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Abbasi H, Behrouzikhah M, Divbandi M, Tabaraei A, Khosravi A, Razavi Nikoo H. Genomic analysis of SARS-CoV-2 variants: diagnosis and vaccination challenges. J Biomol Struct Dyn 2023; 41:14939-14951. [PMID: 37676289 DOI: 10.1080/07391102.2023.2252069] [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: 06/20/2022] [Accepted: 02/18/2023] [Indexed: 09/08/2023]
Abstract
SARS-CoV-2 put a heavy financial burden on the healthcare system, with millions of laboratory-confirmed cases and deaths worldwide in the last 2 years. During the seventh wave of this pandemic, the continuously evolving nature of SARS-CoV-2 resulted in the emergence of new variants that harbor different mutations. Mutations are associated with changes in the virus behavior, including increased transmissibility, increased virulence, and evasion of neutralizing antibodies. Currently, we need detailed and comprehensive genomic information on all SARS-CoV-2 variants. One of the key points in this study was the genome survey of mutation profiles across variants as a genomic data source, to determine the efficiency of RT-qPCR assays. We also used the source to calculate the binding affinity changes of neutralizing antibodies-mutant receptor binding domain (RBD) complexes and determine vaccine efficacy. Our result revealed that the number of nucleotide mismatches is variable in the WHO-recommended primer-probe sets. Mismatches located at the 3' ends of the oligonucleotide, may lead to false-negative results. Only the primer-probe sets designed by the Ministry of Public Health of Thailand were exclusive and cannot detect the omicron variant reliably. Binding affinity changes showed that E484K was more deleterious than other mutations and decreased stability between the mutant RBD protein and neutralizing antibodies. The Omicrons show the highest change in binding affinity which may lead to immune escape and increase transmissibility. Additionally, the 7D6 monoclonal antibody in the 7eam complex could neutralize all variants of SARS-CoV-2. We strongly recommend creating and improving a matrix accuracy by processing a large number of SARS-CoV-2 sequences to update RT-qPCR assays and identified immunogenic residues among conserved RBD. Also, a detail computational analysis is needed to investigate distinctive amino acid substitution patterns which may be foundational in the vaccines. Finally, designing in-vitro studies can help confirm the present study and manage COVID-19 patients.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hamidreza Abbasi
- Department of Medical Biotechnology, Faculty of Advanced Medical Technologies, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mehdi Behrouzikhah
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Marzieh Divbandi
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Alijan Tabaraei
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ayyoob Khosravi
- Stem Cell Research Center, Golestan University of Medical Sciences, Gorgan, Iran
- Department of Molecular Medicine, Faculty of Advanced Medical Technologies, Golestan University of Medical Sciences, Gorgan, Iran
| | - Hadi Razavi Nikoo
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
- Infectious Disease Research Center, Golestan University of Medical Sciences, Gorgan, Iran
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Van Poelvoorde LAE, Picalausa C, Gobbo A, Verhaegen B, Lesenfants M, Herman P, Van Hoorde K, Roosens NHC. Development of a Droplet Digital PCR to Monitor SARS-CoV-2 Omicron Variant BA.2 in Wastewater Samples. Microorganisms 2023; 11:microorganisms11030729. [PMID: 36985302 PMCID: PMC10059707 DOI: 10.3390/microorganisms11030729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
Wastewater-based surveillance can be used as a complementary method to other SARS-CoV-2 surveillance systems. It allows the emergence and spread of infections and SARS-CoV-2 variants to be monitored in time and place. This study presents an RT-ddPCR method that targets the T19I amino acid mutation in the spike protein of the SARS-CoV-2 genomes, which is specific to the BA.2 variant (omicron). The T19I assay was evaluated both in silico and in vitro for its inclusivity, sensitivity, and specificity. Moreover, wastewater samples were used as a proof of concept to monitor and quantify the emergence of the BA.2 variant from January until May 2022 in the Brussels-Capital Region which covers a population of more than 1.2 million inhabitants. The in silico analysis showed that more than 99% of the BA.2 genomes could be characterized using the T19I assay. Subsequently, the sensitivity and specificity of the T19I assay were successfully experimentally evaluated. Thanks to our specific method design, the positive signal from the mutant probe and wild-type probe of the T19I assay was measured and the proportion of genomes with the T19I mutation, characteristic of the BA.2 mutant, compared to the entire SARS-CoV-2 population was calculated. The applicability of the proposed RT-ddPCR method was evaluated to monitor and quantify the emergence of the BA.2 variant over time. To validate this assay as a proof of concept, the measurement of the proportion of a specific circulating variant with genomes containing the T19I mutation in comparison to the total viral population was carried out in wastewater samples from wastewater treatment plants in the Brussels-Capital Region in the winter and spring of 2022. This emergence and proportional increase in BA.2 genomes correspond to what was observed in the surveillance using respiratory samples; however, the emergence was observed slightly earlier, which suggests that wastewater sampling could be an early warning system and could be an interesting alternative to extensive human testing.
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Affiliation(s)
| | - Corinne Picalausa
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Andrea Gobbo
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | | | - Marie Lesenfants
- Epidemiology of Infectious Diseases, Sciensano, 1050 Brussels, Belgium
| | | | | | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
- Correspondence:
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Combined Use of RT-qPCR and NGS for Identification and Surveillance of SARS-CoV-2 Variants of Concern in Residual Clinical Laboratory Samples in Miami-Dade County, Florida. Viruses 2023; 15:v15030593. [PMID: 36992302 PMCID: PMC10059866 DOI: 10.3390/v15030593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Over the course of the COVID-19 pandemic, SARS-CoV-2 variants of concern (VOCs) with increased transmissibility and immune escape capabilities, such as Delta and Omicron, have triggered waves of new COVID-19 infections worldwide, and Omicron subvariants continue to represent a global health concern. Tracking the prevalence and dynamics of VOCs has clinical and epidemiological significance and is essential for modeling the progression and evolution of the COVID-19 pandemic. Next generation sequencing (NGS) is recognized as the gold standard for genomic characterization of SARS-CoV-2 variants, but it is labor and cost intensive and not amenable to rapid lineage identification. Here we describe a two-pronged approach for rapid, cost-effective surveillance of SARS-CoV-2 VOCs by combining reverse-transcriptase quantitative polymerase chain reaction (RT-qPCR) and periodic NGS with the ARTIC sequencing method. Variant surveillance by RT-qPCR included the commercially available TaqPath COVID-19 Combo Kit to track S-gene target failure (SGTF) associated with the spike protein deletion H69-V70, as well as two internally designed and validated RT-qPCR assays targeting two N-terminal-domain (NTD) spike gene deletions, NTD156-7 and NTD25-7. The NTD156-7 RT-qPCR assay facilitated tracking of the Delta variant, while the NTD25-7 RT-qPCR assay was used for tracking Omicron variants, including the BA.2, BA.4, and BA.5 lineages. In silico validation of the NTD156-7 and NTD25-7 primers and probes compared with publicly available SARS-CoV-2 genome databases showed low variability in regions corresponding to oligonucleotide binding sites. Similarly, in vitro validation with NGS-confirmed samples showed excellent correlation. RT-qPCR assays allow for near-real-time monitoring of circulating and emerging variants allowing for ongoing surveillance of variant dynamics in a local population. By performing periodic sequencing of variant surveillance by RT-qPCR methods, we were able to provide ongoing validation of the results obtained by RT-qPCR screening. Rapid SARS-CoV-2 variant identification and surveillance by this combined approach served to inform clinical decisions in a timely manner and permitted better utilization of sequencing resources.
