1
|
Valli MB, Schiavone ML, Rueca M, Berno G, Spezia PG, Gruber CEM, Forbici F, Fabeni L, Focosi D, Girardi E, Meledandri M, Maggi F. Partial N-gene target failure in the Seegene Allplex SARS-CoV-2 Master Assay as a proxy of SARS-CoV-2 BA.2.86. Microbiol Spectr 2024; 12:e0017924. [PMID: 38647335 DOI: 10.1128/spectrum.00179-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Affiliation(s)
- Maria Beatrice Valli
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | | | - Martina Rueca
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Giulia Berno
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Pietro Giorgio Spezia
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | | | - Federica Forbici
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Lavinia Fabeni
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Enrico Girardi
- Scientific Direction, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Marcello Meledandri
- UOC Microbiology and Virology, San Filippo Neri Hospital, ASL Roma 1, Rome, Italy
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Hilti D, Wehrli F, Roditscheff A, Risch M, Risch L, Egli A, Bodmer T, Wohlwend N. SARS-CoV-2 Nucleocapsid Protein Mutations Found in Switzerland Disrupt N-Gene Amplification in Commonly Used Multiplex RT-PCR Assay. Pathogens 2023; 12:1383. [PMID: 38133268 PMCID: PMC10745585 DOI: 10.3390/pathogens12121383] [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: 10/11/2023] [Revised: 11/11/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023] Open
Abstract
At the end of 2021, we observed an increase in N-gene target failures (NGTF) with the TaqPathTM COVID-19 CE-IVD RT-PCR Kit from Thermo Fisher Scientific (TaqPath). We subsequently used whole-genome sequencing (Oxford Nanopore Technology) to identify potential issues with N-gene PCR efficacy. Among 168,101 positive samples with a cycle threshold (CT) value <30 from August 2021 to May 2022, 194 specimens without N-gene amplification by PCR were identified (0.12%). Most NGTF samples originated from a wave of infection attributable to the Delta variant (B.1.617.2) and its sublineages. Sequencing revealed the nucleotide substitution G28922T (A217S) in 151 samples (88.8%). The substitution G215C, a hallmark mutation for Delta lineages, was concurrently present in all of these samples. Ten samples (5.9%) carried the deletion 28,913-28,918 (del214/215), eight samples (4.7%) the deletion 28,913-28,915 (del214) and one sample (0.6%) the deletion 28,892-28,930 (del207-219). Samples showing intact N-gene amplification by PCR lacked these specific mutations, but delayed-type amplification (i.e., partial or pNGTF) was attributable to the exclusive presence of A217S. As the N gene is a common target in many RT-PCR methods for SARS-CoV-2, an in-depth analysis of single-target failures using a combination with viral whole genome sequencing may allow for the identification of diagnostic flaws and eventual new variants.
Collapse
Affiliation(s)
- Dominique Hilti
- Laboratory Dr. Risch, 9470 Buchs, Switzerland; (F.W.); (M.R.); (L.R.); (N.W.)
- Faculty of Medical Science, Private University in the Principality of Liechtenstein (UFL), 9495 Triesen, Liechtenstein;
| | - Faina Wehrli
- Laboratory Dr. Risch, 9470 Buchs, Switzerland; (F.W.); (M.R.); (L.R.); (N.W.)
| | - Anna Roditscheff
- Faculty of Medical Science, Private University in the Principality of Liechtenstein (UFL), 9495 Triesen, Liechtenstein;
- Laboratory Dr. Risch, Liebefeld, 3097 Köniz, Switzerland
| | - Martin Risch
- Laboratory Dr. Risch, 9470 Buchs, Switzerland; (F.W.); (M.R.); (L.R.); (N.W.)
- Zentrallabor, Kantonsspital Graubünden, 7000 Chur, Switzerland
| | - Lorenz Risch
- Laboratory Dr. Risch, 9470 Buchs, Switzerland; (F.W.); (M.R.); (L.R.); (N.W.)
- Faculty of Medical Science, Private University in the Principality of Liechtenstein (UFL), 9495 Triesen, Liechtenstein;
| | - Adrian Egli
- Department of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland;
| | - Thomas Bodmer
- Laboratory Dr. Risch, Liebefeld, 3097 Köniz, Switzerland
| | - Nadia Wohlwend
- Laboratory Dr. Risch, 9470 Buchs, Switzerland; (F.W.); (M.R.); (L.R.); (N.W.)
| |
Collapse
|
4
|
Kia P, Katagirya E, Kakembo FE, Adera DA, Nsubuga ML, Yiga F, Aloyo SM, Aujat BR, Anguyo DF, Katabazi FA, Kigozi E, Joloba ML, Kateete DP. Genomic characterization of SARS-CoV-2 from Uganda using MinION nanopore sequencing. Sci Rep 2023; 13:20507. [PMID: 37993530 PMCID: PMC10665338 DOI: 10.1038/s41598-023-47379-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 11/13/2023] [Indexed: 11/24/2023] Open
Abstract
SARS-CoV-2 undergoes frequent mutations, affecting COVID-19 diagnostics, transmission and vaccine efficacy. Here, we describe the genetic diversity of 49 SARS-CoV-2 samples from Uganda, collected during the COVID-19 waves of 2020/2021. Overall, the samples were similar to previously reported SARS-CoV-2 from Uganda and the Democratic Republic of Congo (DRC). The main lineages were AY.46 and A.23, which are considered to be Delta SARS-CoV-2 variants. Further, a total of 268 unique single nucleotide variants and 1456 mutations were found, with more than seventy percent mutations in the ORF1ab and S genes. The most common mutations were 2042C>G (83.4%), 14143C>T (79.5%), 245T>C (65%), and 1129G>T (51%), which occurred in the S, ORF1ab, ORF7a and N genes, respectively. As well, 28 structural variants-21 insertions and 7 deletions, occurred in 16 samples. Our findings point to the possibility that most SARS-CoV-2 infections in Uganda at the time arose from local spread and were not newly imported. Moreover, the relatedness of variants from Uganda and the DRC reflects high human mobility and interaction between the two countries, which is peculiar to this region of the world.
