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Ogo N, Ikegame S, Hotta T, Kan-O K, Yoneshima Y, Shiraishi Y, Tsubouchi K, Tanaka K, Okamoto I. The Utility and Limitations of Universal Polymerase Chain Reaction Screening for SARS-CoV-2 During Hospital Admission. Cureus 2024; 16:e61470. [PMID: 38953084 PMCID: PMC11215299 DOI: 10.7759/cureus.61470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2024] [Indexed: 07/03/2024] Open
Abstract
OBJECTIVE Universal polymerase chain reaction (PCR) screening for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on hospital admission is an effective approach to preventing coronavirus disease 2019 (COVID-19) outbreaks in medical facilities. However, false-positive test results due to a recent infection are a concern. We investigated the usefulness and limitations of universal PCR screening for SARS-CoV-2 on hospital admission in a real-world setting. METHODS We retrospectively analyzed 1320 attempted hospital admissions for 775 patients at the Department of Respiratory Medicine, Kyushu University Hospital, between January 1, 2022, and May 2, 2023. RESULTS Thirty-nine out of 1201 PCR tests (3.2%) yielded a positive result, with 22 of these results being considered false positives on the basis of a recent infection. We found that 39% of cases showed a positive PCR result between 31 and 60 days after the onset of COVID-19, although the threshold cycle (Ct) for target 1 (ORF1ab gene) of the Cobas SARS-CoV-2 test (Roche Diagnostics, Basel, Switzerland) was >30 in most instances. CONCLUSION Hospital admission based on the results of PCR screening for SARS-CoV-2 should take into account not only PCR positivity but also the Ct value and recent COVID-19 history.
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Affiliation(s)
- Naruhiko Ogo
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, JPN
| | - Satoshi Ikegame
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, JPN
| | - Taeko Hotta
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, Fukuoka, JPN
| | - Keiko Kan-O
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, JPN
| | - Yasuto Yoneshima
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, JPN
| | - Yoshimasa Shiraishi
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, JPN
| | - Kazuya Tsubouchi
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, JPN
| | - Kentaro Tanaka
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, JPN
| | - Isamu Okamoto
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, JPN
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2
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Mostafa HH. Is It Possible to Test for Viral Infectiousness?: The Use Case of (SARS-CoV-2). Clin Lab Med 2024; 44:85-93. [PMID: 38280800 DOI: 10.1016/j.cll.2023.10.008] [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] [Indexed: 01/29/2024]
Abstract
Identifying and managing individuals with active or chronic disease, implementing appropriate infection control measures, and mitigating the spread of the COVID-19 pandemic highlighted the need for tests of infectiousness. The gold standard for assessing infectiousness has been the recovery of infectious virus in cell culture. Using cycle threshold values, antigen testing, and SARS-CoV-2, replication intermediate strands were used to assess infectiousness, with many limitations. Infectiousness can be influenced by host factors (eg, preexisting immune responses) and virus factors (eg, evolution).
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Affiliation(s)
- Heba H Mostafa
- Johns Hopkins School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD 21287, USA.
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3
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McCracken GR, Gaston D, Pettipas J, Loder A, Majer A, Grudeski E, Labbé G, Joy BK, Patriquin G, LeBlanc JJ. Neglected SARS-CoV-2 variants and potential concerns for molecular diagnostics: a framework for nucleic acid amplification test target site quality assurance. Microbiol Spectr 2023; 11:e0076123. [PMID: 37815347 PMCID: PMC10715164 DOI: 10.1128/spectrum.00761-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/02/2023] [Indexed: 10/11/2023] Open
Abstract
IMPORTANCE Molecular tests like polymerase chain reaction were widely used during the COVID-19 pandemic but as the pandemic evolved, so did SARS-CoV-2. This virus acquired mutations, prompting concerns that mutations could compromise molecular test results and be falsely negative. While some manufacturers may have in-house programs for monitoring mutations that could impact their assay performance, it is important to promptly report mutations in circulating viral strains that could adversely impact a diagnostic test result. However, commercial test target sites are proprietary, making independent monitoring difficult. In this study, SARS-CoV-2 test target sites were sequenced to monitor and assess mutations impact, and 29 novel mutations impacting SARS-CoV-2 detection were identified. This framework for molecular test target site quality assurance could be adapted to any molecular test, ensuring accurate diagnostic test results and disease diagnoses.