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Sharma D, Notarte KI, Fernandez RA, Lippi G, Gromiha MM, Henry BM. In silico evaluation of the impact of Omicron variant of concern sublineage BA.4 and BA.5 on the sensitivity of RT-qPCR assays for SARS-CoV-2 detection using whole genome sequencing. J Med Virol 2023; 95:e28241. [PMID: 36263448 PMCID: PMC9874926 DOI: 10.1002/jmv.28241] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/10/2022] [Accepted: 10/17/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of concern (VoC) Omicron (B.1.1.529) has rapidly spread around the world, presenting a new threat to global public human health. Due to the large number of mutations accumulated by SARS-CoV-2 Omicron, concerns have emerged over potentially reduced diagnostic accuracy of reverse-transcription polymerase chain reaction (RT-qPCR), the gold standard diagnostic test for diagnosing coronavirus disease 2019 (COVID-19). Thus, we aimed to assess the impact of the currently endemic Omicron sublineages BA.4 and BA.5 on the integrity and sensitivity of RT-qPCR assays used for coronavirus disease 2019 (COVID-19) diagnosis via in silico analysis. We employed whole genome sequencing data and evaluated the potential for false negatives or test failure due to mismatches between primers/probes and the Omicron VoC viral genome. METHODS In silico sensitivity of 12 RT-qPCR tests (containing 30 primers and probe sets) developed for detection of SARS-CoV-2 reported by the World Health Organization (WHO) or available in the literature, was assessed for specifically detecting SARS-CoV-2 Omicron BA.4 and BA.5 sublineages, obtained after removing redundancy from publicly available genomes from National Center for Biotechnology Information (NCBI) and Global Initiative on Sharing Avian Influenza Data (GISAID) databases. Mismatches between amplicon regions of SARS-CoV-2 Omicron VoC and primers and probe sets were evaluated, and clustering analysis of corresponding amplicon sequences was carried out. RESULTS From the 1164 representative SARS-CoV-2 Omicron VoC BA.4 sublineage genomes analyzed, a substitution in the first five nucleotides (C to T) of the amplicon's 3'-end was observed in all samples resulting in 0% sensitivity for assays HKUnivRdRp/Hel (mismatch in reverse primer) and CoremCharite N (mismatch in both forward and reverse primers). Due to a mismatch in the forward primer's 5'-end (3-nucleotide substitution, GGG to AAC), the sensitivity of the ChinaCDC N assay was at 0.69%. The 10 nucleotide mismatches in the reverse primer resulted in 0.09% sensitivity for Omicron sublineage BA.4 for Thai N assay. Of the 1926 BA.5 sublineage genomes, HKUnivRdRp/Hel assay also had 0% sensitivity. A sensitivity of 3.06% was observed for the ChinaCDC N assay because of a mismatch in the forward primer's 5'-end (3-nucleotide substitution, GGG to AAC). Similarly, due to the 10 nucleotide mismatches in the reverse primer, the Thai N assay's sensitivity was low at 0.21% for sublineage BA.5. Further, eight assays for BA.4 sublineage retained high sensitivity (more than 97%) and 9 assays for BA.5 sublineage retained more than 99% sensitivity. CONCLUSION We observed four assays (HKUnivRdRp/Hel, ChinaCDC N, Thai N, CoremCharite N) that could potentially result in false negative results for SARS-CoV-2 Omicron VoCs BA.4 and BA.5 sublineages. Interestingly, CoremCharite N had 0% sensitivity for Omicron Voc BA.4 but 99.53% sensitivity for BA.5. In addition, 66.67% of the assays for BA.4 sublineage and 75% of the assays for BA.5 sublineage retained high sensitivity. Further, amplicon clustering and additional substitution analysis along with sensitivity analysis could be used for the modification and development of RT-qPCR assays for detecting SARS-CoV-2 Omicron VoC sublineages.
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Affiliation(s)
- Divya Sharma
- Protein Bioinformatics Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of BiosciencesIndian Institute of Technology MadrasChennaiTamil NaduIndia
| | - Kin Israel Notarte
- Department of PathologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Rey Arturo Fernandez
- Ateneo de Manila University Professional SchoolsRockwell CenterMakatiPhilippines
| | - Giuseppe Lippi
- Section of Clinical BiochemistryUniversity of VeronaVeronaItaly
| | - M. Michael Gromiha
- Protein Bioinformatics Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of BiosciencesIndian Institute of Technology MadrasChennaiTamil NaduIndia
| | - Brandon M. Henry
- Clinical Laboratory, Division of Nephrology and HypertensionCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
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Gupta S, Kumar A, Gupta N, Bharti DR, Aggarwal N, Ravi V. A two-step process for in silico screening to assess the performance of qRTPCR kits against variant strains of SARS-CoV-2. BMC Genomics 2022; 23:755. [DOI: 10.1186/s12864-022-08999-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
Abstract
Abstract
Background
Since inception of the COVID-19 pandemic, early detection and isolation of positive cases is one of the key strategies to restrict disease transmission. Real time reverse transcription polymerase chain reaction (qRTPCR) has been the mainstay of diagnosis. Most of the qRTPCR kits were designed against the target genes of original strain of SARS-CoV-2. However, with the emergence of variant strains of SARS-CoV-2, sensitivity of the qRTPCR assays has reportedly reduced. In view of this, it is critical to continuously monitor the performance of the qRTPCR kits in the backdrop of variant strains of SARS-CoV-2. Real world monitoring of assay performance is challenging. Therefore, we developed a two-step in-silico screening process for evaluating the performance of various qRTPCR kits used in India.
Results
We analysed 73 qRT-PCR kits marketed in India, against the two SARS-CoV-2 VoCs. Sequences of both Delta (B.1.617.2) and Omicron (B.1.1.529) VoCs submitted to GISAID within a specific timeframe were downloaded, clustered to identify unique sequences and aligned with primer and probe sequences. Results were analysed following a two-step screening process. Out of 73 kits analysed, seven were unsatisfactory for detection of both Delta and Omicron VoCs, 10 were unsatisfactory for Delta VoC whereas 2 were unsatisfactory for only Omicron VoC.
Conclusion
Overall, we have developed a useful screening process for evaluating the performance of qRTPCR assays against Delta and Omicron VoCs of SARS-CoV-2 which can be used for detecting SARS-CoV-2 VoCs that may emerge in future and can also be redeployed for other evolving pathogens of public health importance.
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Cuypers L, Bode J, Beuselinck K, Laenen L, Dewaele K, Janssen R, Capron A, Lafort Y, Paridaens H, Bearzatto B, Cauchie M, Huwart A, Degosserie J, Fagnart O, Overmeire Y, Rouffiange A, Vandecandelaere I, Deffontaine M, Pilate T, Yin N, Micalessi I, Roisin S, Moons V, Reynders M, Steyaert S, Henin C, Lazarova E, Obbels D, Dufrasne FE, Pirenne H, Schepers R, Collin A, Verhasselt B, Gillet L, Jonckheere S, Van Lint P, Van den Poel B, Van der Beken Y, Stojkovic V, Garrino MG, Segers H, Vos K, Godefroid M, Pede V, Nollet F, Claes V, Verschraegen I, Bogaerts P, Van Gysel M, Leurs J, Saegeman V, Soetens O, Vanhee M, Schiettekatte G, Huyghe E, Martens S, Lemmens A, Nailis H, Laffineur K, Steensels D, Vanlaere E, Gras J, Roussel G, Gijbels K, Boudewijns M, Sion C, Achtergael W, Maurissen W, Iliano L, Chantrenne M, Vanheule G, Flies R, Hougardy N, Berth M, Verbeke V, Morent R, Vankeerberghen A, Bontems S, Kehoe K, Schallier A, Ho G, Bafort K, Raymaekers M, Pypen Y, Heinrichs A, Schuermans W, Cuigniez D, Lali SE, Drieghe S, Ory D, Le Mercier M, Van Laethem K, Thoelen I, Vandamme S, Mansoor I, Vael C, De Sloovere M, Declerck K, Dequeker E, Desmet S, Maes P, Lagrou K, André E. Nationwide Harmonization Effort for Semi-Quantitative Reporting of SARS-CoV-2 PCR Test Results in Belgium. Viruses 2022; 14:1294. [PMID: 35746765 PMCID: PMC9230955 DOI: 10.3390/v14061294] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 02/05/2023] Open
Abstract
From early 2020, a high demand for SARS-CoV-2 tests was driven by several testing indications, including asymptomatic cases, resulting in the massive roll-out of PCR assays to combat the pandemic. Considering the dynamic of viral shedding during the course of infection, the demand to report cycle threshold (Ct) values rapidly emerged. As Ct values can be affected by a number of factors, we considered that harmonization of semi-quantitative PCR results across laboratories would avoid potential divergent interpretations, particularly in the absence of clinical or serological information. A proposal to harmonize reporting of test results was drafted by the National Reference Centre (NRC) UZ/KU Leuven, distinguishing four categories of positivity based on RNA copies/mL. Pre-quantified control material was shipped to 124 laboratories with instructions to setup a standard curve to define thresholds per assay. For each assay, the mean Ct value and corresponding standard deviation was calculated per target gene, for the three concentrations (107, 105 and 103 copies/mL) that determine the classification. The results of 17 assays are summarized. This harmonization effort allowed to ensure that all Belgian laboratories would report positive PCR results in the same semi-quantitative manner to clinicians and to the national database which feeds contact tracing interventions.