Collapse
Affiliation(s)
- Praiscillia Kia
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda.
| | - Eric Katagirya
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Fredrick Elishama Kakembo
- The African Centers of Excellence in Bioinformatics and Date Intensive Sciences, Infectious Disease Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Doreen Ato Adera
- Multifunctional Research Laboratories, Gulu University, Gulu, Uganda
| | - Moses Luutu Nsubuga
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Fahim Yiga
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Sharley Melissa Aloyo
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Brendah Ronah Aujat
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Fred Ashaba Katabazi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Edgar Kigozi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Moses L Joloba
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - David Patrick Kateete
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda.
| |
Collapse
|
5
|
Peñas-Utrilla D, Sanz A, Catalán P, Veintimilla C, Alcalá L, Alonso R, Muñoz P, Pérez-Lago L, García de Viedma D. A mutation responsible for impaired detection by the Xpert SARS-CoV-2 assay independently emerged in different lineages during the SARS-CoV-2 pandemic. BMC Microbiol 2023; 23:190. [PMID: 37460980 DOI: 10.1186/s12866-023-02924-8] [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: 12/22/2022] [Accepted: 06/29/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND COVID-19 diagnosis lies on the detection of SARS-CoV-2 on nasopharyngeal specimens by RT-PCR. The Xpert-Xpress SARS-CoV-2 assay provides results in less than one hour from specimen reception, which makes it suitable for clinical/epidemiological circumstances that require faster responses. The analysis of a COVID-19 outbreak suspected in the neonatology ward from our institution showed that the Ct values obtained for the targeted genes in the Xpert assay were markedly different within each specimen (N Ct value > 20 cycles above the E Ct value). RESULTS We identified the mutation C29200T in the N gene as responsible for an impairment in the N gene amplification by performing whole genome sequencing of the specimens involved in the outbreak (Omicron variant). Subsequently, a retrospective analysis of all specimens sequenced in our institution allowed us to identify the same SNP as responsible for similar impairments in another 12 cases (42% of the total cases reported in the literature). Finally, we found that the same SNP emerged in five different lineages independently, throughout almost all the COVID-19 pandemic. CONCLUSIONS We demonstrated for the first time the impact of this SNP on the Xpert assay, when harbored by new Omicron variants. We extend our observation period throughout almost all the COVID-19 pandemic, offering the most updated observations of this phenomenon, including sequences from the seventh pandemic wave, until now absent in the reports related to this issue. Continuous monitoring of emerging SNPs that could affect the performance of the most commonly used diagnostic tests, is required to redesign the tests to restore their correct performance.
Collapse
Affiliation(s)
- Daniel Peñas-Utrilla
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, 28007, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Amadeo Sanz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, 28007, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Pilar Catalán
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, 28007, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Cristina Veintimilla
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, 28007, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Luis Alcalá
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, 28007, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Roberto Alonso
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, 28007, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Departamento de Medicina, Universidad Complutense, Madrid, Spain
| | - Patricia Muñoz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, 28007, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Departamento de Medicina, Universidad Complutense, Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Laura Pérez-Lago
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, 28007, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Darío García de Viedma
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, 28007, Madrid, Spain.
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain.
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias (CIBERES), Madrid, Spain.
| |
Collapse
|
6
|
Saldivar-Espinoza B, Garcia-Segura P, Novau-Ferré N, Macip G, Martínez R, Puigbò P, Cereto-Massagué A, Pujadas G, Garcia-Vallve S. The Mutational Landscape of SARS-CoV-2. Int J Mol Sci 2023; 24:ijms24109072. [PMID: 37240420 DOI: 10.3390/ijms24109072] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Mutation research is crucial for detecting and treating SARS-CoV-2 and developing vaccines. Using over 5,300,000 sequences from SARS-CoV-2 genomes and custom Python programs, we analyzed the mutational landscape of SARS-CoV-2. Although almost every nucleotide in the SARS-CoV-2 genome has mutated at some time, the substantial differences in the frequency and regularity of mutations warrant further examination. C>U mutations are the most common. They are found in the largest number of variants, pangolin lineages, and countries, which indicates that they are a driving force behind the evolution of SARS-CoV-2. Not all SARS-CoV-2 genes have mutated in the same way. Fewer non-synonymous single nucleotide variations are found in genes that encode proteins with a critical role in virus replication than in genes with ancillary roles. Some genes, such as spike (S) and nucleocapsid (N), show more non-synonymous mutations than others. Although the prevalence of mutations in the target regions of COVID-19 diagnostic RT-qPCR tests is generally low, in some cases, such as for some primers that bind to the N gene, it is significant. Therefore, ongoing monitoring of SARS-CoV-2 mutations is crucial. The SARS-CoV-2 Mutation Portal provides access to a database of SARS-CoV-2 mutations.
