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Christodoulou A, Katsarou MS, Emmanouil C, Gavrielatos M, Georgiou D, Tsolakou A, Papasavva M, Economou V, Nanou V, Nikolopoulos I, Daganou M, Argyraki A, Stefanidis E, Metaxas G, Panagiotou E, Michalopoulos I, Drakoulis N. A Machine Learning-Based Web Tool for the Severity Prediction of COVID-19. BIOTECH 2024; 13:22. [PMID: 39051337 PMCID: PMC11270362 DOI: 10.3390/biotech13030022] [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: 12/31/2023] [Revised: 06/13/2024] [Accepted: 06/20/2024] [Indexed: 07/27/2024] Open
Abstract
Predictive tools provide a unique opportunity to explain the observed differences in outcome between patients of the COVID-19 pandemic. The aim of this study was to associate individual demographic and clinical characteristics with disease severity in COVID-19 patients and to highlight the importance of machine learning (ML) in disease prognosis. The study enrolled 344 unvaccinated patients with confirmed SARS-CoV-2 infection. Data collected by integrating questionnaires and medical records were imported into various classification machine learning algorithms, and the algorithm and the hyperparameters with the greatest predictive ability were selected for use in a disease outcome prediction web tool. Of 111 independent features, age, sex, hypertension, obesity, and cancer comorbidity were found to be associated with severe COVID-19. Our prognostic tool can contribute to a successful therapeutic approach via personalized treatment. Although at the present time vaccination is not considered mandatory, this algorithm could encourage vulnerable groups to be vaccinated.
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Affiliation(s)
- Avgi Christodoulou
- Research Group of Clinical Pharmacology and Pharmacogenomics Faculty of Pharmacy, School oh Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece; (A.C.); (M.-S.K.); (A.T.); (V.E.); (N.D.)
- Sotiria Thoracic Diseases Hospital of Athens, 11527 Athens, Greece; (V.N.); (I.N.); (M.D.); (A.A.); (E.S.); (G.M.); (E.P.)
| | - Martha-Spyridoula Katsarou
- Research Group of Clinical Pharmacology and Pharmacogenomics Faculty of Pharmacy, School oh Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece; (A.C.); (M.-S.K.); (A.T.); (V.E.); (N.D.)
| | - Christina Emmanouil
- Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (C.E.); (M.G.); (D.G.)
- Department of Biology, National and Kapodistrian University of Athens, 15772 Athens, Greece
- Institute for Bioinnovation, Biomedical Sciences Research Center ‘Alexander Fleming’, 16672 Vari, Greece
| | - Marios Gavrielatos
- Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (C.E.); (M.G.); (D.G.)
- Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, 16122 Athens, Greece
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Dimitrios Georgiou
- Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (C.E.); (M.G.); (D.G.)
- School of Electrical and Computer Engineering, National and Technical University of Athens, 15773 Athens, Greece
| | - Annia Tsolakou
- Research Group of Clinical Pharmacology and Pharmacogenomics Faculty of Pharmacy, School oh Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece; (A.C.); (M.-S.K.); (A.T.); (V.E.); (N.D.)
| | - Maria Papasavva
- Department of Pharmacy, School of Health Sciences, Frederick University, 1036 Nicosia, Cyprus;
| | - Vasiliki Economou
- Research Group of Clinical Pharmacology and Pharmacogenomics Faculty of Pharmacy, School oh Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece; (A.C.); (M.-S.K.); (A.T.); (V.E.); (N.D.)
| | - Vasiliki Nanou
- Sotiria Thoracic Diseases Hospital of Athens, 11527 Athens, Greece; (V.N.); (I.N.); (M.D.); (A.A.); (E.S.); (G.M.); (E.P.)
| | - Ioannis Nikolopoulos
- Sotiria Thoracic Diseases Hospital of Athens, 11527 Athens, Greece; (V.N.); (I.N.); (M.D.); (A.A.); (E.S.); (G.M.); (E.P.)
| | - Maria Daganou
- Sotiria Thoracic Diseases Hospital of Athens, 11527 Athens, Greece; (V.N.); (I.N.); (M.D.); (A.A.); (E.S.); (G.M.); (E.P.)
| | - Aikaterini Argyraki
- Sotiria Thoracic Diseases Hospital of Athens, 11527 Athens, Greece; (V.N.); (I.N.); (M.D.); (A.A.); (E.S.); (G.M.); (E.P.)
