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Sarkar M, Madabhavi I. COVID-19 mutations: An overview. World J Methodol 2024; 14:89761. [DOI: 10.5662/wjm.v14.i3.89761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 02/07/2024] [Accepted: 04/17/2024] [Indexed: 06/25/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) belongs to the genus Beta coronavirus and the family of Coronaviridae. It is a positive-sense, non-segmented single-strand RNA virus. Four common types of human coronaviruses circulate globally, particularly in the fall and winter seasons. They are responsible for 10%-30% of all mild upper respiratory tract infections in adults. These are 229E, NL63 of the Alfacoronaviridae family, OC43, and HKU1 of the Betacoronaviridae family. However, there are three highly pathogenic human coronaviruses: SARS-CoV-2, Middle East respiratory syndrome coronavirus, and the latest pandemic caused by the SARS-CoV-2 infection. All viruses, including SARS-CoV-2, have the inherent tendency to evolve. SARS-CoV-2 is still evolving in humans. Additionally, due to the development of herd immunity, prior infection, use of medication, vaccination, and antibodies, the viruses are facing immune pressure. During the replication process and due to immune pressure, the virus may undergo mutations. Several SARS-CoV-2 variants, including the variants of concern (VOCs), such as B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617/B.1.617.2 (Delta), P.1 (Gamma), and B.1.1.529 (Omicron) have been reported from various parts of the world. These VOCs contain several important mutations; some of them are on the spike proteins. These mutations may lead to enhanced infectivity, transmissibility, and decreased neutralization efficacy by monoclonal antibodies, convalescent sera, or vaccines. Mutations may also lead to a failure of detection by molecular diagnostic tests, leading to a delayed diagnosis, increased community spread, and delayed treatment. We searched PubMed, EMBASE, Covariant, the Stanford variant Database, and the CINAHL from December 2019 to February 2023 using the following search terms: VOC, SARS-CoV-2, Omicron, mutations in SARS-CoV-2, etc. This review discusses the various mutations and their impact on infectivity, transmissibility, and neutralization efficacy.
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Affiliation(s)
- Malay Sarkar
- Department of Pulmonary Medicine, Indira Gandhi Medical College, Shimla 171001, Himachal Pradesh, India
| | - Irappa Madabhavi
- Department of Medical and Pediatric Oncology and Hematology, J N Medical College, and KAHER, Belagavi, Karnataka 590010, India
- Department of Medical and Pediatric Oncology and Hematology, Kerudi Cancer Hospital, Bagalkot, Karnataka 587103, India
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2
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Pasev M, Trifonova A, Velichkov A, Terzieva V. Duration of antibody response to the receptor binding domain of SARS-CoV-2 in infected or vaccinated individuals - A one year retrospective cohort study. Int Immunopharmacol 2024; 133:112084. [PMID: 38621337 DOI: 10.1016/j.intimp.2024.112084] [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: 11/21/2023] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
The 2019 coronavirus (COVID-19) pandemic raised many scientific and medical questions. Of interest are the duration and effectiveness of the humoral immune response, especially since part of the pandemic occurred in the presence of anti-SARS-CoV-2 vaccines. We retrospectively studied 564 serum samples from 393 post-infected and vaccinated individuals to investigate the longevity and magnitude of the anti-spike IgG response. Our results showed that SARS-CoV-2 anti-spike IgG antibodies are retained for nine-twelve months, in both groups. In the vaccinated group we found higher IgG levels, but with a steeper decrease in titer over the study period. The recovered group's antibody levels correlated well with the national infection trendline for 2021. Both groups showed different, but distinct neutralizing capabilities towards RBD. The anti-Spike IgG response was sustained and efficient, independently of the triggering event, infection or vaccination, with the adaptive capacity against new viral variants being more valuable after infection.
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Affiliation(s)
- Martin Pasev
- Department of Clinical Microbiology and Virology, University Hospital Lozenetz, Sofia University "Sv. Kliment Ohridski", Sofia, Bulgaria
| | - Angelina Trifonova
- Department of Clinical Microbiology and Virology, University Hospital Lozenetz, Sofia University "Sv. Kliment Ohridski", Sofia, Bulgaria
| | - Andrey Velichkov
- Laboratory of Reproductive OMICs Technologies, Institute of Biology and Immunology of Reproduction "Acad. Kiril Bratanov", Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Velislava Terzieva
- Department of Clinical Microbiology and Virology, University Hospital Lozenetz, Sofia University "Sv. Kliment Ohridski", Sofia, Bulgaria; Laboratory of Reproductive OMICs Technologies, Institute of Biology and Immunology of Reproduction "Acad. Kiril Bratanov", Bulgarian Academy of Sciences, Sofia, Bulgaria.
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3
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Kumar A, Tripathi P, Kumar P, Shekhar R, Pathak R. From Detection to Protection: Antibodies and Their Crucial Role in Diagnosing and Combatting SARS-CoV-2. Vaccines (Basel) 2024; 12:459. [PMID: 38793710 PMCID: PMC11125746 DOI: 10.3390/vaccines12050459] [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: 03/13/2024] [Revised: 04/20/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
Understanding the antibody response to SARS-CoV-2, the virus responsible for COVID-19, is crucial to comprehending disease progression and the significance of vaccine and therapeutic development. The emergence of highly contagious variants poses a significant challenge to humoral immunity, underscoring the necessity of grasping the intricacies of specific antibodies. This review emphasizes the pivotal role of antibodies in shaping immune responses and their implications for diagnosing, preventing, and treating SARS-CoV-2 infection. It delves into the kinetics and characteristics of the antibody response to SARS-CoV-2 and explores current antibody-based diagnostics, discussing their strengths, clinical utility, and limitations. Furthermore, we underscore the therapeutic potential of SARS-CoV-2-specific antibodies, discussing various antibody-based therapies such as monoclonal antibodies, polyclonal antibodies, anti-cytokines, convalescent plasma, and hyperimmunoglobulin-based therapies. Moreover, we offer insights into antibody responses to SARS-CoV-2 vaccines, emphasizing the significance of neutralizing antibodies in order to confer immunity to SARS-CoV-2, along with emerging variants of concern (VOCs) and circulating Omicron subvariants. We also highlight challenges in the field, such as the risks of antibody-dependent enhancement (ADE) for SARS-CoV-2 antibodies, and shed light on the challenges associated with the original antigenic sin (OAS) effect and long COVID. Overall, this review intends to provide valuable insights, which are crucial to advancing sensitive diagnostic tools, identifying efficient antibody-based therapeutics, and developing effective vaccines to combat the evolving threat of SARS-CoV-2 variants on a global scale.
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Affiliation(s)
- Anoop Kumar
- Molecular Diagnostic Laboratory, National Institute of Biologicals, Noida 201309, India
| | - Prajna Tripathi
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA;
| | - Prashant Kumar
- R. Ken Coit College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA
| | - Ritu Shekhar
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Rajiv Pathak
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
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Wralstad EC, Raines RT. Sensitive detection of SARS-CoV-2 main protease 3CL pro with an engineered ribonuclease zymogen. Protein Sci 2024; 33:e4916. [PMID: 38501598 PMCID: PMC10949392 DOI: 10.1002/pro.4916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/13/2024] [Accepted: 01/17/2024] [Indexed: 03/20/2024]
Abstract
Alongside vaccines and antiviral therapeutics, diagnostic tools are a crucial aid in combating the COVID-19 pandemic caused by the etiological agent SARS-CoV-2. All common assays for infection rely on the detection of viral sub-components, including structural proteins of the virion or fragments of the viral genome. Selective pressure imposed by human intervention of COVID-19 can, however, induce viral mutations that decrease the sensitivity of diagnostic assays based on biomolecular structure, leading to an increase in false-negative results. In comparison, mutations are unlikely to alter the function of viral proteins, and viral machinery is under less selective pressure from vaccines and therapeutics. Accordingly, diagnostic assays that rely on biomolecular function can be more robust than ones that rely on biopolymer structure. Toward this end, we used a split intein to create a circular ribonuclease zymogen that is activated by the SARS-CoV-2 main protease, 3CLpro . Zymogen activation by 3CLpro leads to a >300-fold increase in ribonucleolytic activity, which can be detected with a highly sensitive fluorogenic substrate. This coupled assay can detect low nanomolar concentrations of 3CLpro within a timeframe comparable to that of common antigen-detection protocols. More generally, the concept of detecting a protease by activating a ribonuclease could be the basis of diagnostic tools for other indications.
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Affiliation(s)
- Evans C. Wralstad
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Ronald T. Raines
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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Xu X, Deng Y, Ding J, Shi X, Zheng X, Wang D, Yang Y, Liu L, Wang C, Li S, Gu H, Poon LLM, Zhang T. Refining detection methods for emerging SARS-CoV-2 mutants in wastewater: A case study on the Omicron variants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166215. [PMID: 37591380 DOI: 10.1016/j.scitotenv.2023.166215] [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: 04/10/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/19/2023]
Abstract
COVID-19 is an ongoing public health threat worldwide driven by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Wastewater surveillance has emerged as a complementary tool to clinical surveillance to control the COVID-19 pandemic. With the emergence of new variants of SARS-CoV-2, accumulated mutations that occurred in the SARS-CoV-2 genome raise new challenges for RT-qPCR diagnosis used in wastewater surveillance. There is a pressing need to develop refined methods for modifying primer/probes to better detect these emerging variants in wastewater. Here, we exemplified this process by focusing on the Omicron variants, for which we have developed and validated a modified detection method. We first modified the primers/probe mismatches of three assays commonly used in wastewater surveillance according to in silico analysis results for the mutations of 882 sequences collected during the fifth-wave outbreak in Hong Kong, and then evaluated them alongside the seven original assays. The results showed that five of seven original assays had better sensitivity for detecting Omicron variants, with the limits of detection (LoDs) ranging from 1.53 to 2.76 copies/μL. UCDC-N1 and Charité-E sets had poor performances, having LoDs higher than 10 copies/μL and false-positive/false-negative results in wastewater testing, probably due to the mismatch and demonstrating the need for modification of primer/probe sequences. The modified assays exhibited higher sensitivity and specificity, along with better reproducibility in detecting 81 wastewater samples. In addition, the sequencing results of six wastewater samples by Illumina also validated the presence of mismatches in the primer/probe binding sites of the three assays. This study highlights the importance of re-configuration of the primer-probe sets and refinements for the sequences to ensure the diagnostic effectiveness of RT-qPCR detection.
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Affiliation(s)
- Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jiahui Ding
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xianghui Shi
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiawan Zheng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Dou Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yu Yang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Shuxian Li
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Haogao Gu
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong, China
| | - Leo L M Poon
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong, China; HKU-Pasteur Research Pole, The University of Hong Kong, Sassoon Road, Hong Kong, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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de Mello Malta F, Amgarten D, Marra AR, Petroni RC, da Silva Nali LH, Siqueira RA, Neto MC, Oler SC, Pinho JRR. Nucleocapsid single point-mutation associated with drop-out on RT-PCR assay for SARS-CoV-2 detection. BMC Infect Dis 2023; 23:714. [PMID: 37872472 PMCID: PMC10591358 DOI: 10.1186/s12879-023-08707-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023] Open
Abstract
BACKGROUND Since its beginning, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been a challenge for clinical and molecular diagnostics, because it has been caused by a novel viral agent. Whole-genome sequencing assisted in the characterization and classification of SARS-CoV-2, and it is an essential tool to genomic surveillance aiming to identify potentials hot spots that could impact on vaccine immune response and on virus diagnosis. We describe two cases of failure at the N2 target of the RT-PCR test Xpert® Xpress SARS-CoV-2. METHODS Total nucleic acid from the Nasopharyngeal (NP) and oropharyngeal (OP) swab samples and cell supernatant isolates were obtained. RNA samples were submitted to random amplification. Raw sequencing data were subjected to sequence quality controls, removal of human contaminants by aligning against the HG19 reference genome, taxonomic identification of other pathogens and genome recovery through assembly and manual curation. RT-PCR test Xpert® Xpress SARS-CoV-2 was used for molecular diagnosis of SARS-CoV-2 infection, samples were tested in duplicates. RESULTS We identified 27 samples positive for SARS-CoV-2 with a nucleocapsid (N) gene drop out on Cepheid Xpert® Xpress SARS-CoV-2 assay. Sequencing of 2 of 27 samples revealed a single common mutation in the N gene C29197T, potentially involved in the failed detection of N target. CONCLUSIONS This study highlights the importance of genomic data to update molecular tests and vaccines.
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Affiliation(s)
- Fernanda de Mello Malta
- Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil
| | - Deyvid Amgarten
- Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil
| | - Alexandre Rodrigues Marra
- Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil
| | - Roberta Cardoso Petroni
- Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil
| | - Luiz Henrique da Silva Nali
- Post-Graduation Program in Health Sciences, Santo Amaro University, Rua Prof. Enéas de Siqueira Neto, 340 - Jardim das Imbuias, Sao Paulo, SP, Brazil
| | - Ricardo Andreotti Siqueira
- Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil
| | - Miguel Cendoroglo Neto
- Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil
| | - Silvia Cassiano Oler
- Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil
| | - João Renato Rebello Pinho
- Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil.
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Lim HGM, Fann YC, Lee YCG. COWID: an efficient cloud-based genomics workflow for scalable identification of SARS-COV-2. Brief Bioinform 2023; 24:bbad280. [PMID: 37738400 PMCID: PMC10516370 DOI: 10.1093/bib/bbad280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 07/15/2023] [Accepted: 07/19/2023] [Indexed: 09/24/2023] Open
Abstract
Implementing a specific cloud resource to analyze extensive genomic data on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a challenge when resources are limited. To overcome this, we repurposed a cloud platform initially designed for use in research on cancer genomics (https://cgc.sbgenomics.com) to enable its use in research on SARS-CoV-2 to build Cloud Workflow for Viral and Variant Identification (COWID). COWID is a workflow based on the Common Workflow Language that realizes the full potential of sequencing technology for use in reliable SARS-CoV-2 identification and leverages cloud computing to achieve efficient parallelization. COWID outperformed other contemporary methods for identification by offering scalable identification and reliable variant findings with no false-positive results. COWID typically processed each sample of raw sequencing data within 5 min at a cost of only US$0.01. The COWID source code is publicly available (https://github.com/hendrick0403/COWID) and can be accessed on any computer with Internet access. COWID is designed to be user-friendly; it can be implemented without prior programming knowledge. Therefore, COWID is a time-efficient tool that can be used during a pandemic.