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Affiliation(s)
- Lize Cuypers
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium; (J.B.); (K.B.); (L.L.); (K.D.); (R.J.); (E.D.); (S.D.); (K.L.); (E.A.)
| | - Jannes Bode
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium; (J.B.); (K.B.); (L.L.); (K.D.); (R.J.); (E.D.); (S.D.); (K.L.); (E.A.)
| | - Kurt Beuselinck
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium; (J.B.); (K.B.); (L.L.); (K.D.); (R.J.); (E.D.); (S.D.); (K.L.); (E.A.)
| | - Lies Laenen
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium; (J.B.); (K.B.); (L.L.); (K.D.); (R.J.); (E.D.); (S.D.); (K.L.); (E.A.)
| | - Klaas Dewaele
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium; (J.B.); (K.B.); (L.L.); (K.D.); (R.J.); (E.D.); (S.D.); (K.L.); (E.A.)
| | - Reile Janssen
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium; (J.B.); (K.B.); (L.L.); (K.D.); (R.J.); (E.D.); (S.D.); (K.L.); (E.A.)
| | - Arnaud Capron
- Epidemiology of Infectious Diseases and Quality Service Unit, Scientific Directorate of Epidemiology and Public Health, Sciensano, 1000 Brussels, Belgium; (A.C.); (Y.L.)
| | - Yves Lafort
- Epidemiology of Infectious Diseases and Quality Service Unit, Scientific Directorate of Epidemiology and Public Health, Sciensano, 1000 Brussels, Belgium; (A.C.); (Y.L.)
| | - Henry Paridaens
- Clinical Laboratory, Centre Hospitalier Régional de la Citadelle, 4000 Liège, Belgium;
| | - Bertrand Bearzatto
- Federal Testing Platform COVID-19, Centre des Technologies Moléculaires Appliquées (CTMA), Institute of Experimental and Clinical Research (IREC), Cliniques Universitaires Saint-Luc and Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium;
| | | | | | - Jonathan Degosserie
- Federal Testing Platform COVID-19, Department of Laboratory Medicine, CHU UCL Namur, 5530 Yvoir, Belgium;
| | - Olivier Fagnart
- Saint-Jean Hospital Laboratory, Cebiodi, 1000 Brussels, Belgium;
| | - Yarah Overmeire
- Microbiology, Labo Nuytinck, Anacura, 9940 Evergem, Belgium;
| | | | | | - Marine Deffontaine
- Laboratory of Clinical Biology, Centre Hopsitalier de Mouscron, 7700 Mouscron, Belgium;
| | - Thomas Pilate
- Clinical Laboratory, Laboratory Medicine, AZ Diest, 3290 Diest, Belgium;
| | - Nicolas Yin
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles—Universitair Laboratorium Brussel (LHUB-ULB), Université de Bruxelles (ULB), 1000 Brussels, Belgium;
| | - Isabel Micalessi
- Clinical Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium;
| | - Sandrine Roisin
- Microbiology, Centre Hospitalier Universitaire de Tivoli, 7100 La Louvière, Belgium;
| | - Veronique Moons
- Microbiology, LKO-LMC Medical Laboratory, 3800 Sint-Truiden, Belgium;
| | - Marijke Reynders
- Laboratory Medicine, AZ Sint-Jan Brugge-Oostende AV, 8000 Brugge, Belgium;
| | - Sophia Steyaert
- Clinical Laboratory, AZ Maria Middelares, 9000 Gent, Belgium;
| | - Coralie Henin
- Federal Testing Platform COVID-19, Université Libre de Bruxelles, 1070 Brussels, Belgium;
| | - Elena Lazarova
- Centre Hospitalier Régional de la Haute Senne, Department of Clinical Biology, 7060 Soignies, Belgium;
| | - Dagmar Obbels
- Imelda, Clinical Laboratory, 2820 Bonheiden, Belgium;
| | | | - Hendri Pirenne
- Synlab Belgium, Synlab Laboratory Collard, 4020 Liège, Belgium;
| | - Raf Schepers
- Synlab Belgium, Synlab Laboratory Heppignies, 6220 Heppignies, Belgium;
| | | | - Bruno Verhasselt
- Federal Testing Platform COVID-19, Department of Laboratory Medicine, Ghent University and Ghent University Hospital, 9000 Gent, Belgium;
| | - Laurent Gillet
- Federal Testing Platform COVID-19, University of Liège, 4000 Liège, Belgium;
| | - Stijn Jonckheere
- Jan Yperman Hospital, Laboratory of Clinical Biology, 8900 Ieper, Belgium;
| | | | - Bea Van den Poel
- Clinical Laboratory, General Hospital Jan Portaels, 1800 Vilvoorde, Belgium;
| | - Yolien Van der Beken
- Military Medicine Lab Capacity, Military Hospital Queen Astrid, 1120 Brussels, Belgium;
| | - Violeta Stojkovic
- Centre Hospitalier Bois de l’Abbaye, Laboratory Service, 4100 Seraing, Belgium;
| | | | | | - Kevin Vos
- RZ Heilig Hart Tienen, Clinical Biology, 3300 Tienen, Belgium;
| | | | - Valerie Pede
- AZ Sint-Elisabeth Zottegem, Laboratory of Clinical Biology, 9600 Zottegem, Belgium;
| | - Friedel Nollet
- Biogazelle NV, Diagnostic Testing, 9052 Zwijnaarde, Belgium;
| | - Vincent Claes
- Institute of Clinical Biology ULB-IBC, 1170 Brussels, Belgium;
| | | | - Pierre Bogaerts
- CHU UCL Namur, Department of Laboratory Medicine, Molecular Diagnostics Center, 5530 Yvoir, Belgium;
| | | | | | | | - Oriane Soetens
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, 1090 Brussels, Belgium;
| | - Merijn Vanhee
- Clinical Laboratory, Laboratory Medicine, AZ Delta, 8800 Roeselare, Belgium;
| | | | - Evelyne Huyghe
- ZNA Middelheim, Clinical Laboratory, 2020 Antwerp, Belgium;
| | | | - Ann Lemmens
- AZ Sint-Maarten, Laboratory of Clinical Biology, 2800 Mechelen, Belgium;
| | | | | | - Deborah Steensels
- Clinical Laboratory, Campus Sint-Jan, Hospital Oost-Limburg, 3600 Genk, Belgium;
| | - Elke Vanlaere
- Clinical Laboratory, AZ Sint-Lucas Hospital, 9000 Gent, Belgium;
| | - Jérémie Gras
- Institute of Pathology and Genetics, 6041 Gosselies, Belgium;
| | - Gatien Roussel
- Clinique Saint Pierre, Laboratory, 1340 Ottignies, Belgium;
| | | | - Michael Boudewijns
- Clinical Laboratory, Campus Kennedylaan, AZ Groeninge, 8500 Kortrijk, Belgium;
| | - Catherine Sion
- Grand Hôpital de Charleroi, Clinical Biology and Microbiology, 6060 Gilly, Belgium;
| | - Wim Achtergael
- Clinical Laboratory, Algemeen Stedelijk Ziekenhuis Aalst, 9300 Aalst, Belgium;
| | | | - Luc Iliano
- Laboratory for Medical Biology Iliano, 9070 Destelbergen, Belgium;
| | | | | | | | - Nicolas Hougardy
- Clinical Biology Unit, Vivalia Clinique du Sud-Luxembourg, 6700 Arlon, Belgium;
| | - Mario Berth
- Clinical Laboratory, AZ Alma, 9900 Eeklo, Belgium;
| | | | - Robin Morent
- Department of Laboratory Medicine, Campus Henri Serruys, AZ Sint-Jan Brugge, 8400 Oostende, Belgium;
| | - Anne Vankeerberghen
- Laboratory of Molecular Biology, Campus Aalst-Asse-Ninove, Onze-Lieve-Vrouwziekenhuis, 9300 Aalst, Belgium;
| | - Sébastien Bontems
- Clinical Laboratory, Unit of Clinical Microbiology, CHU Liège, 4000 Liège, Belgium;
| | - Kaat Kehoe
- Microbiology, Algemeen Medisch Laboratorium, 2020 Antwerp, Belgium;
| | | | - Giang Ho
- Laboratory, Clinique du MontLégia, Groupe Santé CHC, 4000 Liège, Belgium;
| | - Kristof Bafort
- Clinical Laboratory, Mariaziekenhuis Noorderhart, 3900 Pelt, Belgium;
| | - Marijke Raymaekers
- Laboratory for Molecular Diagnostics, Jessa Hospital, 3500 Hasselt, Belgium;
| | - Yolande Pypen
- Microbiology, Laboratory Somedi, 2220 Heist-op-den-Berg, Belgium;
| | - Amelie Heinrichs
- Laboratory of Clinical Biology, Hospital Arlon—Vivalia, 6700 Arlon, Belgium;
| | - Wim Schuermans
- Clinical Laboratory, Ziekenhuis Geel, 2440 Geel, Belgium;
| | | | | | - Stefanie Drieghe
- Microbiology, Algemeen Medisch Laboratorium West, 8850 Ardooie, Belgium;
| | - Dieter Ory
- Clinical Laboratory, Heilig Hart Ziekenhuis Mol, 2400 Mol, Belgium;
| | - Marie Le Mercier
- Federal Testing Platform COVID-19, University Hospitals Antwerp, 2650 Edegem, Belgium;
| | - Kristel Van Laethem
- Federal Testing Platform COVID-19, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium;
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Rega Institute for Medical Research, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium;
| | - Inge Thoelen
- Clinical Laboratory, AZ Vesalius Tongeren, 3700 Tongeren, Belgium;
| | - Sarah Vandamme