| | - Evaggelos Stefanidis
- Sotiria Thoracic Diseases Hospital of Athens, 11527 Athens, Greece; (V.N.); (I.N.); (M.D.); (A.A.); (E.S.); (G.M.); (E.P.)
| | - Gerasimos Metaxas
- Sotiria Thoracic Diseases Hospital of Athens, 11527 Athens, Greece; (V.N.); (I.N.); (M.D.); (A.A.); (E.S.); (G.M.); (E.P.)
| | - Emmanouil Panagiotou
- Sotiria Thoracic Diseases Hospital of Athens, 11527 Athens, Greece; (V.N.); (I.N.); (M.D.); (A.A.); (E.S.); (G.M.); (E.P.)
| | - Ioannis Michalopoulos
- Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (C.E.); (M.G.); (D.G.)
| | - Nikolaos Drakoulis
- Research Group of Clinical Pharmacology and Pharmacogenomics Faculty of Pharmacy, School oh Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece; (A.C.); (M.-S.K.); (A.T.); (V.E.); (N.D.)
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Saidi LK, Md Rani ZZ, Sulaiman SA, Jamal R, Ismail A, Alim AA, Ayob SNSA, Dee CF, Hamzah AA, Abdul Murad NA. Development of DNA-Based Lateral Flow Assay for Detection of LDLR Gene Mutation for Familial Hypercholesterolemia. Malays J Med Sci 2024; 31:92-106. [PMID: 38984253 PMCID: PMC11229576 DOI: 10.21315/mjms2024.31.3.6] [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: 05/16/2023] [Accepted: 06/29/2023] [Indexed: 07/11/2024] Open
Abstract
Background The techniques for detecting single nucleotide polymorphisms (SNP) require lengthy and complex experimental procedures and expensive instruments that may only be available in some laboratories. Thus, a deoxyribonucleic acid (DNA)-based lateral flow assay (LFA) was developed as a point-of-care test (POCT) diagnostic tool for genotyping. In this study, single nucleotide variation (E101K) in the low-density lipoprotein receptor (LDLR) gene leading to familial hypercholesterolemia (FH) was chosen as a model. Methods Hypercholesterolemic individuals (n = 103) were selected from the Malaysian Cohort project (UKM Medical Molecular Biology Institute) while the control samples were selected from the Biobank (UKM Medical Molecular Biology Institute). The DNA samples were isolated from whole blood. Polymerase chain reaction (PCR) amplification process was performed using bifunctional labelled primers specifically designed to correspond to the variant that differentiates wild-type and mutant DNA for visual detection on LFA. The variant was confirmed using Sanger sequencing, and the sensitivity and specificity of the LFA detection method were validated using the Agena MassARRAY® technique. Results Out of 103 hypercholesterolemic individuals, 5 individuals (4.8%) tested positive for E101K, LDLR mutation and the rest, including healthy control individuals, tested negative. This result was concordant with Sanger sequencing and Agena MassARRAY®. These five individuals could be classified as Definite FH, as the DNA diagnosis was confirmed. The sensitivity and specificity of the variant detection by LFA is 100% compared to results using the genotyping method using Agena MassARRAY®. Conclusion The developed LFA can potentially be used in the POC setting for detecting the E101K variant in the LDLR gene. This LFA can also be used to screen family members with E101K variant in the LDLR gene and is applicable for other SNP's detection.