Collapse
Affiliation(s)
- Bryan Saldivar-Espinoza
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Pol Garcia-Segura
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Nil Novau-Ferré
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Guillem Macip
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | | | - Pere Puigbò
- Department of Biology, University of Turku, 20500 Turku, Finland
- Department of Biochemistry and Biotechnology, Rovira i Virgili University, 43007 Tarragona, Spain
- Eurecat, Technology Centre of Catalonia, Unit of Nutrition and Health, 43204 Reus, Spain
| | - Adrià Cereto-Massagué
- EURECAT Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), 43204 Reus, Spain
| | - Gerard Pujadas
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Santiago Garcia-Vallve
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| |
Collapse
|
7
|
Yamashita K, Taniguchi T, Niizeki N, Nagao Y, Suzuki A, Toguchi A, Takebayashi S, Ishikawa J, Nagura O, Furuhashi K, Iwaizumi M, Maekawa M. Cycle Threshold (Ct) Values of SARS-CoV-2 Detected with the GeneXpert ® System and a Mutation Associated with Different Target Gene Failure. Curr Issues Mol Biol 2023; 45:4124-4134. [PMID: 37232731 DOI: 10.3390/cimb45050262] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/30/2023] [Accepted: 05/03/2023] [Indexed: 05/27/2023] Open
Abstract
SARS-CoV-2 nucleic acid detection tests enable rapid virus detection; however, it is challenging to identify genotypes to comprehend the local epidemiology and infection routes in real-time qRT-PCR. At the end of June 2022, our hospital experienced an in-hospital cluster of COVID-19. When examined using the GeneXpert® System, the cycle threshold (Ct) value of the N2 region of the nucleocapsid gene of SARS-CoV-2 was approximately 10 cycles higher than that of the envelope gene. Sanger sequencing revealed a G29179T mutation in the primer and probe binding sites. A review of past test results revealed differences in Ct values in 21 of 345 SARS-CoV-2-positive patients, of which 17 cases were cluster-related and 4 were not. Including these 21 cases, 36 cases in total were selected for whole-genome sequencing (WGS). The viral genomes in the cluster-related cases were identified as BA.2.10, and those in the non-cluster cases were closely related and classified as being downstream of BA.2.10 and other lineages. Although WGS can provide comprehensive information, its use is limited in various laboratory settings. A measurement platform reporting and comparing Ct values of different target genes can improve test accuracy, enhance our understanding of infection spread, and be applied to the quality control of reagents.
Collapse
Affiliation(s)
- Keita Yamashita
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Terumi Taniguchi
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Noriyasu Niizeki
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Yuki Nagao
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Akira Suzuki
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Akihiro Toguchi
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Shiori Takebayashi
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Jinko Ishikawa
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Osanori Nagura
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Kazuki Furuhashi
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Moriya Iwaizumi
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Masato Maekawa
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| |
Collapse
|
8
|
Kami W, Kinjo T, Hashioka H, Arakaki W, Uechi K, Takahashi A, Oki H, Tanaka K, Motooka D, Nakamura S, Nakamatsu M, Maeda S, Yamamoto K, Fujita J. Impact of G29179T mutation on two commercial PCR assays for SARS-CoV-2 detection. J Virol Methods 2023; 314:114692. [PMID: 36796678 PMCID: PMC9930255 DOI: 10.1016/j.jviromet.2023.114692] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023]
Abstract
Nucleic acid amplification test (NAAT) is the gold standard for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. However, genetic mutations in the virus can affect the result. Cycle threshold (Ct) values of N genes and their association with mutations using SARS-CoV-2 positive specimens diagnosed by the Xpert Xpress SARS-CoV-2 were examined in this study. In total, 196 nasopharyngeal swab specimens were tested for SARS-CoV-2 infection using the Xpert Xpress SARS-CoV-2, and 34 were positive. WGS was performed for four outlier samples with increased ΔCt identified by Scatterplot analysis as well as seven control samples without increased ΔCt in the Xpert Xpress SARS-CoV-2. The presence of the G29179T mutation was identified as a cause of increased ΔCt. PCR using the Allplex™ SARS-CoV-2 Assay did not show a similar increase in ΔCt. Previous reports focusing on N-gene mutations and their effects on SARS-CoV-2 testing including the Xpert Xpress SARS-CoV-2 were also summarized. While a single mutation that impacts one target of a multiplex NAAT is not a true detection failure, mutation compromising NAAT target region can cause confusion of the results and render the assay susceptible to diagnostic failure.
Collapse
Affiliation(s)
- Wakaki Kami
- First Department of Internal Medicine, Division of Infectious, Respiratory, and Digestive Medicine, University of the Ryukyus Graduate School of Medicine, 207 Uehara Nishihara, Okinawa 903-0215, Japan
| | - Takeshi Kinjo
- First Department of Internal Medicine, Division of Infectious, Respiratory, and Digestive Medicine, University of the Ryukyus Graduate School of Medicine, 207 Uehara Nishihara, Okinawa 903-0215, Japan.