- Microbiology Laboratory, University Hospitals Antwerp, 2650 Edegem, Belgium;
| | - Iqbal Mansoor
- Clinical Laboratory, Hospital Hornu Epicura, 7301 Boussu, Belgium;
| | - Carl Vael
- Clinical Laboratory, AZ Klina, 2930 Brasschaat, Belgium;
| | | | | | - Elisabeth Dequeker
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium; (J.B.); (K.B.); (L.L.); (K.D.); (R.J.); (E.D.); (S.D.); (K.L.); (E.A.)
| | - Stefanie Desmet
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium; (J.B.); (K.B.); (L.L.); (K.D.); (R.J.); (E.D.); (S.D.); (K.L.); (E.A.)
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Piet Maes
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Rega Institute for Medical Research, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium;
| | - Katrien Lagrou
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium; (J.B.); (K.B.); (L.L.); (K.D.); (R.J.); (E.D.); (S.D.); (K.L.); (E.A.)
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Emmanuel André
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium; (J.B.); (K.B.); (L.L.); (K.D.); (R.J.); (E.D.); (S.D.); (K.L.); (E.A.)
- Federal Testing Platform COVID-19, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium;
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
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7
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Abstract
A fast and highly specific detection of COVID-19 infections is essential in managing the virus dissemination networks. The most relevant technologies developed for SARS-CoV-2 detection, along with their advantages and limitations, will be presented and fully explored. Additionally, some of the newest and emerging COVID-19 diagnosis tools, such as biosensing platforms, will also be introduced. Considering the extreme relevance that all these technologies assume in pandemic control, it is of the utmost relevance to have an intrinsic knowledge of the parameters that need to be taken into consideration before choosing the most adequate test for a particular situation. Moreover, the new variants of the virus and their potential impact on the detection method’s effectiveness will be discussed. In order to better manage the pandemic, it is essential to maintain continuous research into the SARS-CoV-2 genome and updated genomic surveillance at the global level. This will allow for timely detection of new mutations and viral variants, which may affect the performance of COVID-19 detection tests.
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8
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Negrón DA, Kang J, Mitchell S, Holland MY, Wist S, Voss J, Brinkac L, Jennings K, Guertin S, Goodwin BG, Sozhamannan S. Impact of SARS-CoV-2 Mutations on PCR Assay Sequence Alignment. Front Public Health 2022; 10:889973. [PMID: 35570946 PMCID: PMC9096222 DOI: 10.3389/fpubh.2022.889973] [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: 03/04/2022] [Accepted: 04/05/2022] [Indexed: 11/28/2022] Open
Abstract
Real-time reverse transcription polymerase chain reaction (RT-PCR) assays are the most widely used molecular tests for the detection of SARS-CoV-2 and diagnosis of COVID-19 in clinical samples. PCR assays target unique genomic RNA regions to identify SARS-CoV-2 with high sensitivity and specificity. In general, assay development incorporates the whole genome sequences available at design time to be inclusive of all target species and exclusive of near neighbors. However, rapid accumulation of mutations in viral genomes during sustained growth in the population can result in signature erosion and assay failures, creating situational blind spots during a pandemic. In this study, we analyzed the signatures of 43 PCR assays distributed across the genome against over 1.6 million SARS-CoV-2 sequences. We present evidence of significant signature erosion emerging in just two assays due to mutations, while adequate sequence identity was preserved in the other 41 assays. Failure of more than one assay against a given variant sequence was rare and mostly occurred in the two assays noted to have signature erosion. Assays tended to be designed in regions with statistically higher mutations rates. in silico analyses over time can provide insights into mutation trends and alert users to the emergence of novel variants that are present in the population at low proportions before they become dominant. Such routine assessment can also potentially highlight false negatives in test samples that may be indicative of mutations having functional consequences in the form of vaccine and therapeutic failures. This study highlights the importance of whole genome sequencing and expanded real-time monitoring of diagnostic PCR assays during a pandemic.
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Affiliation(s)
| | - June Kang
- Noblis, Inc., Reston, VA, United States
| | | | | | | | - Jameson Voss
- Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), Joint Project Lead for CBRND Enabling Biotechnologies (JPL CBRND EB), Frederick, MD, United States
| | | | | | | | - Bruce G Goodwin
- Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), Joint Project Lead for CBRND Enabling Biotechnologies (JPL CBRND EB), Frederick, MD, United States
| | - Shanmuga Sozhamannan
- Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), Joint Project Lead for CBRND Enabling Biotechnologies (JPL CBRND EB), Frederick, MD, United States.,Logistics Management Institute, Tysons, VA, United States
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9
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Hernandez MM, Banu R, Gonzalez-Reiche AS, Gray B, Shrestha P, Cao L, Chen F, Shi H, Hanna A, Ramírez JD, van de Guchte A, Sebra R, Gitman MR, Nowak MD, Cordon-Cardo C, Schutzbank TE, Simon V, van Bakel H, Sordillo EM, Paniz-Mondolfi AE. RT-PCR and Matrix-Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry Diagnostic Target Performance Reflects Circulating Severe Acute Respiratory Syndrome Coronavirus 2 Variant Diversity in New York City. J Mol Diagn 2022; 24:738-749. [PMID: 35525388 PMCID: PMC9067105 DOI: 10.1016/j.jmoldx.2022.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/07/2022] [Accepted: 04/06/2022] [Indexed: 12/20/2022] Open
Abstract
As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to circulate, multiple variants of concern have emerged. New variants pose challenges for diagnostic platforms because sequence diversity can alter primer/probe-binding sites (PBSs), causing false-negative results. The Agena MassARRAY SARS-CoV-2 Panel (Agena Bioscience) uses RT-PCR and mass spectrometry to detect five multiplex targets across N and ORF1ab genes. Herein, we use a data set of 256 SARS-CoV-2-positive specimens collected between April 11, 2021, and August 28, 2021, to evaluate target performance with paired sequencing data. During this time frame, two targets in the N gene (N2 and N3) were subject to the greatest sequence diversity. In specimens with N3 dropout, 69% harbored the Alpha-specific A28095U polymorphism that introduces a 3'-mismatch to the N3 forward PBS and increases risk of target dropout relative to specimens with 28095A (relative risk, 20.02; 95% CI, 11.36 to 35.72; P < 0.0001). Furthermore, among specimens with N2 dropout, 90% harbored the Delta-specific G28916U polymorphism that creates a 3'-mismatch to the N2 probe PBS and increases target dropout risk (relative risk, 11.92; 95% CI, 8.17 to 14.06; P < 0.0001). These findings highlight the robust capability of Agena MassARRAY SARS-CoV-2 Panel target results to reveal circulating virus diversity, and they underscore the power of multitarget design to capture variants of concern.