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Affiliation(s)
- Lina Khalida Saidi
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Zam Zureena Md Rani
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Siti Aishah Sulaiman
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Aziah Ismail
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Kelantan, Malaysia
| | - Anis Amirah Alim
- Institute of Microengineering and Nanoelectronics (IMEN), Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - Sharipah Nadzirah Syed Ahmad Ayob
- Institute of Microengineering and Nanoelectronics (IMEN), Universiti Kebangsaan Malaysia, Selangor, Malaysia
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis, Perlis, Malaysia
| | - Chang Fu Dee
- Institute of Microengineering and Nanoelectronics (IMEN), Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - Azrul Azlan Hamzah
- Institute of Microengineering and Nanoelectronics (IMEN), Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - Nor Azian Abdul Murad
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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González Ramírez M, Hoyos Muñoz JA, Moreno Gómez GA, Aguirre Flórez M, Gómez González JF. Relationship between steroid use and superinfections in SARS-CoV-2 patients. A systematic review and meta-analysis. Infect Ecol Epidemiol 2023; 13:2277000. [PMID: 38187166 PMCID: PMC10769522 DOI: 10.1080/20008686.2023.2277000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/25/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction: The use of steroids has been proposed as a pharmacological approach to treat the SARS-CoV-2 infection to improve outcomes. However, there are doubts about safety against the development of superinfections and their worse outcomes. Objective: To establish the relative frequency of superinfection associated with using steroids in patients with SARS-CoV-2 infection. Materials and methods: We conducted a systematic literature review and meta-analysis using PRISMA standards in 5 databases (PubMed/Scopus/Cochrane/EMBASE/Google Scholar). The search was carried out between February 2020 and May 2023. The search terms were 'steroids' or 'superinfection' 'and' followed by 'SARS-CoV-2' or 'COVID-19'. Results: We found 77 studies, but only 10 with 3539 patients were included in the systematic review. All patients developed severe disease. The documented OR for superinfection through the meta-analysis was 1.437 (95% IC 0.869-2.378) with a p-value of 0.158 without showing a risk attributed to steroids and the development of superinfections. In the Funnel-plot analysis, no publication biases were found. Conclusion: No relationship was found between using steroids and superinfection in patients with SARS-CoV-2.
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Affiliation(s)
- Melissa González Ramírez
- Medical Doctor; Specialist in critical medicine and intensive care. Universidad Tecnológica de Pereira, Pereira, Risaralda, Colombia
| | - Jaime Andrés Hoyos Muñoz
- Medical Doctor; Specialist in critical medicine and intensive care. Universidad Tecnológica de Pereira, Pereira, Risaralda, Colombia
| | - Germán Alberto Moreno Gómez
- Medical Doctor; Clinical Epidemiologist. Ph.D. in Public Health. Universidad Tecnológica de Pereira, Pereira, Risaralda, Colombia
| | - Mateo Aguirre Flórez
- Medical Doctor. Universidad Tecnológica de Pereira, Pereira, Risaralda, Colombia
| | - José Fernando Gómez González
- Medical Doctor; Specialist in critical medicine and intensive care. Grupo de investigación en Medicina Crítica y Cuidado Intensivo (GIMCCI). Universidad Tecnológica de Pereira, Pereira, Risaralda, Colombia
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Anderson M, Holzmayer V, Harris B, Hodges A, Olivo A, Fortney T, Goldstein Y, Hirschhorn J, Pytel D, Faron ML, Cloherty G, Rodgers MA. The diversification of SARS-CoV-2 Omicron variants and evaluation of their detection with molecular and rapid antigen assays. J Clin Virol 2023; 166:105532. [PMID: 37459763 DOI: 10.1016/j.jcv.2023.105532] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/30/2023] [Accepted: 07/05/2023] [Indexed: 08/16/2023]
Abstract
BACKGROUND The SARS-CoV-2 pandemic saw the rapid rise, global spread, and diversification of the omicron variant in 2022. Given the overwhelming dominance of this variant globally and its diverse lineages, there is an urgent need to ensure that diagnostic assays are capable of detecting widely circulating omicron sub-lineages. STUDY DESIGN Remnant clinical VTM samples from SARS-CoV-2 PCR confirmed infections (n = 733) collected in Wisconsin (n = 94), New York (n = 267), and South Carolina (n = 372) throughout 2022 were sequenced, classified, and tested with m2000 RealTime SARS-CoV-2, Alinity m SARS-CoV-2, ID NOW COVID-19 v2.0, BinaxNOW COVID-19 Ag Card, and Panbio COVID-19 Rapid Test Device assays. RESULTS Sequences and lineage classifications were obtained for n = 641/733 (87.4%) samples and included delta (n = 6) and representatives from all major SARS-CoV-2 omicron variants circulating in 2022 (BA.1, BA.2, BA.3, BA.4, BA.5, BE, BF, BQ.1, and XBB). Panels of diverse omicron lineages were tested by molecular assays RealTime (n = 624), Alinity m (n = 80), and ID NOW v2.0 (n = 88) with results showing 100% detection for all samples. BinaxNOW and Panbio had sensitivities of 494/533 (92.7%) and 416/469 (88.7%), respectively for specimens with >4 log10 copies/test, consistent with expected performance for frozen specimens. Furthermore, BinaxNOW demonstrated SARS-CoV-2 detection in clinical samples 1-4 days, and up to 18 days post-symptom onset in BA.1 infected patients with >4 log10 copies/test. CONCLUSIONS This data highlights the rise and diversification of SARS-CoV-2 omicron variants over the course of 2022 and demonstrate that each of the 5 tested assays can detect the breadth of omicron variants circulating globally.