| | - Hiroe Hashioka
- First Department of Internal Medicine, Division of Infectious, Respiratory, and Digestive Medicine, University of the Ryukyus Graduate School of Medicine, 207 Uehara Nishihara, Okinawa 903-0215, Japan
| | - Wakako Arakaki
- First Department of Internal Medicine, Division of Infectious, Respiratory, and Digestive Medicine, University of the Ryukyus Graduate School of Medicine, 207 Uehara Nishihara, Okinawa 903-0215, Japan
| | - Kohei Uechi
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, 207 Uehara Nishihara, Okinawa 903-0215, Japan
| | - Ami Takahashi
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, 207 Uehara Nishihara, Okinawa 903-0215, Japan
| | - Hiroya Oki
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kentaro Tanaka
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masashi Nakamatsu
- Infection Control Center, University of the Ryukyus Hospital, 207 Uehara Nishihara, Okinawa 903-0215, Japan
| | - Shiro Maeda
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, 207 Uehara Nishihara, Okinawa 903-0215, Japan
| | - Kazuko Yamamoto
- First Department of Internal Medicine, Division of Infectious, Respiratory, and Digestive Medicine, University of the Ryukyus Graduate School of Medicine, 207 Uehara Nishihara, Okinawa 903-0215, Japan
| | - Jiro Fujita
- First Department of Internal Medicine, Division of Infectious, Respiratory, and Digestive Medicine, University of the Ryukyus Graduate School of Medicine, 207 Uehara Nishihara, Okinawa 903-0215, Japan
| |
Collapse
|
9
|
Yang WW, Hsu CW, Chan YJ, Su SB, Feng IJ, Hou CY, Huang CY. Using Real-Time PCR Fluorescence Reaction Values to Improve SARS-CoV-2 Virus Detection and Benefit Clinical Decision-Making. Life (Basel) 2023; 13:life13030683. [PMID: 36983837 PMCID: PMC10057560 DOI: 10.3390/life13030683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/05/2023] [Accepted: 02/24/2023] [Indexed: 03/06/2023] Open
Abstract
This study aimed to compare the SARS-CoV-2 nucleic acid detection results of the BD MAX™ System and other platforms to formulate an optimized laboratory verification process. The re-examination of 400 samples determined as positive by BD MAX™ indicated that the inconsistency rate between BD MAX™ and the other platforms was 65.8%; the inconsistency rate of single-gene-positive results was as high as 99.2%. A receiver operating characteristic curve was drawn for the relative light unit (RLU) values of samples positive for a single gene, and RLU 800 was used as the cutoff. After setting the retest standard as single-gene positive and RLU ≥ 800, the number of the 260 BD MAX™ single-gene positives that needed to be confirmed again was 36 (13.8%) and the number that could be directly reported as negative was 224 (86.2%). This verification process can shorten the reporting period and speed up the epidemic adjustment time and turnover rate of special wards, thereby improving SARS-CoV-2 detection efficiency and clinical decision-making.
Collapse
Affiliation(s)
- Wan-Wen Yang
- Department of Clinical Pathology, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
| | - Chin-Wen Hsu
- Department of Family Medicine, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
| | - Yu-Ju Chan
- Department of Family Medicine, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
| | - Shih-Bin Su
- Division of Occupational Medicine, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
- Division of Occupational Medicine, Chi-Mei Medical Center, Tainan 710402, Taiwan
| | - I-Jung Feng
- Institute of Precision Medicine, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
| | - Chia-Yi Hou
- Department of Clinical Pathology, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
- Correspondence: (C.-Y.H.); (C.-Y.H.)
| | - Chien-Yuan Huang
- Division of Occupational Medicine, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
- Division of Occupational Medicine, Chi-Mei Medical Center, Tainan 710402, Taiwan
- Correspondence: (C.-Y.H.); (C.-Y.H.)
| |
Collapse
|
10
|
Abbasian MH, Mahmanzar M, Rahimian K, Mahdavi B, Tokhanbigli S, Moradi B, Sisakht MM, Deng Y. Global landscape of SARS-CoV-2 mutations and conserved regions. J Transl Med 2023; 21:152. [PMID: 36841805 PMCID: PMC9958328 DOI: 10.1186/s12967-023-03996-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/15/2023] [Indexed: 02/27/2023] Open
Abstract
BACKGROUND At the end of December 2019, a novel strain of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) disease (COVID-19) has been identified in Wuhan, a central city in China, and then spread to every corner of the globe. As of October 8, 2022, the total number of COVID-19 cases had reached over 621 million worldwide, with more than 6.56 million confirmed deaths. Since SARS-CoV-2 genome sequences change due to mutation and recombination, it is pivotal to surveil emerging variants and monitor changes for improving pandemic management. METHODS 10,287,271 SARS-CoV-2 genome sequence samples were downloaded in FASTA format from the GISAID databases from February 24, 2020, to April 2022. Python programming language (version 3.8.0) software was utilized to process FASTA files to identify variants and sequence conservation. The NCBI RefSeq SARS-CoV-2 genome (accession no. NC_045512.2) was considered as the reference sequence. RESULTS Six mutations had more than 50% frequency in global SARS-CoV-2. These mutations include the P323L (99.3%) in NSP12, D614G (97.6) in S, the T492I (70.4) in NSP4, R203M (62.8%) in N, T60A (61.4%) in Orf9b, and P1228L (50.0%) in NSP3. In the SARS-CoV-2 genome, no mutation was observed in more than 90% of nsp11, nsp7, nsp10, nsp9, nsp8, and nsp16 regions. On the other hand, N, nsp3, S, nsp4, nsp12, and M had the maximum rate of mutations. In the S protein, the highest mutation frequency was observed in aa 508-635(0.77%) and aa 381-508 (0.43%). The highest frequency of mutation was observed in aa 66-88 (2.19%), aa 7-14, and aa 164-246 (2.92%) in M, E, and N proteins, respectively. CONCLUSION Therefore, monitoring SARS-CoV-2 proteomic changes and detecting hot spots mutations and conserved regions could be applied to improve the SARS-CoV-2 diagnostic efficiency and design safe and effective vaccines against emerging variants.
