351
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Gobeille Paré S, Bestman-Smith J, Fafard J, Doualla-Bell F, Jacob-Wagner M, Lavallée C, Charest H, Beauchemin S, Coutlée F, Dumaresq J, Busque L, St-Hilaire M, Lépine G, Boucher V, Desforges M, Goupil-Sormany I, Labbé AC. Natural spring water gargle samples as an alternative to nasopharyngeal swabs for SARS-CoV-2 detection using a laboratory-developed test. J Med Virol 2021; 94:985-993. [PMID: 34672374 PMCID: PMC8661969 DOI: 10.1002/jmv.27407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/28/2021] [Accepted: 10/18/2021] [Indexed: 01/23/2023]
Abstract
The objective of this study was to validate the use of spring water gargle (SWG) as an alternative to oral and nasopharyngeal swab (ONPS) for SARS‐CoV‐2 detection with a laboratory‐developed test. Healthcare workers and adults from the general population, presenting to one of two COVID‐19 screening clinics in Montréal and Québec City, were prospectively recruited to provide a gargle sample in addition to the standard ONPS. The paired specimens were analyzed using thermal lysis followed by a laboratory‐developed nucleic acid amplification test (LD‐NAAT) to detect SARS‐CoV‐2, and comparative performance analysis was performed. An individual was considered infected if a positive result was obtained on either sample. A total of 1297 adult participants were recruited. Invalid results (n = 18) were excluded from the analysis. SARS‐CoV‐2 was detected in 144/1279 (11.3%) participants: 126 from both samples, 15 only from ONPS, and 3 only from SWG. Overall, the sensitivity was 97.9% (95% CI: 93.7–99.3) for ONPS and 89.6% (95% CI: 83.4–93.6; p = 0.005) for SWG. The mean ONPS cycle threshold (Ct) value was significantly lower for the concordant paired samples as compared to discordant ones (22.9 vs. 32.1; p < 0.001). In conclusion, using an LD‐NAAT with thermal lysis, SWG is a less sensitive sampling method than the ONPS. However, the higher acceptability of SWG might enable a higher rate of detection from a population‐based perspective. Nonetheless, in patients with a high clinical suspicion of COVID‐19, a repeated analysis with ONPS should be considered. The sensitivity of SWG using NAAT preceded by chemical extraction should be evaluated. Using a laboratory‐developed NAAT preceded by thermal lysis, the overall percent agreement between spring water gargle (SWG) and oral combined with nasopharyngeal swab (ONPS), sampled at the same time among 1297 participants, is excellent (98.6%). Although the SARS‐CoV‐2 NAAT from SWG is globally less sensitive than from ONPS (89.6% vs. 97.9%), the difference is markedly less in individuals symptomatic for <3 days (2.7%; p=NS) than in those whose symptoms started ≥7 days before testing (35.7%; p= 0.005).
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Affiliation(s)
- Sarah Gobeille Paré
- Département de microbiologie-infectiologie et d'immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Julie Bestman-Smith
- Département de microbiologie-infectiologie et d'immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada.,Département de microbiologie et d'infectiologie du Centre hospitalier universitaire (CHU) de Québec, Québec, Québec, Canada
| | - Judith Fafard
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Québec, Canada.,Département de microbiologie, infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Florence Doualla-Bell
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Québec, Canada
| | - Mariève Jacob-Wagner
- Département de microbiologie et d'infectiologie du Centre hospitalier universitaire (CHU) de Québec, Québec, Québec, Canada
| | - Christian Lavallée
- Département de microbiologie, infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada.,Département des laboratoires de biologie médicale, Grappe Optilab-CHUM, Centre hospitalier de l'Université de Montréal, Montréal, Québec, Canada.,Service de maladies infectieuses, CIUSSS de l'Est-de-l'Île-de-Montréal, Montréal, Québec, Canada
| | - Hugues Charest
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Québec, Canada.,Département de microbiologie, infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Stéphanie Beauchemin
- Département des laboratoires de biologie médicale, Grappe Optilab-CHUM, Centre hospitalier de l'Université de Montréal, Montréal, Québec, Canada
| | - François Coutlée
- Département de microbiologie, infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada.,Département des laboratoires de biologie médicale, Grappe Optilab-CHUM, Centre hospitalier de l'Université de Montréal, Montréal, Québec, Canada
| | - Jeannot Dumaresq
- Département de microbiologie-infectiologie et d'immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada.,Département de microbiologie et d'Infectiologie, CISSS de Chaudière-Appalaches, Lévis, Québec, Canada
| | - Lambert Busque
- Département des laboratoires de biologie médicale, Grappe Optilab-CHUM, Centre hospitalier de l'Université de Montréal, Montréal, Québec, Canada
| | - Manon St-Hilaire