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Affiliation(s)
- Mark Anderson
- Abbott Diagnostics Division, Infectious Disease Research, Abbott Park, IL, United States of America.
| | - Vera Holzmayer
- Abbott Diagnostics Division, Infectious Disease Research, Abbott Park, IL, United States of America
| | - Barbara Harris
- Abbott Diagnostics Division, Infectious Disease Research, Abbott Park, IL, United States of America
| | - Austin Hodges
- Abbott Diagnostics Division, Infectious Disease Research, Abbott Park, IL, United States of America
| | - Ana Olivo
- Abbott Diagnostics Division, Infectious Disease Research, Abbott Park, IL, United States of America
| | - Tiffany Fortney
- Abbott Diagnostics Division, Infectious Disease Research, Abbott Park, IL, United States of America
| | - Yitz Goldstein
- Montefiore Medical Center, Department of Pathology and Laboratory Medicine, Bronx, New York, United States of America
| | - Julie Hirschhorn
- Medical University of South Carolina, Department of Pathology and Laboratory Medicine, Charleston, South Carolina, United States of America
| | - Dariusz Pytel
- Medical University of South Carolina, Department of Pathology and Laboratory Medicine, Charleston, South Carolina, United States of America
| | - Matthew L Faron
- Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Gavin Cloherty
- Abbott Diagnostics Division, Infectious Disease Research, Abbott Park, IL, United States of America
| | - Mary A Rodgers
- Abbott Diagnostics Division, Infectious Disease Research, Abbott Park, IL, United States of America
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Widyasari K, Kim S. Efficacy of novel SARS-CoV-2 rapid antigen tests in the era of omicron outbreak. PLoS One 2023; 18:e0289990. [PMID: 37561721 PMCID: PMC10414561 DOI: 10.1371/journal.pone.0289990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/30/2023] [Indexed: 08/12/2023] Open
Abstract
Following the outbreak of Omicron and its subvariants, many of the currently available rapid Ag tests (RATs) showed a decrease in clinical performance. In this study, we evaluated the clinical sensitivity of the SARS-CoV-2 Rapid Antigen Test 2.0 for nasopharyngeal swabs and SARS-CoV-2 Rapid Antigen Test 2.0 Nasal for nasal swabs in 56 symptomatic individuals by comparing the results between RATs, RT-PCR, Omicron RT-PCR, and whole-genome sequencing (WGS). Furthermore, sequences of the Omicron subvariants' spike proteins were subjected to phylogenetic analysis. Both novel RATs demonstrated a high sensitivity of up to 92.86%, (95% CI 82.71%- 98.02%), 94.23%, (95% CI 83.07%- 98.49%), and 97.95% (95% CI 87.76%- 99.89%) compared to the RT-PCR, Omicron RT-PCR, and WGS, respectively. The clinical sensitivity of RATs was at its highest when the Ct value was restricted to 15≤Ct<25, with a sensitivity of 97.05% for RdRp genes. The Omicron RT-PCR analysis revealed subvariants BA.4 or BA.5 (76.8%) and BA.2.75 (16.1%). Subsequently, the WGS analysis identified BA.5 (65.5%) as the dominant subvariant. Phylogenetic analysis of the spike protein of Omicron's subvariants showed a close relationship between BA.4, BA.5, and BA.2.75. These results demonstrated that SARS-CoV-2 Rapid Antigen Test 2.0 and SARS-CoV-2 Rapid Antigen Test 2.0 Nasal are considered useful and efficient RATs for the detection of SARS-CoV-2, particularly during the current Omicron subvariants wave.
