distribution of pain was 313 (80.41%) muscle pain, 264 (70.61%) joint pain, 299 (77.1%) headache, 208 (53.6%) low back pain, 312 (80.41%) sore throat, and 157 (40.46%) abdominal pain. Out of 388 patients, 292 (75.25%) had diffuse pain. Conclusions Acute pain including myalgia, sore throat, arthralgia, headache, and low back pain were the most common symptoms of COVID-19 patients. Viral diseases such as COVID-19 may trigger the immune system to release cytokines that lead to muscle pain. Patients presenting to healthcare centers with complaints of pain should be evaluated for suspected COVID-19 infection.
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Affiliation(s)
- Ali Mohammadian Erdi
- Department of Anesthesiology, School of Medicine, Adabil University of Medical Scienes, Ardabil, Iran
| | - Minoo Zakavi
- Department of Physiology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Mohammad Amani
- Department of Physiology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Shahnaz Fooladi
- Department of Anesthesiology, School of Medicine, Adabil University of Medical Scienes, Ardabil, Iran
| | - Ali Abedi
- Department of Physiology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
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19
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Jiju P, Matalliotakis M, Lane S, Wong W, Hedrich CM, Pain CE. Demographic, clinical and laboratory differences between paediatric acute COVID-19 and PIMS-TS-results from a single centre study in the UK. Front Pediatr 2023; 11:1219654. [PMID: 38027272 PMCID: PMC10667694 DOI: 10.3389/fped.2023.1219654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Background Paediatric symptomatic SARS-CoV-2 infections associate with two presentations, acute COVID-19 and paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS). Phenotypic comparisons, and reports on predictive markers for disease courses are sparse and preliminary. Methods A chart review of COVID-19 and PIMS-TS patients (≤19 years) admitted to Alder Hey Children's NHS Foundation Trust, a tertiary centre in the North-West of England, was performed (02/2020-09/2022). Results A total of 161 symptomatic COVID-19 and 50 PIMS-TS patients were included. Peaks in admissions of patients with PIMS-TS occurred approximately 4 weeks after those for acute COVID-19. The incidence of in-patients with PIMS-TS reduced over time, and there were no admissions after February 2022. When compared to acute COVID-19, PIMS-TS patients were older (median: 10.3 years vs. 2.03 years; p < 0.001). There were no differences in gender distribution, but minority ethnicities were over-represented among PIMS-TS patients. Regional ethnic distribution was reflected among acute COVID-19 patients (66% vs. 84.5% White Caucasian, p = 0.01). Pre-existing comorbidities were more common among acute COVID-19 patients (54.7% vs. 8%, p < 0.001). PIMS-TS patients more commonly presented with abdominal symptoms (92% vs. 50.3%), neurological symptoms (28% vs. 10.6%) and skin rashes (72% vs. 16.8%), (p ≤ 0.01) when compared with acute COVID-19, where respiratory symptoms were more common (51.6% vs. 32%, p = 0.016). PIMS-TS more frequently required intensive care admission (64% vs. 16.8%), and inotropic support (64% vs. 9.3%) (all p < 0.05). More deaths occurred among acute COVID-19 patients [0 vs. 7 (4.4%)], with 5/7 (71%) in the context of pre-existing comorbidities. When compared to acute COVID-19, PIMS-TS patients exhibited more lymphopenia and thrombocytopenia, a more pronounced acute phase reaction, and more hyponatraemia (p < 0.05). Partial least square discriminant analysis of routine laboratory parameters allowed (incomplete) separation of patients at diagnosis, and variable importance projection (VIP) scoring revealed elevated CRP and low platelets as the most discriminatory parameters. Conclusion Admissions for PIMS-TS reduced with increasing seroconversion rates in the region. Young age and pre-existing comorbidities associate with hospital admission for acute COVID-19. While PIMS-TS may present more acutely with increased need for intensive care, acute COVID-19 had an increased risk of mortality in this cohort.
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Affiliation(s)
- Prince Jiju
- Department of Paediatric Medicine, Alder Hey Children’s NHS Foundation Trust, Liverpool, United Kingdom
| | - Michail Matalliotakis
- Department of Paediatric Rheumatology, Alder Hey Children’s NHS Foundation Trust, Liverpool, United Kingdom
| | - Steven Lane
- Department of Biostatistics, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Waison Wong
- Department of Paediatric Infectious Diseases and Immunology, Alder Hey Children’s NHS Foundation Trust, Liverpool, United Kingdom
| | - Christian M. Hedrich
- Department of Paediatric Rheumatology, Alder Hey Children’s NHS Foundation Trust, Liverpool, United Kingdom
- Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Clare E. Pain
- Department of Paediatric Rheumatology, Alder Hey Children’s NHS Foundation Trust, Liverpool, United Kingdom
- Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
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20
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Wang WB, Ma YB, Lei ZH, Zhang XF, Li J, Li SS, Dong ZY, Liang Y, Li QM, Su JG. Identification of key mutations responsible for the enhancement of receptor-binding affinity and immune escape of SARS-CoV-2 Omicron variant. J Mol Graph Model 2023; 124:108540. [PMID: 37352723 PMCID: PMC10254043 DOI: 10.1016/j.jmgm.2023.108540] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/25/2023]
Abstract
The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has raised concerns worldwide due to its enhanced transmissibility and immune escapability. The first dominant Omicron BA.1 subvariant harbors more than 30 mutations in the spike protein from the prototype virus, of which 15 mutations are located at the receptor binding domain (RBD). These mutations in the RBD region attracted significant attention, which potentially enhance the binding of the receptor human angiotensin-converting enzyme 2 (hACE2) and decrease the potency of neutralizing antibodies/nanobodies. This study applied the molecular dynamics simulations combined with the molecular mechanics-generalized Born surface area (MMGBSA) method, to investigate the molecular mechanism behind the impact of the mutations acquired by Omicron on the binding affinity between RBD and hACE2. Our results indicate that five key mutations, i.e., N440K, T478K, E484A, Q493R, and G496S, contributed significantly to the enhancement of the binding affinity by increasing the electrostatic interactions of the RBD-hACE2 complex. Moreover, fourteen neutralizing antibodies/nanobodies complexed with RBD were used to explore the effects of the mutations in Omicron RBD on their binding affinities. The calculation results indicate that the key mutations E484A and Y505H reduce the binding affinities to RBD for most of the studied neutralizing antibodies/nanobodies, mainly attributed to the elimination of the original favorable gas-phase electrostatic and hydrophobic interactions between them, respectively. Our results provide valuable information for developing effective vaccines and antibody/nanobody drugs.
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Affiliation(s)
- Wei Bu Wang
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China
| | - Yi Bo Ma
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China
| | - Ze Hua Lei
- National Engineering Center for New Vaccine Research, Beijing, China; The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
| | - Xue Feng Zhang
- National Engineering Center for New Vaccine Research, Beijing, China; The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
| | - Jiao Li
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China
| | - Shan Shan Li
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China
| | - Ze Yuan Dong
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China
| | - Yu Liang
- National Engineering Center for New Vaccine Research, Beijing, China; The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
| | - Qi Ming Li
- National Engineering Center for New Vaccine Research, Beijing, China; The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China.
| | - Ji Guo Su
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China.
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21
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Geyer CE, Chen HJ, Bye AP, Manz XD, Guerra D, Caniels TG, Bijl TP, Griffith GR, Hoepel W, de Taeye SW, Veth J, Vlaar AP, Vidarsson G, Bogaard HJ, Aman J, Gibbins JM, van Gils MJ, de Winther MP, den Dunnen J. Identification of new drugs to counteract anti-spike IgG-induced hyperinflammation in severe COVID-19. Life Sci Alliance 2023; 6:e202302106. [PMID: 37699657 PMCID: PMC10497933 DOI: 10.26508/lsa.202302106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/14/2023] Open
Abstract
Previously, we and others have shown that SARS-CoV-2 spike-specific IgG antibodies play a major role in disease severity in COVID-19 by triggering macrophage hyperactivation, disrupting endothelial barrier integrity, and inducing thrombus formation. This hyperinflammation is dependent on high levels of anti-spike IgG with aberrant Fc tail glycosylation, leading to Fcγ receptor hyperactivation. For development of immune-regulatory therapeutics, drug specificity is crucial to counteract excessive inflammation whereas simultaneously minimizing the inhibition of antiviral immunity. We here developed an in vitro activation assay to screen for small molecule drugs that specifically counteract antibody-induced pathology. We identified that anti-spike-induced inflammation is specifically blocked by small molecule inhibitors against SYK and PI3K. We identified SYK inhibitor entospletinib as the most promising candidate drug, which also counteracted anti-spike-induced endothelial dysfunction and thrombus formation. Moreover, entospletinib blocked inflammation by different SARS-CoV-2 variants of concern. Combined, these data identify entospletinib as a promising treatment for severe COVID-19.
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Affiliation(s)
- Chiara E Geyer
- https://ror.org/05grdyy37 Center for Experimental and Molecular Medicine, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Hung-Jen Chen
- https://ror.org/05grdyy37 Center for Experimental and Molecular Medicine, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Alexander P Bye
- Institute for Cardiovascular and Metabolic Research, and School of Biological Sciences, University of Reading, Reading, UK
- Molecular and Clinical Sciences Research Institute, St George's University, London, UK
- School of Pharmacy, University of Reading, Reading, UK
| | - Xue D Manz
- https://ror.org/05grdyy37 Pulmonary Medicine, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Denise Guerra
- https://ror.org/05grdyy37 Medical Microbiology and Infection Prevention, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Tom G Caniels
- https://ror.org/05grdyy37 Medical Microbiology and Infection Prevention, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Tom Pl Bijl
- https://ror.org/05grdyy37 Medical Microbiology and Infection Prevention, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Guillermo R Griffith
- https://ror.org/05grdyy37 Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Atherosclerosis & Ischemic Syndromes, Amsterdam Institute for Infection and Immunity, Inflammatory Diseases, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Willianne Hoepel
- https://ror.org/05grdyy37 Center for Experimental and Molecular Medicine, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Steven W de Taeye
- https://ror.org/05grdyy37 Medical Microbiology and Infection Prevention, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Jennifer Veth
- https://ror.org/05grdyy37 Center for Experimental and Molecular Medicine, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Alexander Pj Vlaar
- https://ror.org/05grdyy37 Department of Intensive Care Medicine, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Gestur Vidarsson
- Experimental Immunohematology, Sanquin Research, Amsterdam, Netherlands
- Department of Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Harm Jan Bogaard
- https://ror.org/05grdyy37 Pulmonary Medicine, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Jurjan Aman
- https://ror.org/05grdyy37 Pulmonary Medicine, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Jonathan M Gibbins
- Institute for Cardiovascular and Metabolic Research, and School of Biological Sciences, University of Reading, Reading, UK
| | - Marit J van Gils
- https://ror.org/05grdyy37 Medical Microbiology and Infection Prevention, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Menno Pj de Winther
- https://ror.org/05grdyy37 Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Atherosclerosis & Ischemic Syndromes, Amsterdam Institute for Infection and Immunity, Inflammatory Diseases, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Jeroen den Dunnen
- https://ror.org/05grdyy37 Center for Experimental and Molecular Medicine, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, Netherlands
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22
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Wijkström J, Caldinelli A, Bruchfeld A, Nowak A, Artborg A, Stendahl M, Segelmark M, Lindholm B, Bellocco R, Rydell H, Evans M. Results of the first nationwide cohort study of outcomes in dialysis and kidney transplant patients before and after vaccination for COVID-19. Nephrol Dial Transplant 2023; 38:2607-2616. [PMID: 37433606 PMCID: PMC10615630 DOI: 10.1093/ndt/gfad151] [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: 01/27/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Patients on kidney replacement therapy (KRT) have been identified as a vulnerable group during the coronavirus disease 2019 (COVID-19) pandemic. This study reports the outcomes of COVID-19 in KRT patients in Sweden, a country where patients on KRT were prioritized early in the vaccination campaign. METHODS Patients on KRT between January 2019 and December 2021 in the Swedish Renal Registry were included. Data were linked to national healthcare registries. The primary outcome was monthly all-cause mortality over 3 years of follow-up. The secondary outcomes were monthly COVID-19-related deaths and hospitalizations. The results were compared with the general population using standardized mortality ratios. The difference in risk for COVID-19-related outcomes between dialysis and kidney transplant recipients (KTRs) was assessed in multivariable logistic regression models before and after vaccinations started. RESULTS On 1 January 2020, there were 4097 patients on dialysis (median age 70 years) and 5905 KTRs (median age 58 years). Between March 2020 and February 2021, mean all-cause mortality rates increased by 10% (from 720 to 804 deaths) and 22% (from 158 to 206 deaths) in dialysis and KTRs, respectively, compared with the same period in 2019. After vaccinations started, all-cause mortality rates during the third wave (April 2021) returned to pre-COVID-19 mortality rates among dialysis patients, while mortality rates remained increased among transplant recipients. Dialysis patients had a higher risk for COVID-19 hospitalizations and death before vaccinations started {adjusted odds ratio [aOR] 2.1 [95% confidence interval (CI) 1.7-2.5]} but a lower risk after vaccination [aOR 0.5 (95% CI 0.4-0.7)] compared with KTRs. CONCLUSIONS The COVID-19 pandemic in Sweden resulted in increased mortality and hospitalization rates among KRT patients. After vaccinations started, a distinct reduction in hospitalization and mortality rates was observed among dialysis patients, but not in KTRs. Early and prioritized vaccinations of KRT patients in Sweden probably saved many lives.