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Affiliation(s)
- Hendrick Gao-Min Lim
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan 11031
- Department of Medical Research, Tzu Chi Hospital Indonesia, Pantai Indah Kapuk, Greater Jakarta, Indonesia 14470
| | - Yang C Fann
- IT and Bioinformatics Program, Division of Intramural, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA 20892
| | - Yuan-Chii Gladys Lee
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan 11031
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Murray A, Ojeda J, El Merhebi O, Calvo-Marzal P, Gerasimova Y, Chumbimuni-Torres K. Cost-Effective Modular Biosensor for SARS-CoV-2 and Influenza A Detection. BIOSENSORS 2023; 13:874. [PMID: 37754108 PMCID: PMC10526333 DOI: 10.3390/bios13090874] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/03/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023]
Abstract
A modular, multi-purpose, and cost-effective electrochemical biosensor based on a five-stranded four-way junction (5S-4WJ) system was developed for SARS-CoV-2 (genes S and N) and Influenza A virus (gene M) detection. The 5S-4WJ structure consists of an electrode-immobilized universal stem-loop (USL) strand, two auxiliary DNA strands, and a universal methylene blue redox strand (UMeB). This design allows for the detection of specific nucleic acid sequences using square wave voltammetry (SWV). The sequence-specific auxiliary DNA strands (m and f) ensure selectivity of the biosensor for target recognition utilizing the same USL and UMeB components. An important feature of this biosensor is the ability to reuse the USL-modified electrodes to detect the same or alternative targets in new samples. This is accomplished by a simple procedure involving rinsing the electrodes with water to disrupt the 5S-4WJ structure and subsequent re-hybridization of the USL strand with the appropriate set of strands for a new analysis. The biosensor exhibited minimal loss in signal after rehybridization, demonstrating its potential as a viable multiplex assay for both current and future pathogens, with a low limit of quantification (LOQ) of as low as 17 pM.
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Affiliation(s)
| | | | | | | | | | - Karin Chumbimuni-Torres
- Department of Chemistry, University of Central Florida, Orlando, FL 32816, USA; (A.M.); (J.O.); (O.E.M.); (P.C.-M.); (Y.G.)
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Vierbaum L, Wojtalewicz N, Grunert HP, Zimmermann A, Scholz A, Goseberg S, Kaiser P, Duehring U, Drosten C, Corman V, Niemeyer D, Rabenau HF, Obermeier M, Nitsche A, Michel J, Puyskens A, Huggett JF, O'Sullivan DM, Busby E, Cowen S, Vallone PM, Cleveland MH, Falak S, Kummrow A, Schellenberg I, Zeichhardt H, Kammel M. Results of German external quality assessment schemes for SARS-CoV-2 antigen detection. Sci Rep 2023; 13:13206. [PMID: 37580353 PMCID: PMC10425338 DOI: 10.1038/s41598-023-40330-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 08/08/2023] [Indexed: 08/16/2023] Open
Abstract
The COVID-19 pandemic illustrated the important role of diagnostic tests, including lateral flow tests (LFTs), in identifying patients and their contacts to slow the spread of infections. INSTAND performed external quality assessments (EQA) for SARS-CoV-2 antigen detection with lyophilized and chemically inactivated cell culture supernatant of SARS-CoV-2 infected Vero cells. A pre-study demonstrated the suitability of the material. Participants reported qualitative and/or quantitative antigen results using either LFTs or automated immunoassays for five EQA samples per survey. 711 data sets were reported for LFT detection in three surveys in 2021. This evaluation focused on the analytical sensitivity of different LFTs and automated immunoassays. The inter-laboratory results showed at least 94% correct results for non-variant of concern (VOC) SARS-CoV-2 antigen detection for viral loads of ≥ 4.75 × 106 copies/mL and SARS-CoV-2 negative samples. Up to 85% had success for a non-VOC viral load of ~ 1.60 × 106 copies/mL. A viral load of ~ 1.42 × 107 copies/mL of the Delta VOC was reported positive in > 96% of results. A high specificity was found with almost 100% negative SARS-CoV-2 antigen results for HCoV 229E and HCoV NL63 positive samples. Quantitative results correlated with increasing SARS-CoV-2 viral load but showed a broad scatter. This study shows promising SARS-CoV-2 antigen test performance of the participating laboratories, but further investigations with the now predominant Omicron VOC are needed.
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Affiliation(s)
- Laura Vierbaum
- INSTAND E.V., Society for Promoting Quality Assurance in Medical Laboratories, Ubierstr. 20, 40223, Düsseldorf, Germany.
| | - Nathalie Wojtalewicz
- INSTAND E.V., Society for Promoting Quality Assurance in Medical Laboratories, Ubierstr. 20, 40223, Düsseldorf, Germany
| | - Hans-Peter Grunert
- GBD Gesellschaft für Biotechnologische Diagnostik mbH, Berlin, Potsdamer Chaussee 80, 14129, Berlin, Germany
| | - Anika Zimmermann
- IQVD GmbH, Institut für Qualitätssicherung in der Virusdiagnostik, Berlin, Potsdamer Chaussee 80, 14129, Berlin, Germany
| | - Annemarie Scholz
- IQVD GmbH, Institut für Qualitätssicherung in der Virusdiagnostik, Berlin, Potsdamer Chaussee 80, 14129, Berlin, Germany
| | - Sabine Goseberg
- INSTAND E.V., Society for Promoting Quality Assurance in Medical Laboratories, Ubierstr. 20, 40223, Düsseldorf, Germany
| | - Patricia Kaiser
- INSTAND E.V., Society for Promoting Quality Assurance in Medical Laboratories, Ubierstr. 20, 40223, Düsseldorf, Germany
| | - Ulf Duehring
- GBD Gesellschaft für Biotechnologische Diagnostik mbH, Berlin, Potsdamer Chaussee 80, 14129, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité - University Medicine Berlin; National Consultant Laboratory for Coronaviruses; German Centre for Infection Research, Berlin, Berlin, Germany
| | - Victor Corman
- Institute of Virology, Charité - University Medicine Berlin; National Consultant Laboratory for Coronaviruses; German Centre for Infection Research, Berlin, Berlin, Germany
| | - Daniela Niemeyer
- Institute of Virology, Charité - University Medicine Berlin; National Consultant Laboratory for Coronaviruses; German Centre for Infection Research, Berlin, Berlin, Germany
| | - Holger F Rabenau
- Institute of Virology, Charité - University Medicine Berlin; National Consultant Laboratory for Coronaviruses; German Centre for Infection Research, Berlin, Berlin, Germany
| | - Martin Obermeier
- Institute for Medical Virology, University Hospital, Goethe University Frankfurt, Frankfurt, Hessen, Germany
| | | | - Janine Michel
- Robert Koch Institute, Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Andreas Puyskens
- Robert Koch Institute, Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Jim F Huggett
- National Measurement Laboratory, LGC, Teddington, Middlesex, UK
- School of Biosciences and Medicine, Faculty of Health and Medical Science, University of Surrey, Guildford, UK
| | | | - Eloise Busby
- National Measurement Laboratory, LGC, Teddington, Middlesex, UK
| | - Simon Cowen
- National Measurement Laboratory, LGC, Teddington, Middlesex, UK
| | - Peter M Vallone
- NIST, National Institute of Standards and Technology, Applied Genetics Group, Biomolecular Measurement Division, Materials Measurement Laboratory, Gaithersburg, MD, USA
| | - Megan H Cleveland
- NIST, National Institute of Standards and Technology, Applied Genetics Group, Biomolecular Measurement Division, Materials Measurement Laboratory, Gaithersburg, MD, USA
| | - Samreen Falak
- Physikalisch-Technische Bundesanstalt, Berlin, Germany
| | | | - Ingo Schellenberg
- INSTAND E.V., Society for Promoting Quality Assurance in Medical Laboratories, Ubierstr. 20, 40223, Düsseldorf, Germany
- Institute of Bioanalytical Sciences, Center of Life Sciences, Anhalt University of Applied Sciences, Bernburg, Saxony-Anhalt, Germany
| | - Heinz Zeichhardt
- INSTAND E.V., Society for Promoting Quality Assurance in Medical Laboratories, Ubierstr. 20, 40223, Düsseldorf, Germany
- IQVD GmbH, Institut für Qualitätssicherung in der Virusdiagnostik, Berlin, Potsdamer Chaussee 80, 14129, Berlin, Germany
- GBD Gesellschaft für Biotechnologische Diagnostik mbH, Berlin, Potsdamer Chaussee 80, 14129, Berlin, Germany
| | - Martin Kammel
- INSTAND E.V., Society for Promoting Quality Assurance in Medical Laboratories, Ubierstr. 20, 40223, Düsseldorf, Germany
- IQVD GmbH, Institut für Qualitätssicherung in der Virusdiagnostik, Berlin, Potsdamer Chaussee 80, 14129, Berlin, Germany
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Yaghoobizadeh F, Roayaei Ardakani M, Ranjbar MM, Khosravi M, Galehdari H. Preparation, Purification and Performance Evaluation of Polyclonal Antibody Against SARS-CoV-2 Produced in Rat. Adv Pharm Bull 2023; 13:563-572. [PMID: 37646054 PMCID: PMC10460799 DOI: 10.34172/apb.2023.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 08/21/2022] [Accepted: 11/02/2022] [Indexed: 09/01/2023] Open
Abstract
Purpose Among all known human coronaviruses, some viruses (e.g., SARS-CoV-2) cause severe pneumonia or even death. With the regard to its spread and the importance of its rapid identification/treatment, and because pAbs are relatively cheap, able to bind to more sites on antigens and even neutralize them, this study was done for the production and purification of anti-SARS-CoV-2 polyclonal antibodies (pAb) in rats. Methods Viral antigen purification was performed by PEG/NaCl precipitation. The efficiency of the sucrose cushion method was also investigated to produce a purer antigen. Immunization was done and antibody purification was performed by ammonium sulfate precipitation (33%), dialysis, and ion-exchange chromatography. Western blotting and enzyme-linked immunosorbent assay (ELISA) were performed to verify the antibody specificity. All data were analyzed by SPSS software. Results The results showed that the amount of concentrated virus increased with the increase of PEG concentration. Moreover, the sucrose cushion method increased its purity. Besides, induction of immune response in rats for pAb production with high titers was reached via these antigens and ELISA/western blot results indicated a suitable antibody-antigen interaction. Additionally, it was shown that ion-exchange chromatography could be a suitable technique for IgG purification. Conclusion Herein, we presented a simple and cheap method for the purification of whole viral particles with relatively high quality. The results verified that these antigens could elicit a good immune response in the rat. The obtained pAbs showed a good specificity toward SARS-CoV-2 antigens. Accordingly, this study proposes a promising method for viral vaccine development.
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Affiliation(s)
- Fatemeh Yaghoobizadeh
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, Iran
| | - Mohammad Roayaei Ardakani
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, Iran
| | | | - Mohammad Khosravi
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, Iran
| | - Hamid Galehdari
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, Iran
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11
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Dong T, Wang M, Liu J, Ma P, Pang S, Liu W, Liu A. Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives. Chem Sci 2023; 14:6149-6206. [PMID: 37325147 PMCID: PMC10266450 DOI: 10.1039/d2sc06665c] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/03/2023] [Indexed: 06/17/2023] Open
Abstract
The disastrous spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has induced severe public healthcare issues and weakened the global economy significantly. Although SARS-CoV-2 infection is not as fatal as the initial outbreak, many infected victims suffer from long COVID. Therefore, rapid and large-scale testing is critical in managing patients and alleviating its transmission. Herein, we review the recent advances in techniques to detect SARS-CoV-2. The sensing principles are detailed together with their application domains and analytical performances. In addition, the advantages and limits of each method are discussed and analyzed. Besides molecular diagnostics and antigen and antibody tests, we also review neutralizing antibodies and emerging SARS-CoV-2 variants. Further, the characteristics of the mutational locations in the different variants with epidemiological features are summarized. Finally, the challenges and possible strategies are prospected to develop new assays to meet different diagnostic needs. Thus, this comprehensive and systematic review of SARS-CoV-2 detection technologies may provide insightful guidance and direction for developing tools for the diagnosis and analysis of SARS-CoV-2 to support public healthcare and effective long-term pandemic management and control.
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Affiliation(s)
- Tao Dong
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
- School of Pharmacy, Medical College, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Mingyang Wang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Junchong Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Pengxin Ma
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Shuang Pang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Wanjian Liu
- Qingdao Hightop Biotech Co., Ltd 369 Hedong Road, Hi-tech Industrial Development Zone Qingdao 266112 China
| | - Aihua Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
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12
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Park SJ, Lee S, Lee D, Lee NE, Park JS, Hong JH, Jang JW, Kim H, Roh S, Lee G, Lee D, Cho SY, Park C, Lee DG, Lee R, Nho D, Yoon DS, Yoo YK, Lee JH. PCR-like performance of rapid test with permselective tunable nanotrap. Nat Commun 2023; 14:1520. [PMID: 36934093 PMCID: PMC10024276 DOI: 10.1038/s41467-023-37018-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/24/2023] [Indexed: 03/20/2023] Open
Abstract
Highly sensitive rapid testing for COVID-19 is essential for minimizing virus transmission, especially before the onset of symptoms and in asymptomatic cases. Here, we report bioengineered enrichment tools for lateral flow assays (LFAs) with enhanced sensitivity and specificity (BEETLES2), achieving enrichment of SARS-CoV-2 viruses, nucleocapsid (N) proteins and immunoglobulin G (IgG) with 3-minute operation. The limit of detection is improved up to 20-fold. We apply this method to clinical samples, including 83% with either intermediate (35%) or low viral loads (48%), collected from 62 individuals (n = 42 for positive and n = 20 for healthy controls). We observe diagnostic sensitivity, specificity, and accuracy of 88.1%, 100%, and 91.9%, respectively, compared with commercial LFAs alone achieving 14.29%, 100%, and 41.94%, respectively. BEETLES2, with permselectivity and tunability, can enrich the SARS-CoV-2 virus, N proteins, and IgG in the nasopharyngeal/oropharyngeal swab, saliva, and blood serum, enabling reliable and sensitive point-of-care testing, facilitating fast early diagnosis.