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Affiliation(s)
- Kristin Widyasari
- Gyeongsang Institute of Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Sunjoo Kim
- Gyeongsang Institute of Medical Science, Gyeongsang National University, Jinju, Republic of Korea
- Department of Laboratory Medicine, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
- Department of Laboratory Medicine, Gyeongsang National University Changwon Hospital, Changwon, Republic of Korea
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Menting S, Erhart A, Schallig HDFH. Laboratory Evaluation of a SARS-CoV-2 RT-LAMP Test. Trop Med Infect Dis 2023; 8:320. [PMID: 37368738 DOI: 10.3390/tropicalmed8060320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/30/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
There is a need to have more accessible molecular diagnostic tests for the diagnosis of severe acute respiratory syndrome coronavirus 2 disease in low- and middle-income countries. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) may provide an attractive option as this technology does not require a complex infrastructure. In this study, the diagnostic performance of a SARS-CoV-2 RT-LAMP was evaluated using RT-PCR-confirmed clinical specimens of COVID-19-positive (n = 55) and -negative patients (n = 55) from the Netherlands. The observed sensitivity of the RT-LAMP test was 97.2% (95% CI: 82.4-98.0%) and the specificity was 100% (95% CI: 93.5-100%). The positive predictive value of the RT-LAMP was 100%, the negative predictive value 93.2% (95% CI: 84.3-97.3%), and the diagnostic accuracy was 96.4% (95% CI: 91.0-99.0%). The agreement between the RT-LAMP and the RT-PCR was "almost perfect" (κ-value: 0.92). The evaluated RT-LAMP might provide an attractive alternative molecular diagnostic tool for SARS-CoV-2 in resource limited settings.
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Affiliation(s)
- Sandra Menting
- Amsterdam University Medical Centres, Academic Medical Centre at the University of Amsterdam, Laboratory for Experimental Parasitology, Department of Clinical Microbiology and Infection Prevention, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Annette Erhart
- MRC Unit The Gambia at the LSHTM, Atlantic Boulevard, Fajara, Banjul P.O. Box 273, The Gambia
| | - Henk D F H Schallig
- Amsterdam University Medical Centres, Academic Medical Centre at the University of Amsterdam, Laboratory for Experimental Parasitology, Department of Clinical Microbiology and Infection Prevention, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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Marinov TT, Marinova RS, Marinov RT, Shelby N. Novel Approach for Identification of Basic and Effective Reproduction Numbers Illustrated with COVID-19. Viruses 2023; 15:1352. [PMID: 37376651 DOI: 10.3390/v15061352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
This paper presents a novel numerical technique for the identification of effective and basic reproduction numbers, Re and R0, for long-term epidemics, using an inverse problem approach. The method is based on the direct integration of the SIR (Susceptible-Infectious-Removed) system of ordinary differential equations and the least-squares method. Simulations were conducted using official COVID-19 data for the United States and Canada, and for the states of Georgia, Texas, and Louisiana, for a period of two years and ten months. The results demonstrate the applicability of the method in simulating the dynamics of the epidemic and reveal an interesting relationship between the number of currently infectious individuals and the effective reproduction number, which is a useful tool for predicting the epidemic dynamics. For all conducted experiments, the results show that the local maximum (and minimum) values of the time-dependent effective reproduction number occur approximately three weeks before the local maximum (and minimum) values of the number of currently infectious individuals. This work provides a novel and efficient approach for the identification of time-dependent epidemics parameters.
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Affiliation(s)
- Tchavdar T Marinov
- Department of Natural Sciences, Southern University at New Orleans, 6801 Press Drive, New Orleans, LA 70126, USA
| | - Rossitza S Marinova
- Department of Mathematical & Physical Sciences, Concordia University of Edmonton, 7128 Ada Boulevard, Edmonton, AB T5B 4E4, Canada
- Department Computer Science, Varna Free University, 9007 Varna, Bulgaria
| | - Radoslav T Marinov
- Rescale, 33 New Montgomery Street, Suite 950, San Francisco, CA 94105, USA
| | - Nicci Shelby
- Department of Natural Sciences, Southern University at New Orleans, 6801 Press Drive, New Orleans, LA 70126, USA
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Sakai-Tagawa Y, Yamayoshi S, Halfmann PJ, Wilson N, Bobholz M, Vuyk WC, Wei W, Ries H, O'Connor DH, Friedrich TC, Sordillo EM, van Bakel H, Simon V, Kawaoka Y. Sensitivity of rapid antigen tests for Omicron subvariants of SARS-CoV-2. J Med Virol 2023; 95:e28788. [PMID: 37212288 DOI: 10.1002/jmv.28788] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/22/2023] [Accepted: 05/02/2023] [Indexed: 05/23/2023]
Abstract
Diagnosis by rapid antigen tests (RATs) is useful for early initiation of antiviral treatment. Because RATs are easy to use, they can be adapted for self-testing. Several kinds of RATs approved for such use by the Japanese regulatory authority are available from drug stores and websites. Most RATs for COVID-19 are based on antibody detection of the SARS-CoV-2 N protein. Since Omicron and its subvariants have accumulated several amino acid substitutions in the N protein, such amino acid changes might affect the sensitivity of RATs. Here, we investigated the sensitivity of seven RATs available in Japan, six of which are approved for public use and one of which is approved for clinical use, for the detection of BA.5, BA.2.75, BF.7, XBB.1, and BQ.1.1, as well as the delta variant (B.1.627.2). All tested RATs detected the delta variant with a detection level between 7500 and 75 000 pfu per test, and all tested RATs showed similar sensitivity to the Omicron variant and its subvariants (BA.5, BA.2.75, BF.7, XBB.1, and BQ.1.1). Human saliva did not reduce the sensitivity of the RATs tested. Espline SARS-CoV-2 N showed the highest sensitivity followed by Inspecter KOWA SARS-CoV-2 and V Trust SARS-CoV-2 Ag. Since the RATs failed to detect low levels of infectious virus, individuals whose specimens contained less infectious virus than the detection limit would be considered negative. Therefore, it is important to note that RATs may miss individuals shedding low levels of infectious virus.