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Affiliation(s)
- Matthew M Hernandez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Radhika Banu
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Brandon Gray
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Paras Shrestha
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Liyong Cao
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Feng Chen
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Huanzhi Shi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ayman Hanna
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Juan David Ramírez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Sema4, a Mount Sinai venture, Stamford, Connecticut
| | - Melissa R Gitman
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Michael D Nowak
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Carlos Cordon-Cardo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Viviana Simon
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York; Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Alberto E Paniz-Mondolfi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York.
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10
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Duarte CM, Ketcheson DI, Eguíluz VM, Agustí S, Fernández-Gracia J, Jamil T, Laiolo E, Gojobori T, Alam I. Rapid evolution of SARS-CoV-2 challenges human defenses. Sci Rep 2022; 12:6457. [PMID: 35440671 PMCID: PMC9017738 DOI: 10.1038/s41598-022-10097-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 03/23/2022] [Indexed: 12/25/2022] Open
Abstract
The race between pathogens and their hosts is a major evolutionary driver, where both reshuffle their genomes to overcome and reorganize the defenses for infection, respectively. Evolutionary theory helps formulate predictions on the future evolutionary dynamics of SARS-CoV-2, which can be monitored through unprecedented real-time tracking of SARS-CoV-2 population genomics at the global scale. Here we quantify the accelerating evolution of SARS-CoV-2 by tracking the SARS-CoV-2 mutation globally, with a focus on the Receptor Binding Domain (RBD) of the spike protein determining infection success. We estimate that the > 820 million people that had been infected by October 5, 2021, produced up to 1021 copies of the virus, with 12 new effective RBD variants appearing, on average, daily. Doubling of the number of RBD variants every 89 days, followed by selection of the most infective variants challenges our defenses and calls for a shift to anticipatory, rather than reactive tactics involving collaborative global sequencing and vaccination.
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Affiliation(s)
- Carlos M Duarte
- Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia. .,Computational Bioscience Research Centre (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
| | - David I Ketcheson
- Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Víctor M Eguíluz
- Instituto de Física Interdisciplinar y Sistemas Complejos IFISC (UIB-CSIC), Palma de Mallorca, Spain
| | - Susana Agustí
- Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Juan Fernández-Gracia
- Instituto de Física Interdisciplinar y Sistemas Complejos IFISC (UIB-CSIC), Palma de Mallorca, Spain
| | - Tahira Jamil
- Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.,Computational Bioscience Research Centre (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Elisa Laiolo
- Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.,Computational Bioscience Research Centre (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Centre (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Intikhab Alam
- Computational Bioscience Research Centre (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
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11
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A deletion in the N gene of SARS-CoV-2 may reduce test sensitivity for detection of SARS-CoV-2. Diagn Microbiol Infect Dis 2022; 102:115631. [PMID: 35045382 PMCID: PMC8715644 DOI: 10.1016/j.diagmicrobio.2021.115631] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 01/25/2023]
Abstract
One SARS-CoV-2-positive sample demonstrated impaired detection of the N1 target by RT-PCR using US CDC primer/probe sets. A 3 nucleotide deletion was discovered that overlaps the forward primer binding site. This finding underscores the importance of continued SARS-CoV-2 mutation surveillance and assessment of the impact on diagnostic test performance.
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12
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Gdoura M, Abouda I, Mrad M, Ben Dhifallah I, Belaiba Z, Fares W, Chouikha A, Khedhiri M, Layouni K, Touzi H, Sadraoui A, Hammemi W, Meddeb Z, Hogga N, Ben Fadhel S, Haddad-Boubaker S, Triki H. SARS-CoV2 RT-PCR assays: In vitro comparison of 4 WHO approved protocols on clinical specimens and its implications for real laboratory practice through variant emergence. Virol J 2022; 19:54. [PMID: 35346227 PMCID: PMC8959265 DOI: 10.1186/s12985-022-01784-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 03/14/2022] [Indexed: 11/10/2022] Open
Abstract
Introduction RT-PCR testing on nasopharyngeal swabs is a key component in the COVID-19 fighting, provided to use sensitive and specific SARS-CoV2 genome targets. In this study, we aimed to evaluate and to compare 4 widely used WHO approved RT-PCR protocols on real clinical specimens, to decrypt the reasons of the diverging results and to propose recommendations for the choice of the genome targets. Methods 260 nasopharyngeal samples were randomly selected among the samples tested between Week-16, 2020 and week-16 2021, in the Institut Pasteur de Tunis, Tunisia, one of the referent laboratories of COVID-19 in Tunisia. All samples were tested by Charité, Berlin protocol (singleplex envelop (E) and singleplex RNA-dependent RNA polymerase (RdRp)), Hong Kong Universiy, China protocol (singleplex nucleoprotein (N) and singleplex Open reading frame Orf1b), commercial test DAAN Gene® (using the CDC China protocol), (triplex N, Orf1ab with internal control) and Institut Pasteur Paris protocol (IPP) (triplex IP2(nsp9) and IP4 (nsp12) with internal control). For IPP, a selection from samples positive by IP2 but negative with IP4 was re-tested by exactly the same protocol but this time in singleplex. New results were described and analyzed. Results In vitro analysis showed discordant results in 29.2% of cases (76 out of 260). The most discordant protocol is DAAN Gene® due to the false positive late signals with N target. Discordant results between the two protocol’s targets are more frequent when viral load are low (high Ct values). Our results demonstrated that the multiplexing has worsened the sensitivity of the IP4 target. Conclusion We provide concise recommendations for the choice of the genome targets, the interpretation of the results and the alarm signals which makes suspect a gene mutation.
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Affiliation(s)
- Mariem Gdoura
- Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia. .,Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia. .,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.
| | - Imen Abouda
- Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia.,Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Mehdi Mrad
- Laboratory of Biochemistry and Hormonology, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Imen Ben Dhifallah
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Zeineb Belaiba
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Wasfi Fares
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Anissa Chouikha
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Maroua Khedhiri
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Kaouther Layouni
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Henda Touzi
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Amel Sadraoui
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Walid Hammemi
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Zina Meddeb
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Nahed Hogga
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Sihem Ben Fadhel
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Sondes Haddad-Boubaker
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Henda Triki
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
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13
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Abstract
Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with enhanced transmissibility, pathogenicity, and immune escape ability have ravaged many countries and regions, which has brought substantial challenges to pandemic prevention and control. Real-time reverse transcriptase PCR (rRT-PCR) is widely used for SARS-CoV-2 detection but may be limited by the continuous evolution of the virus. However, the sensitivity of Chinese commercial rRT-PCR kits to critical SARS-CoV-2 variants remains unknown. In this study, contrived MS2 virus-like particles were used as reference materials to evaluate the analytical sensitivity of Daan, BioGerm, EasyDiagnosis, Liferiver, and Sansure kits when detecting six important variants (Alpha, Beta, Gamma, Delta, Omicron, and Fin-796H). The Beta and Delta variants adversely affected the analytical sensitivity of the BioGerm ORF1ab gene assay (9.52% versus 42.96%, P = 0.014, and 14.29% versus 42.96%, P = 0.040, respectively), whereas the N gene assay completely failed in terms of the Fin-796H variant. The Gamma and Fin-796H variants impeded the PCR amplification efficiency for the Sansure ORF1ab gene assay (33.33% versus 66.67%, P = 0.031, and 66.67% versus 95.24%, P = 0.040, respectively), and the Delta variant compromised the E gene assay (52.38% versus 85.71%, P = 0.019). The Alpha and Omicron variants had no significant effect on the kits. This study highlights the necessity of identifying the potential effect of viral mutations on the efficacy and sensitivity of clinical detection assays. It can also provide helpful insights regarding the development and optimization of diagnostic assays and aid the strategic management of the ongoing pandemic.