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Affiliation(s)
- Seong Jun Park
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea
| | - Seungmin Lee
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea
- School of Biomedical Engineering, Korea University, 145 Anam-ro, Seongbuk, Seoul, 02841, Republic of Korea
| | - Dongtak Lee
- School of Biomedical Engineering, Korea University, 145 Anam-ro, Seongbuk, Seoul, 02841, Republic of Korea
| | - Na Eun Lee
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Jeong Soo Park
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea
| | - Ji Hye Hong
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea
- School of Biomedical Engineering, Korea University, 145 Anam-ro, Seongbuk, Seoul, 02841, Republic of Korea
| | - Jae Won Jang
- School of Biomedical Engineering, Korea University, 145 Anam-ro, Seongbuk, Seoul, 02841, Republic of Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, Republic of Korea
| | - Hyunji Kim
- School of Biomedical Engineering, Korea University, 145 Anam-ro, Seongbuk, Seoul, 02841, Republic of Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, Republic of Korea
| | - Seokbeom Roh
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, Republic of Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong, 30019, Korea
| | - Gyudo Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, Republic of Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong, 30019, Korea
| | - Dongho Lee
- CALTH Inc., Changeop-ro 54, Seongnam, Gyeonggi, 13449, Republic of Korea
| | - Sung-Yeon Cho
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Chulmin Park
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Dong-Gun Lee
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Raeseok Lee
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Dukhee Nho
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Dae Sung Yoon
- School of Biomedical Engineering, Korea University, 145 Anam-ro, Seongbuk, Seoul, 02841, Republic of Korea.
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, Republic of Korea.
- Astrion Inc, Seoul, 02841, Republic of Korea.
| | - Yong Kyoung Yoo
- Department of Electronic Engineering, Catholic Kwandong University, 24, Beomil-ro 579 beon-gil, Gangneung-si, Gangwon-do, 25601, Republic of Korea.
| | - Jeong Hoon Lee
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea.
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13
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Seymen AA, Gulten E, Ozgur E, Ortaç B, Akdemir I, Cinar G, Saricaoglu EM, Guney-Esken G, Akkus E, Can F, Karahan ZC, Azap A, Tuncay E. Clinical evaluation of DIAGNOVIR SARS-CoV-2 ultra-rapid antigen test performance compared to PCR-based testing. Sci Rep 2023; 13:4438. [PMID: 36932107 PMCID: PMC10021059 DOI: 10.1038/s41598-023-31177-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 03/07/2023] [Indexed: 03/19/2023] Open
Abstract
Coronavirus Disease-19 (COVID-19) is a highly contagious infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The development of rapid antigen tests has contributed to easing the burden on healthcare and lifting restrictions by detecting infected individuals to help prevent further transmission of the virus. We developed a state-of-art rapid antigen testing system, named DIAGNOVIR, based on immune-fluorescence analysis, which can process and give the results in a minute. In our study, we assessed the performance of the DIAGNOVIR and compared the results with those of the qRT-PCR test. Our results demonstrated that the sensitivity and specificity of the DIAGNOVIR were 94% and 99.2%, respectively, with a 100% sensitivity and 96.97% specificity, among asymptomatic patients. In addition, DIAGNOVIR can detect SARS‑CoV‑2 with 100% sensitivity up to 5 days after symptom onset. We observed that the DIAGNOVIR Rapid Antigen Test's limit of detection (LoD) was not significantly affected by the SARS‑CoV‑2 variants including Wuhan, alpha (B1.1.7), beta (B.1.351), delta (B.1.617.2) and omicron (B.1.1.529) variants, and LoD was calculated as 8 × 102, 6.81 × 101.5, 3.2 × 101.5, 1 × 103, and 1 × 103.5 TCID50/mL, respectively. Our results indicated that DIAGNOVIR can detect all SARS-CoV-2 variants in just seconds with higher sensitivity and specificity lower testing costs and decreased turnover time.
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Affiliation(s)
- Ali Aytac Seymen
- EA Teknoloji LLC Bilkent CyberPark, 06800, Ankara, Turkey
- Felisya Biyomedikal, Bilkent, 06800, Ankara, Turkey
- Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, 06800, Turkey
| | - Ezgi Gulten
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Ankara University, Ankara, 06230, Turkey
| | - Erol Ozgur
- EA Teknoloji LLC Bilkent CyberPark, 06800, Ankara, Turkey
- James C. Wyant College of Optical Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Bülend Ortaç
- EA Teknoloji LLC Bilkent CyberPark, 06800, Ankara, Turkey
- Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, 06800, Turkey
| | - Irem Akdemir
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Ankara University, Ankara, 06230, Turkey
| | - Gule Cinar
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Ankara University, Ankara, 06230, Turkey
| | - Elif Mukime Saricaoglu
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Ankara University, Ankara, 06230, Turkey
| | - Gulen Guney-Esken
- Koc University IsBank Research Center for Infectious Diseases (KUISCID), Istanbul, Turkey
| | - Erman Akkus
- Department of Internal Medicine, Faculty of Medicine, Ankara University, Ankara, 06230, Turkey
| | - Fusun Can
- School of Medicine, Department of Medical Microbiology, Koc University, Istanbul, Turkey
- Koc University IsBank Research Center for Infectious Diseases (KUISCID), Istanbul, Turkey
| | - Zeynep Ceren Karahan
- Department of Medical Microbiology, Faculty of Medicine, Ankara University, Ankara, 06230, Turkey
| | - Alpay Azap
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Ankara University, Ankara, 06230, Turkey
| | - Erkan Tuncay
- Departments of Biophysics, Faculty of Medicine, Ankara University, Ankara, 06230, Turkey.
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14
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Li J, Shi J, Zhou Z, Yang B, Cao J, Cao Z, Zeng Q, Hu Z, Yang X. Development of an Antigen Detection Kit Capable of Discriminating the Omicron Mutants of SARS-CoV-2. Vaccines (Basel) 2023; 11:vaccines11020303. [PMID: 36851181 PMCID: PMC9964912 DOI: 10.3390/vaccines11020303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
INTRODUCTION Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread around the world, caused millions of deaths and a severe illness which poses a serious threat to human health. OBJECTIVE To develop an antigen detection kit that can identify Omicron novel coronavirus mutants. METHODS BALB/c mice were immunized with the nucleocapsid protein of SARS-CoV-2 Omicron mutant treated with β-propiolactone. After fusion of myeloma cells with immune cells, Elisa was used to screen the cell lines capable of producing monoclonal antibodies. The detection kit was prepared by colloidal gold immunochromatography. Finally, the sensitivity, specificity and anti-interference of the kit were evaluated by simulating positive samples. RESULTS The sensitivity of the SARS-CoV-2 antigen detection kit can reach 62.5 TCID50/mL, and it has good inclusiveness for different SARS-CoV-2 strains. The kit had no cross-reaction with common respiratory pathogens, and its sensitivity was still not affected under the action of different concentrations of interferences, indicating that it had good specificity and stability. CONCLUSION In this study, monoclonal antibodies with high specificity to the N protein of the Omicron mutant strain were obtained by monoclonal antibody screening technology. Colloidal gold immunochromatography technology was used to prepare an antigen detection kit with high sensitivity to detect and identify the mutant Omicron strain.
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Affiliation(s)
- Jiaji Li
- School of Bioengineering and Food Science, Hubei University of Technology, Wuhan 430068, China
| | - Jinrong Shi
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Zhijun Zhou
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Bo Yang
- School of Bioengineering and Food Science, Hubei University of Technology, Wuhan 430068, China
| | - Jiamin Cao
- School of Bioengineering and Food Science, Hubei University of Technology, Wuhan 430068, China
| | - Zhongsen Cao
- School of Bioengineering and Food Science, Hubei University of Technology, Wuhan 430068, China
| | | | - Zheng Hu
- School of Bioengineering and Food Science, Hubei University of Technology, Wuhan 430068, China
- Correspondence: (Z.H.); (X.Y.)
| | - Xiaoming Yang
- China National Biotec Group Company Limited, Beijing 100029, China
- National Engineering Technology Research Center for Combined Vaccines, Wuhan 430207, China
- Correspondence: (Z.H.); (X.Y.)
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15
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Zhou B, Zhou H, Zhang X, Xu X, Chai Y, Zheng Z, Kot AC, Zhou Z. TEMPO: A transformer-based mutation prediction framework for SARS-CoV-2 evolution. Comput Biol Med 2023; 152:106264. [PMID: 36535209 PMCID: PMC9747230 DOI: 10.1016/j.compbiomed.2022.106264] [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: 09/18/2022] [Revised: 10/16/2022] [Accepted: 10/30/2022] [Indexed: 12/15/2022]
Abstract
The widespread of SARS-CoV-2 presents a significant threat to human society, as well as public health and economic development. Extensive efforts have been undertaken to battle against the pandemic, whereas effective approaches such as vaccination would be weakened by the continuous mutations, leading to considerable attention being attracted to the mutation prediction. However, most previous studies lack attention to phylogenetics. In this paper, we propose a novel and effective model TEMPO for predicting the mutation of SARS-CoV-2 evolution. Specifically, we design a phylogenetic tree-based sampling method to generate sequence evolution data. Then, a transformer-based model is presented for the site mutation prediction after learning the high-level representation of these sequence data. We conduct experiments to verify the effectiveness of TEMPO, leveraging a large-scale SARS-CoV- 2 dataset. Experimental results show that TEMPO is effective for mutation prediction of SARS- CoV-2 evolution and outperforms several state-of-the-art baseline methods. We further perform mutation prediction experiments of other infectious viruses, to explore the feasibility and robustness of TEMPO, and experimental results verify its superiority. The codes and datasets are freely available at https://github.com/ZJUDataIntelligence/TEMPO.
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Affiliation(s)
- Binbin Zhou
- Department of Computer Science and Computing, Zhejiang University City College, No. 48 Huzhou Street, Hangzhou, 310015, China; Industry Brain Institute, Zhejiang University City College, Hangzhou, 310015, China.
| | - Hang Zhou
- Department of Computer Science and Computing, Zhejiang University City College, No. 48 Huzhou Street, Hangzhou, 310015, China; College of Computer Science and Technology, Zhejiang University, Hangzhou, 310027, China.
| | - Xue Zhang
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Xiaobin Xu
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Yi Chai
- ZJU-UoE Institute, Zhejiang University, Haining, 314400, China.
| | - Zengwei Zheng
- Department of Computer Science and Computing, Zhejiang University City College, No. 48 Huzhou Street, Hangzhou, 310015, China; Industry Brain Institute, Zhejiang University City College, Hangzhou, 310015, China.
| | - Alex Chichung Kot
- School of Electrical and Electronic Engineering, Nanyang Technological University, 639798, Singapore.
| | - Zhan Zhou
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China; The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 310058, China.
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16
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Silva CS, Tryndyak VP, Camacho L, Orloff MS, Porter A, Garner K, Mullis L, Azevedo M. Temporal dynamics of SARS-CoV-2 genome and detection of variants of concern in wastewater influent from two metropolitan areas in Arkansas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 849:157546. [PMID: 35914602 PMCID: PMC9338166 DOI: 10.1016/j.scitotenv.2022.157546] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/14/2022] [Accepted: 07/17/2022] [Indexed: 06/15/2023]
Abstract
Although SARS-CoV-2 can cause severe illness and death, a percentage of the infected population is asymptomatic. This, along with other factors, such as insufficient diagnostic testing and underreporting due to self-testing, contributes to the silent transmission of SARS-CoV-2 and highlights the importance of implementing additional surveillance tools. The fecal shedding of the virus from infected individuals enables its detection in community wastewater, and this has become a valuable public health tool worldwide as it allows the monitoring of the disease on a populational scale. Here, we monitored the presence of SARS-CoV-2 and its dynamic genomic changes in wastewater sampled from two metropolitan areas in Arkansas during major surges of COVID-19 cases and assessed how the viral titers in these samples related to the clinical case counts between late April 2020 and January 2022. The levels of SARS-CoV-2 RNA were quantified by reverse-transcription quantitative polymerase chain reaction (RT-qPCR) using a set of TaqMan assays targeting three different viral genes (encoding ORF1ab polyprotein, surface glycoprotein, and nucleocapsid phosphoprotein). An allele-specific RT-qPCR approach was used to screen the samples for SARS-CoV-2 mutations. The identity and genetic diversity of the virus were further investigated through amplicon-based RNA sequencing, and SARS-CoV-2 variants of concern were detected in wastewater samples throughout the duration of this study. Our data show how changes in the virus genome can affect the sensitivity of specific RT-qPCR assays used in COVID-19 testing with the surge of new variants. A significant association was observed between viral titers in wastewater and recorded number of COVID-19 cases in the areas studied, except when assays failed to detect targets due to the presence of particular variants. These findings support the use of wastewater surveillance as a reliable complementary tool for monitoring SARS-CoV-2 and its genetic variants at the community level.
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Affiliation(s)
- Camila S Silva
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA.
| | - Volodymyr P Tryndyak
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Luísa Camacho
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Mohammed S Orloff
- Department of Epidemiology, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Center for the Studies of Tobacco, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Austin Porter
- Department of Health Policy and Management, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Arkansas Department of Health, Little Rock, AR, USA
| | - Kelley Garner
- Department of Epidemiology, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Arkansas Department of Health, Little Rock, AR, USA
| | - Lisa Mullis
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Marli Azevedo
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
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17
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Fluorescent nanodiamond-based spin-enhanced lateral flow immunoassay for detection of SARS-CoV-2 nucleocapsid protein and spike protein from different variants. Anal Chim Acta 2022; 1230:340389. [PMID: 36192062 PMCID: PMC9472599 DOI: 10.1016/j.aca.2022.340389] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/30/2022] [Accepted: 09/09/2022] [Indexed: 11/24/2022]
Abstract
SARS-CoV-2 viruses, responsible for the COVID-19 pandemic, continues to evolve into new mutations, which poses a significant threat to public health. Current testing methods have some limitations, such as long turnaround times, high costs, and professional laboratory requirements. In this report, the novel Spin-Enhanced Lateral Flow Immunoassay (SELFIA) platform and fluorescent nanodiamond (FND) reporter were utilized for the rapid detection of SARS-CoV-2 nucleocapsid and spike antigens from different variants, including wild-type (Wuhan-1), Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (B.1.1.529). The SARS-CoV-2 antibodies were conjugated with FND via nonspecific binding, enabling the detection of SARS-CoV-2 antigens via both direct and competitive SELFIA format. Direct SELFIA was performed by directly adding the SARS-CoV-2 antibodies-conjugated FND on the antigens-immobilized nitrocellulose (NC) membrane. Conversely, the SARS-CoV-2 antigen-containing sample was first incubated with the antibodies-conjugated FND, and then dropped on the antigen-immobilized NC membrane to carry out the competitive SELFIA. The results suggested that S44F anti-S IgG antibody can be efficiently used for the detection of wild-type, Alpha, Delta, and Omicron variants spike antigens. Findings were comparable in direct SELFIA, competitive SELFIA, and ELISA. A detection limit of 1.94, 0.77, 1.14, 1.91, and 1.68 ng/mL can be achieved for SARS-CoV-2 N protein, wild-type, Alpha, Delta, and Omicron S proteins, respectively, via competitive SELFIA assay. These results suggest that a direct SELFIA assay can be used for antibody/antigen pair screening in diagnosis development, while the competitive SELFIA assay can serve as an accurate quantitative diagnostic tool. The simplicity and rapidity of the SELFIA platform were demonstrated, which can be leveraged in the detection of other infectious diseases in the near future.