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Affiliation(s)
- Gregory R. McCracken
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health (NSH), Halifax, Nova Scotia, Canada
| | - Daniel Gaston
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, Nova Scotia Health (NSH), Halifax, Nova Scotia, Canada
| | - Janice Pettipas
- Nova Scotia Provincial Public Health Laboratory Network (PPHLN), Halifax, Nova Scotia, Canada
| | - Allana Loder
- National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC), Winnipeg, Manitoba, Canada
| | - Anna Majer
- National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC), Winnipeg, Manitoba, Canada
| | - Elsie Grudeski
- National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC), Winnipeg, Manitoba, Canada
| | - Geneviève Labbé
- National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC), Winnipeg, Manitoba, Canada
| | - Bryn K. Joy
- Medical Sciences Program, Faculty of Sciences, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Glenn Patriquin
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health (NSH), Halifax, Nova Scotia, Canada
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jason J. LeBlanc
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health (NSH), Halifax, Nova Scotia, Canada
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Medicine (Infectious Diseases), Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
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4
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Koné A, Diallo D, Kané F, Diarra B, Coulibaly TA, Sameroff SC, Diarra HB, Diakité MT, Camara F, Maiga O, Keita D, Dolo O, Somboro A, Coulibaly Y, Bane S, Togo AC, Somboro AM, Togo J, Coulibaly M, Coulibaly G, Kone M, Degoga B, Dramé HB, Traoré FG, Diallo F, Sanogo F, Kone K, Diallo IB, Sanogo M, Diakité M, Mishra N, Neal A, Saliba-Shaw K, Sow Y, Hensley L, Lane HC, Briese T, Lipkin WI, Doumbia S. Dynamics of SARS-CoV-2 variants characterized during different COVID-19 waves in Mali. IJID REGIONS 2023; 6:24-28. [PMID: 36448028 PMCID: PMC9691504 DOI: 10.1016/j.ijregi.2022.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022]
Abstract
Background The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants may have contributed to prolonging the pandemic, and increasing morbidity and mortality related to coronavirus disease 2019 (COVID-19). This article describes the dynamics of circulating SARS-CoV-2 variants identified during the different COVID-19 waves in Mali between April and October 2021. Methods The respiratory SARS-CoV-2 complete spike (S) gene from positive samples was sequenced. Generated sequences were aligned by Variant Reporter v3.0 using the Wuhan-1 strain as the reference. Mutations were noted using the GISAID and Nextclade platforms. Results Of 16,797 nasopharyngeal swab samples tested, 6.0% (1008/16,797) tested positive for SARS-CoV-2 on quantitative reverse transcription polymerase chain reaction. Of these, 16.07% (162/1008) had a cycle threshold value ≤28 and were amplified and sequenced. The complete S gene sequence was recovered from 80 of 162 (49.8%) samples. Seven distinct variants were identified: Delta (62.5%), Alpha (1.2%), Beta (1.2%), Eta (30.0%), 20B (2.5%), 19B (1.2%) and 20A (1.2%). Conclusions and perspectives Several SARS-CoV-2 variants were present during the COVID-19 waves in Mali between April and October 2021. The continued emergence of new variants highlights the need to strengthen local real-time sequencing capacity and genomic surveillance for better and coordinated national responses to SARS-CoV-2.