Collapse
Affiliation(s)
- Mohammad Hadi Abbasian
- Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
| | - Mohammadamin Mahmanzar
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, 96813, USA
| | - Karim Rahimian
- Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Bahar Mahdavi
- Department of Computer Science, Tarbiat Modares University, Tehran, Iran
| | - Samaneh Tokhanbigli
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, Australia
| | - Bahman Moradi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mahsa Mollapour Sisakht
- Department of Biochemistry, Erasmus University Medical Center, 2040, 3000 CA, Rotterdam, The Netherlands
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, 96813, USA.
| |
Collapse
|
11
|
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.
Collapse
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.
| |
Collapse
|
12
|
Yip CCY, Sridhar S, Chan WM, Ip JD, Chu AWH, Leung KH, Cheng VCC, Yuen KY, To KKW. Development and Validation of a Novel COVID-19 nsp8 One-Tube RT-LAMP-CRISPR Assay for SARS-CoV-2 Diagnosis. Microbiol Spectr 2022; 10:e0196222. [PMID: 36445095 PMCID: PMC9769742 DOI: 10.1128/spectrum.01962-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 11/09/2022] [Indexed: 12/02/2022] Open
Abstract
Accurate and simple diagnostic tests for coronavirus disease 2019 (COVID-19) are essential components of the pandemic response. In this study, we evaluated a one-tube reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay coupled with clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein-mediated endpoint detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in clinical samples. RT-LAMP-CRISPR is fast and affordable, does not require bulky thermocyclers, and minimizes carryover contamination risk. Results can be read either visually or with a fluorometer. RT-LAMP-CRISPR assays using primers targeting a highly expressed nsp8 gene and previously described nucleocapsid (N) gene primers were designed. The analytical characteristics and diagnostic performance of RT-LAMP-CRISPR assays were compared to those of a commercial real-time RT-PCR E gene assay. The limits of detection (LODs) of the nsp8 and N RT-LAMP-CRISPR assays were 750 and 2,000 copies/mL, which were higher than that of the commercial real-time RT-PCR assay (31.3 copies/mL). Despite the higher LOD, RT-LAMP-CRISPR assays showed diagnostic sensitivity and specificity of 98.6% and 100%, respectively, equivalent to those of the real-time RT-PCR assay (P = 0.5). The median fluorescence reading from the nsp8 assay (378.3 raw fluorescence unit [RFU] [range, 215.6 to 592.6]) was significantly higher than that of the N gene assay (342.0 RFU [range, 143.0 to 576.6]) (P < 0.0001). In conclusion, we demonstrate that RT-LAMP-CRISPR assays using primers rationally designed from highly expressed gene targets are highly sensitive, specific, and easy to perform. Such assays are a valuable asset in resource-limited settings. IMPORTANCE Accurate tests for the diagnosis of SARS-CoV-2, the virus causing coronavirus disease 2019 (COVID-19), are important for timely treatment and infection control decisions. Conventional tests such as real-time reverse transcription-PCR (RT-PCR) require specialized equipment and are expensive. On the other hand, rapid antigen tests suffer from a lack of sensitivity. In this study, we describe a novel assay format for the diagnosis of COVID-19 that is based on principles of loop-mediated isothermal amplification (LAMP) and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas chemistry. A major advantage of this assay format is that it does not require expensive equipment to perform, and results can be read visually. This method proved to be fast, easy to perform, and inexpensive. The test compared well against an RT-PCR assay in terms of the ability to detect SARS-CoV-2 RNA in clinical samples. No false-positive test results were observed. The new assay format is ideal for SARS-CoV-2 diagnosis in resource-limited settings.