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18
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Chiba R, Miyakawa K, Aoki K, Morikawa TJ, Moriizumi Y, Degawa T, Arai Y, Segawa O, Tanaka K, Tajima H, Arai S, Yoshinaga H, Tsukada R, Tani A, Fuji H, Sato A, Ishii Y, Tateda K, Ryo A, Yoshimura T. Development of a Fully Automated Desktop Analyzer and Ultrahigh Sensitivity Digital Immunoassay for SARS-CoV-2 Nucleocapsid Antigen Detection. Biomedicines 2022; 10:biomedicines10092291. [PMID: 36140390 PMCID: PMC9496537 DOI: 10.3390/biomedicines10092291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/09/2022] [Accepted: 09/11/2022] [Indexed: 11/21/2022] Open
Abstract
Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak has had a significant impact on public health and the global economy. Several diagnostic tools are available for the detection of infectious diseases, with reverse transcription-polymerase chain reaction (RT-PCR) testing specifically recommended for viral RNA detection. However, this diagnostic method is costly, complex, and time-consuming. Although it does not have sufficient sensitivity, antigen detection by an immunoassay is an inexpensive and simpler alternative to RT-PCR. Here, we developed an ultrahigh sensitivity digital immunoassay (d-IA) for detecting SARS-CoV-2 nucleocapsid (N) protein as antigens using a fully automated desktop analyzer based on a digital enzyme-linked immunosorbent assay. Methods: We developed a fully automated d-IA desktop analyzer and measured the viral N protein as an antigen in nasopharyngeal (NP) swabs from patients with coronavirus disease. We studied nasopharyngeal swabs of 159 and 88 patients who were RT-PCR-negative and RT-PCR-positive, respectively. Results: The limit of detection of SARS-CoV-2 d-IA was 0.0043 pg/mL of N protein. The cutoff value was 0.029 pg/mL, with a negative RT-PCR distribution. The sensitivity of RT-PCR-positive specimens was estimated to be 94.3% (83/88). The assay time was 28 min. Conclusions: Our d-IA system, which includes a novel fully automated desktop analyzer, enabled detection of the SARS-CoV-2 N-protein with a comparable sensitivity to RT-PCR within 30 min. Thus, d-IA shows potential for SARS-CoV-2 detection across multiple diagnostic centers including small clinics, hospitals, airport quarantines, and clinical laboratories.
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Affiliation(s)
- Ryotaro Chiba
- Research and Development, Abbott Japan LLC, Matsudo 270-2214, Japan
| | - Kei Miyakawa
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Kotaro Aoki
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo 143-8540, Japan
| | | | | | - Takuma Degawa
- Research and Development, Abbott Japan LLC, Matsudo 270-2214, Japan
| | - Yoshiyuki Arai
- Research and Development, Abbott Japan LLC, Matsudo 270-2214, Japan
| | - Osamu Segawa
- Precision System Science Co., Ltd., Matsudo 271-0064, Japan
| | - Kengo Tanaka
- Precision System Science Co., Ltd., Matsudo 271-0064, Japan
| | - Hideji Tajima
- Precision System Science Co., Ltd., Matsudo 271-0064, Japan
| | - Susumu Arai
- Sumitomo Bakelite Co., Ltd., Tokyo 140-0002, Japan
| | | | | | - Akira Tani
- Olympus Corporation, Hachioji 192-8507, Japan
| | | | | | - Yoshikazu Ishii
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo 143-8540, Japan
| | - Kazuhiro Tateda
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo 143-8540, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
- Correspondence: (A.R.); (T.Y.)
| | - Toru Yoshimura
- Research and Development, Abbott Japan LLC, Matsudo 270-2214, Japan
- Correspondence: (A.R.); (T.Y.)
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19
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Ghosh N, Saha I, Sharma N, Nandi S. Bioinformatics pipeline unveils genetic variability to synthetic vaccine design for Indian SARS-CoV-2 genomes. Int Immunopharmacol 2022; 112:109224. [PMID: 36116149 PMCID: PMC9444899 DOI: 10.1016/j.intimp.2022.109224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/30/2022]
Abstract
In the worrisome scenarios of various waves of SARS-CoV-2 pandemic, a comprehensive bioinformatics pipeline is essential to analyse the virus genomes in order to understand its evolution, thereby identifying mutations as signature SNPs, conserved regions and subsequently to design epitope based synthetic vaccine. We have thus performed multiple sequence alignment of 4996 Indian SARS-CoV-2 genomes as a case study using MAFFT followed by phylogenetic analysis using Nextstrain to identify virus clades. Furthermore, based on the entropy of each genomic coordinate of the aligned sequences, conserved regions are identified. After refinement of the conserved regions, based on its length, one conserved region is identified for which the primers and probes are reported for virus detection. The refined conserved regions are also used to identify T-cell and B-cell epitopes along with their immunogenic and antigenic scores. Such scores are used for selecting the most immunogenic and antigenic epitopes. By executing this pipeline, 40 unique signature SNPs are identified resulting in 23 non-synonymous signature SNPs which provide 28 amino acid changes in protein. On the other hand, 12 conserved regions are selected based on refinement criteria out of which one is selected as the potential target for virus detection. Additionally, 22 MHC-I and 21 MHC-II restricted T-cell epitopes with 10 unique HLA alleles each and 17 B-cell epitopes are obtained for 12 conserved regions. All the results are validated both quantitatively and qualitatively which show that from genetic variability to synthetic vaccine design, the proposed pipeline can be used effectively to combat SARS-CoV-2.
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Affiliation(s)
- Nimisha Ghosh
- Department of Computer Science and Information Technology, Institute of Technical Education and Research, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Indrajit Saha
- Department of Computer Science and Engineering, National Institute of Technical Teachers' Training and Research, Kolkata, West Bengal, India.
| | - Nikhil Sharma
- Department of Electronics and Communication Engineering, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India
| | - Suman Nandi
- Department of Computer Science and Engineering, National Institute of Technical Teachers' Training and Research, Kolkata, West Bengal, India
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20
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Xu J, Kerr L, Jiang Y, Suo W, Zhang L, Lao T, Chen Y, Zhang Y. Rapid Antigen Diagnostics as Frontline Testing in the COVID-19 Pandemic. SMALL SCIENCE 2022; 2:2200009. [PMID: 35942171 PMCID: PMC9349911 DOI: 10.1002/smsc.202200009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/25/2022] [Indexed: 11/09/2022] Open
Abstract
The ongoing global COVID-19 pandemic, caused by the SARS-CoV-2 virus, has resulted in significant loss of life since December 2019. Timely and precise virus detection has been proven as an effective solution to reduce the spread of the virus and to track the epidemic. Rapid antigen diagnostics has played a significant role in the frontline of COVID-19 testing because of its convenience, low cost, and high accuracy. Herein, different types of recently innovated in-lab and commercial antigen diagnostic technologies with emphasis on the strengths and limitations of these technologies including the limit of detection, sensitivity, specificity, affordability, and usability are systematically reviewed. The perspectives of assay development are looked into.
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Affiliation(s)
- Jiang Xu
- Department of Systems BiologyBlavatnik InstituteHarvard Medical SchoolBostonMA02115USA
- Department of Molecular VirologyVirogin Biotech Ltd.3800 Wesbrook MallVancouverBCV6S 2L9Canada
| | - Liam Kerr
- Department of Mechanical EngineeringCenter for Intelligent MachinesMcGill UniversityMontrealQCH3A0C3Canada
| | - Yue Jiang
- China-Australia Institute for Advanced Materials and ManufacturingJiaxing UniversityJiaxing314001China
| | - Wenhao Suo
- Dana-Farber Cancer InstituteHarvard Medical SchoolBostonMA02215USA
- Department of PathologyThe First Affiliated Hospital of Xiamen University55 Zhenhai RoadXiamen361003China
| | - Lei Zhang
- Department of Chemical EngineeringWaterloo Institute for NanotechnologyUniversity of Waterloo200 University Avenue WestWaterlooONN2L3G1Canada
| | - Taotao Lao
- Department of Molecular DiagnosticsBoston Molecules Inc.564 Main StreetWalthamMA02452USA
- Center for Immunology and Inflammatory DiseasesMassachusetts General HospitalHarvard Medical SchoolCharlestownMA02114USA
| | - Yuxin Chen
- Department of Laboratory MedicineNanjing Drum Tower HospitalNanjing University Medical SchoolNanjingJiangsu210008China
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery and High-EfficiencyCollaborative Innovation Center of Chemical Science and EngineeringSchool of Pharmaceutical Science and TechnologyTianjin UniversityTianjin300072China
- Frontiers Science Center for Synthetic Biology (Ministry of Education)Tianjin UniversityTianjin300072China
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21
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Zhao H, Han K, Gao C, Madhira V, Topaloglu U, Lu Y, Jin G. VOC-alarm: mutation-based prediction of SARS-CoV-2 variants of concern. Bioinformatics 2022; 38:3549-3556. [PMID: 35640977 PMCID: PMC9272809 DOI: 10.1093/bioinformatics/btac370] [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: 01/20/2022] [Revised: 04/03/2022] [Accepted: 05/26/2022] [Indexed: 11/14/2022] Open
Abstract
SUMMARY Mutation is the key for a variant of concern (VOC) to overcome selective pressures, but this process is still unclear. Understanding the association of the mutational process with VOCs is an unmet need. Motivation: Here, we developed VOC-alarm, a method to predict VOCs and their caused COVID surges, using mutations of about 5.7 million SARS-CoV-2 complete sequences. We found that VOCs rely on lineage-level entropy value of mutation numbers to compete with other variants, suggestive of the importance of population-level mutations in the virus evolution. Thus, we hypothesized that VOCs are a result of a mutational process across the globe. Results: Analyzing the mutations from January 2020 to December 2021, we simulated the mutational process by estimating the pace of evolution, and thus divided the time period, January 2020-March 2022, into eight stages. We predicted Alpha, Delta, Delta Plus (AY.4.2) and Omicron (B.1.1.529) by their mutational entropy values in the Stages I, III, V and VII with accelerated paces, respectively. In late November 2021, VOC-alarm alerted that Omicron strongly competed with Delta and Delta plus to become a highly transmissible variant. Using simulated data, VOC-alarm also predicted that Omicron could lead to another COVID surge from January 2022 to March 2022. AVAILABILITY AND IMPLEMENTATION Our software implementation is available at https://github.com/guangxujin/VOC-alarm. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hongyu Zhao
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Kun Han
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Chao Gao
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin 300052, China
| | | | - Umit Topaloglu
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
- Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC 27157, USA
- Wake Forest School of Medicine, Center for Biomedical Informatics, NC 27101, USA
| | - Yong Lu
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
- Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC 27157, USA
| | - Guangxu Jin
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
- Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC 27157, USA
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22
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Islam MM, Koirala D. Toward a next-generation diagnostic tool: A review on emerging isothermal nucleic acid amplification techniques for the detection of SARS-CoV-2 and other infectious viruses. Anal Chim Acta 2022; 1209:339338. [PMID: 35569864 PMCID: PMC8633689 DOI: 10.1016/j.aca.2021.339338] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 01/09/2023]
Abstract
As the COVID-19 pandemic continues to affect human health across the globe rapid, simple, point-of-care (POC) diagnosis of infectious viruses such as SARS-CoV-2 remains challenging. Polymerase chain reaction (PCR)-based diagnosis has risen to meet these demands and despite its high-throughput and accuracy, it has failed to gain traction in the rapid, low-cost, point-of-test settings. In contrast, different emerging isothermal amplification-based detection methods show promise in the rapid point-of-test market. In this comprehensive study of the literature, several promising isothermal amplification methods for the detection of SARS-CoV-2 are critically reviewed that can also be applied to other infectious viruses detection. Starting with a brief discussion on the SARS-CoV-2 structure, its genomic features, and the epidemiology of the current pandemic, this review focuses on different emerging isothermal methods and their advancement. The potential of isothermal amplification combined with the revolutionary CRISPR/Cas system for a more powerful detection tool is also critically reviewed. Additionally, the commercial success of several isothermal methods in the pandemic are highlighted. Different variants of SARS-CoV-2 and their implication on isothermal amplifications are also discussed. Furthermore, three most crucial aspects in achieving a simple, fast, and multiplexable platform are addressed.
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23
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Gong W, Parkkila S, Wu X, Aspatwar A. SARS-CoV-2 variants and COVID-19 vaccines: Current challenges and future strategies. Int Rev Immunol 2022; 42:393-414. [PMID: 35635216 DOI: 10.1080/08830185.2022.2079642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/23/2022] [Accepted: 05/09/2022] [Indexed: 12/23/2022]
Abstract
The ongoing COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global threat. Despite strict control measures implemented worldwide and immunization using novel vaccines, the pandemic continues to rage due to emergence of several variants of SARS-CoV-2 with increased transmission and immune escape. The rapid spread of variants of concern (VOC) in the recent past has created a massive challenge for the control of COVID-19 pandemic via the currently used vaccines. Vaccines that are safe and effective against the current and future variants of SARS-CoV-2 are essential in controlling the COVID-19 pandemic. Rapid production and massive rollout of next-generation vaccines against the variants are key steps to control the COVID-19 pandemic and to help us return to normality. Coordinated surveillance of SARS-CoV-2, rapid redesign of new vaccines and extensive vaccination are needed to counter the current SARS-CoV-2 variants and prevent the emergence of new variants. In this article, we review the latest information on the VOCs and variants of interest (VOIs) and present the information on the clinical trials that are underway on evaluating the effectiveness of COVID-19 vaccines on VOCs. We also discuss the current challenges posed by the VOCs in controlling the COVID-19 pandemic and future strategies to overcome the threat posed by the highly virulent and rapidly transmissible variants of SARS-CoV2.