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Affiliation(s)
- Amadou Koné
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Dramane Diallo
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Fousseyni Kané
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Bassirou Diarra
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Tenin Aminatou Coulibaly
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Hawa B. Diarra
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mahamane T. Diakité
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Fatoumata Camara
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Oumou Maiga
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Daouda Keita
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Oumar Dolo
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Amadou Somboro
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Youssouf Coulibaly
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sidy Bane
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Antieme C.G. Togo
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Anou M. Somboro
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Josué Togo
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mariam Coulibaly
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Gagni Coulibaly
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mahamadou Kone
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Boureima Degoga
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Hawa Baye Dramé
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Fah Gaoussou Traoré
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Fatimata Diallo
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Fanta Sanogo
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Kadidia Kone
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Ibrahima B. Diallo
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Moumine Sanogo
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mahamadou Diakité
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Nischay Mishra
- Center for Infection and Immunity, Columbia University, New York, NY, USA
| | - Aaron Neal
- Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Katy Saliba-Shaw
- Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ydrissa Sow
- Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lisa Hensley
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - H. Clifford Lane
- Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Thomas Briese
- Center for Infection and Immunity, Columbia University, New York, NY, USA
| | - W. Ian Lipkin
- Center for Infection and Immunity, Columbia University, New York, NY, USA
| | - Seydou Doumbia
- University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
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Jiang M, Chen W, Chen Y, Chen J, Zhang Y, Yin H, Li Y, Liu W. Analytical performance of rapid nucleic acid detection assays and routine RT-qPCR assays for detection of SARS-CoV-2 in Shanghai, China in 2022. Diagn Microbiol Infect Dis 2023; 105:115860. [PMID: 36459887 PMCID: PMC9708047 DOI: 10.1016/j.diagmicrobio.2022.115860] [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: 08/02/2022] [Revised: 10/28/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
Abstract
Diagnostic accuracy of COVID-19 varies among different assays. In this study, the analytical performance of 1 rapid nucleic acid detection assay (Coyote assay) and 2 routine RT-qPCR assays (BioGerm assay and DaAn assay) was evaluated, using 1196 clinical samples. Disagreement in the results of 2 paired targets occurred in all 3 assays. The Coyote assay failed to detect 15 samples, and the DaAn assay failed to detect 5 samples. The Cohen's kappa coefficient was 0.970 between the BioGerm and DaAn assays, 0.907 between the Coyote and BioGerm assays, and 0.936 between the Coyote and DaAn assays. The positive percent agreement, and negative percent agreement of the Coyote assay were 84.04%, and 100%, respectively. Our study revealed that the results of the Coyote, BioGerm, and DaAn assays were highly consistent, which provided reference for the application of these assays for diagnosis of COVID-19.
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Affiliation(s)
- Min Jiang
- Department of Laboratory Medicine, LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Department of Laboratory Medicine and Central Laboratory, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Weiqin Chen
- Department of Laboratory Medicine, LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yong Chen
- Department of Laboratory Medicine, LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jia Chen
- Department of Laboratory Medicine, LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yue Zhang
- Department of Laboratory Medicine, LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hongmei Yin
- Department of Laboratory Medicine, LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yi Li
- Department of Nephropathy, LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Weiwei Liu
- Department of Laboratory Medicine, LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
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6
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Wang X, Hu M, Liu B, Xu H, Jin Y, Wang B, Zhao Y, Wu J, Yue J, Ren H. Evaluating the effect of SARS-CoV-2 spike mutations with a linear doubly robust learner. Front Cell Infect Microbiol 2023; 13:1161445. [PMID: 37153142 PMCID: PMC10154619 DOI: 10.3389/fcimb.2023.1161445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/03/2023] [Indexed: 05/09/2023] Open
Abstract
Driven by various mutations on the viral Spike protein, diverse variants of SARS-CoV-2 have emerged and prevailed repeatedly, significantly prolonging the pandemic. This phenomenon necessitates the identification of key Spike mutations for fitness enhancement. To address the need, this manuscript formulates a well-defined framework of causal inference methods for evaluating and identifying key Spike mutations to the viral fitness of SARS-CoV-2. In the context of large-scale genomes of SARS-CoV-2, it estimates the statistical contribution of mutations to viral fitness across lineages and therefore identifies important mutations. Further, identified key mutations are validated by computational methods to possess functional effects, including Spike stability, receptor-binding affinity, and potential for immune escape. Based on the effect score of each mutation, individual key fitness-enhancing mutations such as D614G and T478K are identified and studied. From individual mutations to protein domains, this paper recognizes key protein regions on the Spike protein, including the receptor-binding domain and the N-terminal domain. This research even makes further efforts to investigate viral fitness via mutational effect scores, allowing us to compute the fitness score of different SARS-CoV-2 strains and predict their transmission capacity based solely on their viral sequence. This prediction of viral fitness has been validated using BA.2.12.1, which is not used for regression training but well fits the prediction. To the best of our knowledge, this is the first research to apply causal inference models to mutational analysis on large-scale genomes of SARS-CoV-2. Our findings produce innovative and systematic insights into SARS-CoV-2 and promotes functional studies of its key mutations, serving as reliable guidance about mutations of interest.