Collapse
Grants
- Health@InnoHK, Innovation and Technology Commission of Hong Kong
- Donations from Richard Yu and Carol Yu, the Shaw Foundation Hong Kong, Michael Seak-Kan Tong, The Hui Ming, Chan Yin Chuen Memorial Charitable Foundation
- Donations from Marina Man-Wai Lee, the Jessie & George Ho Charitable Foundation, Kai Chong Tong, Tse Kam Ming Laurence, Foo Oi Foundation Limited, Betty Hing-Chu Lee, and Ping Cham So
- Hui Hoy and Chow Sin Lan Charity Fund (許海周倩蘭慈善基金有限公司)
Collapse
Affiliation(s)
- Cyril Chik-Yan Yip
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
| | - Siddharth Sridhar
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Clinical Microbiology and Infection, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Wan-Mui Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jonathan Daniel Ip
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Allen Wing-Ho Chu
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kit-Hang Leung
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Vincent Chi-Chung Cheng
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kwok-Yung Yuen
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Clinical Microbiology and Infection, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Sha Tin, Hong Kong Special Administrative Region, China
| | - Kelvin Kai-Wang To
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Clinical Microbiology and Infection, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Sha Tin, Hong Kong Special Administrative Region, China
| |
Collapse
|
13
|
Sit BHM, Po KHL, Cheung YY, Tsang AKL, Leung PKL, Zheng J, Lam AYT, Lam ETK, Ng KHL, Chan RCW. Detection of SARS-CoV-2 VOC-Omicron using commercial sample-to-answer real-time RT-PCR platforms and melting curve-based SNP assays. JOURNAL OF CLINICAL VIROLOGY PLUS 2022; 2:100091. [PMID: 35761832 PMCID: PMC9213017 DOI: 10.1016/j.jcvp.2022.100091] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 05/27/2022] [Accepted: 06/13/2022] [Indexed: 12/03/2022] Open
Abstract
Objectives The World Health Organization (WHO) had designated the SARS-CoV-2 lineage B.1.1.529 as the new Variant of Concern Omicron (VOC-Omicron) on 26th November 20211. Real-time reverse transcription polymerase chain reaction (RT-PCR), single nucleotide polymorphisms (SNP) and whole genome sequencing (WGS) tests were widely employed to detect SARS-CoV-2 and its variant. Yet, the SARS-CoV-2 Omicron detection performance of commercial real-time RT-PCR platforms and SARS-CoV-2 spike SNP assays remain to be elucidated. Methods In the first part of this study, we evaluated the VOC-Omicron detection performance of three commercial RT-PCR sample-to-answer platforms i.e. Roche cobas® 6800/8800, Roche cobas® Liat®, and Cepheid GeneXpert® systems. The detection performances were compared to one commercial conventional real-time RT-PCR assay (TIB MOLBIOL LightMix Modular SARS and Wuhan CoV E-gene) and one in-house real-time RT-PCR assay targeting RNA-dependent RNA polymerase (RdRP) gene of SARS-CoV-2 in the WHO COVID-19 Reference Laboratory at Public Health Laboratory Services Branch, Centre for Health Protection, Department of Health, The Government of the Hong Kong Special Administrative Region. In the second part of this study, we evaluated the SNP detection performance of four TIB MOLBIOL melting curve-based assays (1. Spike S371L/S373P, 2. Spike E484A, 3. Spike E484K and 4. Spike N501Y) in clinical samples obtained from hospitalized COVID-19 patients in Hong Kong. The SNP results were compared to whole genome sequences generated by Illumina platform. Results The VOC-Omicron detection limits of three commercial sample-to-answer assays were tested to be ≤ 2.35 Log10 dC/ml. The detection performances of the sample-to-answer platforms were comparable to the two tested conventional real-time RT-PCR assays. The test sensitivities of TIB MOLBIOL VirSNiP SARS-CoV-2 Spike S371L/S373P assay and the Spike E484A assays were 100% and 96.6% respectively and the test specificities of both assays were 100%. An aberrant melting peak at Tm 42-44°C was observed when the specimens with Omicron variant were tested with the TIB MOLBIOL VirSNiP SARS-CoV-2 Spike E484K assay. Notably, the TIB MOLBIOL VirSNiP SARS-CoV-2 Spike N501Y assay failed to detect the spike N501Y mutation of Omicron variant in the tested specimens. Conclusions The SARS-CoV-2 detection sensitivity of three commercial platforms, Roche cobas® 6800/8800, Roche cobas® Liat®, and Cepheid GeneXpert® systems were shown not to be impacted by the large number of mutations of VOC-Omicron. Also, the signature mutations i.e. Spike S371L/Spike S373P and Spike E484A in VOC-Omicron were correctly identified by the TIB MOLBIOL VirSNiP SARS-CoV-2 Spike S371L/S373P and VirSNiP SARS-CoV-2 Spike E484A assays. Unexpected findings including a shifted melting peak or absence of amplification curve/melting peak were observed when specimens with Omicron variant were tested with the TIB MOLBIOL VirSNiP SARS-CoV-2 Spike E484K assay and Spike N501Y assay, suggesting a potential alert for Omicron variant, prior confirmation by whole genome sequencing.
Collapse
Affiliation(s)
- Brian H M Sit
- Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Department of Health, Hong Kong SAR, China
| | - Kathy Hiu Laam Po
- Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Department of Health, Hong Kong SAR, China
| | - Yuk-Yam Cheung
- Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Department of Health, Hong Kong SAR, China
| | - Alan K L Tsang
- Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Department of Health, Hong Kong SAR, China
| | - Patricia K L Leung
- Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Department of Health, Hong Kong SAR, China
| | - J Zheng
- Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Department of Health, Hong Kong SAR, China
| | - Alison Y T Lam
- Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Department of Health, Hong Kong SAR, China
| | - Edman T K Lam
- Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Department of Health, Hong Kong SAR, China
| | - Ken H L Ng
- Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Department of Health, Hong Kong SAR, China
| | - Rickjason C W Chan
- Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Department of Health, Hong Kong SAR, China
| |
Collapse
|
14
|
Chakraborty C, Bhattacharya M, Sharma AR, Dhama K, Lee SS. Continent-wide evolutionary trends of emerging SARS-CoV-2 variants: dynamic profiles from Alpha to Omicron. GeroScience 2022; 44:2371-2392. [PMID: 35831773 PMCID: PMC9281186 DOI: 10.1007/s11357-022-00619-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/27/2022] [Indexed: 01/06/2023] Open
Abstract
The ongoing SARS-CoV-2 evolution process has generated several variants due to its continuous mutations, making pandemics more critical. The present study illustrates SARS-CoV-2 evolution and its emerging mutations in five directions. First, the significant mutations in the genome and S-glycoprotein were analyzed in different variants. Three linear models were developed with the regression line to depict the mutational load for S-glycoprotein, total genome excluding S-glycoprotein, and whole genome. Second, the continent-wide evolution of SARS-CoV-2 and its variants with their clades and divergence were evaluated. It showed the region-wise evolution of the SARS-CoV-2 variants and their clustering event. The major clades for each variant were identified. One example is clade 21K, a major clade of the Omicron variant. Third, lineage dynamics and comparison between SARS-CoV-2 lineages across different countries are also illustrated, demonstrating dominant variants in various countries over time. Fourth, gene-wise mutation patterns and genetic variability of SARS-CoV-2 variants across various countries are illustrated. High mutation patterns were found in the ORF10, ORF6, S, and low mutation pattern E genes. Finally, emerging AA point mutations (T478K, L452R, N501Y, S477N, E484A, Q498R, and Y505H), their frequencies, and country-wise occurrence were identified, and the highest event of two mutations (T478K and L452R) was observed.