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Affiliation(s)
- Wenping Gong
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing 100091, China
| | - Seppo Parkkila
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Ltd, Tampere University Hospital, Tampere, Finland
| | - Xueqiong Wu
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing 100091, China
| | - Ashok Aspatwar
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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24
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Chen Y, Liu F, Lee LP. Quantitative and ultrasensitive in situ immunoassay technology for SARS-CoV-2 detection in saliva. SCIENCE ADVANCES 2022; 8:eabn3481. [PMID: 35613342 PMCID: PMC9132547 DOI: 10.1126/sciadv.abn3481] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/11/2022] [Indexed: 05/26/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has become an immense global health crisis. However, the lack of efficient and sensitive on-site testing methods limits early detection for timely isolation and intervention. Here, we present a quantitative and ultrasensitive in situ immunoassay technology for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection in saliva (QUIT SARS-CoV-2). Our nanoporous membrane resonator generates a rapid oscillating flow to purify and concentrate fully intact SARS-CoV-2 virus in saliva by 40-fold for in situ detection of viral antigens based on chemiluminescent immunoassay within 20 min. This method can not only achieve a detection sensitivity below 100 copies/ml of virus, comparable to the bench-top PCR equipment; it can also improve detection specificity via direct monitoring of viral loads. The integrated portable QUIT SARS-CoV-2 system, which enables rapid and accurate on-site viral screening with a high-throughput sample pooling strategy, can be performed in primary care settings and substantially improve the detection and prevention of COVID-19.
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Affiliation(s)
- Yuchao Chen
- WellSIM Biomedical Technologies Inc., 626 Bancroft Way, Suite A, Berkeley, CA, USA
| | - Fei Liu
- WellSIM Biomedical Technologies Inc., 626 Bancroft Way, Suite A, Berkeley, CA, USA
| | - Luke P. Lee
- Harvard Medical School, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Bioengineering and Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, CA, USA
- Institute of Quantum Biophysics, Department of Biophysics, Sungkyunkwan University, Suwon, Gyeonggi-do, Korea
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25
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Khudhair YI, Saleh ZF, Ayyez HN. First study on microscopic and molecular evidences of two bovine hemoplasma species in cattle herds in Al-Qadisiyah Province, Iraq. Vet World 2022; 15:1323-1327. [PMID: 35765475 PMCID: PMC9210837 DOI: 10.14202/vetworld.2022.1323-1327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/25/2022] [Indexed: 11/18/2022] Open
Abstract
Background and Aim: Hemotropic Mycoplasmas are small epierythrocytic bacteria that cause infectious anemia in several livestock species and in humans. Several reports have been made on hemoplasma infections in the south and north of Iraq, but there have been no studies in the middle Euphrates of Iraq. This study aimed to evaluate the presence of hemoplasma species in cattle in Al-Qadisiyah Province, Iraq. Materials and Methods: Two hundred blood samples were collected from cattle with pale mucous membrane from regions with heavy tick endemicity. The samples were analyzed for the presence of Rickettsia pathogens using thin blood smears and the Diff-Quik stains. All the samples were also examined using polymerase chain reaction (PCR) to amplify the 16S ribosomal ribonucleic acid (rRNA) gene to confirm the presence of the smear-identified microorganisms. Ten PCR positive samples were subjected to 16S rRNA partial gene sequencing to identify the species. Results: The findings uncovered positivity in 68 (34%) blood smears. PCR revealed positive confirmation in 18 (9%) of the 200 blood samples. Mycoplasma wenyonii and Candidatus mycoplasma hemobos were identified from 10 PCR positive samples. The nucleotide sequences of the isolates were closely related to isolates from cattle, buffalo, and dogs in Vietnam, Cuba, India, and Germany. Conclusion: Bovine hemoplasma infections are prevalent in cattle in the Al-Qadisiyah Province in Iraq. Our results may have significance for the development of control programs.
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Affiliation(s)
- Yahia Ismail Khudhair
- Department of Internal and Preventive Medicine, College of Veterinary Medicine, University of Al-Qadisiyah, Al Diwaniyah, Iraq
| | - Zeena Fouad Saleh
- Unit of Zoonotic Disease Research, College of Veterinary Medicine, Al-Qadisiyah University, Al Diwaniyah, Iraq
| | - Hayder N. Ayyez
- Unit of Zoonotic Disease Research, College of Veterinary Medicine, Al-Qadisiyah University, Al Diwaniyah, Iraq
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26
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Saravanan KA, Panigrahi M, Kumar H, Rajawat D, Nayak SS, Bhushan B, Dutt T. Role of genomics in combating COVID-19 pandemic. Gene 2022; 823:146387. [PMID: 35248659 PMCID: PMC8894692 DOI: 10.1016/j.gene.2022.146387] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/17/2022] [Accepted: 02/28/2022] [Indexed: 12/20/2022]
Abstract
The coronavirus disease 2019 (COVID-19) quickly swept over the world, becoming one of the most devastating outbreaks in human history. Being the first pandemic in the post-genomic era, advancements in genomics contributed significantly to scientific understanding and public health response to COVID-19. Genomic technologies have been employed by researchers all over the world to better understand the biology of SARS-CoV-2 and its origin, genomic diversity, and evolution. Worldwide genomic resources have greatly aided in the investigation of the COVID-19 pandemic. The pandemic has ushered in a new era of genomic surveillance, wherein scientists are tracking the changes of the SARS-CoV-2 genome in real-time at the international and national levels. Availability of genomic and proteomic information enables the rapid development of molecular diagnostics and therapeutics. The advent of high-throughput sequencing and genome editing technologies led to the development of modern vaccines. We briefly discuss the impact of genomics in the ongoing COVID-19 pandemic in this review.
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Affiliation(s)
- K A Saravanan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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27
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Dumache R, Enache A, Macasoi I, Dehelean CA, Dumitrascu V, Mihailescu A, Popescu R, Vlad D, Vlad CS, Muresan C. SARS-CoV-2: An Overview of the Genetic Profile and Vaccine Effectiveness of the Five Variants of Concern. Pathogens 2022; 11:pathogens11050516. [PMID: 35631037 PMCID: PMC9144800 DOI: 10.3390/pathogens11050516] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 12/13/2022] Open
Abstract
With the onset of the COVID-19 pandemic, enormous efforts have been made to understand the genus SARS-CoV-2. Due to the high rate of global transmission, mutations in the viral genome were inevitable. A full understanding of the viral genome and its possible changes represents one of the crucial aspects of pandemic management. Structural protein S plays an important role in the pathogenicity of SARS-CoV-2, mutations occurring at this level leading to viral forms with increased affinity for ACE2 receptors, higher transmissibility and infectivity, resistance to neutralizing antibodies and immune escape, increasing the risk of infection and disease severity. Thus, five variants of concern are currently being discussed, Alpha, Beta, Gamma, Delta and Omicron. In the present review, a comprehensive summary of the following critical aspects regarding SARS-CoV-2 has been made: (i) the genomic characteristics of SARS-CoV-2; (ii) the pathological mechanism of transmission, penetration into the cell and action on specific receptors; (iii) mutations in the SARS-CoV-2 genome; and (iv) possible implications of mutations in diagnosis, treatment, and vaccination.
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Affiliation(s)
- Raluca Dumache
- Ethics and Human Identification Research Center, Department of Neurosciences, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (R.D.); (A.E.); (A.M.); (C.M.)
| | - Alexandra Enache
- Ethics and Human Identification Research Center, Department of Neurosciences, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (R.D.); (A.E.); (A.M.); (C.M.)
| | - Ioana Macasoi
- Departament of Toxicology and Drug Industry, Faculty of Pharmacy, “Victor Babeş” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timişoara, Romania
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
- Correspondence: (I.M.); (C.A.D.)
| | - Cristina Adriana Dehelean
- Departament of Toxicology and Drug Industry, Faculty of Pharmacy, “Victor Babeş” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timişoara, Romania
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
- Correspondence: (I.M.); (C.A.D.)
| | - Victor Dumitrascu
- Department of Pharmacology and Biochemistry, Discipline of Pharmacology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (V.D.); (D.V.); (C.S.V.)
| | - Alexandra Mihailescu
- Ethics and Human Identification Research Center, Department of Neurosciences, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (R.D.); (A.E.); (A.M.); (C.M.)
- Genetics, Genomic Medicine Research Center, Department of Microscopic Morphology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania
| | - Roxana Popescu
- Department of Microscopic Morphology, Discipline of Molecular and Cell Biology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania;
| | - Daliborca Vlad
- Department of Pharmacology and Biochemistry, Discipline of Pharmacology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (V.D.); (D.V.); (C.S.V.)
| | - Cristian Sebastian Vlad
- Department of Pharmacology and Biochemistry, Discipline of Pharmacology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (V.D.); (D.V.); (C.S.V.)
| | - Camelia Muresan
- Ethics and Human Identification Research Center, Department of Neurosciences, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (R.D.); (A.E.); (A.M.); (C.M.)
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28
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Jaiswal V, Lee HJ. Conservation and Evolution of Antigenic Determinants of SARS-CoV-2: An Insight for Immune Escape and Vaccine Design. Front Immunol 2022; 13:832106. [PMID: 35444664 PMCID: PMC9014086 DOI: 10.3389/fimmu.2022.832106] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/07/2022] [Indexed: 11/20/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is the most devastating pandemic of the century, which is still far from over. The remarkable success of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines is the working hope, but the evolving variants are the huge concern that can turn the tide. Potential immune escape mutations (PIEMs) in the past and circulating variants were not studied at large scale (all available data). Hence, the conservation of antigenic determinants (epitopes) was analyzed in all available sequences of SARS-CoV-2 according to time (months), proteins, hosts, and variants. Numerous highly conserved B- and T-cell epitopes were identified in 24 proteins of SARS-CoV-2. A decrease in the conservation of epitopes with time was observed in almost all proteins, which was more rapid in neutralizing epitopes. Delta variant still has the highest PIEM in the circulating strains, which pose threat to the effectiveness of current vaccines. The inclusion of identified, highly conserved, and important epitopes in subunit vaccines can increase vaccine effectiveness against evolving variants. Trends in the conservation of epitopes in different proteins, hosts, and variants with time may also help to inspire the counter measure against the current pandemic.
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Affiliation(s)
- Varun Jaiswal
- Department of Food and Nutrition, College of BioNano Technology, Gachon University, Seongnam-si, South Korea
| | - Hae-Jeung Lee
- Department of Food and Nutrition, College of BioNano Technology, Gachon University, Seongnam-si, South Korea.,Institute for Aging and Clinical Nutrition Research, Gachon University, Seongnam-si, South Korea.,Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon, South Korea
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29
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Lim HGM, Hsiao SH, Fann YC, Lee YCG. Robust Mutation Profiling of SARS-CoV-2 Variants from Multiple Raw Illumina Sequencing Data with Cloud Workflow. Genes (Basel) 2022. [PMID: 35456492 DOI: 10.3390/genes1304068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023] Open
Abstract
Several variants of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are emerging all over the world. Variant surveillance from genome sequencing has become crucial to determine if mutations in these variants are rendering the virus more infectious, potent, or resistant to existing vaccines and therapeutics. Meanwhile, analyzing many raw sequencing data repeatedly with currently available code-based bioinformatics tools is tremendously challenging to be implemented in this unprecedented pandemic time due to the fact of limited experts and computational resources. Therefore, in order to hasten variant surveillance efforts, we developed an installation-free cloud workflow for robust mutation profiling of SARS-CoV-2 variants from multiple Illumina sequencing data. Herein, 55 raw sequencing data representing four early SARS-CoV-2 variants of concern (Alpha, Beta, Gamma, and Delta) from an open-access database were used to test our workflow performance. As a result, our workflow could automatically identify mutated sites of the variants along with reliable annotation of the protein-coding genes at cost-effective and timely manner for all by harnessing parallel cloud computing in one execution under resource-limitation settings. In addition, our workflow can also generate a consensus genome sequence which can be shared with others in public data repositories to support global variant surveillance efforts.
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Affiliation(s)
- Hendrick Gao-Min Lim
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Shih-Hsin Hsiao
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Division of Pulmonary Medicine, Department of Internal Medicine, Taipei Medical University Hospital, Taipei 11031, Taiwan
| | - Yang C Fann
- IT and Bioinformatics Program, Division of Intramural, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yuan-Chii Gladys Lee
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
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30
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Lim HGM, Hsiao SH, Fann YC, Lee YCG. Robust Mutation Profiling of SARS-CoV-2 Variants from Multiple Raw Illumina Sequencing Data with Cloud Workflow. Genes (Basel) 2022; 13:genes13040686. [PMID: 35456492 PMCID: PMC9028989 DOI: 10.3390/genes13040686] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/06/2022] [Accepted: 04/12/2022] [Indexed: 02/04/2023] Open
Abstract
Several variants of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are emerging all over the world. Variant surveillance from genome sequencing has become crucial to determine if mutations in these variants are rendering the virus more infectious, potent, or resistant to existing vaccines and therapeutics. Meanwhile, analyzing many raw sequencing data repeatedly with currently available code-based bioinformatics tools is tremendously challenging to be implemented in this unprecedented pandemic time due to the fact of limited experts and computational resources. Therefore, in order to hasten variant surveillance efforts, we developed an installation-free cloud workflow for robust mutation profiling of SARS-CoV-2 variants from multiple Illumina sequencing data. Herein, 55 raw sequencing data representing four early SARS-CoV-2 variants of concern (Alpha, Beta, Gamma, and Delta) from an open-access database were used to test our workflow performance. As a result, our workflow could automatically identify mutated sites of the variants along with reliable annotation of the protein-coding genes at cost-effective and timely manner for all by harnessing parallel cloud computing in one execution under resource-limitation settings. In addition, our workflow can also generate a consensus genome sequence which can be shared with others in public data repositories to support global variant surveillance efforts.
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Affiliation(s)
- Hendrick Gao-Min Lim
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
| | - Shih-Hsin Hsiao
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
- Division of Pulmonary Medicine, Department of Internal Medicine, Taipei Medical University Hospital, Taipei 11031, Taiwan
| | - Yang C. Fann
- IT and Bioinformatics Program, Division of Intramural, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Yuan-Chii Gladys Lee
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
- Correspondence:
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31
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Ghosh N, Nandi S, Saha I. Phylogenetic analysis of 17271 Indian SARS-CoV-2 genomes to identify temporal and spatial hotspot mutations. PLoS One 2022; 17:e0265579. [PMID: 35344550 PMCID: PMC8959188 DOI: 10.1371/journal.pone.0265579] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 03/07/2022] [Indexed: 11/25/2022] Open
Abstract
The second wave of SARS-CoV-2 has hit India hard and though the vaccination drive has started, moderate number of COVID affected patients is still present in the country, thereby leading to the analysis of the evolving virus strains. In this regard, multiple sequence alignment of 17271 Indian SARS-CoV-2 sequences is performed using MAFFT followed by their phylogenetic analysis using Nextstrain. Subsequently, mutation points as SNPs are identified by Nextstrain. Thereafter, from the aligned sequences temporal and spatial analysis are carried out to identify top 10 hotspot mutations in the coding regions based on entropy. Finally, to judge the functional characteristics of all the non-synonymous hotspot mutations, their changes in proteins are evaluated as biological functions considering the sequences by using PolyPhen-2 while I-Mutant 2.0 evaluates their structural stability. For both temporal and spatial analysis, there are 21 non-synonymous hotspot mutations which are unstable and damaging.