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14
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Angulo J, Martinez-Valdebenito C, Pardo-Roa C, Almonacid LI, Fuentes-Luppichini E, Contreras AM, Maldonado C, Le Corre N, Melo F, Medina RA, Ferrés M. Assessment of Mutations Associated With Genomic Variants of SARS-CoV-2: RT-qPCR as a Rapid and Affordable Tool to Monitoring Known Circulating Variants in Chile, 2021. Front Med (Lausanne) 2022; 9:841073. [PMID: 35280916 PMCID: PMC8914012 DOI: 10.3389/fmed.2022.841073] [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: 12/21/2021] [Accepted: 02/02/2022] [Indexed: 11/13/2022] Open
Abstract
Since the first report of SARS-CoV-2 infection in humans, the virus has mutated to develop new viral variants with higher infection rates and more resistance to neutralization by antibodies elicited after natural SARS-CoV-2 infection or by vaccines. Therefore, rapid identification of viral variants circulating in the population is crucial for epidemiological assessment and efforts to contain the resurgence of the pandemic. Between January and November 2021, we performed a large variant RT-qPCR-based screening of mutations in the spike protein of 1851 SARS-CoV-2-positive samples derived from outpatients from the UC-Christus Health Network in Chile. In a portion of samples (n = 636), we validated our RT-qPCR-pipeline by WGS, obtaining a 99.2% concordance. Our results indicate that from January to March 2021 there was a dominance of non-identifiable variants by the RT-qPCR-based screening; however, throughout WGS we were able to identify the Lambda (C.37) variant of interest (VOI). From March to July, we observed the rapid emergence of mutations associated with the Gamma variant (P.1), which was quickly replaced by the appearance of a combination of samples harboring mutations associated with the Delta variant (B.1.617.2), which predominated until the end of the study. Our results highlight the applicability of cost-effective RT-qPCR-based screening of mutations associated with known variants of concern (VOC), VOI and variants under monitoring (VUM) of SARS-CoV-2, being a rapid and reliable tool that complements WGS-based surveillance.
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Affiliation(s)
- Jenniffer Angulo
- Departamento de Enfermedades Infeciosas e Inmmunologia Pediatricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Infectious Disease and Molecular Virology Laboratory, Red Salud UC-Christus, Santiago, Chile
| | - Constanza Martinez-Valdebenito
- Departamento de Enfermedades Infeciosas e Inmmunologia Pediatricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Infectious Disease and Molecular Virology Laboratory, Red Salud UC-Christus, Santiago, Chile
| | - Catalina Pardo-Roa
- Departamento de Enfermedades Infeciosas e Inmmunologia Pediatricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Advanced Interdisciplinary Rehabilitation Register – COVID-19 Working Group, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Leonardo I. Almonacid
- Molecular Bioinformatics Laboratory, Department of Molecular Genetics and Microbiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Ana Maria Contreras
- Infectious Disease and Molecular Virology Laboratory, Red Salud UC-Christus, Santiago, Chile
| | - Constanza Maldonado
- Infectious Disease and Molecular Virology Laboratory, Red Salud UC-Christus, Santiago, Chile
| | - Nicole Le Corre
- Departamento de Enfermedades Infeciosas e Inmmunologia Pediatricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Infectious Disease and Molecular Virology Laboratory, Red Salud UC-Christus, Santiago, Chile
| | - Francisco Melo
- Molecular Bioinformatics Laboratory, Department of Molecular Genetics and Microbiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rafael A. Medina
- Departamento de Enfermedades Infeciosas e Inmmunologia Pediatricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Advanced Interdisciplinary Rehabilitation Register – COVID-19 Working Group, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Marcela Ferrés
- Departamento de Enfermedades Infeciosas e Inmmunologia Pediatricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Infectious Disease and Molecular Virology Laboratory, Red Salud UC-Christus, Santiago, Chile
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15
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Kiryanov SA, Levina TA, Konopleva MV, Suslov AP. Identification of Hotspot Mutations in the N Gene of SARS-CoV-2 in Russian Clinical Samples That May Affect the Detection by Reverse Transcription-PCR. Diagnostics (Basel) 2022; 12:diagnostics12010147. [PMID: 35054314 PMCID: PMC8774456 DOI: 10.3390/diagnostics12010147] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/28/2021] [Accepted: 01/04/2022] [Indexed: 12/27/2022] Open
Abstract
Sensitive and reliable diagnostic test systems based on real-time PCR are of great importance in the fight against the ongoing SARS-CoV-2 pandemic. The genetic variability of the SARS-CoV-2 virus leads to the accumulation of mutations, some of which may affect the sensitivity of modern PCR assays. The aim of this study was to search in Russian clinical samples for new mutations in SARS-CoV-2 gene N that can affect the detection by RT-PCR. In this study, the polymorphisms in the regions of the target gene N causing failed or poor detection of the target N in the RT-PCR assay on 12 selected samples were detected. Sequencing the entire N and E genes in these samples along with other 195 samples that were positive for both target regions was performed. Here, we identified a number of nonsynonymous mutations and one novel deletion in the N gene that affected the ability to detect a target in the N gene as well a few mutations in the E gene of SARS-CoV-2 that did not affect detection. Sequencing revealed that majority of the mutations in the N gene were located in the variable region between positions 193 and 235 aa, inside and nearby the phosphorylated serine-rich region of the protein N. This study highlights the importance of the further characterization of the genetic variability and evolution of gene N, the most common target for detecting SARS-CoV-2. The use of at least two targets for detecting SARS-CoV-2, including one for the E gene, will be necessary for reliable diagnostics.
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Affiliation(s)
- Sergei A. Kiryanov
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (T.A.L.); (M.V.K.); (A.P.S.)
- Correspondence:
| | - Tatiana A. Levina
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (T.A.L.); (M.V.K.); (A.P.S.)
- OOO “DNA-Technology”, 117587 Moscow, Russia
| | - Maria V. Konopleva
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (T.A.L.); (M.V.K.); (A.P.S.)
| | - Anatoly P. Suslov
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (T.A.L.); (M.V.K.); (A.P.S.)
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16
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Rosato AE, Msiha E, Weng B, Mesisca M, Gnass R, Gnass S, Bol C, Tabuenca A, Rosato RR. Rapid detection of the widely circulating B.1.617.2 (Delta) SARS-CoV-2 variant. Pathology 2022; 54:351-356. [PMID: 35221043 PMCID: PMC8801325 DOI: 10.1016/j.pathol.2022.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/21/2021] [Accepted: 01/10/2022] [Indexed: 02/03/2023]
Abstract
The emergence of the B.1.617.2 (Delta) variant of the severe acute syndrome coronavirus (SARS-CoV-2) that emerged in 2019 (COVID-19), resulted in a surge of cases in India and has expanded and been detected across the world, including in the United States. The B.1.617.2 (Delta) variant has been seen to be twice more transmissible coupled with potential increases in disease severity and immune escape. As a result, case numbers and hospitalisations are once again on the rise in the USA. On 16 July 2021, the Centers for Disease Control and Prevention (CDC) reported a 7-day average 69.3% increase in new cases and a 35% increase in hospitalisations. Although the gold standard for SARS-CoV-2 variants identification remains genomic sequencing, this approach is not accessible to many clinical laboratories. The main goal of this study was to validate and implement the detection of the B.1.617.2 (Delta) variant utilising an open reverse transcription polymerase chain reaction (RT-PCR) platform by explicitly detecting the S-gene target failure (SGTF) corresponding to the deletion of two amino acids (ΔE156/ΔF157) characteristic of B.1.617.2 (Delta) variant. This approach was conceived as a rapid screening of B.1.617.2 (Delta) variant in conjunction with CDC’s recommended N1 (nucleocapsid gene), N2, and RP (human RNase P) genes, as a pre-screening tool prior to viral genomic sequencing. We assessed 4,937 samples from 5 July to 5 September 2021. We identified the B.1.617.2 (Delta) variant in 435 of 495 positive samples (87.8%); the additional positive samples (7 samples, 1.4%) were found to belong to the B.1.1.7 (Alpha, UK) lineage and the remaining 53 samples (10.7%) were reported as ‘other’ lineages. Whole genome sequencing of 46 randomly selected samples validated the strains identified as positive and negative for the B.1.617.2 (Delta) variant and confirmed the S gene deletion in addition to B.1.617.2 characteristic mutations including L452R, T478K, P681R and D950N located in the spike protein. This modality has been used as routine testing at the Riverside University System Health (RUHS) Medical Center as a method for detection of B.1.617.2 (Delta) to pre-screen samples before genome sequencing. The assay can be easily implemented in clinical laboratories, most notably those with limited economic resources and access to genomic platforms.