- Département des laboratoires de biologie médicale, Grappe Optilab-CHUM, Centre hospitalier de l'Université de Montréal, Montréal, Québec, Canada
| | - Guylaine Lépine
- Département des laboratoires de biologie médicale, Grappe Optilab-CHUM, Centre hospitalier de l'Université de Montréal, Montréal, Québec, Canada
| | - Valérie Boucher
- Centre de recherche du CHU de Québec-Université Laval, Québec, Canada
| | - Marc Desforges
- Département de microbiologie, infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada.,Département clinique de médecine de laboratoire, CHU Ste-Justine, Montréal, Québec, Canada
| | - Isabelle Goupil-Sormany
- Direction de la vigie sanitaire, Ministère de la Santé et des Services sociaux du Québec, Québec, Québec, Canada
| | - Annie-Claude Labbé
- Département de microbiologie, infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada.,Département des laboratoires de biologie médicale, Grappe Optilab-CHUM, Centre hospitalier de l'Université de Montréal, Montréal, Québec, Canada.,Service de maladies infectieuses, CIUSSS de l'Est-de-l'Île-de-Montréal, Montréal, Québec, Canada
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352
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Hu YL, Ding T. Clinical characteristics of COVID-19 patients in Xiaogan, China: comparison between recent imported cases and earlier local cases. Am J Transl Res 2021; 13:11999-12005. [PMID: 34786134 PMCID: PMC8581891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/08/2021] [Indexed: 06/13/2023]
Abstract
OBJECT In this study, we aim to investigate if there exists some change in the pathogenicity of SARS-CoV-2 by comparing the clinical characteristics between recent imported patients and earlier local patients. METHODS 227 local COVID-19 patients diagnosed before February 15, 2020 (local group) and 23 imported COVID-19 patients diagnosed between July 1, 2020, and January 15, 2021 (imported group) were included in this study. Baseline characteristics and characteristics of computed tomography (CT), routine blood test, liver functions, and infectious markers upon admission were collected and compared. RESULTS The neutrophil-to-lymphocyte ratio (NLR) of the imported group was 3.21 ± 1.25, which was significantly higher than that of the local group (2.55 ± 1.19) with a P-value of 0.030. The concentration of C-reactive protein of the imported group was 12.34 ± 5.25, which was significantly higher than that of the local group (7.76 ± 6.54 mg/L) with a P-value of 0.0005. No significant difference was observed in the rest characteristics. CONCLUSION The recent imported cases had higher NLR and C-reactive protein levels than the earlier local cases, indicating that the pathogenicity of SARS-CoV-2 is getting worse during the pandemic.
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Affiliation(s)
- Yan-Lan Hu
- Hanchuan People's Hospital Hanchuan 431600, Hubei, China
| | - Tao Ding
- Hanchuan People's Hospital Hanchuan 431600, Hubei, China
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353
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Graber TE, Mercier É, Bhatnagar K, Fuzzen M, D'Aoust PM, Hoang HD, Tian X, Towhid ST, Plaza-Diaz J, Eid W, Alain T, Butler A, Goodridge L, Servos M, Delatolla R. Near real-time determination of B.1.1.7 in proportion to total SARS-CoV-2 viral load in wastewater using an allele-specific primer extension PCR strategy. WATER RESEARCH 2021; 205:117681. [PMID: 34619611 PMCID: PMC8459324 DOI: 10.1016/j.watres.2021.117681] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/15/2021] [Accepted: 09/17/2021] [Indexed: 05/02/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has claimed millions of lives to date. Antigenic drift has resulted in viral variants with putatively greater transmissibility, virulence, or both. Early and near real-time detection of these variants of concern (VOC) and the ability to accurately follow their incidence and prevalence in communities is wanting. Wastewater-based epidemiology (WBE), which uses nucleic acid amplification tests to detect viral fragments, is a reliable proxy of COVID-19 incidence and prevalence, and thus offers the potential to monitor VOC viral load in a given population. Here, we describe and validate a primer extension PCR strategy targeting a signature mutation in the N gene of SARS-CoV-2. This allows quantification of B.1.1.7 versus non-B.1.1.7 allele frequency in wastewater without the need to employ quantitative RT-PCR standard curves. We show that the wastewater B.1.1.7 profile correlates with its clinical counterpart and benefits from a near real-time and facile data collection and reporting pipeline. This assay can be quickly implemented within a current SARS-CoV-2 WBE framework with minimal cost; allowing early and contemporaneous estimates of B.1.1.7 community transmission prior to, or in lieu of, clinical screening and identification. Our study demonstrates that this strategy can provide public health units with an additional and much needed tool to rapidly triangulate VOC incidence/prevalence with high sensitivity and lineage specificity.