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Affiliation(s)
- Nimisha Ghosh
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
- Department of Computer Science and Information Technology, Institute of Technical Education and Research, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Suman Nandi
- Department of Computer Science and Engineering, National Institute of Technical Teachers’ Training and Research, Kolkata, West Bengal, India
| | - Indrajit Saha
- Department of Computer Science and Engineering, National Institute of Technical Teachers’ Training and Research, Kolkata, West Bengal, India
- * E-mail:
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32
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Dong Y, Zhao Y, Li S, Wan Z, Lu R, Yang X, Yu G, Reboud J, Cooper JM, Tian Z, Zhang C. Multiplex, Real-Time, Point-of-care RT-LAMP for SARS-CoV-2 Detection Using the HFman Probe. ACS Sens 2022; 7:730-739. [PMID: 35192340 PMCID: PMC8887655 DOI: 10.1021/acssensors.1c02079] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/08/2022] [Indexed: 12/11/2022]
Abstract
Viral evolution impacts diagnostic test performance through the emergence of variants with sequences affecting the efficiency of primer binding. Such variants that evade detection by nucleic acid-based tests are subject to selective pressure, enabling them to spread more efficiently. Here, we report a variant-tolerant diagnostic test for SARS-CoV-2 using a loop-mediated isothermal nucleic acid-based amplification (LAMP) assay containing high-fidelity DNA polymerase and a high-fidelity DNA polymerase-medicated probe (HFman probe). In addition to demonstrating a high tolerance to variable SARS-CoV-2 viral sequences, the mechanism also overcomes frequently observed limitations of LAMP assays arising from non-specific amplification within multiplexed reactions performed in a single "pot". Results showed excellent clinical performance (sensitivity 94.5%, specificity 100%, n = 190) when compared directly to a commercial gold standard reverse transcription quantitative polymerase chain reaction assay for the extracted RNA from nasopharyngeal samples and the capability of detecting a wide range of sequences containing at least alpha and delta variants. To further validate the test with no sample processing, directly from nasopharyngeal swabs, we also detected SARS-CoV-2 in positive clinical samples (n = 49), opening up the possibility for the assay's use in decentralized testing.
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Affiliation(s)
- Yajuan Dong
- College
of Life Sciences, Henan Normal University, Xinxiang 453007, China
- Shanghai
Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yongjuan Zhao
- Shanghai
Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Shenwei Li
- Shanghai
International Travel Healthcare Center, Shanghai 200335, China
| | - Zhenzhou Wan
- Medical
Laboratory of Taizhou Fourth People’s Hospital, Taizhou 225300, China
| | - Renfei Lu
- Clinical
Laboratory, Nantong Third Hospital Affiliated
to Nantong University, Nantong 226006, China
| | - Xianguang Yang
- College
of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Guoying Yu
- College
of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Julien Reboud
- Division
of Biomedical Engineering, University of
Glasgow, G12 8LT Glasgow, U.K.
| | - Jonathan M. Cooper
- Division
of Biomedical Engineering, University of
Glasgow, G12 8LT Glasgow, U.K.
| | - Zhengan Tian
- Shanghai
International Travel Healthcare Center, Shanghai 200335, China
| | - Chiyu Zhang
- Shanghai
Public Health Clinical Center, Fudan University, Shanghai 201508, China
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33
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Kim D, Han S, Ji Y, Youn H, Kim H, Ko O, Lee JB. RNA polymerization actuating nucleic acid membrane (RANAM)-based biosensing for universal RNA virus detection. Biosens Bioelectron 2022; 199:113880. [PMID: 34915215 PMCID: PMC8662841 DOI: 10.1016/j.bios.2021.113880] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 11/18/2022]
Abstract
The coronavirus disease (COVID-19) pandemic has shown the importance of early disease diagnosis in preventing further infection and mortality. Despite major advances in the development of highly precise and rapid detection approaches, the time-consuming process of designing a virus-specific diagnostic kit has been a limiting factor in the early management of the pandemic. Here, we propose an RNA polymerase activity-sensing strategy utilizing an RNA polymerization actuating nucleic acid membrane (RANAM) partially metallized with gold for colorimetric RNA virus detection. Following RANAM-templated amplification of newly synthesized RNA, the presence of the RNA polymerase was determined by visualization of the inhibition of an oxidation/reduction (redox) reaction between 3,3',5,5'-tetramethylbenzidine (TMB) and blocked Au3+. As a proof of concept, a viral RNA-dependent RNA polymerase (RdRP), which is found in various RNA virus-infected cells, was chosen as a target molecule. With this novel RANAM biosensor, as little as 10 min of RdRP incubation could significantly reduce the colorimetric signal. Further development into an easy-to-use prototype kit in viral infection diagnosis detected RdRP present at levels even as low as 100 aM. Color formation based on the presence of RdRP could be simply and clearly confirmed through smartphone-assisted color imaging of the prototype kit. This study provides a non-PCR-based RNA virus detection including its variants using RdRP-mediated polymerization.
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Affiliation(s)
- Dajeong Kim
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea
| | - Sangwoo Han
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea
| | - Yoonbin Ji
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea
| | - Heejeong Youn
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea
| | - Hyejin Kim
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea
| | - Ohsung Ko
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea
| | - Jong Bum Lee
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea.
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34
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Thakur S, Sasi S, Pillai SG, Nag A, Shukla D, Singhal R, Phalke S, Velu GSK. SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Front Med (Lausanne) 2022; 9:815389. [PMID: 35273977 PMCID: PMC8902153 DOI: 10.3389/fmed.2022.815389] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/04/2022] [Indexed: 12/11/2022] Open
Abstract
With the high rate of COVID-19 infections worldwide, the emergence of SARS-CoV-2 variants was inevitable. Several mutations have been identified in the SARS-CoV-2 genome, with the spike protein as one of the mutational hot spots. Specific amino acid substitutions such as D614G and N501Y were found to alter the transmissibility and virulence of the virus. The WHO has classified the variants identified with fitness-enhancing mutations as variants of concern (VOC), variants of interest (VOI) or variants under monitoring (VUM). The VOCs pose an imminent threat as they exhibit higher transmissibility, disease severity and ability to evade vaccine-induced and natural immunity. Here we review the mutational landscape on the SARS-CoV-2 structural and non-structural proteins and their impact on diagnostics, therapeutics and vaccines. We also look at the effectiveness of approved vaccines, antibody therapy and convalescent plasma on the currently prevalent VOCs, which are B.1.17, B.1.351, P.1, B.1.617.2 and B.1.1.529. We further discuss the possible factors influencing mutation rates and future directions.
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Affiliation(s)
- Suresh Thakur
- Trivitron Healthcare Pvt., Ltd., Visakhapatnam, India
| | - Shalitha Sasi
- Blue Horizon International Therapeutic Sciences, Hackensack, NJ, United States
| | | | | | - Dhananjay Shukla
- Department of Biotechnology, Guru Ghasidas Vishwavidyalaya (A Central University), Bilaspur, India
| | - Ritu Singhal
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Disease, New Delhi, India
| | - Sameer Phalke
- Trivitron Healthcare Pvt., Ltd., Visakhapatnam, India
| | - G. S. K. Velu
- Trivitron Healthcare Pvt., Ltd., Visakhapatnam, India
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35
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Gan SKE, Phua SX, Yeo JY. Sagacious epitope selection for vaccines, and both antibody-based therapeutics and diagnostics: tips from virology and oncology. Antib Ther 2022; 5:63-72. [PMID: 35372784 PMCID: PMC8972324 DOI: 10.1093/abt/tbac005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/24/2022] [Accepted: 02/12/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
The target of an antibody plays a significant role in the success of antibody-based therapeutics and diagnostics, and vaccine development. This importance is focused on the target binding site—epitope, where epitope selection as a part of design thinking beyond traditional antigen selection using whole cell or whole protein immunization can positively impact success. With purified recombinant protein production and peptide synthesis to display limited/selected epitopes, intrinsic factors that can affect the functioning of resulting antibodies can be more easily selected for. Many of these factors stem from the location of the epitope that can impact accessibility of the antibody to the epitope at a cellular or molecular level, direct inhibition of target antigen activity, conservation of function despite escape mutations, and even non-competitive inhibition sites. By incorporating novel computational methods for predicting antigen changes to model-informed drug discovery and development, superior vaccines and antibody-based therapeutics or diagnostics can be easily designed to mitigate failures. With detailed examples, this review highlights the new opportunities, factors and methods of predicting antigenic changes for consideration in sagacious epitope selection.
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Affiliation(s)
- Samuel Ken-En Gan
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
- APD SKEG Pte Ltd, Singapore 439444, Singapore
| | - Ser-Xian Phua
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Joshua Yi Yeo
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
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36
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Salehi-Vaziri M, Fazlalipour M, Seyed Khorrami SM, Azadmanesh K, Pouriayevali MH, Jalali T, Shoja Z, Maleki A. The ins and outs of SARS-CoV-2 variants of concern (VOCs). Arch Virol 2022; 167:327-344. [PMID: 35089389 PMCID: PMC8795292 DOI: 10.1007/s00705-022-05365-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/16/2021] [Indexed: 02/07/2023]
Abstract
SARS-CoV-2, a newly emerging coronavirus that caused the COVID-19 epidemic, has been spreading quickly throughout the world. Despite immunization and some fairly effective therapeutic regimens, SARS-CoV-2 has been ravaging patients, health workers, and the economy. SARS-CoV-2 mutates and evolves to adapt to its host as a result of extreme selection pressure. As a consequence, new SARS-CoV-2 variants have emerged, some of which are classified as variants of concern (VOC) because they exhibit greater transmissibility, cause more-severe disease, are better able to escape immunity, or cause higher mortality than the original Wuhan strain. Here, we introduce these VOCs and review their characteristics, such as transmissibility, immune escape, mortality risk, and diagnostics.
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Affiliation(s)
- Mostafa Salehi-Vaziri
- COVID-19 National Reference Laboratory, Pasteur Institute of Iran, 69 Pasteur Ave, 1316943551, Tehran, Iran
- Department of Arboviruses and Viral Hemorrhagic Fevers (National Reference Laboratory), Pasteur Institute of Iran, Tehran, Iran
- Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Mehdi Fazlalipour
- COVID-19 National Reference Laboratory, Pasteur Institute of Iran, 69 Pasteur Ave, 1316943551, Tehran, Iran
| | | | - Kayhan Azadmanesh
- Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
- Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Hassan Pouriayevali
- COVID-19 National Reference Laboratory, Pasteur Institute of Iran, 69 Pasteur Ave, 1316943551, Tehran, Iran
- Department of Arboviruses and Viral Hemorrhagic Fevers (National Reference Laboratory), Pasteur Institute of Iran, Tehran, Iran
| | - Tahmineh Jalali
- COVID-19 National Reference Laboratory, Pasteur Institute of Iran, 69 Pasteur Ave, 1316943551, Tehran, Iran
- Department of Arboviruses and Viral Hemorrhagic Fevers (National Reference Laboratory), Pasteur Institute of Iran, Tehran, Iran
| | - Zabihollah Shoja
- Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran
| | - Ali Maleki
- COVID-19 National Reference Laboratory, Pasteur Institute of Iran, 69 Pasteur Ave, 1316943551, Tehran, Iran.
- Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran.
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37
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Lee JH, Jung Y, Lee SK, Kim J, Lee CS, Kim S, Lee JS, Kim NH, Kim HG. Rapid Biosensor of SARS-CoV-2 Using Specific Monoclonal Antibodies Recognizing Conserved Nucleocapsid Protein Epitopes. Viruses 2022; 14:v14020255. [PMID: 35215848 PMCID: PMC8879994 DOI: 10.3390/v14020255] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/13/2022] [Accepted: 01/21/2022] [Indexed: 02/04/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is characterized by symptoms such as fever, fatigue, a sore throat, diarrhea, and coughing. Although various new vaccines against COVID-19 have been developed, early diagnostics, isolation, and prevention remain important due to virus mutations resulting in rapid and high disease transmission. Amino acid substitutions in the major diagnostic target antigens of SARS-CoV-2 may lower the sensitivity for the detection of SARS-CoV-2. For this reason, we developed specific monoclonal antibodies that bind to epitope peptides as antigens for the rapid detection of SARS-CoV-2 NP. The binding affinity between antigenic peptides and monoclonal antibodies was investigated, and a sandwich pair for capture and detection was employed to develop a rapid biosensor for SARS-CoV-2 NP. The rapid biosensor, based on a monoclonal antibody pair binding to conserved epitopes of SARS-CoV-2 NP, detected cultured virus samples of SARS-CoV-2 (1.4 × 103 TCID50/reaction) and recombinant NP (1 ng/mL). Laboratory confirmation of the rapid biosensor was performed with clinical specimens (n = 16) from COVID-19 patients and other pathogens. The rapid biosensor consisting of a monoclonal antibody pair (75E12 for capture and the 54G6/54G10 combination for detection) binding to conserved epitopes of SARS-CoV-2 NP could assist in the detection of SARS-CoV-2 NP under the circumstance of spreading SARS-CoV-2 variants.
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Affiliation(s)
- Jong-Hwan Lee
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea; (J.-H.L.); (Y.J.); (S.-K.L.); (J.K.); (S.K.); (J.-S.L.)
| | - Yujin Jung
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea; (J.-H.L.); (Y.J.); (S.-K.L.); (J.K.); (S.K.); (J.-S.L.)
| | - Sung-Kyun Lee
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea; (J.-H.L.); (Y.J.); (S.-K.L.); (J.K.); (S.K.); (J.-S.L.)
| | - Jung Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea; (J.-H.L.); (Y.J.); (S.-K.L.); (J.K.); (S.K.); (J.-S.L.)
| | - Chang-Seop Lee
- Department of Internal Medicine, Jeonbuk National University Medical School, Jeonju 54896, Jeollabuk-do, Korea;
- Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju 54907, Jeollabuk-do, Korea
| | - Soohyun Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea; (J.-H.L.); (Y.J.); (S.-K.L.); (J.K.); (S.K.); (J.-S.L.)
| | - Ji-Seon Lee
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea; (J.-H.L.); (Y.J.); (S.-K.L.); (J.K.); (S.K.); (J.-S.L.)
| | - Nam-Hoon Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea; (J.-H.L.); (Y.J.); (S.-K.L.); (J.K.); (S.K.); (J.-S.L.)