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Affiliation(s)
- Yuko Sakai-Tagawa
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Seiya Yamayoshi
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Peter J Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nancy Wilson
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Max Bobholz
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - William C Vuyk
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Wanting Wei
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Hunter Ries
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, Wisconsin, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, Wisconsin, USA
| | - Emilia M Sordillo
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Viviana Simon
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yoshihiro Kawaoka
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Infection and Advanced Research Center, The University of Tokyo Pandemic Preparedness, Tokyo, Japan
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Mohammadie ZE, Akhlaghi S, Samaeinasab S, Shaterzadeh-Bojd S, Jamialahmadi T, Sahebkar A. Clinical performance of rapid antigen tests in comparison to RT-PCR for SARS-COV-2 diagnosis in Omicron variant: A systematic review and meta-analysis. Rev Med Virol 2023; 33:e2428. [PMID: 36790832 DOI: 10.1002/rmv.2428] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/21/2023] [Accepted: 01/29/2023] [Indexed: 02/16/2023]
Abstract
The Omicron variant of concern has a high level of mutations in different genes that has raised awareness about the performance of immunological products such as vaccines and antigen detection kits. In this systematic review and meta-analysis, we investigated whether Omicron had a significant influence on rapid antigen test (RAT) performance in comparison to PCR. We registered this systematic review and meta-analysis in PROSPERO with the registration number CRD42022355510. We searched PubMed, Scopus, Embase, and Web of Science databases systematically to 1 August 2022. After article screening, we assessed the quality of the included studies based on the JBI checklist. Following data extraction, we performed a meta-analysis using R software. We included 18 qualified articles presenting sufficient data about RATs performance in comparison to RT-PCR in Omicron infections. The pooled specificity and sensitivity of RATs were 1.000 (0.997-1.000) and 0.671 (0.595-0.721), respectively. The FDA-approved kits showed a better performance than WHO-approved ones with a sensitivity of 0.728 (0.620-0.815). The use of RATs with nasal swabs showed a higher sensitivity compared with nasopharyngeal swabs. The sensitivity for samples with a CT-value >25 was 0.108 (0.048-0.227). Rapid antigen tests show impaired performance for COVID-19 diagnosis when the Omicron variant is circulating, particularly in samples with low viral loads.