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Affiliation(s)
- Julia Wijkström
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Department of Renal Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Aurora Caldinelli
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- University of Milano-Bicocca, Department of Statistics and Quantitative Methods, Milano, Italy
| | - Annette Bruchfeld
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
| | - Alexandra Nowak
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Department of Renal Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Angelica Artborg
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Department of Renal Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Stendahl
- Department of Internal Medicine, Ryhov Hospital, Jönköping, Sweden
- Swedish Renal Register, Jönköping, Sweden
| | - Mårten Segelmark
- Swedish Renal Register, Jönköping, Sweden
- Department of Clinical Sciences, Lund University, Lund, Sweden
- Department of Endocrinology, Nephrology and Rheumatology, Skane University Hospital, Lund, Sweden
| | - Bengt Lindholm
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Rino Bellocco
- University of Milano-Bicocca, Department of Statistics and Quantitative Methods, Milano, Italy
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Helena Rydell
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Department of Renal Medicine, Karolinska University Hospital, Stockholm, Sweden
- Swedish Renal Register, Jönköping, Sweden
| | - Marie Evans
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Department of Renal Medicine, Karolinska University Hospital, Stockholm, Sweden
- Swedish Renal Register, Jönköping, Sweden
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23
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Mohan A, Iyer VA, Kumar D, Batra L, Dahiya P. Navigating the Post-COVID-19 Immunological Era: Understanding Long COVID-19 and Immune Response. Life (Basel) 2023; 13:2121. [PMID: 38004261 PMCID: PMC10672162 DOI: 10.3390/life13112121] [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: 07/06/2023] [Revised: 09/25/2023] [Accepted: 09/30/2023] [Indexed: 11/26/2023] Open
Abstract
The COVID-19 pandemic has affected the world unprecedentedly, with both positive and negative impacts. COVID-19 significantly impacted the immune system, and understanding the immunological consequences of COVID-19 is essential for developing effective treatment strategies. The purpose of this review is to comprehensively explore and provide insights into the immunological aspects of long COVID-19, a phenomenon where individuals continue to experience a range of symptoms and complications, even after the acute phase of COVID-19 infection has subsided. The immune system responds to the initial infection by producing various immune cells and molecules, including antibodies, T cells, and cytokines. However, in some patients, this immune response becomes dysregulated, leading to chronic inflammation and persistent symptoms. Long COVID-19 encompasses diverse persistent symptoms affecting multiple organ systems, including the respiratory, cardiovascular, neurological, and gastrointestinal systems. In the post-COVID-19 immunological era, long COVID-19 and its impact on immune response have become a significant concern. Post-COVID-19 immune pathology, including autoimmunity and immune-mediated disorders, has also been reported in some patients. This review provides an overview of the current understanding of long COVID-19, its relationship to immunological responses, and the impact of post-COVID-19 immune pathology on patient outcomes. Additionally, the review addresses the current and potential treatments for long COVID-19, including immunomodulatory therapies, rehabilitation programs, and mental health support, all of which aim to improve the quality of life for individuals with long COVID-19. Understanding the complex interplay between the immune system and long COVID-19 is crucial for developing targeted therapeutic strategies and providing optimal care in the post-COVID-19 era.
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Affiliation(s)
- Aditi Mohan
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida Sector-125, Noida 201313, Uttar Pradesh, India; (A.M.); (V.A.I.)
| | - Venkatesh Anand Iyer
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida Sector-125, Noida 201313, Uttar Pradesh, India; (A.M.); (V.A.I.)
| | - Dharmender Kumar
- Department of Biotechnology, Deenbandhu Chhotu Ram University of Science &Technology, Murthal, Sonipat 131309, Haryana, India;
| | - Lalit Batra
- Regional Biocontainment Laboratory, Center for Predictive Medicine, University of Louisville, Louisville, KY 40222, USA
| | - Praveen Dahiya
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida Sector-125, Noida 201313, Uttar Pradesh, India; (A.M.); (V.A.I.)
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24
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Vinzón SE, Lopez MV, Cafferata EGA, Soto AS, Berguer PM, Vazquez L, Nusblat L, Pontoriero AV, Belotti EM, Salvetti NR, Viale DL, Vilardo AE, Avaro MM, Benedetti E, Russo ML, Dattero ME, Carobene M, Sánchez-Lamas M, Afonso J, Heitrich M, Cristófalo AE, Otero LH, Baumeister EG, Ortega HH, Edelstein A, Podhajcer OL. Cross-protection and cross-neutralization capacity of ancestral and VOC-matched SARS-CoV-2 adenoviral vector-based vaccines. NPJ Vaccines 2023; 8:149. [PMID: 37794010 PMCID: PMC10550992 DOI: 10.1038/s41541-023-00737-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 09/15/2023] [Indexed: 10/06/2023] Open
Abstract
COVID-19 vaccines were originally designed based on the ancestral Spike protein, but immune escape of emergent Variants of Concern (VOC) jeopardized their efficacy, warranting variant-proof vaccines. Here, we used preclinical rodent models to establish the cross-protective and cross-neutralizing capacity of adenoviral-vectored vaccines expressing VOC-matched Spike. CoroVaxG.3-D.FR, matched to Delta Plus Spike, displayed the highest levels of nAb to the matched VOC and mismatched variants. Cross-protection against viral infection in aged K18-hACE2 mice showed dramatic differences among the different vaccines. While Delta-targeted vaccines fully protected mice from a challenge with Gamma, a Gamma-based vaccine offered only partial protection to Delta challenge. Administration of CorovaxG.3-D.FR in a prime/boost regimen showed that a booster was able to increase the neutralizing capacity of the sera against all variants and fully protect aged K18-hACE2 mice against Omicron BA.1, as a BA.1-targeted vaccine did. The neutralizing capacity of the sera diminished in all cases against Omicron BA.2 and BA.5. Altogether, the data demonstrate that a booster with a vaccine based on an antigenically distant variant, such as Delta or BA.1, has the potential to protect from a wider range of SARS-CoV-2 lineages, although careful surveillance of breakthrough infections will help to evaluate combination vaccines targeting antigenically divergent variants yet to emerge.
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Affiliation(s)
- Sabrina E Vinzón
- Laboratorio de Terapia Molecular y Celular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - María V Lopez
- Laboratorio de Terapia Molecular y Celular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Eduardo G A Cafferata
- Laboratorio de Terapia Molecular y Celular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Ariadna S Soto
- Laboratorio de Microbiología e Inmunología Molecular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Paula M Berguer
- Laboratorio de Microbiología e Inmunología Molecular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Luciana Vazquez
- Unidad Operativa Centro de Contención Biológica, ANLIS Dr. Carlos G. Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Leonora Nusblat
- Unidad Operativa Centro de Contención Biológica, ANLIS Dr. Carlos G. Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Andrea V Pontoriero
- Servicio Virosis Respiratorias, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Laboratorio Nacional de Referencia de SARS-CoV-2/COVID-19 OPS/OMS, INEI-ANLIS Dr Carlos G Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Eduardo M Belotti
- Centro de Medicina Comparada, ICiVet-Litoral, Universidad Nacional del Litoral-CONICET; Esperanza, Santa Fe, 3080, Argentina
| | - Natalia R Salvetti
- Centro de Medicina Comparada, ICiVet-Litoral, Universidad Nacional del Litoral-CONICET; Esperanza, Santa Fe, 3080, Argentina
| | - Diego L Viale
- Laboratorio de Terapia Molecular y Celular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Ariel E Vilardo
- Unidad Operativa Centro de Contención Biológica, ANLIS Dr. Carlos G. Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Martin M Avaro
- Servicio Virosis Respiratorias, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Laboratorio Nacional de Referencia de SARS-CoV-2/COVID-19 OPS/OMS, INEI-ANLIS Dr Carlos G Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Estefanía Benedetti
- Servicio Virosis Respiratorias, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Laboratorio Nacional de Referencia de SARS-CoV-2/COVID-19 OPS/OMS, INEI-ANLIS Dr Carlos G Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Mara L Russo
- Servicio Virosis Respiratorias, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Laboratorio Nacional de Referencia de SARS-CoV-2/COVID-19 OPS/OMS, INEI-ANLIS Dr Carlos G Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - María E Dattero
- Servicio Virosis Respiratorias, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Laboratorio Nacional de Referencia de SARS-CoV-2/COVID-19 OPS/OMS, INEI-ANLIS Dr Carlos G Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Mauricio Carobene
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (UBA-CONICET), Ciudad Autónoma de Buenos Aires, C1121ABG, Buenos Aires, Argentina
| | | | - Jimena Afonso
- Area de Bioterio, Fundación Instituto Leloir; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Mauro Heitrich
- Laboratorio de Terapia Molecular y Celular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Alejandro E Cristófalo
- Centro de Re-diseño e Ingeniería de Proteínas (CRIP), Universidad Nacional de San Martín, San Martin, Buenos Aires, 1650, Argentina
| | - Lisandro H Otero
- Centro de Re-diseño e Ingeniería de Proteínas (CRIP), Universidad Nacional de San Martín, San Martin, Buenos Aires, 1650, Argentina
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Instituto de Biotecnología Ambiental y Salud, CONICET, Universidad Nacional de Río Cuarto, Córdoba, X5804BYA, Argentina
| | - Elsa G Baumeister
- Servicio Virosis Respiratorias, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Laboratorio Nacional de Referencia de SARS-CoV-2/COVID-19 OPS/OMS, INEI-ANLIS Dr Carlos G Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Hugo H Ortega
- Centro de Medicina Comparada, ICiVet-Litoral, Universidad Nacional del Litoral-CONICET; Esperanza, Santa Fe, 3080, Argentina
| | - Alexis Edelstein
- Unidad Operativa Centro de Contención Biológica, ANLIS Dr. Carlos G. Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Osvaldo L Podhajcer
- Laboratorio de Terapia Molecular y Celular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina.