- Correspondence: (N.-H.K.); (H.-G.K.)
| | - Hong-Gi Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea; (J.-H.L.); (Y.J.); (S.-K.L.); (J.K.); (S.K.); (J.-S.L.)
- Correspondence: (N.-H.K.); (H.-G.K.)
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38
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Yin B, Ho WKH, Zhang Q, Li C, Huang Y, Yan J, Yang H, Hao J, Wong SHD, Yang M. Magnetic-Responsive Surface-Enhanced Raman Scattering Platform with Tunable Hot Spot for Ultrasensitive Virus Nucleic Acid Detection. ACS APPLIED MATERIALS & INTERFACES 2022; 14:4714-4724. [PMID: 35081679 DOI: 10.1021/acsami.1c21173] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Surface-enhanced Raman scattering (SERS)-based biosensors are promising tools for virus nucleic acid detection. However, it remains challenging for SERS-based biosensors using a sandwiching strategy to detect long-chain nucleic acids such as nucleocapsid (N) gene of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) because the extension of the coupling distance (CD) between the two tethered metallic nanostructures weakens electric field and SERS signals. Herein, we report a magnetic-responsive substrate consisting of heteoronanostructures that controls the CD for ultrasensitive and highly selective detection of the N gene of SARS-CoV-2. Significantly, our findings show that this platform reversibly shortens the CD and enhances SERS signals with a 10-fold increase in the detection limit from 1 fM to 100 aM, compared to those without magnetic modulation. The optical simulation that emulates the CD shortening process confirms the CD-dependent electric field strength and further supports the experimental results. Our study provides new insights into designing a stimuli-responsive SERS-based platform with tunable hot spots for long-chain nucleic acid detection.
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Affiliation(s)
- Bohan Yin
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
| | - Willis Kwun Hei Ho
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
| | - Qin Zhang
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
| | - Chuanqi Li
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
| | - Yingying Huang
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
| | - Jiaxiang Yan
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
| | - Hongrong Yang
- Department of Bioengineering, College of Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Jianhua Hao
- Department of Applied Physics, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
| | - Siu Hong Dexter Wong
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
| | - Mo Yang
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
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Arana C, Liang C, Brock M, Zhang B, Zhou J, Chen L, Cantarel B, SoRelle J, Hooper LV, Raj P. A short plus long-amplicon based sequencing approach improves genomic coverage and variant detection in the SARS-CoV-2 genome. PLoS One 2022; 17:e0261014. [PMID: 35025877 PMCID: PMC8757904 DOI: 10.1371/journal.pone.0261014] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 11/22/2021] [Indexed: 12/01/2022] Open
Abstract
High viral transmission in the COVID-19 pandemic has enabled SARS-CoV-2 to acquire new mutations that may impact genome sequencing methods. The ARTIC.v3 primer pool that amplifies short amplicons in a multiplex-PCR reaction is one of the most widely used methods for sequencing the SARS-CoV-2 genome. We observed that some genomic intervals are poorly captured with ARTIC primers. To improve the genomic coverage and variant detection across these intervals, we designed long amplicon primers and evaluated the performance of a short (ARTIC) plus long amplicon (MRL) sequencing approach. Sequencing assays were optimized on VR-1986D-ATCC RNA followed by sequencing of nasopharyngeal swab specimens from fifteen COVID-19 positive patients. ARTIC data covered 94.47% of the virus genome fraction in the positive control and patient samples. Variant analysis in the ARTIC data detected 217 mutations, including 209 single nucleotide variants (SNVs) and eight insertions & deletions. On the other hand, long-amplicon data detected 156 mutations, of which 80% were concordant with ARTIC data. Combined analysis of ARTIC + MRL data improved the genomic coverage to 97.03% and identified 214 high confidence mutations. The combined final set of 214 mutations included 203 SNVs, 8 deletions and 3 insertions. Analysis showed 26 SARS-CoV-2 lineage defining mutations including 4 known variants of concern K417N, E484K, N501Y, P618H in spike gene. Hybrid analysis identified 7 nonsynonymous and 5 synonymous mutations across the genome that were either ambiguous or not called in ARTIC data. For example, G172V mutation in the ORF3a protein and A2A mutation in Membrane protein were missed by the ARTIC assay. Thus, we show that while the short amplicon (ARTIC) assay provides good genomic coverage with high throughput, complementation of poorly captured intervals with long amplicon data can significantly improve SARS-CoV-2 genomic coverage and variant detection.
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Affiliation(s)
- Carlos Arana
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
- Microbiome and Genomics core, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Chaoying Liang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
- Microbiome and Genomics core, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Matthew Brock
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
- Microbiome and Genomics core, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Bo Zhang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Jinchun Zhou
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
- Microbiome and Genomics core, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Li Chen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Brandi Cantarel
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Jeffrey SoRelle
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Lora V. Hooper
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Prithvi Raj
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
- Microbiome and Genomics core, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
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Hart CR, McLendon PM, Naik RR. Dealing with a Pandemic: Emerging Tools, Solutions, and Challenges. Health Secur 2022; 20:109-115. [PMID: 35021893 DOI: 10.1089/hs.2021.0145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
As a result of the COVID-19 pandemic, nations across the globe have responded by attempting to understand how the virus was spreading in their communities, in order to isolate cases, reduce morbidity and mortality, and avoid overwhelming healthcare facilities. In this article, we describe the global response to tracking the virus, and discuss new technological advances in molecular testing that have been deployed and developed to track and mitigate COVID-19. We also discuss how the successes and failures observed in the COVID-19 pandemic can be extrapolated to improve our ability to respond to the next pandemic.
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Affiliation(s)
- Corey R Hart
- Corey R. Hart, PhD, is a Senior Physiologist/Technical Integration Manager and Rajesh R. Naik, PhD, is Chief Scientist; both in the 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH. Patrick M. McLendon, PhD, is a Senior Scientist/Senior Technical Program Manager, Integrative Health and Performance Sciences Division, UES, Inc., Dayton, OH. The views expressed are those of the authors and do not reflect the official guidance or position of the United States Government, the Department of Defense or of the United States Air Force
| | - Patrick M McLendon
- Corey R. Hart, PhD, is a Senior Physiologist/Technical Integration Manager and Rajesh R. Naik, PhD, is Chief Scientist; both in the 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH. Patrick M. McLendon, PhD, is a Senior Scientist/Senior Technical Program Manager, Integrative Health and Performance Sciences Division, UES, Inc., Dayton, OH. The views expressed are those of the authors and do not reflect the official guidance or position of the United States Government, the Department of Defense or of the United States Air Force
| | - Rajesh R Naik
- Corey R. Hart, PhD, is a Senior Physiologist/Technical Integration Manager and Rajesh R. Naik, PhD, is Chief Scientist; both in the 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH. Patrick M. McLendon, PhD, is a Senior Scientist/Senior Technical Program Manager, Integrative Health and Performance Sciences Division, UES, Inc., Dayton, OH. The views expressed are those of the authors and do not reflect the official guidance or position of the United States Government, the Department of Defense or of the United States Air Force
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Zepeda-Cervantes J, Martínez-Flores D, Ramírez-Jarquín JO, Tecalco-Cruz ÁC, Alavez-Pérez NS, Vaca L, Sarmiento-Silva RE. Implications of the Immune Polymorphisms of the Host and the Genetic Variability of SARS-CoV-2 in the Development of COVID-19. Viruses 2022; 14:94. [PMID: 35062298 PMCID: PMC8778858 DOI: 10.3390/v14010094] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 01/08/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the current pandemic affecting almost all countries in the world. SARS-CoV-2 is the agent responsible for coronavirus disease 19 (COVID-19), which has claimed millions of lives around the world. In most patients, SARS-CoV-2 infection does not cause clinical signs. However, some infected people develop symptoms, which include loss of smell or taste, fever, dry cough, headache, severe pneumonia, as well as coagulation disorders. The aim of this work is to report genetic factors of SARS-CoV-2 and host-associated to severe COVID-19, placing special emphasis on the viral entry and molecules of the immune system involved with viral infection. Besides this, we analyze SARS-CoV-2 variants and their structural characteristics related to the binding to polymorphic angiotensin-converting enzyme type 2 (ACE2). Additionally, we also review other polymorphisms as well as some epigenetic factors involved in the immunopathogenesis of COVID-19. These factors and viral variability could explain the increment of infection rate and/or in the development of severe COVID-19.
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Affiliation(s)
- Jesús Zepeda-Cervantes
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Daniel Martínez-Flores
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Josué Orlando Ramírez-Jarquín
- Departamento de Neuropatología Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Ángeles C. Tecalco-Cruz
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México (UACM), Mexico City 06720, Mexico;
| | - Noé Santiago Alavez-Pérez
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Mexico City 07340, Mexico;
| | - Luis Vaca
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Rosa Elena Sarmiento-Silva
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
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Bano I, Sharif M, Alam S. Genetic drift in the genome of SARS COV-2 and its global health concern. J Med Virol 2022; 94:88-98. [PMID: 34524697 PMCID: PMC8661852 DOI: 10.1002/jmv.27337] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/12/2021] [Indexed: 01/04/2023]
Abstract
The outbreak of the current coronavirus disease (COVID-19) occurred in late 2019 and quickly spread all over the world. The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) belongs to a genetically diverse group that mutates continuously leading to the emergence of multiple variants. Although a few antiviral agents and anti-inflammatory medicines are available, thousands of individuals have passed away due to emergence of new viral variants. Thus, proper surveillance of the SARS-CoV-2 genome is needed for the rapid identification of developing mutations over time, which are of the major concern if they occur specifically in the surface spike proteins of the virus (neutralizing analyte). This article reviews the potential mutations acquired by the SARS-CoV2 since the pandemic began and their significant impact on the neutralizing efficiency of vaccines and validity of the diagnostic assays.
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Affiliation(s)
- Iqra Bano
- Department of MicrobiologyThe University of HaripurHaripurPakistan
| | - Mehmoona Sharif
- Department of MicrobiologyQuaid I Azam UniversityIslamabadPakistan
| | - Sadia Alam
- Department of MicrobiologyThe University of HaripurHaripurPakistan
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Huang X, Tang G, Ismail N, Wang X. Developing RT-LAMP assays for rapid diagnosis of SARS-CoV-2 in saliva. EBioMedicine 2022; 75:103736. [PMID: 34922321 PMCID: PMC8674011 DOI: 10.1016/j.ebiom.2021.103736] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 11/13/2021] [Accepted: 11/22/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has killed millions of people worldwide. The current crisis has created an unprecedented demand for rapid test of SARS-CoV-2 infection. METHODS Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a fast and convenient method to amplify and identify the transcripts of a targeted pathogen. However, the sensitivity and specificity of RT-LAMP were generally regarded as inferior when compared with the gold standard RT-qPCR. To address this issue, we combined bioinformatic and experimental analyses to improve the assay performance for COVID-19 diagnosis. FINDINGS First, by experimental screening as well as high-throughput sequencing studies, we discovered new primer features that impacted LAMP sensitivity and specificity. These features were then used to build an improved bioinformatics algorithm to design LAMP primers targeting SARS-CoV-2. We further rigorously validated these new assays for their efficacy and specificity. We demonstrated that multiplexed RT-LAMP assay could directly detect as low as 1.5 copies/µL of SARS-CoV-2 particles in saliva, without the need of RNA isolation. We further tested this ultra-sensitive and specific RT-LAMP assay using saliva samples from COVID-19 patients. Clinical validation results indicated that the new RT-LAMP assay was comparable to standard RT-qPCR in overall assay sensitivity and specificity. INTERPRETATION In summary, our new LAMP primer design algorithm along with the validated assays provide a fast and reliable method for the diagnosis of COVID-19 cases. FUNDING National Institutes of Health.
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Affiliation(s)
- Xin Huang
- Department of Pharmacology and Regenerative Medicine, University of Illinois Chicago Chicago, IL, United States; University of Illinois Cancer Center, Chicago, IL, United States
| | - Gongyu Tang
- Department of Pharmacology and Regenerative Medicine, University of Illinois Chicago Chicago, IL, United States; University of Illinois Cancer Center, Chicago, IL, United States
| | - Nahed Ismail
- Department of Pathology, University of Illinois Chicago; Chicago, IL, United States
| | - Xiaowei Wang
- Department of Pharmacology and Regenerative Medicine, University of Illinois Chicago Chicago, IL, United States; University of Illinois Cancer Center, Chicago, IL, United States.
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44
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Kaur N, Sahoo SS, Chhabra HS, Kaur A, Singh N, Garg S. High-resolution chest computed tomography findings of coronavirus disease 2019 (COVID-19) - A retrospective single center study of 152 patients. J Family Med Prim Care 2021; 10:3753-3759. [PMID: 34934676 PMCID: PMC8653456 DOI: 10.4103/jfmpc.jfmpc_173_21] [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: 01/24/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 11/15/2022] Open
Abstract
Introduction: Coronavirus disease 2019 (COVID-19) pandemic has engulfed the world, within a short span of time crippling many health systems. The disease in its ever-evolving course is exhibiting a myriad of symptoms and imaging manifestations. This retrospective study was conducted to generate evidence from the chest computed tomography (CT) findings of patients with COVID-19 pneumonia to aid in the diagnosis and disease management. Methods: This retrospective study included all patients with reverse transcriptase polymerase chain reaction confirmed COVID-19 disease who underwent chest CT between 1st June to 31st December 2020 at a tertiary care institute of North India. Anonymized data of 152 COVID-19 positive patients was used for the evaluation of the clinical profile and imaging findings. Results: The common presenting clinical symptoms were fever, cough, myalgia and sore throat. The most frequent CT imaging feature consisted of ground-glass opacities (GGOs), consolidation and crazy paving distributed bilaterally, peripherally in subpleural location with a predilection for the posterior parts of lungs. Reverse halo sign was observed in 12 patients and halo sign in 3 patients. Dilated pulmonary vessels with mild bronchiolectasis were observed in the involved lung parenchyma. Less common findings included pleural effusion, mediastinal lymphadenopathy, and pericardial effusion. The mean CT severity score gradually increased with increasing age. Conclusion: The predominant imaging finding of COVID-19 pneumonia was peripheral GGO's distributed bilaterally in peripheral subpleural region and having predilection for the posterior parts of the lungs which gradually evolve into organizing pneumonia patterns. Although COVID-19 shares imaging findings with other viral pneumonias, however in the context of the current pandemic, we must keep COVID-19 a differential diagnosis, in all patients with fever and respiratory symptoms.