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17
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Guest PC, Zahedipour F, Majeed M, Jamialahmadi T, Sahebkar A. Multiplex Technologies in COVID-19 Research, Diagnostics, and Prognostics: Battling the Pandemic. Methods Mol Biol 2022; 2511:3-20. [PMID: 35838948 DOI: 10.1007/978-1-0716-2395-4_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Due to continuous technical developments and new insights into the high complexity of infectious diseases such as COVID-19, there is an increasing need for multiplex biomarkers to aid clinical management and support the development of new drugs and vaccines. COVID-19 disease requires rapid diagnosis and stratification to enable the most appropriate treatment course for the best possible outcomes for patients. In addition, these tests should be rapid, specific, and sensitive. They should rule out other potential causes of illness with simultaneous testing for other diseases. Elevated levels of specific biomarkers can be used to establish severity risks of chronic diseases so that patients can be provided the proper medication at the right time. This review describes the state-of-the-art technologies in proteomics, transcriptomics, and metabolomics, for multiplex biomarker approaches in COVID-19 research.
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Affiliation(s)
- Paul C Guest
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Fatemeh Zahedipour
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Tannaz Jamialahmadi
- Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Nutrition, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- School of Medicine, The University of Western Australia, Perth, Australia.
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18
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Hernandez MM, Banu R, Gonzalez-Reiche AS, van de Guchte A, Khan Z, Shrestha P, Cao L, Chen F, Shi H, Hanna A, Alshammary H, Fabre S, Amoako A, Obla A, Alburquerque B, Patiño LH, Ramírez JD, Sebra R, Gitman MR, Nowak MD, Cordon-Cardo C, Schutzbank TE, Simon V, van Bakel H, Sordillo EM, Paniz-Mondolfi AE. Robust clinical detection of SARS-CoV-2 variants by RT-PCR/MALDI-TOF multitarget approach. J Med Virol 2021; 94:1606-1616. [PMID: 34877674 DOI: 10.1002/jmv.27510] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 12/24/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has sparked the rapid development of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostics. However, emerging variants pose the risk for target dropout and false-negative results secondary to primer/probe binding site (PBS) mismatches. The Agena MassARRAY® SARS-CoV-2 Panel combines reverse-transcription polymerase chain reaction and matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry to probe for five targets across N and ORF1ab genes, which provides a robust platform to accommodate PBS mismatches in divergent viruses. Herein, we utilize a deidentified data set of 1262 SARS-CoV-2-positive specimens from Mount Sinai Health System (New York City) from December 2020 to April 2021 to evaluate target results and corresponding sequencing data. Overall, the level of PBS mismatches was greater in specimens with target dropout. Of specimens with N3 target dropout, 57% harbored an A28095T substitution that is highly specific for the Alpha (B.1.1.7) variant of concern. These data highlight the benefit of redundancy in target design and the potential for target performance to illuminate the dynamics of circulating SARS-CoV-2 variants.
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Affiliation(s)
- Matthew M Hernandez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Radhika Banu
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Zenab Khan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Paras Shrestha
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Liyong Cao
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Feng Chen
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Huanzhi Shi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ayman Hanna
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Hala Alshammary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Shelcie Fabre
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Angela Amoako
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ajay Obla
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Bremy Alburquerque
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Luz Helena Patiño
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sema4, a Mount Sinai Venture, Stamford, Connecticut, USA
| | - Melissa R Gitman
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Michael D Nowak
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ted E Schutzbank
- Senior Scientific Affairs Manager, Infectious Diseases, Agena Bioscience, San Diego, California, USA
| | - Viviana Simon
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Alberto E Paniz-Mondolfi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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19
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Yaniv K, Ozer E, Lewis Y, Kushmaro A. RT-qPCR assays for SARS-CoV-2 variants of concern in wastewater reveals compromised vaccination-induced immunity. WATER RESEARCH 2021; 207:117808. [PMID: 34753092 PMCID: PMC8551083 DOI: 10.1016/j.watres.2021.117808] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 05/02/2023]
Abstract
SARS-CoV-2 variants of concern, demonstrating higher infection rate and lower vaccine effectiveness as compared with the original virus, are important factors propelling the ongoing COVID-19 global outbreak. Therefore, prompt identification of these variants in the environment is essential for pandemic assessment and containment efforts. One well established tool for such viral monitoring is the use of wastewater systems. Here, we describe continuous monitoring of traces of SARS-CoV-2 viruses in the municipal wastewater of a large city in Israel. By observing morbidity fluctuations (during three main COVID-19 surges) occurring in parallel with Pfizer-BioNTech COVID-19 vaccine vaccination rate, compromised immunity was revealed in the current morbidity peak. RT-qPCR assays for the Original (D614G), Alpha and Beta variants had been previously developed and are being employed for wastewater surveillance. In the present study we developed a sensitive RT-qPCR assay designed for the rapid, direct detection of Gamma and Delta variants of concern. Sensitive quantification and detection of the various variants showed the prevalence of the original variant during the first morbidity peak. The dominance of the Alpha variant over the original variant correlated with the second morbidity peak. These variants decreased concurrently with an increase in vaccinations (Feb-March 2021) and the observed decrease in morbidity. The appearance and subsequent rise of the Delta variant became evident and corresponded to the third morbidity peak (June-August 2021). These results suggest a high vaccine neutralization efficiency towards the Alpha variant compared to its neutralization efficiency towards the Delta variant. Moreover, the third vaccination dose (booster) seems to regain neutralization efficiency towards the Delta variant. The developed assays and wastewater-based epidemiology are important tools aiding in morbidity surveillance and disclosing vaccination efforts and immunity dynamics in the community.
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Affiliation(s)
- Karin Yaniv
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben- Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Eden Ozer
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | | | - Ariel Kushmaro
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben- Gurion University of the Negev, Beer-Sheva 84105, Israel; The Ilse Katz Center for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
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20
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Van Poelvoorde LAE, Gand M, Fraiture MA, De Keersmaecker SCJ, Verhaegen B, Van Hoorde K, Cay AB, Balmelle N, Herman P, Roosens N. Strategy to Develop and Evaluate a Multiplex RT-ddPCR in Response to SARS-CoV-2 Genomic Evolution. Curr Issues Mol Biol 2021; 43:1937-1949. [PMID: 34889894 PMCID: PMC8928932 DOI: 10.3390/cimb43030134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/08/2021] [Accepted: 11/02/2021] [Indexed: 12/12/2022] Open
Abstract
The worldwide emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) since 2019 has highlighted the importance of rapid and reliable diagnostic testing to prevent and control the viral transmission. However, inaccurate results may occur due to false negatives (FN) caused by polymorphisms or point mutations related to the virus evolution and compromise the accuracy of the diagnostic tests. Therefore, PCR-based SARS-CoV-2 diagnostics should be evaluated and evolve together with the rapidly increasing number of new variants appearing around the world. However, even by using a large collection of samples, laboratories are not able to test a representative collection of samples that deals with the same level of diversity that is continuously evolving worldwide. In the present study, we proposed a methodology based on an in silico and in vitro analysis. First, we used all information offered by available whole-genome sequencing data for SARS-CoV-2 for the selection of the two PCR assays targeting two different regions in the genome, and to monitor the possible impact of virus evolution on the specificity of the primers and probes of the PCR assays during and after the development of the assays. Besides this first essential in silico evaluation, a minimal set of testing was proposed to generate experimental evidence on the method performance, such as specificity, sensitivity and applicability. Therefore, a duplex reverse-transcription droplet digital PCR (RT-ddPCR) method was evaluated in silico by using 154 489 whole-genome sequences of SARS-CoV-2 strains that were representative for the circulating strains around the world. The RT-ddPCR platform was selected as it presented several advantages to detect and quantify SARS-CoV-2 RNA in clinical samples and wastewater. Next, the assays were successfully experimentally evaluated for their sensitivity and specificity. A preliminary evaluation of the applicability of the developed method was performed using both clinical and wastewater samples.