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Xu R, Chang Z, Wen D, Liu Y, Wang C, Qu W, Tang X, Jia H, Li J, Cai J, Li G, Jiang B, Zha L. A preliminary exploration for co-detecting RNA virus and STR type on capillary electrophoresis in forensic practice. Electrophoresis 2023; 44:1579-1587. [PMID: 37528696 DOI: 10.1002/elps.202300051] [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: 03/11/2023] [Revised: 07/04/2023] [Accepted: 07/23/2023] [Indexed: 08/03/2023]
Abstract
RNA virus infection such as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection shows severe respiratory symptoms on human and could be an obvious individual characteristic for investigations in forensic science. As for biological samples suspected to contain RNA virus in forensic casework, it requires respective detection of viral RNA and human DNA: reverse transcriptase polymerase chain reaction and DNA type (short tandem repeat [STR] analysis). Capillary electrophoresis (CE) has been shown to be a versatile technique and used for a variety of applications, so we preliminarily explored the co-detection of RNA virus and STR type on CE by developing a system of co-detecting SARS-CoV-2 and STR type under ensuring both the efficiency of forensic DNA analysis and safety of the laboratory. This study investigated the development and validation of the system, including N and ORF1ab primer designs, polymerase chain reaction amplification, allelic ladder, CE detection, thermal cycling parameters, concordance, sensitivity, species specificity, precision, and contrived and real SARS-CoV-2 sample studies. Final results showed the system could simultaneously detect SARS-CoV-2 and STR type, further indicating that CE has possibilities in the multi-detection of RNA viruses/STR type to help to prompt individual characteristics (viral infection) and narrow the scope of investigation in forensic science.
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Affiliation(s)
- Ruyi Xu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, P. R. China
| | - Zhaorui Chang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, P. R. China
| | - Dan Wen
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, P. R. China
| | - Yi Liu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, P. R. China
| | - Chudong Wang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, P. R. China
| | - Weifeng Qu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, P. R. China
| | - Xuan Tang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, P. R. China
| | - Hongtao Jia
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, P. R. China
| | - Jienan Li
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, P. R. China
| | - Jifeng Cai
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, P. R. China
| | - Guanlin Li
- Department of Clinical Laboratory, First Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
| | - Bowei Jiang
- The first Research Institute of the Ministry of public security P.R.C, Beijing, P. R. China
| | - Lagabaiyila Zha
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, P. R. China
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D'Carmo Sodré MM, Dos Santos UR, Povoas HP, Guzmán JL, Junqueira C, Trindade TO, Gadelha SR, Romano CC, da Conceição AO, Gross E, Silva A, Rezende RP, Fontana R, da Mata CPSM, Marin LJ, de Carvalho LD. Relationship between clinical-epidemiological parameters and outcomes of patients with COVID-19 admitted to the intensive care unit: a report from a Brazilian hospital. Front Public Health 2023; 11:1241444. [PMID: 37808991 PMCID: PMC10556466 DOI: 10.3389/fpubh.2023.1241444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/28/2023] [Indexed: 10/10/2023] Open
Abstract
Background People in low-income countries, especially those with low socio-economic conditions, are likelier to test positive for SARS-CoV-2. The unequal conditions of public health systems also increase the infection rate and make early identification and treatment of at-risk patients difficult. Here, we aimed to characterize the epidemiological profile of COVID-19 patients in intensive care and identify laboratory and clinical markers associated with death. Materials and methods We conducted an observational, descriptive, and cross-sectional study in a reference hospital for COVID-19 treatment in the Southern Region of Bahia State, in Brazil, to evaluate the epidemiological, clinical, and laboratory characteristics of COVID-19 patients admitted to the intensive care unit (ICU). Additionally, we used the area under the curve (AUC) to classify survivors and non-survivors and a multivariate logistic regression analysis to assess factors associated with death. Data was collected from the hospital databases between April 2020 and July 2021. Results The use of bladder catheters (OR 79.30; p < 0.0001) and central venous catheters (OR, 45.12; p < 0.0001) were the main factors associated with death in ICU COVID-19 patients. Additionally, the number of non-survivors increased with age (p < 0.0001) and prolonged ICU stay (p < 0.0001). Besides, SAPS3 presents a higher sensibility (77.9%) and specificity (63.1%) to discriminate between survivors and non-survivor with an AUC of 0.79 (p < 0.0001). Conclusion We suggest that multi-laboratory parameters can predict patient prognosis and guide healthcare teams toward more assertive clinical management, better resource allocation, and improved survival of COVID-19 patients admitted to the ICU.
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Affiliation(s)
| | | | | | | | - Caroline Junqueira
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
- René Rachou Institute, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | | | - Sandra Rocha Gadelha
- Department of Biological Sciences, Santa Cruz State University, Ilhéus, Bahia, Brazil
| | - Carla Cristina Romano
- Department of Biological Sciences, Santa Cruz State University, Ilhéus, Bahia, Brazil
| | | | - Eduardo Gross
- Department of Biological Sciences, Santa Cruz State University, Ilhéus, Bahia, Brazil
| | - Aline Silva
- Department of Biological Sciences, Santa Cruz State University, Ilhéus, Bahia, Brazil
| | - Rachel Passos Rezende
- Department of Biological Sciences, Santa Cruz State University, Ilhéus, Bahia, Brazil
| | - Renato Fontana
- Department of Biological Sciences, Santa Cruz State University, Ilhéus, Bahia, Brazil
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Xie G, Wang L, Zhang J. How are countries responding differently to COVID-19: a systematic review of guidelines on isolation measures. Front Public Health 2023; 11:1190519. [PMID: 37719732 PMCID: PMC10502310 DOI: 10.3389/fpubh.2023.1190519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/08/2023] [Indexed: 09/19/2023] Open
Abstract
Introduction Isolation strategies have been implemented in numerous countries worldwide during the ongoing community transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, various countries and organizations have implemented their isolation measures at varying intensities, even during the same period. Therefore, we systematically reviewed the key information contained in currently available guidelines regarding the isolation of the general population, aiming to better identify the heterogeneity of the current isolation strategies. Methods We conducted searches in four evidence-based medicine (EBM) databases and five guideline websites to identify guidelines, guidance, protocols, and policy documents published by authoritative advisory bodies or healthcare organizations, which provided information on the implementation of isolation for general populations with COVID-19. One author extracted data using a standardized data extraction checklist, and a second author double-checked all extractions for completeness and correctness. Discrepancies were resolved through discussion. The information extracted from the included articles was summarized both narratively and using tables. Results We included 15 articles that provided information on isolation measures recommended by nine different countries and organizations. The included articles consistently recommended isolating individuals with a positive COVID-19 test, regardless of the presence of symptoms. However, there were variations in the duration of isolation, and substantial differences also existed in the criteria for ending the isolation of COVID-19 patients. Conclusion Different countries and organizations have substantial differences in their isolation policies. This reminds us that scientifically sound guidelines on isolation that balance the risk of prematurely ending isolation with the burden of prolonged isolation are a crucial topic of discussion when faced with a pandemic.
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Affiliation(s)
- Guangmei Xie
- Reproductive Medicine Center, Gansu Maternal and Child Health Care Hospital, Lanzhou, Gansu, China
- Reproductive Medicine Center, Gansu Provincial Central Hospital, Lanzhou, Gansu, China
| | - Li Wang
- Reproductive Medicine Center, Gansu Maternal and Child Health Care Hospital, Lanzhou, Gansu, China
- Reproductive Medicine Center, Gansu Provincial Central Hospital, Lanzhou, Gansu, China
| | - Jun Zhang
- School of Nursing, Gansu University of Chinese Medicine, Lanzhou, Gansu, China
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Hussein HA, Kandeil A, Gomaa M, Hassan RYA. Double-antibody-based nano-biosensing system for the onsite monitoring of SARS-CoV-2 variants. MICROSYSTEMS & NANOENGINEERING 2023; 9:105. [PMID: 37614970 PMCID: PMC10442362 DOI: 10.1038/s41378-023-00578-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 08/25/2023]
Abstract
The fast and reliable diagnosis of COVID-19 is the foremost priority for promoting public health interventions. Therefore, double-antibody-based immunobiosensor chips were designed, constructed, and exploited for clinical diagnosis. Gold nanoparticles/tungsten oxide/carbon nanotubes (AuNPs/WO3/CNTs) were used as the active working sensor surface to support the chemical immobilization of a mixture of SARS-CoV-2 antibodies (anti-RBD-S and anti-RBD-S-anti-Llama monoclonal antibodies). The morphology and chemical functionalization of the fabricated disposable immunochips was characterized using scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy, cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS). After full assay optimization, the immunobiosensor showed a high sensitivity to detect SARS-CoV-2-S protein with limits of detection and quantification of 1.8 and 5.6 pg/mL, respectively. On the other hand, for the SARS-CoV-2 whole virus particle analysis, the detection and quantification limits were determined to be 5.7 and 17 pg/mL, respectively. The biosensor showed a highly selective response toward SARS-CoV-2, even in the presence of influenza, nontargeting human coronaviruses, and Middle East respiratory syndrome coronavirus (MERS-CoV). The immunochips exhibited distinct responses toward the variants of concern: B.1>C.36.3>Omicron> Delta> Alpha coronavirus variants. For biosensor validation, twenty-nine clinical specimens were analyzed, and the impedimetric responses were positively detected for two Delta samples, eighteen Omicron samples, and six B.1-type samples in addition to three negative samples. Eventually, the immunobiosensor was fabricated in the form of ready-to-use chips capable of sensitive detection of virus variants, especially variants of concern (VOC) and interest, in a specimen within 15 min. The chips provided instantaneous detection with the direct application of clinical samples and are considered a point-of-care device that could be used in public places and hot spots.
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Affiliation(s)
- Heba A. Hussein
- Virology Department, Animal Health Research Institute (AHRI), Agricultural Research Center (ARC), Giza, 12619 Egypt
- Biosensors Research Laboratory, Zewail City of Science and Technology, 6th October City, Giza, 12578 Egypt
| | - Ahmed Kandeil
- Center of Scientific Excellence for Influenza Viruses, Environmental Research Division, National Research Centre, Giza, 12622 Egypt
| | - Mokhtar Gomaa
- Center of Scientific Excellence for Influenza Viruses, Environmental Research Division, National Research Centre, Giza, 12622 Egypt
| | - Rabeay Y. A. Hassan
- Biosensors Research Laboratory, Zewail City of Science and Technology, 6th October City, Giza, 12578 Egypt
- Nanoscience Program, University of Science and Technology (UST), Zewail City of Science and Technology, Giza, 12578 Egypt
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29
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Rollin J, Bester R, Brostaux Y, Caglayan K, De Jonghe K, Eichmeier A, Foucart Y, Haegeman A, Koloniuk I, Kominek P, Maree H, Onder S, Posada Céspedes S, Roumi V, Šafářová D, Schumpp O, Ulubas Serce C, Sõmera M, Tamisier L, Vainio E, van der Vlugt RAA, Massart S. Detection of single nucleotide polymorphisms in virus genomes assembled from high-throughput sequencing data: large-scale performance testing of sequence analysis strategies. PeerJ 2023; 11:e15816. [PMID: 37601254 PMCID: PMC10439718 DOI: 10.7717/peerj.15816] [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: 02/20/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
Recent developments in high-throughput sequencing (HTS) technologies and bioinformatics have drastically changed research in virology, especially for virus discovery. Indeed, proper monitoring of the viral population requires information on the different isolates circulating in the studied area. For this purpose, HTS has greatly facilitated the sequencing of new genomes of detected viruses and their comparison. However, bioinformatics analyses allowing reconstruction of genome sequences and detection of single nucleotide polymorphisms (SNPs) can potentially create bias and has not been widely addressed so far. Therefore, more knowledge is required on the limitations of predicting SNPs based on HTS-generated sequence samples. To address this issue, we compared the ability of 14 plant virology laboratories, each employing a different bioinformatics pipeline, to detect 21 variants of pepino mosaic virus (PepMV) in three samples through large-scale performance testing (PT) using three artificially designed datasets. To evaluate the impact of bioinformatics analyses, they were divided into three key steps: reads pre-processing, virus-isolate identification, and variant calling. Each step was evaluated independently through an original, PT design including discussion and validation between participants at each step. Overall, this work underlines key parameters influencing SNPs detection and proposes recommendations for reliable variant calling for plant viruses. The identification of the closest reference, mapping parameters and manual validation of the detection were recognized as the most impactful analysis steps for the success of the SNPs detections. Strategies to improve the prediction of SNPs are also discussed.