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Affiliation(s)
- Navdeep Kaur
- Department of Radiodiagnosis, All India Institute of Medical Sciences, Bathinda, Punjab, India
| | - Soumya S Sahoo
- Department of Community and Family Medicine, All India Institute of Medical Sciences, Bathinda, Punjab, India
| | - Harvinder S Chhabra
- Department of Forensic Medicine, GGS Medical College and Hospital, Faridkot, Punjab, India
| | - Amandeep Kaur
- General Medicine, All India Institute of Medical Sciences, Bathinda, Punjab, India
| | - Navdeep Singh
- Department of Radiodiagnosis, Delhi Heart Hospital and Multispeciality Institute, Bathinda, Punjab, India
| | - Shivane Garg
- Department of Radiodiagnosis, All India Institute of Medical Sciences, Bathinda, Punjab, India
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45
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Dubey A, Choudhary S, Kumar P, Tomar S. Emerging SARS-CoV-2 Variants: Genetic Variability and Clinical Implications. Curr Microbiol 2021; 79:20. [PMID: 34905108 PMCID: PMC8669229 DOI: 10.1007/s00284-021-02724-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/08/2021] [Indexed: 12/12/2022]
Abstract
The sudden rise in COVID-19 cases in 2020 and the incessant emergence of fast-spreading variants have created an alarming situation worldwide. Besides the continuous advancements in the design and development of vaccines to combat this deadly pandemic, new variants are frequently reported, possessing mutations that rapidly outcompeted an existing population of circulating variants. As concerns grow about the effects of mutations on the efficacy of vaccines, increased transmissibility, immune escape, and diagnostic failures are few other apprehensions liable for more deadly waves of COVID-19. Although the phenomenon of antigenic drift in new variants of SARS-CoV-2 is still not validated, it is conceived that the virus is acquiring new mutations as a fitness advantage for rapid transmission or to overcome immunological resistance of the host cell. Considerable evolution of SARS-CoV-2 has been observed since its first appearance in 2019, and despite the progress in sequencing efforts to characterize the mutations, their impacts in many variants have not been analyzed. The present article provides a substantial review of literature explaining the emerging variants of SARS-CoV-2 circulating globally, key mutations in viral genome, and the possible impacts of these new mutations on prevention and therapeutic strategies currently administered to combat this pandemic. Rising infections, mortalities, and hospitalizations can possibly be tackled through mass vaccination, social distancing, better management of available healthcare infrastructure, and by prioritizing genome sequencing for better serosurveillance studies and community tracking.
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Affiliation(s)
- Aakriti Dubey
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Shweta Choudhary
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India.
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Tong F, Li J, Qu W, Song W, Zhao D. SCOPE2: A Platform for Sars-COv-2 Primer covErage Evaluation. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2021; 2021:2197-2200. [PMID: 34891723 DOI: 10.1109/embc46164.2021.9630187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Currently, there is an increasing number and speed of SARS-CoV-2 mutation taking place around the world, posing a threat to promising public health and challenge to existing diagnostic tools. RT-PCR technology is recognized as the gold standard diagnosing methodology but has shown inaccuracy under some mutated SARS-CoV-2 circumstances. In this study, we developed a platform named SCOPE2 (Sars-COv-2 Primer covErage Evaluation) based on our previous publication. Testing by commonly-used SARS-COV-2 PCR primers, SCOPE2 is proved to effectively and efficiently assess the quality in terms of detection coverage, which may provide a practical tool for primer selection acceleration and primer design improvement.Clinical Relevance-This assists in single SARS-COV-2 Primer selection and suggestion of different SARS-COV-2 Primer combinations.
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47
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Bai C, Wang J, Chen G, Zhang H, An K, Xu P, Du Y, Ye RD, Saha A, Zhang A, Warshel A. Predicting Mutational Effects on Receptor Binding of the Spike Protein of SARS-CoV-2 Variants. J Am Chem Soc 2021; 143:17646-17654. [PMID: 34648291 PMCID: PMC8525340 DOI: 10.1021/jacs.1c07965] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Indexed: 12/17/2022]
Abstract
The pandemic caused by SARS-CoV-2 has cost millions of lives and tremendous social/financial loss. The virus continues to evolve and mutate. In particular, the recently emerged "UK", "South Africa", and Delta variants show higher infectivity and spreading speed. Thus, the relationship between the mutations of certain amino acids and the spreading speed of the virus is a problem of great importance. In this respect, understanding the mutational mechanism is crucial for surveillance and prediction of future mutations as well as antibody/vaccine development. In this work, we used a coarse-grained model (that was used previously in predicting the importance of mutations of N501) to calculate the free energy change of various types of single-site or combined-site mutations. This was done for the UK, South Africa, and Delta mutants. We investigated the underlying mechanisms of the binding affinity changes for mutations at different spike protein domains of SARS-CoV-2 and provided the energy basis for the resistance of the E484 mutant to the antibody m396. Other potential mutation sites were also predicted. Furthermore, the in silico predictions were assessed by functional experiments. The results establish that the faster spreading of recently observed mutants is strongly correlated with the binding-affinity enhancement between virus and human receptor as well as with the reduction of the binding to the m396 antibody. Significantly, the current approach offers a way to predict new variants and to assess the effectiveness of different antibodies toward such variants.
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Affiliation(s)
- Chen Bai
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Road, Shenzhen 518172, China
| | - Junlin Wang
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Road, Shenzhen 518172, China
| | - Geng Chen
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Road, Shenzhen 518172, China
| | - Honghui Zhang
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Road, Shenzhen 518172, China
| | - Ke An
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Road, Shenzhen 518172, China
| | - Peiyi Xu
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Road, Shenzhen 518172, China
| | - Yang Du
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Road, Shenzhen 518172, China
| | - Richard D Ye
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Road, Shenzhen 518172, China
| | - Arjun Saha
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089-1062, U.S.A
| | - Aoxuan Zhang
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089-1062, U.S.A
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089-1062, U.S.A
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Jindal H, Jain S, Suvvari TK, Kutikuppala LVS, Rackimuthu S, Rocha ICN, Goyal S, Radha. False-Negative RT-PCR Findings and Double Mutant Variant as Factors of an Overwhelming Second Wave of COVID-19 in India: an Emerging Global Health Disaster. SN COMPREHENSIVE CLINICAL MEDICINE 2021; 3:2383-2388. [PMID: 34568761 PMCID: PMC8453462 DOI: 10.1007/s42399-021-01059-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Accepted: 09/01/2021] [Indexed: 12/17/2022]
Abstract
RT-PCR is considered to be the standard gold diagnostic test for detecting COVID-19 causing SARS-CoV-2. Recent reports and recent pieces of evidence from scientific literature, however, tell a different story. There have been speculations of SARS-CoV-2 escaping the RT-PCR because of the series of mutations it has gone through. It is possible that host-dependent RNA editing and high person-to-person transmission have equipped the virus with mutations enabling it to spread faster and even evade the RT-PCR. Added to this is burnout among healthcare workers and technicians handling the RT-PCR machines and sampling. All of these factors may be working in unison to result in the deluge of false-negative cases India is facing during the second COVID-19 wave. The mutant strains are spreading to other parts, posing challenges to the whole world. These circumstances warrant supplementary diagnostic tests such as serological and radiological findings to deal with cases of high clinical suspicion. Even one misdiagnosed COVID-19 patient poses a risk to hundreds of others in the vicinity. Healthcare workers' burnout also has to be dealt with. Erroneous staff should be re-trained.
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Affiliation(s)
- Himanshu Jindal
- Ganesh Shankar Vidyarthi Memorial Medical College, Kanpur, India
| | | | | | - LVSimhachalam Kutikuppala
- Konaseema Institute of Medical Sciences and Research Foundation (KIMS&RF), Amalapuram, Andhra Pradesh India
| | | | | | | | - Radha
- Kasturba Medical College, Manipal, India
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Wang C, Cheng X, Liu L, Zhang X, Yang X, Zheng S, Rong Z, Wang S. Ultrasensitive and Simultaneous Detection of Two Specific SARS-CoV-2 Antigens in Human Specimens Using Direct/Enrichment Dual-Mode Fluorescence Lateral Flow Immunoassay. ACS APPLIED MATERIALS & INTERFACES 2021; 13:40342-40353. [PMID: 34412466 PMCID: PMC8386037 DOI: 10.1021/acsami.1c11461] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/12/2021] [Indexed: 05/18/2023]
Abstract
Sensitive point-of-care methods for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigens in clinical specimens are urgently needed to achieve rapid screening of viral infection. We developed a magnetic quantum dot-based dual-mode lateral flow immunoassay (LFIA) biosensor for the high-sensitivity simultaneous detection of SARS-CoV-2 spike (S) and nucleocapsid protein (NP) antigens, which is beneficial for improving the detection accuracy and efficiency of SARS-CoV-2 infection in the point-of-care testing area. A high-performance magnetic quantum dot with a triple-QD shell (MagTQD) nanotag was first fabricated and integrated into the LFIA system to provide superior fluorescence signals, enrichment ability, and detectability for S/NP antigen testing. Two detection modes were provided by the proposed MagTQD-LFIA. The direct mode was used for rapid screening or urgent detection of suspected samples within 10 min, and the enrichment mode was used for the highly sensitive and quantitative analysis of SARS-CoV-2 antigens in biological samples without the interference of the "hook effect." The simultaneous detection of SARS-CoV-2 S/NP antigens was conducted in one LFIA strip, and the detection limits for two antigens under direct and enrichment modes were 1 and 0.5 pg/mL, respectively. The MagTQD-LFIA showed high accuracy, specificity, and stability in saliva and nasal swab samples and is an efficient tool with flexibility to meet the testing requirements for SARS-CoV-2 antigens in various situations.
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Affiliation(s)
- Chongwen Wang
- College
of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China
- Beijing
Institute of Radiation Medicine, Beijing 100850, P. R.
China
- Beijing
Key Laboratory of New Molecular Diagnosis Technologies for Infectious
Diseases, Beijing 100850, P. R. China
| | - Xiaodan Cheng
- College
of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China
- Beijing
Institute of Radiation Medicine, Beijing 100850, P. R.
China
| | - Liyan Liu
- Beijing
Institute of Radiation Medicine, Beijing 100850, P. R.
China
| | - Xiaochang Zhang
- Beijing
Institute of Radiation Medicine, Beijing 100850, P. R.
China
| | - Xingsheng Yang
- College
of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China
- Beijing
Institute of Radiation Medicine, Beijing 100850, P. R.
China
| | - Shuai Zheng
- College
of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Zhen Rong
- Beijing
Institute of Radiation Medicine, Beijing 100850, P. R.
China
| | - Shengqi Wang
- Beijing
Institute of Radiation Medicine, Beijing 100850, P. R.
China
- Beijing
Key Laboratory of New Molecular Diagnosis Technologies for Infectious
Diseases, Beijing 100850, P. R. China
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Osterman A, Iglhaut M, Lehner A, Späth P, Stern M, Autenrieth H, Muenchhoff M, Graf A, Krebs S, Blum H, Baiker A, Grzimek-Koschewa N, Protzer U, Kaderali L, Baldauf HM, Keppler OT. Comparison of four commercial, automated antigen tests to detect SARS-CoV-2 variants of concern. Med Microbiol Immunol 2021; 210:263-275. [PMID: 34415422 PMCID: PMC8377707 DOI: 10.1007/s00430-021-00719-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 08/13/2021] [Indexed: 12/23/2022]
Abstract
A versatile portfolio of diagnostic tests is essential for the containment of the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) pandemic. Besides nucleic acid-based test systems and point-of-care (POCT) antigen (Ag) tests, quantitative, laboratory-based nucleocapsid Ag tests for SARS-CoV-2 have recently been launched. Here, we evaluated four commercial Ag tests on automated platforms and one POCT to detect SARS-CoV-2. We evaluated PCR-positive (n = 107) and PCR-negative (n = 303) respiratory swabs from asymptomatic and symptomatic patients at the end of the second pandemic wave in Germany (February–March 2021) as well as clinical isolates EU1 (B.1.117), variant of concern (VOC) Alpha (B.1.1.7) or Beta (B.1.351), which had been expanded in a biosafety level 3 laboratory. The specificities of automated SARS-CoV-2 Ag tests ranged between 97.0 and 99.7% (Lumipulse G SARS-CoV-2 Ag (Fujirebio): 97.03%, Elecsys SARS-CoV-2 Ag (Roche Diagnostics): 97.69%; LIAISON® SARS-CoV-2 Ag (Diasorin) and SARS-CoV-2 Ag ELISA (Euroimmun): 99.67%). In this study cohort of hospitalized patients, the clinical sensitivities of tests were low, ranging from 17.76 to 52.34%, and analytical sensitivities ranged from 420,000 to 25,000,000 Geq/ml. In comparison, the detection limit of the Roche Rapid Ag Test (RAT) was 9,300,000 Geq/ml, detecting 23.58% of respiratory samples. Receiver-operating-characteristics (ROCs) and Youden’s index analyses were performed to further characterize the assays’ overall performance and determine optimal assay cutoffs for sensitivity and specificity. VOCs carrying up to four amino acid mutations in nucleocapsid were detected by all five assays with characteristics comparable to non-VOCs. In summary, automated, quantitative SARS-CoV-2 Ag tests show variable performance and are not necessarily superior to a standard POCT. The efficacy of any alternative testing strategies to complement nucleic acid-based assays must be carefully evaluated by independent laboratories prior to widespread implementation.
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Affiliation(s)
- Andreas Osterman
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Iglhaut
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Andreas Lehner
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Patricia Späth
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Marcel Stern
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Hanna Autenrieth
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Muenchhoff
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Armin Baiker
- Public Health Microbiology Unit, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Natascha Grzimek-Koschewa
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Ulrike Protzer
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Hanna-Mari Baldauf
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
- Max Von Pettenkofer Institute, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany.
| | - Oliver T Keppler
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany.
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.
- Max Von Pettenkofer Institute, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany.
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