Collapse
Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126 India
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore, 756020 Odisha India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252 Gangwon-do Republic of Korea
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122 Uttar Pradesh India
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252 Gangwon-do Republic of Korea
| |
Collapse
|
15
|
Stoykova Z, Kostadinova T, Todorova T, Niyazi D, Bozhkova M, Bizheva S, Stoeva T. Dealing with inconclusive SARS-CoV-2 PCR samples-Our experience. PLoS One 2022; 17:e0268187. [PMID: 35560147 PMCID: PMC9106147 DOI: 10.1371/journal.pone.0268187] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 04/25/2022] [Indexed: 11/18/2022] Open
Abstract
Purpose Early confirmation of SARS-CoV-2 is a key point in the timely management of infected patients and contact persons. Routine diagnostics of COVID-19 cases relies on RT-PCR detection of two or three unique sequences of the virus. A serious problem for the laboratories is how to interpret inconclusive samples which are positive for only one of the SARS-CoV-2 specific genes. Materials and methods A total of 16364 naso-oropharyngeal swabs were collected and tested with SARS-CoV-2 Real-TM kit (Sacace Biotechnologies, Italy) between May and September 2020. We retrospectively analyzed their amplification plots to determine the number of inconclusive samples. We also reviewed the medical records to summarize the patient’s COVID-19 testing history and basic demographic characteristics. Results We obtained 136 (0.8%) inconclusive samples with amplification signal only for the N-gene. Thirty-nine of the samples were excluded from further analysis as no additional data were available for them. Of the rest of the samples, the majority– 48% (95% CI 38–59%) had a previous history of SARS-CoV-2 positivity, 14% (95% CI 8–23%)–a subsequent history of positivity and 37% (95% CI 28–48%) were considered as false positive. Conclusion A substantial proportion of the inconclusive results should be considered as positive samples at the beginning or the end of the infection. However, the number of false-positive results is also significant and each patient’s result should be analyzed separately following the clinical symptoms and epidemiological data.
Collapse
Affiliation(s)
- Zhivka Stoykova
- Department of Microbiology and Virology, Medical University Varna, Varna, Bulgaria
- Laboratory of Virology, University Hospital “St. Marina”, Varna, Bulgaria
| | - Tsvetelina Kostadinova
- Laboratory of Virology, University Hospital “St. Marina”, Varna, Bulgaria
- Medical College, Medical University Varna, Varna, Bulgaria
| | - Tatina Todorova
- Department of Microbiology and Virology, Medical University Varna, Varna, Bulgaria
- Laboratory of Virology, University Hospital “St. Marina”, Varna, Bulgaria
- * E-mail:
| | - Denis Niyazi
- Department of Microbiology and Virology, Medical University Varna, Varna, Bulgaria
- Laboratory of Microbiology, University Hospital “St. Marina”, Varna, Bulgaria
| | - Milena Bozhkova
- Department of Microbiology and Virology, Medical University Varna, Varna, Bulgaria
- Laboratory of Microbiology, University Hospital “St. Marina”, Varna, Bulgaria
| | - Svetomira Bizheva
- Laboratory of Microbiology, University Hospital “St. Marina”, Varna, Bulgaria
| | - Temenuga Stoeva
- Department of Microbiology and Virology, Medical University Varna, Varna, Bulgaria
- Laboratory of Microbiology, University Hospital “St. Marina”, Varna, Bulgaria
| |
Collapse
|
16
|
Choi H, Hwang M, Lukey J, Jinadatha C, Navarathna DH. Presumptive positive with the Cepheid Xpert Xpress SARS-CoV-2 Assay due to N mutations in the Delta variant. Diagn Microbiol Infect Dis 2022; 103:115699. [PMID: 35569431 PMCID: PMC9023076 DOI: 10.1016/j.diagmicrobio.2022.115699] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 11/19/2022]
Abstract
The Cepheid Xpert® Xpress SARS-CoV-2 assay is 1 of the several real-time reverse transcription polymerase chain reaction (RT-PCR) assays that received Emergency Use Authorization from the United States Food and Drug Administration (FDA) for detection of SARS-CoV-2. Here we report 4 SARS-CoV-2 samples that were reported as presumptive positives on the Cepheid platform while reported as positives on alternative RT-PCR platforms. Whole genome sequencing indicated that the samples were Delta variants and had point mutations in the N gene which potentially interfered with SARS-CoV-2 detection. Two types of point mutations were found in these samples in the US CDC 2019-nCoV Real time PCR N2 Probe region: C29203T and C29200T. C29203T is a novel point mutation, and C29200T has not been previously reported in the Delta variants. This underlines the fact that mutations in the real-time RT-PCR assay target region could hinder accurate detection of SARS-CoV-2.