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Affiliation(s)
- Johan Rollin
- Laboratory of Plant Pathology—TERRA—Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Rachelle Bester
- Citrus Research International, Matieland, South Africa
- Department of Genetics, Stellenbosch University, Matieland, South Africa
| | - Yves Brostaux
- Laboratory of Statistics, Computer Science and Modelling Applied to Bioengineering, TERRA, Gembloux Agro-Bio Tech, Teaching and Research Centre, University of Liège, Gembloux, Belgium
| | - Kadriye Caglayan
- Plant Protection Department, Agricultural Faculty, Hatay Mustafa Kemal University, Hatay, Turkey
| | - Kris De Jonghe
- Fisheries and Food (ILVO), Plant Sciences Unit, Flanders Research Institute for Agriculture, Merelbeke, Belgium
| | - Ales Eichmeier
- Mendeleum—Institute of Genetics, Faculty of Horticulture, Mendel University in Brno, Lednice, Czech Republic
| | - Yoika Foucart
- Fisheries and Food (ILVO), Plant Sciences Unit, Flanders Research Institute for Agriculture, Merelbeke, Belgium
| | - Annelies Haegeman
- Fisheries and Food (ILVO), Plant Sciences Unit, Flanders Research Institute for Agriculture, Merelbeke, Belgium
| | - Igor Koloniuk
- Biology Centre CAS, Ceske Budejovice, Czech Republic
| | | | - Hans Maree
- Citrus Research International, Matieland, South Africa
- Department of Genetics, Stellenbosch University, Matieland, South Africa
| | - Serkan Onder
- Department of Plant Protection, Faculty of Agriculture, Eskişehir Osmangazi University, Eskişehir, Turkey
| | - Susana Posada Céspedes
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland
- Swiss Institute of Bioinformatics (SIB), Basel, Switzerland
| | - Vahid Roumi
- Plant Protection Department, Faculty of Agriculture, University of Maragheh, Maragheh, Iran
| | - Dana Šafářová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | | | - Cigdem Ulubas Serce
- Plant Production and Technologies Department, Ayhan Şahenk Faculty of Agricultural Science and Technologies, Niğde Ömer Halisdemir University, Niğde, Turkey
| | - Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Lucie Tamisier
- Pathologie Végétale, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Montfavet, France
- GAFL, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Montfavet, France
| | - Eeva Vainio
- Natural Resources Institute Finland, Helsinki, Finland
| | | | - Sebastien Massart
- Laboratory of Plant Pathology—TERRA—Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
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España PP, Bilbao-González A, Larrea N, Castillo-Sintes I, García-Gutiérrez S, Portuondo J, Villanueva A, Uranga A, Legarreta MJ, Gascon M, Quintana JM. Impact of prior SARS-COV-2 infection and vaccination on COVID-19 hospital admission and mortality amongst nursing home residents. Aging Clin Exp Res 2023; 35:1771-1778. [PMID: 37249860 PMCID: PMC10228436 DOI: 10.1007/s40520-023-02446-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/17/2023] [Indexed: 05/31/2023]
Abstract
BACKGROUND Nursing home residents (NHRs) have experienced disproportionately high risk of severe outcomes due to COVID-19 infection. AIM We investigated the impact of COVID-19 vaccinations and previous SARS-CoV-2 episodes in preventing hospitalization and mortality in NHRs. METHODS Retrospective study of a cohort of all NHRs in our area who were alive at the start of the vaccination campaign. The first three doses of SARS-CoV-2 vaccine and prior COVID-19 infections were registered. The main outcomes were hospital admission and mortality during each follow up. Random effects time-varying Cox models adjusted for age, sex, and comorbidities were fitted to estimate hazard ratios (HRs) according to vaccination status. RESULTS COVID-19 hospitalization and death rates for unvaccinated NHRs were respectively 2.39 and 1.42 per 10,000 person-days, falling after administration of the second dose (0.37 and 0.34) and rising with the third dose (1.08 and 0.8). Rates were much lower amongst people who had previously had COVID-19. Adjusted HRs indicated a significant decrease in hospital admission amongst those with a two- and three-dose status; those who had had a previous COVID-19 infection had even lower hospital admission rates. Death rates decreased as NHRs received two and three doses, and the probability of death was much lower among those who had previously had the infection. CONCLUSIONS The effectiveness of current vaccines against severe COVID-19 disease in NHRs remains high and SARS-CoV-2 episodes prior to vaccination entail a major reduction in hospitalization and mortality rates. The protection conferred by vaccines appears to decline in the following months. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT04463706.
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Affiliation(s)
- Pedro P España
- Respiratory Service, Osakidetza Basque Health Service, Galdakao-Usansolo University Hospital, Galdakao, Spain.
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.
- Respiratory Unit, Galdakao-Usansolo University Hospital, Galdakao, Spain.
| | - Amaia Bilbao-González
- Research and Innovation Unit, Osakidetza Basque Health Service, Basurto University Hospital, Bilbao, Spain
- Kronikgune Institute for Health Services Research, Barakaldo, Spain
- Health Service Research Network On Chronic Diseases (REDISSEC), Bilbao, Spain
- Network for Research On Chronicity, Primary Care, and Health Promotion (RICAPPS), Galdakao, Spain
| | - Nere Larrea
- Research Unit, Osakidetza Basque Health Service, Galdakao-Usansolo University Hospital, Galdakao, Spain
- Kronikgune Institute for Health Services Research, Barakaldo, Spain
- Health Service Research Network On Chronic Diseases (REDISSEC), Bilbao, Spain
- Network for Research On Chronicity, Primary Care, and Health Promotion (RICAPPS), Galdakao, Spain
| | - Idoia Castillo-Sintes
- Research and Innovation Unit, Osakidetza Basque Health Service, Basurto University Hospital, Bilbao, Spain
- Kronikgune Institute for Health Services Research, Barakaldo, Spain
- Network for Research On Chronicity, Primary Care, and Health Promotion (RICAPPS), Galdakao, Spain
| | - Susana García-Gutiérrez
- Research Unit, Osakidetza Basque Health Service, Galdakao-Usansolo University Hospital, Galdakao, Spain
- Kronikgune Institute for Health Services Research, Barakaldo, Spain
- Health Service Research Network On Chronic Diseases (REDISSEC), Bilbao, Spain
- Network for Research On Chronicity, Primary Care, and Health Promotion (RICAPPS), Galdakao, Spain
| | - Janire Portuondo
- Osakidetza Basque Health Service, Sub-Directorate for Primary Care Coordination, Vitoria-Gasteiz, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Network for Research On Chronicity, Primary Care, and Health Promotion (RICAPPS), Galdakao, Spain
| | - Ane Villanueva
- Research Unit, Osakidetza Basque Health Service, Galdakao-Usansolo University Hospital, Galdakao, Spain
- Kronikgune Institute for Health Services Research, Barakaldo, Spain
- Health Service Research Network On Chronic Diseases (REDISSEC), Bilbao, Spain
- Network for Research On Chronicity, Primary Care, and Health Promotion (RICAPPS), Galdakao, Spain
| | - Ane Uranga
- Respiratory Service, Osakidetza Basque Health Service, Galdakao-Usansolo University Hospital, Galdakao, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Maria J Legarreta
- Research Unit, Osakidetza Basque Health Service, Galdakao-Usansolo University Hospital, Galdakao, Spain
- Kronikgune Institute for Health Services Research, Barakaldo, Spain
- Health Service Research Network On Chronic Diseases (REDISSEC), Bilbao, Spain
- Network for Research On Chronicity, Primary Care, and Health Promotion (RICAPPS), Galdakao, Spain
| | - Maria Gascon
- Research Unit, Osakidetza Basque Health Service, Galdakao-Usansolo University Hospital, Galdakao, Spain
- Kronikgune Institute for Health Services Research, Barakaldo, Spain
- Health Service Research Network On Chronic Diseases (REDISSEC), Bilbao, Spain
- Network for Research On Chronicity, Primary Care, and Health Promotion (RICAPPS), Galdakao, Spain
| | - Jose M Quintana
- Research Unit, Osakidetza Basque Health Service, Galdakao-Usansolo University Hospital, Galdakao, Spain
- Kronikgune Institute for Health Services Research, Barakaldo, Spain
- Health Service Research Network On Chronic Diseases (REDISSEC), Bilbao, Spain
- Network for Research On Chronicity, Primary Care, and Health Promotion (RICAPPS), Galdakao, Spain
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Liu Y, Kumblathan T, Tao J, Xu J, Feng W, Xiao H, Hu J, Huang CV, Wu Y, Zhang H, Li XF, Le XC. Recent advances in RNA sample preparation techniques for the detection of SARS-CoV-2 in saliva and gargle. Trends Analyt Chem 2023; 165:117107. [PMID: 37317683 PMCID: PMC10204347 DOI: 10.1016/j.trac.2023.117107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 05/19/2023] [Accepted: 05/19/2023] [Indexed: 06/16/2023]
Abstract
Molecular detection of SARS-CoV-2 in gargle and saliva complements the standard analysis of nasopharyngeal swabs (NPS) specimens. Although gargle and saliva specimens can be readily obtained non-invasively, appropriate collection and processing of gargle and saliva specimens are critical to the accuracy and sensitivity of the overall analytical method. This review highlights challenges and recent advances in the treatment of gargle and saliva samples for subsequent analysis using reverse transcription polymerase chain reaction (RT-PCR) and isothermal amplification techniques. Important considerations include appropriate collection of gargle and saliva samples, on-site inactivation of viruses in the sample, preservation of viral RNA, extraction and concentration of viral RNA, removal of substances that inhibit nucleic acid amplification reactions, and the compatibility of sample treatment protocols with the subsequent nucleic acid amplification and detection techniques. The principles and approaches discussed in this review are applicable to molecular detection of other microbial pathogens.
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Affiliation(s)
- Yanming Liu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Teresa Kumblathan
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jeffrey Tao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jingyang Xu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Wei Feng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Huyan Xiao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jianyu Hu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Camille V Huang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Yiping Wu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Hongquan Zhang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
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Lin Y, Sun Q, Zhang B, Zhao W, Shen C. The regulation of lncRNAs and miRNAs in SARS-CoV-2 infection. Front Cell Dev Biol 2023; 11:1229393. [PMID: 37576600 PMCID: PMC10416254 DOI: 10.3389/fcell.2023.1229393] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/20/2023] [Indexed: 08/15/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) was a global endemic that continues to cause a large number of severe illnesses and fatalities. There is increasing evidence that non-coding RNAs (ncRNAs) are crucial regulators of viral infection and antiviral immune response and the role of non-coding RNAs in SARS-CoV-2 infection has now become the focus of scholarly inquiry. After SARS-CoV-2 infection, some ncRNAs' expression levels are regulated to indirectly control the expression of antiviral genes and viral gene replication. However, some other ncRNAs are hijacked by SARS-CoV-2 in order to help the virus evade the immune system by suppressing the expression of type I interferon (IFN-1) and controlling cytokine levels. In this review, we summarize the recent findings of long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) among non-coding RNAs in SARS-CoV-2 infection and antiviral response, discuss the potential mechanisms of actions, and prospects for the detection, treatment, prevention and future directions of SARS-CoV-2 infection research.