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Affiliation(s)
- Laura A. E. Van Poelvoorde
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
| | - Mathieu Gand
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
| | - Marie-Alice Fraiture
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
| | - Sigrid C. J. De Keersmaecker
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
| | - Bavo Verhaegen
- Food Pathogens, Sciensano, 1050 Brussels, Belgium; (B.V.); (K.V.H.)
| | | | - Ann Brigitte Cay
- Enzootic, Vector-Borne and Bee Diseases, Sciensano, 1180 Brussels, Belgium; (A.B.C.); (N.B.)
| | - Nadège Balmelle
- Enzootic, Vector-Borne and Bee Diseases, Sciensano, 1180 Brussels, Belgium; (A.B.C.); (N.B.)
| | - Philippe Herman
- Expertise and Service Provision, Sciensano, 1050 Brussels, Belgium;
| | - Nancy Roosens
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
- Correspondence:
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21
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Balaska S, Pilalas D, Takardaki A, Koutra P, Parasidou E, Gkeka I, Tychala A, Meletis G, Fyntanidou B, Metallidis S, Protonotariou E, Skoura L. Evaluation of the Advanta Dx SARS-CoV-2 RT-PCR Assay, a High-Throughput Extraction-Free Diagnostic Test for the Detection of SARS-CoV-2 in Saliva: A Diagnostic Accuracy Study. Diagnostics (Basel) 2021; 11:1766. [PMID: 34679464 PMCID: PMC8534356 DOI: 10.3390/diagnostics11101766] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 12/29/2022] Open
Abstract
Nasopharyngeal swab specimen (NPS) molecular testing is considered the gold standard for SARS-CoV-2 detection. However, saliva is an attractive, noninvasive specimen alternative. The aim of the study was to evaluate the diagnostic accuracy of Advanta Dx SARS-CoV-2 RT-PCR saliva-based assay against paired NPS tested with either NeumoDxTM SARS-CoV-2 assay or Abbott Real Time SARS-CoV-2 assay as the reference method. We prospectively evaluated the method in two settings: a diagnostic outpatient and a healthcare worker screening convenience sample, collected in November-December 2020. SARS-CoV-2 was detected in 27.7% (61/220) of diagnostic samples and in 5% (10/200) of screening samples. Overall, saliva test in diagnostic samples had a sensitivity of 88.5% (77.8-95.3%) and specificity of 98.1% (94.6-99.6%); in screening samples, the sensitivity was 90% (55.5-99.7%) and specificity 100% (98.1-100%). Our data suggests that the Fluidigm Advanta Dx RT-PCR saliva-based assay may be a reliable diagnostic tool for COVID-19 diagnosis in symptomatic individuals and screening asymptomatic healthcare workers.
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Affiliation(s)
- Sofia Balaska
- Department of Microbiology, AHEPA University Hospital, Medical School, Aristotle University οf Thessaloniki, 54636 Thessaloniki, Greece; (S.B.); (A.T.); (P.K.); (E.P.); (I.G.); (A.T.); (G.M.); (E.P.)
| | - Dimitrios Pilalas
- First Propedeutic Department of Internal Medicine, AHEPA University Hospital, Medical School, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece;
| | - Anna Takardaki
- Department of Microbiology, AHEPA University Hospital, Medical School, Aristotle University οf Thessaloniki, 54636 Thessaloniki, Greece; (S.B.); (A.T.); (P.K.); (E.P.); (I.G.); (A.T.); (G.M.); (E.P.)
| | - Paraskevoula Koutra
- Department of Microbiology, AHEPA University Hospital, Medical School, Aristotle University οf Thessaloniki, 54636 Thessaloniki, Greece; (S.B.); (A.T.); (P.K.); (E.P.); (I.G.); (A.T.); (G.M.); (E.P.)
| | - Eleftheria Parasidou
- Department of Microbiology, AHEPA University Hospital, Medical School, Aristotle University οf Thessaloniki, 54636 Thessaloniki, Greece; (S.B.); (A.T.); (P.K.); (E.P.); (I.G.); (A.T.); (G.M.); (E.P.)
| | - Ioanna Gkeka
- Department of Microbiology, AHEPA University Hospital, Medical School, Aristotle University οf Thessaloniki, 54636 Thessaloniki, Greece; (S.B.); (A.T.); (P.K.); (E.P.); (I.G.); (A.T.); (G.M.); (E.P.)
| | - Areti Tychala
- Department of Microbiology, AHEPA University Hospital, Medical School, Aristotle University οf Thessaloniki, 54636 Thessaloniki, Greece; (S.B.); (A.T.); (P.K.); (E.P.); (I.G.); (A.T.); (G.M.); (E.P.)
| | - Georgios Meletis
- Department of Microbiology, AHEPA University Hospital, Medical School, Aristotle University οf Thessaloniki, 54636 Thessaloniki, Greece; (S.B.); (A.T.); (P.K.); (E.P.); (I.G.); (A.T.); (G.M.); (E.P.)
| | - Barbara Fyntanidou
- Emergency Department, AHEPA University Hospital, 54636 Thessaloniki, Greece;
| | - Simeon Metallidis
- First Department of Internal Medicine, Infectious Diseases Division, AHEPA University Hospital, Medical School, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece;
| | - Efthymia Protonotariou
- Department of Microbiology, AHEPA University Hospital, Medical School, Aristotle University οf Thessaloniki, 54636 Thessaloniki, Greece; (S.B.); (A.T.); (P.K.); (E.P.); (I.G.); (A.T.); (G.M.); (E.P.)
| | - Lemonia Skoura
- Department of Microbiology, AHEPA University Hospital, Medical School, Aristotle University οf Thessaloniki, 54636 Thessaloniki, Greece; (S.B.); (A.T.); (P.K.); (E.P.); (I.G.); (A.T.); (G.M.); (E.P.)
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22
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Ferrari L, Nigro S, Bordini L, Carugno M, Bollati V. SARS-CoV-2 tests in occupational settings: what you look for is what you get. LA MEDICINA DEL LAVORO 2021; 112:183-193. [PMID: 34142672 PMCID: PMC8223938 DOI: 10.23749/mdl.v112i3.11472] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/19/2021] [Indexed: 01/13/2023]
Abstract
During the last month of 2019, a new Coronavirus from China started to spread all around the world causing a pandemic emergency still ongoing. The outbreak made imperative the need for diagnostic and screening tests that could identify the current and past infection state of an individual. Occupational medicine is facing a very demanding challenge, as the pandemic set off the need to re-evaluate many aspects of workplace safety. A fundamental role has been played by tests used to diagnose COVID-19 and to isolate infected asymptomatic subjects, with a view to the viral evolution and the emerging variants. However, the need for the urgent set-up of new methods for assessing both new and past infections has resulted in a large number of methods, not always comparable with each other, in terms of laboratory techniques, viral antigens used for detection, and class of antibodies detected. These factors make it difficult to understand the serological test results and their possible application. In this paper, we reviewed the types of assays currently available, to address some key aspects that characterize each technique, and might have an impact on results interpretation.
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Affiliation(s)
- Luca Ferrari
- EPIGET Lab, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy.
| | - Simona Nigro
- EPIGET Lab, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy.
| | - Lorenzo Bordini
- Occupational Health Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
| | - Michele Carugno
- EPIGET Lab, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy.
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