Collapse
Affiliation(s)
- Hosoon Choi
- Department of Research, Central Texas Veterans Health Care System, Temple, TX, USA
| | - Munok Hwang
- Department of Research, Central Texas Veterans Health Care System, Temple, TX, USA
| | - Janell Lukey
- Department of Pathology and Laboratory Medicine Services, Central Texas Veterans Health Care System, Temple, TX, USA
| | - Chetan Jinadatha
- Department of Medicine, Central Texas Veterans Health Care System, Temple, TX, USA; Department of Medicine, College of Medicine, Texas A&M University, Bryan, TX, USA
| | - Dhammika H Navarathna
- Department of Pathology and Laboratory Medicine Services, Central Texas Veterans Health Care System, Temple, TX, USA.
| |
Collapse
|
17
|
Foster CS, Madden M, Chan R, Agapiou D, Bull RA, Rawlinson WD, Van Hal SJ. SARS-CoV-2 N-gene mutation leading to Xpert Xpress SARS-CoV-2 assay instability. Pathology 2022; 54:499-501. [PMID: 35440368 PMCID: PMC9012949 DOI: 10.1016/j.pathol.2022.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/31/2022] [Accepted: 02/09/2022] [Indexed: 11/21/2022]
|
18
|
Domnich A, Orsi A, Panatto D, De Pace V, Ricucci V, Caligiuri P, Guarona G, Chessa V, Ferone D, Boccotti S, Bruzzone B, Icardi G. Comparative Diagnostic Performance of a Novel Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Kit for the Rapid Detection of SARS-CoV-2. Pathogens 2021; 10:1629. [PMID: 34959584 PMCID: PMC8706056 DOI: 10.3390/pathogens10121629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 11/30/2022] Open
Abstract
Although the reverse transcription-polymerase chain reaction (RT-PCR) is considered a standard-of-care assay for the laboratory diagnosis of SARS-CoV-2, several limitations of this method have been described. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is an alternative molecular assay and is potentially able to overcome some intrinsic shortcomings of RT-PCR. In this study, we evaluated the diagnostic performance of the novel HG COVID-19 RT-LAMP assay. In this retrospective analysis, a total of 400 routinely collected leftover nasopharyngeal samples with a known RT-PCR result were tested by means of the HG COVID-19 RT-LAMP assay. The overall sensitivity and specificity values of HG COVID-19 RT-LAMP versus RT-PCR were 97.0% (95% CI: 93.6-98.9%) and 98.5% (95% CI: 95.7-99.7%), respectively. Inter-assay agreement was almost perfect (κ = 0.96). Concordance was perfect in samples with high viral loads (cycle threshold < 30). The average time to a positive result on RT-LAMP was 17 min. HG COVID-19 RT-LAMP is a reliable molecular diagnostic kit for detecting SARS-CoV-2, and its performance is comparable to that of RT-PCR. Shorter turnaround times and the possibility of performing molecular diagnostics in the point-of-care setting make it a valuable option for facilities without sophisticated laboratory equipment.
Collapse
Affiliation(s)
- Alexander Domnich
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (A.O.); (V.D.P.); (V.R.); (P.C.); (G.G.); (V.C.); (S.B.); (B.B.); (G.I.)
| | - Andrea Orsi
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (A.O.); (V.D.P.); (V.R.); (P.C.); (G.G.); (V.C.); (S.B.); (B.B.); (G.I.)
- Department of Health Sciences, University of Genoa, 16132 Genoa, Italy;
| | - Donatella Panatto
- Department of Health Sciences, University of Genoa, 16132 Genoa, Italy;
| | - Vanessa De Pace
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (A.O.); (V.D.P.); (V.R.); (P.C.); (G.G.); (V.C.); (S.B.); (B.B.); (G.I.)
| | - Valentina Ricucci
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (A.O.); (V.D.P.); (V.R.); (P.C.); (G.G.); (V.C.); (S.B.); (B.B.); (G.I.)
| | - Patrizia Caligiuri
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (A.O.); (V.D.P.); (V.R.); (P.C.); (G.G.); (V.C.); (S.B.); (B.B.); (G.I.)
| | - Giulia Guarona
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (A.O.); (V.D.P.); (V.R.); (P.C.); (G.G.); (V.C.); (S.B.); (B.B.); (G.I.)
| | - Valerio Chessa
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (A.O.); (V.D.P.); (V.R.); (P.C.); (G.G.); (V.C.); (S.B.); (B.B.); (G.I.)
| | - Diego Ferone
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy;
- Endocrinology Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy
| | - Simona Boccotti
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (A.O.); (V.D.P.); (V.R.); (P.C.); (G.G.); (V.C.); (S.B.); (B.B.); (G.I.)
- Department of Health Sciences, University of Genoa, 16132 Genoa, Italy;
| | - Bianca Bruzzone
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (A.O.); (V.D.P.); (V.R.); (P.C.); (G.G.); (V.C.); (S.B.); (B.B.); (G.I.)
| | - Giancarlo Icardi
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (A.O.); (V.D.P.); (V.R.); (P.C.); (G.G.); (V.C.); (S.B.); (B.B.); (G.I.)
- Department of Health Sciences, University of Genoa, 16132 Genoa, Italy;
| |
Collapse
|