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Affiliation(s)
| | | | | | - Wei Zhao
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Chenguang Shen
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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da Silva MF, Dos Santos UR, Ferreira FB, Albuquerque GR, Mariano APM, Fehlberg HF, Santos de Santana ÍT, Dos Santos PR, Santos LC, Silva de Jesus LL, Piton KA, Costa BS, Gomes BSM, Porto VM, Oliveira EDS, Oliveira CL, Fontana R, Maciel BM, Silva MDM, Marin LJ, Gadelha SR. SARS-CoV-2 Infection in Cities from the Southern Region of Bahia State, Brazil: Analysis of Variables Associated in Both Individual and Community Level. Viruses 2023; 15:1583. [PMID: 37515269 PMCID: PMC10383252 DOI: 10.3390/v15071583] [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: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), challenged public health systems worldwide. Individuals in low-income countries/regions are still at individual and community risk concerning inequality, sanitation, and economic conditions. Besides, during the pandemic, the transmission in municipalities and communities in the countryside and less developed regions kept viral spread and required structured and strengthened clinical and laboratory surveillance. Here, we present an observational, analytic, cross-sectional study conducted using secondary data from the Laboratório de Farmacogenômica e Epidemiologia Molecular (LAFEM)-Universidade Estadual de Santa Cruz (UESC), to evaluate individual and community factors associated to SARS-CoV-2 infection in outpatients from different cities from Southern Region of Bahia State, in Brazil. The data were collected between June 2021 and May 2022. The SARS-CoV-2 positivity by RT-qPCR was correlated with low socio-economic indicators, including the Human development index (HDIc) and Average worker salary (AWSc). Besides, in general, females were less likely to test positive for SARS-CoV-2 (OR = 0.752; CI 95% 0.663-0.853; p < 0.0001), while brown individuals had more positivity for infection (p < 0.0001). In addition, those who had clinical symptoms were more likely to test positive for SARS-CoV-2 (OR = 6.000; CI 95% 4.932-7.299; p < 0.0001). Although dry cough, headache, and fever were the most frequent, loss of taste (OR = 5.574; CI 95% 4.334-7.186) and loss of smell (OR = 6.327; CI 95% 4.899-8.144) presented higher odds ratio to be positive to SARS-CoV-2 by RT-qPCR. Nonetheless, the distribution of these characteristics was not homogenous among the different cities, especially for age and gender. The dynamic of SARS-CoV-2 positivity differed between cities and the total population and reinforces the hypothesis that control strategies for prevention needed to be developed based on both individual and community risk levels to mitigate harm to individuals and the health system.
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Affiliation(s)
- Murillo Ferreira da Silva
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
- Pós-Graduação em Ciências da Saúde, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
| | | | - Fabrício Barbosa Ferreira
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
- Laboratório de Imunobiologia, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
| | - George Rego Albuquerque
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
- Programa de Pós-Graduação em Ciência Animal, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
| | - Ana Paula Melo Mariano
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
| | - Hllytchaikra Ferraz Fehlberg
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
- Programa de Pós-Graduação em Ciência Animal, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
| | | | - Pérola Rodrigues Dos Santos
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
- Pós-Graduação em Ciências da Saúde, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
| | - Luciano Cardoso Santos
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
- Programa de Pós-Graduação em Ciência Animal, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
| | - Laine Lopes Silva de Jesus
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
| | - Karoline Almeida Piton
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
| | - Beatriz Santos Costa
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
| | - Beatriz Sena Moreira Gomes
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
| | - Vinicius Moreira Porto
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
| | - Emanuelly da Silva Oliveira
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
| | - Cibele Luz Oliveira
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
| | - Renato Fontana
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
| | - Bianca Mendes Maciel
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
| | - Mylene de Melo Silva
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
| | - Lauro Juliano Marin
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
- Departamento de Ciências da Saúde, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
| | - Sandra Rocha Gadelha
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
- Pós-Graduação em Ciências da Saúde, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
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Cupertino MDC, Freitas AND, Meira GSB, Silva PAMD, Pires SDS, Cosendey TDA, Fernandes TM, Mayers NAJ, Siqueira-Batista R. COVID-19 and One Health: potential role of human and animals in SARS-CoV-2 life cycle. SCIENCE IN ONE HEALTH 2023; 2:100017. [PMID: 39077046 PMCID: PMC10238119 DOI: 10.1016/j.soh.2023.100017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 06/01/2023] [Indexed: 07/31/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes coronavirus disease 2019 (COVID-19) in humans has zoonotic tendencies, which can potentially provoke cross-species transmission, including human-to-animal and animal-to-human infection. Consequently, the objective was to analyze the scientific evidence regarding SARS-CoV-2 animal infections from potential human transmission. A systematic review was executed following the PRISMA guidelines, in the PubMed/MEDLINE, Google Scholar and LILACS, using the descriptors combined in the following way: (("SARS-CoV-2" OR "COVID-19" OR "2019-nCoV") AND (animals OR zoonosis)). The results contemplated the viral susceptibility of about thirty animal species when induced naturally and/or experimentally. The mink & hamster species demonstrated ostensible animal-to-human transmission. Overall, there have been more reports of human contamination by other species than human retransmission from the pathogen. The natural infection of the virus was discovered in domestic dogs & cats, wild cats, deer, minks, rabbits and hamsters. Several animals, including the African green monkeys and rabbits, manifested high levels of viremia, respiratory secretions and fecal excretions of infectious virus conducive to environmental/aerosol transmission. It is still inadequately documented the intrinsic role of such processes, such as the animals' involvement in viral mutations, the emergence of new variants/lineages and the role of the animal host species. Accordingly, this research model type, natural and experimental analysis on varying animal species, corroborates the link between the two aforementioned forms of transmission. Epidemiological surveillance through extensive sequencing of the viral genomes of infected animals and humans can reveal the SARS-CoV-2 transmission routes and anticipate appropriate prophylactic strategies.
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Affiliation(s)
- Marli do Carmo Cupertino
- School of Medicine, Faculdade Dinâmica do Vale do Piranga (FADIP), Ponte Nova, MG, Brazil
- Department of Medicine and Nursing, Federal University of Viçosa (UFV), Viçosa, MG, Brazil
- Department of Veterinary Medicine, Federal University of Viçosa (UFV), Viçosa, MG, Brazil
| | - Ana Nery Dias Freitas
- School of Medicine, Faculdade Dinâmica do Vale do Piranga (FADIP), Ponte Nova, MG, Brazil
| | | | | | - Sarah de Souza Pires
- School of Medicine, Faculdade Dinâmica do Vale do Piranga (FADIP), Ponte Nova, MG, Brazil
| | | | | | | | - Rodrigo Siqueira-Batista
- School of Medicine, Faculdade Dinâmica do Vale do Piranga (FADIP), Ponte Nova, MG, Brazil
- Department of Medicine and Nursing, Federal University of Viçosa (UFV), Viçosa, MG, Brazil
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Rezaei Z, Asaei S, Sepehrpour S, Jamalidoust M, Namayandeh M, Norouzi F, Pourabbas B. SARS-CoV-2 variants circulating in the Fars province, southern Iran, December 2020-March 2021: A cross-sectional study. Health Sci Rep 2023; 6:e1373. [PMID: 37383927 PMCID: PMC10293940 DOI: 10.1002/hsr2.1373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 06/03/2023] [Accepted: 06/11/2023] [Indexed: 06/30/2023] Open
Affiliation(s)
- Zahra Rezaei
- Professor Alborzi Clinical Microbiology Research CenterShiraz University of Medical SciencesShirazIran
| | - Sadaf Asaei
- Professor Alborzi Clinical Microbiology Research CenterShiraz University of Medical SciencesShirazIran
| | - Shima Sepehrpour
- Professor Alborzi Clinical Microbiology Research CenterShiraz University of Medical SciencesShirazIran
| | - Marzieh Jamalidoust
- Professor Alborzi Clinical Microbiology Research CenterShiraz University of Medical SciencesShirazIran
| | - Mandana Namayandeh
- Professor Alborzi Clinical Microbiology Research CenterShiraz University of Medical SciencesShirazIran
| | - Fatemeh Norouzi
- Department of Microbiology, School of MedicineFasa University of Medical SciencesFasaIran
| | - Bahman Pourabbas
- Professor Alborzi Clinical Microbiology Research CenterShiraz University of Medical SciencesShirazIran
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Serwanga J, Baine C, Mugaba S, Ankunda V, Auma BO, Oluka GK, Kato L, Kitabye I, Sembera J, Odoch G, Ejou P, Nalumansi A, Gombe B, Musenero M, Kaleebu P. Seroprevalence and durability of antibody responses to AstraZeneca vaccination in Ugandans with prior mild or asymptomatic COVID-19: implications for vaccine policy. Front Immunol 2023; 14:1183983. [PMID: 37205095 PMCID: PMC10187141 DOI: 10.3389/fimmu.2023.1183983] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/06/2023] [Indexed: 05/21/2023] Open
Abstract
Introduction The duration and timing of immunity conferred by COVID-19 vaccination in sub-Saharan Africa are crucial for guiding pandemic policy interventions, but systematic data for this region is scarce. This study investigated the antibody response after AstraZeneca vaccination in COVID-19 convalescent Ugandans. Methods We recruited 86 participants with a previous rt-PCR-confirmed mild or asymptomatic COVID-19 infection and measured the prevalence and levels of spike-directed IgG, IgM, and IgA antibodies at baseline, 14 and 28 days after the first dose (priming), 14 days after the second dose (boosting), and at six- and nine-months post-priming. We also measured the prevalence and levels of nucleoprotein-directed antibodies to assess breakthrough infections. Results Within two weeks of priming, vaccination substantially increased the prevalence and concentrations of spike-directed antibodies (p < 0.0001, Wilcoxon signed rank test), with 97.0% and 66% of vaccinated individuals possessing S-IgG and S-IgA antibodies before administering the booster dose. S-IgM prevalence changed marginally after the initial vaccination and barely after the booster, consistent with an already primed immune system. However, we also observed a rise in nucleoprotein seroprevalence, indicative of breakthroughs six months after the initial vaccination. Discussion Our results suggest that vaccination of COVID-19 convalescent individuals with the AstraZeneca vaccine induces a robust and differential spike-directed antibody response. The data highlights the value of vaccination as an effective method for inducing immunity in previously infected individuals and the importance of administering two doses to maintain protective immunity. Monitoring anti-spike IgG and IgA when assessing vaccine-induced antibody responses is suggested for this population; assessing S-IgM will underestimate the response. The AstraZeneca vaccine is a valuable tool in the fight against COVID-19. Further research is needed to determine the durability of vaccine-induced immunity and the potential need for booster doses.
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Affiliation(s)
- Jennifer Serwanga
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Claire Baine
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Susan Mugaba
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Violet Ankunda
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Betty Oliver Auma
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Gerald Kevin Oluka
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Laban Kato
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Isaac Kitabye
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Jackson Sembera
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Geoffrey Odoch
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Peter Ejou
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Amina Nalumansi
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Ben Gombe
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Monica Musenero
- Science, Technology, and Innovation Secretariat, Office of the President, Government of Uganda, Kampala, Uganda
| | - Pontiano Kaleebu
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
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37
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Alanzi AR, Parvez MK, Al-Dosari MS. Structure-based virtual identification of natural inhibitors of SARS-CoV-2 and its Delta and Omicron variant proteins. Future Virol 2023; 18:421-438. [PMID: 38051986 PMCID: PMC10241455 DOI: 10.2217/fvl-2022-0184] [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: 10/09/2022] [Accepted: 03/23/2023] [Indexed: 11/02/2023]
Abstract
Aim Structure-based identification of natural compounds against SARS-CoV-2, Delta and Omicron target proteins. Materials & methods Several known antiviral natural compounds were subjected to molecular docking and MD simulation against SARS-CoV-2 Mpro, Helicase and Spike, including Delta and Omicron Spikes. Results Of the docked ligands, 20 selected for each complex exhibited overall good binding affinities (-7.79 to -5.06 kcal/mol) with acceptable physiochemistry following Lipinski's rule. Finally, two best ligands from each complex upon simulation showed structural stability and compactness. Conclusion Quercetin-3-acetyl-glucoside, Rutin, Kaempferol, Catechin, Orientin, Obetrioside and Neridienone A were identified as potential inhibitors of SARS-CoV-2 Mpro, Helicase and Spike, while Orientin and Obetrioside also showed good binding affinities with Omicron Spike. Catechin and Neridienone A formed stable complexes with Delta Spike.