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Affiliation(s)
| | | | | | | | | | | | | | - Jun Wu
- *Correspondence: Hongguang Ren, ; Junjie Yue, ; Jun Wu,
| | - Junjie Yue
- *Correspondence: Hongguang Ren, ; Junjie Yue, ; Jun Wu,
| | - Hongguang Ren
- *Correspondence: Hongguang Ren, ; Junjie Yue, ; Jun Wu,
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7
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Design and Implementation of Improved SARS-CoV-2 Diagnostic Assays To Mitigate the Impact of Genomic Mutations on Target Failure: the Xpert Xpress SARS-CoV-2 Experience. Microbiol Spectr 2022; 10:e0135522. [PMID: 36255326 PMCID: PMC9769917 DOI: 10.1128/spectrum.01355-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In 2020, the U.S. Food and Drug Administration (FDA) enabled manufacturers to request emergency use authorization (EUA) to facilitate the rapid authorization of in vitro diagnostic (IVD) platforms for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Uncommon SARS-CoV-2 point mutations could cause nucleocapsid (N) gene target failure (NGTF) when using first-generation Xpert Xpress assays, so improvements were designed and implemented. In response to NGTF reports and with consideration of viral genomic information in public databases, the Xpress assays were redesigned to mitigate the impact of SARS-CoV-2 mutations on qualitative assay performance. The second-generation assays include a third gene target (RNA-dependent RNA polymerase [RdRp]) and redundant oligonucleotide probes for the N2 target. First- and second-generation assay performances were evaluated using a challenge set of samples. A second-generation assay with updated oligonucleotide chemistry received FDA EUA in September 2021. A prototype assay with oligonucleotide chemistry similar to that of the second-generation assay with FDA EUA successfully detected all three gene targets (N2, envelope [E], and RdRp) in all challenge samples (100%; 50/50), including variants with N gene mutations (g.29197C>T or g.29200C>T), which caused NGTF in the first-generation assays. Investigation and reporting of IVD target failures, public sharing of viral genomic sequence data, and the FDA EUA pathway were essential components in facilitating a short cycle time from the identification of mutations that impact the performance of an IVD assay to the design and implementation of an improved IVD assay. IMPORTANCE The SARS-CoV-2 genome has mutated during the coronavirus disease 2019 (COVID-19) pandemic. Some of these mutations have impacted the performance of nucleic acid amplification tests like PCR, which are commonly used as diagnostic tools to detect an infection. The U.S. Food and Drug Administration (FDA) emergency use authorization (EUA) process enables the rapid reformulation and regulatory authorization of improved PCRs. In our experience, the identification of SARS-CoV-2 mutations that impact PCR performance, the subsequent development of improved PCR chemistry, and the use of the FDA EUA regulatory pathway led to improved diagnostic performance during the SARS-CoV-2 pandemic that is able to keep pace with the rapidly evolving genome of SARS-CoV-2.
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Babady NE, Burckhardt RM, Krammer F, Moore PL, Enquist LW. Building a Resilient Scientific Network for COVID-19 and Beyond. mBio 2022; 13:e0222322. [PMID: 36125317 PMCID: PMC9600431 DOI: 10.1128/mbio.02223-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The continued evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) necessitates that the global scientific community monitor, assess, and respond to the evolving coronavirus disease (COVID-19) pandemic. But the current reactive approach to emerging variants is ill-suited to address the quickly evolving and ever-changing pandemic. To tackle this challenge, investments in pathogen surveillance, systematic variant characterization, and data infrastructure and sharing across public and private sectors will be critical for planning proactive responses to emerging variants. Additionally, an emphasis on incorporating real-time variant identification in point-of-care diagnostics can help inform patient treatment. Active approaches to understand and identify "immunity gaps" can inform design of future vaccines, therapeutics, and diagnostics that will be more resistant to novel variants. Approaches where the scientific community actively plans for and anticipates changes to infectious diseases will result in a more resilient system, capable of adapting to evolving pathogens quickly and effectively.