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Affiliation(s)
- Zahra Eslami Mohammadie
- Student Research Committee, Faculty of Paramedical Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saeed Akhlaghi
- Department of Biostatistics, School of Health, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saeed Samaeinasab
- Immunology Board for Transplantation and Cell-Based Therapeutics (Immuno_TACT), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Shakiba Shaterzadeh-Bojd
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tannaz Jamialahmadi
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhossein Sahebkar
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,School of Medicine, The University of Western Australia, Perth, Australia.,Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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New Monoclonal Antibodies Specific for Different Epitopes of the Spike Protein of SARS-CoV-2 and Its Major Variants: Additional Tools for a More Specific COVID-19 Diagnosis. Biomedicines 2023; 11:biomedicines11020610. [PMID: 36831149 PMCID: PMC9953266 DOI: 10.3390/biomedicines11020610] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/10/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
The emergence of the new pathogen SARS-CoV-2 determined a rapid need for monoclonal antibodies (mAbs) to detect the virus in biological fluids as a rapid tool to identify infected individuals to be treated or quarantined. The majority of commercially available antigenic tests for SARS-CoV-2 rely on the detection of N antigen in biologic fluid using anti-N antibodies, and their capacity to specifically identify subjects infected by SARS-CoV-2 is questionable due to several structural analogies among the N proteins of different coronaviruses. In order to produce new specific antibodies, BALB/c mice were immunized three times at 20-day intervals with a recombinant spike (S) protein. The procedure used was highly efficient, and 40 different specific mAbs were isolated, purified and characterized, with 13 ultimately being selected for their specificity and lack of cross reactivity with other human coronaviruses. The specific epitopes recognized by the selected mAbs were identified through a peptide library and/or by recombinant fragments of the S protein. In particular, the selected mAbs recognized different linear epitopes along the S1, excluding the receptor binding domain, and along the S2 subunits of the S protein of SARS-CoV-2 and its major variants of concern. We identified combinations of anti-S mAbs suitable for use in ELISA or rapid diagnostic tests, with the highest sensitivity and specificity coming from proof-of-concept tests using recombinant antigens, SARS-CoV-2 or biological fluids from infected individuals, that represent important additional tools for the diagnosis of COVID-19.
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11
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Cianci R, Franza L, Pignataro G, Massaro MG, Rio P, Tota A, Ocarino F, Sacco Fernandez M, Franceschi F, Gasbarrini A, Gambassi G, Candelli M. Effect of COVID-19 Vaccination on the In-Hospital Prognosis of Patients Admitted during Delta and Omicron Waves in Italy. Vaccines (Basel) 2023; 11:vaccines11020373. [PMID: 36851251 PMCID: PMC9965237 DOI: 10.3390/vaccines11020373] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/31/2023] [Accepted: 02/04/2023] [Indexed: 02/10/2023] Open
Abstract
All-cause mortality related to the SARS-CoV-2 infection has declined from the first wave to subsequent waves, probably through vaccination programs and the availability of effective antiviral therapies. Our study aimed to evaluate the impact of the SARS-CoV-2 vaccination on the prognosis of infected patients. Overall, we enrolled 545 subjects during the Delta variant wave and 276 ones during the Omicron variant wave. Data were collected concerning vaccination status, clinical parameters, comorbidities, lung involvement, laboratory parameters, and pharmacological treatment. Outcomes were admission to the intensive care unit (ICU) and 30-day all-cause mortality. Overall, the final sample included 821 patients with a mean age of 62 ± 18 years [range 18-100], and 59% were men. Vaccinated patients during the Delta wave were 37% (over ¾ with two doses), while during the Omicron wave they were 57%. Vaccinated patients were older (68 vs. 57 years), and 62% had at least one comorbidity Admission to the ICU was 20%, and the mortality rate at 30 days was 14%. ICU admissions were significantly higher during the Delta wave than during Omicron (OR 1.9, 95% CI 1.2-3.1), while all-cause mortality did not differ. Unvaccinated patients had a higher risk of ICU admission (OR 2.0, 95% CI 1.3-3.1) and 30-day all-cause mortality (OR 1.7, 95% CI 1.3-2.7). Results were consistent for both Delta and Omicron variants. Overall, vaccination with at least two doses was associated with a reduced need for ICU admission. Even one shot of the vaccine was associated with a significantly reduced 30-day mortality.
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Affiliation(s)
- Rossella Cianci
- Department of Translational Medicine and Surgery, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy
| | - Laura Franza
- Emergency Medicine Unit, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy
- Correspondence:
| | - Giulia Pignataro
- Emergency Medicine Unit, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy
| | - Maria Grazia Massaro
- Department of Translational Medicine and Surgery, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy
| | - Pierluigi Rio
- Department of Translational Medicine and Surgery, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy
| | - Antonio Tota
- Department of Translational Medicine and Surgery, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy
| | - Francesca Ocarino
- Department of Translational Medicine and Surgery, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy
| | - Marta Sacco Fernandez
- Emergency Medicine Unit, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy
| | - Francesco Franceschi
- Emergency Medicine Unit, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy
| | - Antonio Gasbarrini
- Department of Translational Medicine and Surgery, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy
| | - Giovanni Gambassi
- Department of Translational Medicine and Surgery, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy
| | - Marcello Candelli
- Emergency Medicine Unit, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy
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