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Affiliation(s)
- Abdullah R Alanzi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Mohammad K Parvez
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Mohammed S Al-Dosari
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
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Prompetchara E, Ketloy C, Alameh MG, Tharakhet K, Kaewpang P, Yostrerat N, Pitakpolrat P, Buranapraditkun S, Manopwisedjaroen S, Thitithanyanont A, Jongkaewwattana A, Hunsawong T, Im-Erbsin R, Reed M, Wijagkanalan W, Patarakul K, Techawiwattanaboon T, Palaga T, Lam K, Heyes J, Weissman D, Ruxrungtham K. Immunogenicity and protective efficacy of SARS-CoV-2 mRNA vaccine encoding secreted non-stabilized spike in female mice. Nat Commun 2023; 14:2309. [PMID: 37085495 PMCID: PMC10120480 DOI: 10.1038/s41467-023-37795-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 03/24/2023] [Indexed: 04/23/2023] Open
Abstract
Establishment of an mRNA vaccine platform in low- and middle-income countries (LMICs) is important to enhance vaccine accessibility and ensure future pandemic preparedness. Here, we describe the preclinical studies of "ChulaCov19", a SARS-CoV-2 mRNA encoding prefusion-unstabilized ectodomain spike protein encapsulated in lipid nanoparticles (LNP). In female BALB/c mice, ChulaCov19 at 0.2, 1, 10, and 30 μg elicits robust neutralizing antibody (NAb) and T cell responses in a dose-dependent relationship. The geometric mean titers (GMTs) of NAb against wild-type (WT, Wuhan-Hu1) virus are 1,280, 11,762, 54,047, and 62,084, respectively. Higher doses induce better cross-NAb against Delta (B.1.617.2) and Omicron (BA.1 and BA.4/5) variants. This elicited immunogenicity is significantly higher than those induced by homologous CoronaVac or AZD1222 vaccination. In a heterologous prime-boost study, ChulaCov19 booster dose generates a 7-fold increase of NAb against Wuhan-Hu1 WT virus and also significantly increases NAb response against Omicron (BA.1 and BA.4/5) when compared to homologous CoronaVac or AZD1222 vaccination. Challenge studies show that ChulaCov19 protects human-ACE-2-expressing female mice from COVID-19 symptoms, prevents viremia and significantly reduces tissue viral load. Moreover, anamnestic NAb response is undetectable in challenge animals. ChulaCov19 is therefore a promising mRNA vaccine candidate either as a primary or boost vaccination and has entered clinical development.
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Affiliation(s)
- Eakachai Prompetchara
- Center of Excellence in Vaccine Research and Development (Chula VRC), Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Department of Laboratory Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Integrated Frontier Biotechnology for Emerging Disease, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chutitorn Ketloy
- Center of Excellence in Vaccine Research and Development (Chula VRC), Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
- Department of Laboratory Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
- Integrated Frontier Biotechnology for Emerging Disease, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Mohamad-Gabriel Alameh
- Division of Infectious Diseases, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Kittipan Tharakhet
- Center of Excellence in Vaccine Research and Development (Chula VRC), Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Department of Laboratory Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Papatsara Kaewpang
- Center of Excellence in Vaccine Research and Development (Chula VRC), Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Nongnaphat Yostrerat
- Center of Excellence in Vaccine Research and Development (Chula VRC), Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Patrawadee Pitakpolrat
- Center of Excellence in Vaccine Research and Development (Chula VRC), Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Department of Laboratory Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Supranee Buranapraditkun
- Center of Excellence in Vaccine Research and Development (Chula VRC), Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Thai Pediatric Gastroenterology, Hepatology and Immunology (TPGHAI) Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | | | - Arunee Thitithanyanont
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Anan Jongkaewwattana
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, 12120, Thailand
| | - Taweewan Hunsawong
- Department of Virology, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, 10400, Thailand
| | - Rawiwan Im-Erbsin
- Department of Veterinary Medicine, USAMD-AFRIMS, Bangkok, 10400, Thailand
| | - Matthew Reed
- Department of Veterinary Medicine, USAMD-AFRIMS, Bangkok, 10400, Thailand
| | | | - Kanitha Patarakul
- Center of Excellence in Vaccine Research and Development (Chula VRC), Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Integrated Frontier Biotechnology for Emerging Disease, Chulalongkorn University, Bangkok, 10330, Thailand
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Teerasit Techawiwattanaboon
- Center of Excellence in Vaccine Research and Development (Chula VRC), Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Tanapat Palaga
- Center of Excellence in Vaccine Research and Development (Chula VRC), Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Kieu Lam
- Genevant Sciences Corporation, Vancouver, BC, V5T 4T5, Canada
| | - James Heyes
- Genevant Sciences Corporation, Vancouver, BC, V5T 4T5, Canada
| | - Drew Weissman
- Division of Infectious Diseases, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Kiat Ruxrungtham
- Center of Excellence in Vaccine Research and Development (Chula VRC), Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Integrated Frontier Biotechnology for Emerging Disease, Chulalongkorn University, Bangkok, 10330, Thailand
- Department of Medicine, and School of Global Health, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
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Tangye SG. Impact of SARS-CoV-2 infection and COVID-19 on patients with inborn errors of immunity. J Allergy Clin Immunol 2023; 151:818-831. [PMID: 36522221 PMCID: PMC9746792 DOI: 10.1016/j.jaci.2022.11.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 12/15/2022]
Abstract
Since the arrival of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019, its characterization as a novel human pathogen, and the resulting coronavirus disease 2019 (COVID-19) pandemic, over 6.5 million people have died worldwide-a stark and sobering reminder of the fundamental and nonredundant roles of the innate and adaptive immune systems in host defense against emerging pathogens. Inborn errors of immunity (IEI) are caused by germline variants, typically in single genes. IEI are characterized by defects in development and/or function of cells involved in immunity and host defense, rendering individuals highly susceptible to severe, recurrent, and sometimes fatal infections, as well as immune dysregulatory conditions such as autoinflammation, autoimmunity, and allergy. The study of IEI has revealed key insights into the molecular and cellular requirements for immune-mediated protection against infectious diseases. Indeed, this has been exemplified by assessing the impact of SARS-CoV-2 infection in individuals with previously diagnosed IEI, as well as analyzing rare cases of severe COVID-19 in otherwise healthy individuals. This approach has defined fundamental aspects of mechanisms of disease pathogenesis, immunopathology in the context of infection with a novel pathogen, and therapeutic options to mitigate severe disease. This review summarizes these findings and illustrates how the study of these rare experiments of nature can inform key features of human immunology, which can then be leveraged to improve therapies for treating emerging and established infectious diseases.
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Affiliation(s)
- Stuart G Tangye
- Garvan Institute of Medical Research, Darlinghurst, Darlinghurst, Australia; St Vincent's Clinical School, University of New South Wales Sydney, Randwick, Randwick, Australia; Clinical Immunogenomics Research Consortium of Australasia (CIRCA).
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40
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Lin Z. More than a key-the pathological roles of SARS-CoV-2 spike protein in COVID-19 related cardiac injury. SPORTS MEDICINE AND HEALTH SCIENCE 2023:S2666-3376(23)00024-0. [PMID: 37361919 PMCID: PMC10062797 DOI: 10.1016/j.smhs.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/13/2023] [Accepted: 03/22/2023] [Indexed: 06/28/2023] Open
Abstract
Cardiac injury is common in hospitalized coronavirus disease 2019 (COVID-19) patients and cardiac abnormalities have been observed in a significant number of recovered COVID-19 patients, portending long-term health issues for millions of infected individuals. To better understand how Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2, CoV-2 for short) damages the heart, it is critical to fully comprehend the biology of CoV-2 encoded proteins, each of which may play multiple pathological roles. For example, CoV-2 spike glycoprotein (CoV-2-S) not only engages angiotensin converting enzyme II (ACE2) to mediate virus infection but also directly activates immune responses. In this work, the goal is to review the known pathological roles of CoV-2-S in the cardiovascular system, thereby shedding lights on the pathogenesis of COVID-19 related cardiac injury.
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Affiliation(s)
- Zhiqiang Lin
- Masonic Medical Research Institute, 2150 Bleecker Street, Utica, NY, 13501, USA
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Nizet S, Rieger J, Sarabi A, Lajtai G, Zatloukal K, Tschegg C. Binding and inactivation of human coronaviruses, including SARS-CoV-2, onto purified clinoptilolite-tuff. Sci Rep 2023; 13:4673. [PMID: 36949092 PMCID: PMC10031168 DOI: 10.1038/s41598-023-31744-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/16/2023] [Indexed: 03/24/2023] Open
Abstract
The current COVID19 pandemic is caused by a positive-sense single-stranded RNA virus, which presents high mutational rates. The development of effective therapeutics and mitigation strategies using vaccination or therapeutic antibodies faces serious challenges because of the regular emergence of immune escape variants of the virus. An efficient approach would involve the use of an agent to non-specifically limit or block viruses contacting the mucosae and therefore entering the body. Here, we investigated the ability of a micronized purified clinoptilolite-tuff to bind and neutralize different viruses from the Coronaviridae family. Using plaque assay, RT-qPCR and immunostaining, the adsorption and inactivation of the seasonal human coronavirus HCoV-229E and of 2 SARS-CoV-2 variants were demonstrated. The resulting data suggest that purified clinoptilolite-tuff could be used as an ingredient in new medical devices and/or pharmaceuticals to prevent or mitigate SARS-CoV-2 dissemination.
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Affiliation(s)
- S Nizet
- Glock Health, Science and Research GmbH, Hausfeldstrasse 17, 2232, Deutsch-Wagram, Austria.
| | - J Rieger
- Diagnostic and Research Institute of Pathology, Medical University Graz, Neue Stiftingtalstrasse 6, 8010, Graz, Austria
| | - A Sarabi
- Glock Health, Science and Research GmbH, Hausfeldstrasse 17, 2232, Deutsch-Wagram, Austria
| | | | - K Zatloukal
- Diagnostic and Research Institute of Pathology, Medical University Graz, Neue Stiftingtalstrasse 6, 8010, Graz, Austria
| | - C Tschegg
- Glock Health, Science and Research GmbH, Hausfeldstrasse 17, 2232, Deutsch-Wagram, Austria
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Molnupiravir: A Versatile Prodrug against SARS-CoV-2 Variants. Metabolites 2023; 13:metabo13020309. [PMID: 36837928 PMCID: PMC9962121 DOI: 10.3390/metabo13020309] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
The nucleoside analog β-D-N4-hydroxycytidine is the active metabolite of the prodrug molnupiravir and is accepted as an efficient drug against COVID-19. Molnupiravir targets the RNA-dependent RNA polymerase (RdRp) enzyme, which is responsible for replicating the viral genome during the replication process of certain types of viruses. It works by disrupting the normal function of the RdRp enzyme, causing it to make mistakes during the replication of the viral genome. These mistakes can prevent the viral RNA from being transcribed, converted into a complementary DNA template, translated, or converted into a functional protein. By disrupting these crucial steps in the viral replication process, molnupiravir can effectively inhibit the replication of the virus and reduce its ability to cause disease. This review article sheds light on the impact of molnupiravir and its metabolite on SARS-CoV-2 variants of concern, such as delta, omicron, and hybrid/recombinant variants. The detailed mechanism and molecular interactions using molecular docking and dynamics have also been covered. The safety and tolerability of molnupiravir in patients with comorbidities have also been emphasized.
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Meurisse M, Catteau L, van Loenhout JAF, Braeye T, De Mot L, Serrien B, Blot K, Cauët E, Van Oyen H, Cuypers L, Robert A, Van Goethem N. Homologous and Heterologous Prime-Boost Vaccination: Impact on Clinical Severity of SARS-CoV-2 Omicron Infection among Hospitalized COVID-19 Patients in Belgium. Vaccines (Basel) 2023; 11:vaccines11020378. [PMID: 36851257 PMCID: PMC9961733 DOI: 10.3390/vaccines11020378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
We investigated effectiveness of (1) mRNA booster vaccination versus primary vaccination only and (2) heterologous (viral vector-mRNA) versus homologous (mRNA-mRNA) prime-boost vaccination against severe outcomes of BA.1, BA.2, BA.4 or BA.5 Omicron infection (confirmed by whole genome sequencing) among hospitalized COVID-19 patients using observational data from national COVID-19 registries. In addition, it was investigated whether the difference between the heterologous and homologous prime-boost vaccination was homogenous across Omicron sub-lineages. Regression standardization (parametric g-formula) was used to estimate counterfactual risks for severe COVID-19 (combination of severity indicators), intensive care unit (ICU) admission, and in-hospital mortality under exposure to different vaccination schedules. The estimated risk for severe COVID-19 and in-hospital mortality was significantly lower with an mRNA booster vaccination as compared to only a primary vaccination schedule (RR = 0.59 [0.33; 0.85] and RR = 0.47 [0.15; 0.79], respectively). No significance difference was observed in the estimated risk for severe COVID-19, ICU admission and in-hospital mortality with a heterologous compared to a homologous prime-boost vaccination schedule, and this difference was not significantly modified by the Omicron sub-lineage. Our results support evidence that mRNA booster vaccination reduced the risk of severe COVID-19 disease during the Omicron-predominant period.