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Affiliation(s)
- N. Esther Babady
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Penny L. Moore
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa, University of Kwazulu-Natal, Durban, South Africa
| | - Lynn W. Enquist
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
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9
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Jiang W, Ji W, Zhang Y, Xie Y, Chen S, Jin Y, Duan G. An Update on Detection Technologies for SARS-CoV-2 Variants of Concern. Viruses 2022; 14:v14112324. [PMID: 36366421 PMCID: PMC9693800 DOI: 10.3390/v14112324] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/15/2022] [Accepted: 10/20/2022] [Indexed: 01/18/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is responsible for the global epidemic of Coronavirus Disease 2019 (COVID-19), with a significant impact on the global economy and human safety. Reverse transcription-quantitative polymerase chain reaction (RT-PCR) is the gold standard for detecting SARS-CoV-2, but because the virus's genome is prone to mutations, the effectiveness of vaccines and the sensitivity of detection methods are declining. Variants of concern (VOCs) include Alpha, Beta, Gamma, Delta, and Omicron, which are able to evade recognition by host immune mechanisms leading to increased transmissibility, morbidity, and mortality of COVID-19. A range of research has been reported on detection techniques for VOCs, which is beneficial to prevent the rapid spread of the epidemic, improve the effectiveness of public health and social measures, and reduce the harm to human health and safety. However, a meaningful translation of this that reduces the burden of disease, and delivers a clear and cohesive message to guide daily clinical practice, remains preliminary. Herein, we summarize the capabilities of various nucleic acid and protein-based detection methods developed for VOCs in identifying and differentiating current VOCs and compare the advantages and disadvantages of each method, providing a basis for the rapid detection of VOCs strains and their future variants and the adoption of corresponding preventive and control measures.
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Affiliation(s)
- Wenjie Jiang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Wangquan Ji
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Yu Zhang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Yaqi Xie
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Shuaiyin Chen
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
- Henan Key Laboratory of Molecular Medicine, Zhengzhou University, Zhengzhou 450001, China
- Correspondence: (S.C.); (Y.J.); (G.D.); Tel.: +86-13523408394 (S.C.); +86-0371-67781453 (Y.J.); +86-0371-67789797 (G.D.)
| | - Yuefei Jin
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
- Correspondence: (S.C.); (Y.J.); (G.D.); Tel.: +86-13523408394 (S.C.); +86-0371-67781453 (Y.J.); +86-0371-67789797 (G.D.)
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
- Henan Key Laboratory of Molecular Medicine, Zhengzhou University, Zhengzhou 450001, China
- Correspondence: (S.C.); (Y.J.); (G.D.); Tel.: +86-13523408394 (S.C.); +86-0371-67781453 (Y.J.); +86-0371-67789797 (G.D.)
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Beheshti Namdar A, Keikha M. BA.2.12.1 is a new omicron offshoot that is a highly contagious but not severe disease. Ann Med Surg (Lond) 2022; 79:104034. [PMID: 35770273 PMCID: PMC9234247 DOI: 10.1016/j.amsu.2022.104034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 06/16/2022] [Indexed: 11/01/2022] Open
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Tiecco G, Storti S, Arsuffi S, Degli Antoni M, Focà E, Castelli F, Quiros-Roldan E. Omicron BA.2 Lineage, the "Stealth" Variant: Is It Truly a Silent Epidemic? A Literature Review. Int J Mol Sci 2022; 23:7315. [PMID: 35806320 PMCID: PMC9266794 DOI: 10.3390/ijms23137315] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/10/2022] [Accepted: 06/27/2022] [Indexed: 12/29/2022] Open
Abstract
The epidemic curve of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is silently rising again. Worldwide, the dominant SARS-CoV-2 variant of concern (VOC) is Omicron, and its virological characteristics, such as transmissibility, pathogenicity, and resistance to both vaccine- and infection-induced immunity as well as antiviral drugs, are an urgent public health concern. The Omicron variant has five major sub-lineages; as of February 2022, the BA.2 lineage has been detected in several European and Asian countries, becoming the predominant variant and the real antagonist of the ongoing surge. Hence, although global attention is currently focused on dramatic, historically significant events and the multi-country monkeypox outbreak, this new epidemic is unlikely to fade away in silence. Many aspects of this lineage are still unclear and controversial, but its apparent replication advantage and higher transmissibility, as well as its ability to escape neutralizing antibodies induced by vaccination and previous infection, are rising global concerns. Herein, we review the latest publications and the most recent available literature on the BA.2 lineage of the Omicron variant.
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Affiliation(s)
| | | | | | | | | | | | - Eugenia Quiros-Roldan
- Unit of Infectious and Tropical Diseases, Department of Clinical and Experimental Sciences, ASST Spedali Civili di Brescia, University of Brescia, 25123 Brescia, Italy; (G.T.); (S.S.); (S.A.); (M.D.A.); (E.F.); (F.C.)
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