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Affiliation(s)
- Marjan Meurisse
- Department of Epidemiology and public health, Sciensano, 1070 Brussels, Belgium
- Department of Epidemiology and Biostatistics, Institut de Recherche Expérimentale et Clinique, Faculty of Public Health, Université Catholique de Louvain, 1200 Woluwe-Saint-Lambert, Belgium
- Correspondence:
| | - Lucy Catteau
- Department of Epidemiology and public health, Sciensano, 1070 Brussels, Belgium
| | | | - Toon Braeye
- Department of Epidemiology and public health, Sciensano, 1070 Brussels, Belgium
| | - Laurane De Mot
- Department of Epidemiology and public health, Sciensano, 1070 Brussels, Belgium
| | - Ben Serrien
- Department of Epidemiology and public health, Sciensano, 1070 Brussels, Belgium
| | - Koen Blot
- Department of Epidemiology and public health, Sciensano, 1070 Brussels, Belgium
| | - Emilie Cauët
- Department of Epidemiology and public health, Sciensano, 1070 Brussels, Belgium
| | - Herman Van Oyen
- Department of Public Health and Primary Care, Ghent University, 9000 Ghent, Belgium
| | - Lize Cuypers
- Department of Laboratory Medicine, National Reference Center for Respiratory Pathogens, University Hospitals Leuven, 3000 Leuven, Belgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | | | | | - Annie Robert
- Department of Epidemiology and Biostatistics, Institut de Recherche Expérimentale et Clinique, Faculty of Public Health, Université Catholique de Louvain, 1200 Woluwe-Saint-Lambert, Belgium
| | - Nina Van Goethem
- Department of Epidemiology and public health, Sciensano, 1070 Brussels, Belgium
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Gravrand V, Mellot F, Ackermann F, Ballester MC, Zuber B, Kirk JT, Navalkar K, Yager TD, Petit F, Pascreau T, Farfour E, Vasse M. Stratification of COVID-19 Severity Using SeptiCyte RAPID, a Novel Host Immune Response Test. Viruses 2023; 15:419. [PMID: 36851633 PMCID: PMC9960895 DOI: 10.3390/v15020419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/20/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
SeptiCyte® RAPID is a gene expression assay measuring the relative expression levels of host response genes PLA2G7 and PLAC8, indicative of a dysregulated immune response during sepsis. As severe forms of COVID-19 may be considered viral sepsis, we evaluated SeptiCyte RAPID in a series of 94 patients admitted to Foch Hospital (Suresnes, France) with proven SARS-CoV-2 infection. EDTA blood was collected in the emergency department (ED) in 67 cases, in the intensive care unit (ICU) in 23 cases and in conventional units in 4 cases. SeptiScore (0-15 scale) increased with COVID-19 severity. Patients in ICU had the highest SeptiScores, producing values comparable to 8 patients with culture-confirmed bacterial sepsis. Receiver operating characteristic (ROC) curve analysis had an area under the curve (AUC) of 0.81 for discriminating patients requiring ICU admission from patients who were immediately discharged or from patients requiring hospitalization in conventional units. SeptiScores increased with the extent of the lung injury. For 68 patients, a chest computed tomography (CT) scan was performed within 24 h of COVID-19 diagnosis. SeptiScore >7 suggested lung injury ≥50% (AUC = 0.86). SeptiCyte RAPID was compared to other biomarkers for discriminating Critical + Severe COVID-19 in ICU, versus Moderate + Mild COVID-19 not in ICU. The mean AUC for SeptiCyte RAPID was superior to that of any individual biomarker or combination thereof. In contrast to C-reactive protein (CRP), correlation of SeptiScore with lung injury was not impacted by treatment with anti-inflammatory agents. SeptiCyte RAPID can be a useful tool to identify patients with severe forms of COVID-19 in ED, as well as during follow-up.
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Affiliation(s)
| | | | - Felix Ackermann
- Internal Medicine Department, Foch Hospital, 92150 Suresnes, France
| | | | - Benjamin Zuber
- Intensive Care Unit, Foch Hospital, 92150 Suresnes, France
| | | | | | | | - Fabien Petit
- Biology Department, Foch Hospital, 92150 Suresnes, France
| | - Tiffany Pascreau
- Biology Department, Foch Hospital, 92150 Suresnes, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR-S1176, 94270 Le Kremlin-Bicêtre, France
| | - Eric Farfour
- Biology Department, Foch Hospital, 92150 Suresnes, France
| | - Marc Vasse
- Biology Department, Foch Hospital, 92150 Suresnes, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR-S1176, 94270 Le Kremlin-Bicêtre, France
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Zhang HP, Sun YL, Wang YF, Yazici D, Azkur D, Ogulur I, Azkur AK, Yang ZW, Chen XX, Zhang AZ, Hu JQ, Liu GH, Akdis M, Akdis CA, Gao YD. Recent developments in the immunopathology of COVID-19. Allergy 2023; 78:369-388. [PMID: 36420736 PMCID: PMC10108124 DOI: 10.1111/all.15593] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 11/01/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022]
Abstract
There has been an important change in the clinical characteristics and immune profile of Coronavirus disease 2019 (COVID-19) patients during the pandemic thanks to the extensive vaccination programs. Here, we highlight recent studies on COVID-19, from the clinical and immunological characteristics to the protective and risk factors for severity and mortality of COVID-19. The efficacy of the COVID-19 vaccines and potential allergic reactions after administration are also discussed. The occurrence of new variants of concerns such as Omicron BA.2, BA.4, and BA.5 and the global administration of COVID-19 vaccines have changed the clinical scenario of COVID-19. Multisystem inflammatory syndrome in children (MIS-C) may cause severe and heterogeneous disease but with a lower mortality rate. Perturbations in immunity of T cells, B cells, and mast cells, as well as autoantibodies and metabolic reprogramming may contribute to the long-term symptoms of COVID-19. There is conflicting evidence about whether atopic diseases, such as allergic asthma and rhinitis, are associated with a lower susceptibility and better outcomes of COVID-19. At the beginning of pandemic, the European Academy of Allergy and Clinical Immunology (EAACI) developed guidelines that provided timely information for the management of allergic diseases and preventive measures to reduce transmission in the allergic clinics. The global distribution of COVID-19 vaccines and emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with reduced pathogenic potential dramatically decreased the morbidity, severity, and mortality of COVID-19. Nevertheless, breakthrough infection remains a challenge for disease control. Hypersensitivity reactions (HSR) to COVID-19 vaccines are low compared to other vaccines, and these were addressed in EAACI statements that provided indications for the management of allergic reactions, including anaphylaxis to COVID-19 vaccines. We have gained a depth knowledge and experience in the over 2 years since the start of the pandemic, and yet a full eradication of SARS-CoV-2 is not on the horizon. Novel strategies are warranted to prevent severe disease in high-risk groups, the development of MIS-C and long COVID-19.
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Affiliation(s)
- Huan-Ping Zhang
- Department of Allergology, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Yuan-Li Sun
- Department of Allergology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yan-Fen Wang
- Department of Pediatrics, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Duygu Yazici
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Dilek Azkur
- Division of Pediatric Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, University of Kirikkale, Kirikkale, Turkey
| | - Ismail Ogulur
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Ahmet Kursat Azkur
- Department of Virology, Faculty of Veterinary Medicine, University of Kirikkale, Kirikkale, Turkey
| | - Zhao-Wei Yang
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiao-Xue Chen
- Department of Allergology, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Ai-Zhi Zhang
- Intensive Care Unit, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Jia-Qian Hu
- Department of Allergology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Guang-Hui Liu
- Department of Allergology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Mübeccel Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Cezmi A Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Ya-Dong Gao
- Department of Allergology, Zhongnan Hospital of Wuhan University, Wuhan, China
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Veneziano C, Marascio N, De Marco C, Quaresima B, Biamonte F, Trecarichi EM, Santamaria G, Quirino A, Torella D, Quattrone A, Matera G, Torti C, De Filippo C, Costanzo FS, Viglietto G. The Spread of SARS-CoV-2 Omicron Variant in CALABRIA: A Spatio-Temporal Report of Viral Genome Evolution. Viruses 2023; 15:v15020408. [PMID: 36851622 PMCID: PMC9963258 DOI: 10.3390/v15020408] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/25/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
We investigated the evolution of SARS-CoV-2 spread in Calabria, Southern Italy, in 2022. A total of 272 RNA isolates from nasopharyngeal swabs of individuals infected with SARS-CoV-2 were sequenced by whole genome sequencing (N = 172) and/or Sanger sequencing (N = 100). Analysis of diffusion of Omicron variants in Calabria revealed the prevalence of 10 different sub-lineages (recombinant BA.1/BA.2, BA.1, BA.1.1, BA.2, BA.2.9, BA.2.10, BA.2.12.1, BA.4, BA.5, BE.1). We observed that Omicron spread in Calabria presented a similar trend as in Italy, with some notable exceptions: BA.1 disappeared in April in Calabria but not in the rest of Italy; recombinant BA.1/BA.2 showed higher frequency in Calabria (13%) than in the rest of Italy (0.02%); BA.2.9, BA.4 and BA.5 emerged in Calabria later than in other Italian regions. In addition, Calabria Omicron presented 16 non-canonical mutations in the S protein and 151 non-canonical mutations in non-structural proteins. Most non-canonical mutations in the S protein occurred mainly in BA.5 whereas non-canonical mutations in non-structural or accessory proteins (ORF1ab, ORF3a, ORF8 and N) were identified in BA.2 and BA.5 sub-lineages. In conclusion, the data reported here underscore the importance of monitoring the entire SARS-CoV-2 genome.
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Affiliation(s)
- Claudia Veneziano
- Department of Experimental and Clinical Medicine, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
- Interdepartmental Center of Services (CIS), Molecular Genomics and Pathology, “Magna Græcia” University of Catanzaro, 88100 Catanzaro, Italy
| | - Nadia Marascio
- Department of Health Sciences, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
| | - Carmela De Marco
- Department of Experimental and Clinical Medicine, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
- Interdepartmental Center of Services (CIS), Molecular Genomics and Pathology, “Magna Græcia” University of Catanzaro, 88100 Catanzaro, Italy
| | - Barbara Quaresima
- Department of Experimental and Clinical Medicine, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
- Interdepartmental Center of Services (CIS), Molecular Genomics and Pathology, “Magna Græcia” University of Catanzaro, 88100 Catanzaro, Italy
| | - Flavia Biamonte
- Department of Experimental and Clinical Medicine, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
- Interdepartmental Center of Services (CIS), Molecular Genomics and Pathology, “Magna Græcia” University of Catanzaro, 88100 Catanzaro, Italy
| | - Enrico Maria Trecarichi
- Department of Medical and Surgical Sciences, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
- “Mater Domini” University Hospital of Catanzaro, 88100 Catanzaro, Italy
| | - Gianluca Santamaria
- Department of Experimental and Clinical Medicine, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
| | - Angela Quirino
- Department of Health Sciences, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
- “Mater Domini” University Hospital of Catanzaro, 88100 Catanzaro, Italy
| | - Daniele Torella
- Department of Experimental and Clinical Medicine, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
- “Mater Domini” University Hospital of Catanzaro, 88100 Catanzaro, Italy
| | - Aldo Quattrone
- Neuroscience Research Center, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
| | - Giovanni Matera
- Department of Health Sciences, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
- “Mater Domini” University Hospital of Catanzaro, 88100 Catanzaro, Italy
| | - Carlo Torti
- Department of Medical and Surgical Sciences, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
- “Mater Domini” University Hospital of Catanzaro, 88100 Catanzaro, Italy
| | | | - Francesco Saverio Costanzo
- Department of Experimental and Clinical Medicine, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
- Interdepartmental Center of Services (CIS), Molecular Genomics and Pathology, “Magna Græcia” University of Catanzaro, 88100 Catanzaro, Italy
- “Mater Domini” University Hospital of Catanzaro, 88100 Catanzaro, Italy
| | - Giuseppe Viglietto
- Department of Experimental and Clinical Medicine, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
- “Mater Domini” University Hospital of Catanzaro, 88100 Catanzaro, Italy
- Correspondence:
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Ong V, Soleimani A, Amirghasemi F, Khazaee Nejad S, Abdelmonem M, Razaviyayn M, Hosseinzadeh P, Comai L, Mousavi MPS. Impedimetric Sensing: An Emerging Tool for Combating the COVID-19 Pandemic. BIOSENSORS 2023; 13:bios13020204. [PMID: 36831970 PMCID: PMC9953732 DOI: 10.3390/bios13020204] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 06/12/2023]
Abstract
The COVID-19 pandemic revealed a pressing need for the development of sensitive and low-cost point-of-care sensors for disease diagnosis. The current standard of care for COVID-19 is quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). This method is sensitive, but takes time, effort, and requires specialized equipment and reagents to be performed correctly. This make it unsuitable for widespread, rapid testing and causes poor individual and policy decision-making. Rapid antigen tests (RATs) are a widely used alternative that provide results quickly but have low sensitivity and are prone to false negatives, particularly in cases with lower viral burden. Electrochemical sensors have shown much promise in filling this technology gap, and impedance spectroscopy specifically has exciting potential in rapid screening of COVID-19. Due to the data-rich nature of impedance measurements performed at different frequencies, this method lends itself to machine-leaning (ML) algorithms for further data processing. This review summarizes the current state of impedance spectroscopy-based point-of-care sensors for the detection of the SARS-CoV-2 virus. This article also suggests future directions to address the technology's current limitations to move forward in this current pandemic and prepare for future outbreaks.
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Affiliation(s)
- Victor Ong
- Alfred E. Mann Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Ali Soleimani
- Alfred E. Mann Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Farbod Amirghasemi
- Alfred E. Mann Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Sina Khazaee Nejad
- Alfred E. Mann Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Mona Abdelmonem
- Alfred E. Mann Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Meisam Razaviyayn
- Daniel J. Epstein Department of Industrial and Systems Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
- Ming Hsieh Department of Electrical and Computer Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
- Department of Computer Science, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Parisa Hosseinzadeh
- Knight Campus Center Department of Bioengineering, University of Oregon, Eugene, OR 97403, USA
| | - Lucio Comai
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Maral P. S. Mousavi
- Alfred E. Mann Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
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48
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AlKalamouni H, Abou Hassan FF, Bou Hamdan M, Page AJ, Lott M, Matthews M, Ghosn N, Rady A, Mahfouz R, Araj GF, Dbaibo G, Zaraket H, Melhem NM, Matar GM. Genomic surveillance of SARS-CoV-2 in COVID-19 vaccinated healthcare workers in Lebanon. BMC Med Genomics 2023; 16:14. [PMID: 36707851 PMCID: PMC9880935 DOI: 10.1186/s12920-023-01443-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The emergence of SARS-CoV-2 variants including the Delta and Omicron along with waning of vaccine-induced immunity over time contributed to increased rates of breakthrough infection specifically among healthcare workers (HCWs). SARS-CoV-2 genomic surveillance is an important tool for timely detection and characterization of circulating variants as well as monitoring the emergence of new strains. Our study is the first national SARS-CoV-2 genomic surveillance among HCWs in Lebanon. METHODS We collected 250 nasopharyngeal swabs from HCWs across Lebanon between December 2021 and January 2022. Data on the date of positive PCR, vaccination status, specific occupation, and hospitalization status of participants were collected. Extracted viral RNA from nasopharyngeal swabs was converted to cDNA, library prepped using the coronaHIT method, followed by whole genome sequencing on the Illumina NextSeq 500 platform. RESULTS A total of 133 (57.1%) samples belonging to the Omicron (BA.1.1) sub-lineage were identified, as well as 44 (18.9%) samples belonging to the BA.1 sub-lineage, 28 (12%) belonging to the BA.2 sub-lineage, and only 15 (6.6%) samples belonging to the Delta variant sub-lineage B.1.617.2. These results show that Lebanon followed the global trend in terms of circulating SARS-CoV-2 variants with Delta rapidly replaced by the Omicron variant. CONCLUSION This study underscores the importance of continuous genomic surveillance programs in Lebanon for the timely detection and characterization of circulating variants. The latter is critical to guide public health policy making and to timely implement public health interventions.
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Affiliation(s)
- Habib AlKalamouni
- grid.22903.3a0000 0004 1936 9801Department of Experimental Pathology, Immunology, and Microbiology, Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, 1107 2020 Lebanon ,grid.22903.3a0000 0004 1936 9801Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Farouk F. Abou Hassan
- grid.22903.3a0000 0004 1936 9801Medical Laboratory Sciences Program, Division of Health Professions, Faculty of Health Sciences, American University of Beirut, Beirut, 1107 2020 Lebanon
| | - Mirna Bou Hamdan
- grid.22903.3a0000 0004 1936 9801Medical Laboratory Sciences Program, Division of Health Professions, Faculty of Health Sciences, American University of Beirut, Beirut, 1107 2020 Lebanon
| | - Andrew J. Page
- grid.420132.6Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Martin Lott
- grid.420132.6Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Michaela Matthews
- grid.420132.6Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Nada Ghosn
- grid.490673.f0000 0004 6020 2237Epidemiological Surveillance Unit, Ministry of Public Health, Beirut, Lebanon
| | | | - Rami Mahfouz
- grid.22903.3a0000 0004 1936 9801Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon ,grid.22903.3a0000 0004 1936 9801Department of Pathology and Laboratory Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - George F. Araj
- grid.22903.3a0000 0004 1936 9801Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon ,grid.22903.3a0000 0004 1936 9801Department of Pathology and Laboratory Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ghassan Dbaibo
- grid.22903.3a0000 0004 1936 9801Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon ,grid.22903.3a0000 0004 1936 9801Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Hassan Zaraket
- grid.22903.3a0000 0004 1936 9801Department of Experimental Pathology, Immunology, and Microbiology, Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, 1107 2020 Lebanon ,grid.22903.3a0000 0004 1936 9801Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Nada M. Melhem
- grid.22903.3a0000 0004 1936 9801Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon ,grid.22903.3a0000 0004 1936 9801Medical Laboratory Sciences Program, Division of Health Professions, Faculty of Health Sciences, American University of Beirut, Beirut, 1107 2020 Lebanon
| | - Ghassan M. Matar
- grid.22903.3a0000 0004 1936 9801Department of Experimental Pathology, Immunology, and Microbiology, Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, 1107 2020 Lebanon ,grid.22903.3a0000 0004 1936 9801Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
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Padilla-Blanco M, Gucciardi F, Rubio V, Lastra A, Lorenzo T, Ballester B, González-Pastor A, Veses V, Macaluso G, Sheth CC, Pascual-Ortiz M, Maiques E, Rubio-Guerri C, Purpari G, Guercio A. A SARS-CoV-2 full genome sequence of the B.1.1 lineage sheds light on viral evolution in Sicily in late 2020. Front Public Health 2023; 11:1098965. [PMID: 36778569 PMCID: PMC9909176 DOI: 10.3389/fpubh.2023.1098965] [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: 11/15/2022] [Accepted: 01/06/2023] [Indexed: 01/27/2023] Open
Abstract
To investigate the influence of geographic constrains to mobility on SARS-CoV-2 circulation before the advent of vaccination, we recently characterized the occurrence in Sicily of viral lineages in the second pandemic wave (September to December 2020). Our data revealed wide prevalence of the then widespread through Europe B.1.177 variant, although some viral samples could not be classified with the limited Sanger sequencing tools used. A particularly interesting sample could not be fitted to a major variant then circulating in Europe and has been subjected here to full genome sequencing in an attempt to clarify its origin, lineage and relations with the seven full genome sequences deposited for that period in Sicily, hoping to provide clues on viral evolution. The obtained genome is unique (not present in databases). It hosts 20 single-base substitutions relative to the original Wuhan-Hu-1 sequence, 8 of them synonymous and the other 12 encoding 11 amino acid substitutions, all of them already reported one by one. They include four highly prevalent substitutions, NSP12:P323L, S:D614G, and N:R203K/G204R; the much less prevalent S:G181V, ORF3a:G49V and N:R209I changes; and the very rare mutations NSP3:L761I, NSP6:S106F, NSP8:S41F and NSP14:Y447H. GISAID labeled this genome as B.1.1 lineage, a lineage that appeared early on in the pandemic. Phylogenetic analysis also confirmed this lineage diagnosis. Comparison with the seven genome sequences deposited in late 2020 from Sicily revealed branching leading to B.1.177 in one branch and to Alpha in the other branch, and suggested a local origin for the S:G118V mutation.
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Affiliation(s)
- Miguel Padilla-Blanco
- Departamento de Farmacia, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU (UCH-CEU), CEU Universities, Valencia, Spain
| | - Francesca Gucciardi
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Palermo, Italy
| | - Vicente Rubio
- Department of Genomics and Proteomics, Instituto de Biomedicina de Valencia del Consejo Superior de Investigaciones Científicas (IBV-CSIC) and Centre for Biomedical Network Research on Rare Diseases of the Instituto de Salud Carlos III (CIBERER-ISCIII), CEU Universities, Valencia, Spain
| | - Antonio Lastra
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Palermo, Italy
| | - Teresa Lorenzo
- Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Beatriz Ballester
- Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Andrea González-Pastor
- Departamento de Medicina, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Veronica Veses
- Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Giusi Macaluso
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Palermo, Italy
| | - Chirag C. Sheth
- Departamento de Medicina, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Marina Pascual-Ortiz
- Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Elisa Maiques
- Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain,*Correspondence: Elisa Maiques ✉
| | - Consuelo Rubio-Guerri
- Departamento de Farmacia, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU (UCH-CEU), CEU Universities, Valencia, Spain,Consuelo Rubio-Guerri ✉
| | - Giuseppa Purpari
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Palermo, Italy,Giuseppa Purpari ✉
| | - Annalisa Guercio
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Palermo, Italy
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Zhang J, Xia Y, Liu X, Liu G. Advanced Vaccine Design Strategies against SARS-CoV-2 and Emerging Variants. Bioengineering (Basel) 2023; 10:bioengineering10020148. [PMID: 36829642 PMCID: PMC9951973 DOI: 10.3390/bioengineering10020148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
Vaccination is the most cost-effective means in the fight against infectious diseases. Various kinds of vaccines have been developed since the outbreak of COVID-19, some of which have been approved for clinical application. Though vaccines available achieved partial success in protecting vaccinated subjects from infection or hospitalization, numerous efforts are still needed to end the global pandemic, especially in the case of emerging new variants. Safe and efficient vaccines are the key elements to stop the pandemic from attacking the world now; novel and evolving vaccine technologies are urged in the course of fighting (re)-emerging infectious diseases. Advances in biotechnology offered the progress of vaccinology in the past few years, and lots of innovative approaches have been applied to the vaccine design during the ongoing pandemic. In this review, we summarize the state-of-the-art vaccine strategies involved in controlling the transmission of SARS-CoV-2 and its variants. In addition, challenges and future directions for rational vaccine design are discussed.
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Affiliation(s)
- Jianzhong Zhang
- Center for Molecular Imaging and Translational Medicine, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Yutian Xia
- Center for Molecular Imaging and Translational Medicine, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Xuan Liu
- Center for Molecular Imaging and Translational Medicine, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Gang Liu
- Center for Molecular Imaging and Translational Medicine, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
- Innovation Center for Cell Biology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
- Correspondence:
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