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Affiliation(s)
- Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, K1H 8L1, Canada
| | - Élisabeth Mercier
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Kamya Bhatnagar
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Meghan Fuzzen
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Patrick M D'Aoust
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Huy-Dung Hoang
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, K1H 8L1, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
| | - Xin Tian
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Syeda Tasneem Towhid
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Julio Plaza-Diaz
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, K1H 8L1, Canada
| | - Walaa Eid
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, K1H 8L1, Canada
| | - Tommy Alain
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, K1H 8L1, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
| | - Ainslie Butler
- Simcoe Muskoka District Health Unit, Barrie, Ontario, L4M 6K9, Canada
| | - Lawrence Goodridge
- Department of Food Science, Canadian Research Institute for Food Safety, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Mark Servos
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada.
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354
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Hristov DR, Gomez-Marquez J, Wade D, Hamad-Schifferli K. SARS-CoV-2 and approaches for a testing and diagnostic strategy. J Mater Chem B 2021; 9:8157-8173. [PMID: 34494642 DOI: 10.1039/d1tb00674f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The COVID-19 pandemic has led to an unprecedented global health challenge, creating sudden, massive demands for diagnostic testing, treatment, therapies, and vaccines. In particular, the development of diagnostic assays for SARS-CoV-2 has been pursued as they are needed for quarantine, disease surveillance, and patient treatment. One of the major lessons the pandemic highlighted was the need for fast, cheap, scalable and reliable diagnostic methods, such as paper-based assays. Furthermore, it has previously been suggested that paper-based tests may be more suitable for settings with lower resource availability and may help alleviate some supply chain challenges which arose during the COVID-19 pandemic. Therefore, we explore how such devices may fit in a comprehensive diagnostic strategy and how some of the challenges to the technology, e.g. low sensitivity, may be addressed. We discuss the properties of the SARS-CoV-2 virus itself, the COVID-19 disease pathway, and the immune response. We then describe the different diagnostic strategies that have been pursued, focusing on molecular strategies for viral genetic material, antigen tests, and serological assays, and innovations for improving the diagnostic sensitivity and capabilities. Finally, we discuss pressing issues for the future, and what needs to be addressed for the ongoing pandemic and future outbreaks.
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Affiliation(s)
- Delyan R Hristov
- Department of Engineering, University of Massachusetts Boston, Boston, MA, USA.
| | - Jose Gomez-Marquez
- Little Devices Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Djibril Wade
- iLEAD (Innovation in Laboratory Engineered Accelerated Diagnostics), Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formations (IRESSEF), Dakar, Senegal
| | - Kimberly Hamad-Schifferli
- Department of Engineering, University of Massachusetts Boston, Boston, MA, USA. .,School for the Environment, University of Massachusetts Boston, Boston, MA, USA
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355
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Ngaba GP, Kalla GCM, Assob JCN, Njouendou AJ, Jembe CN, Mboudou ET, Mbopi-Keou FX. Comparative analysis of two molecular tests for the detection of COVID-19 in Cameroon. Pan Afr Med J 2021; 39:214. [PMID: 34630826 PMCID: PMC8486926 DOI: 10.11604/pamj.2021.39.214.30718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 07/16/2021] [Indexed: 11/11/2022] Open
Abstract
Introduction COVID-19 equation in Cameroon is yet to be resolved. There is an urgent need for a rapid response strategy to the increasing demand of polymerase chain reaction (PCR) test results for both patients, travelers and competitors to various games. We assessed the diagnostic performance of the AmpliQuick® SARS-CoV-2 against the classic Reverse transcription polymerase chain reaction (RT-PCR). Methods a cross-sectional and comparative study was conducted from April 27th to May 29th, 2021 in the city of Douala, Cameroon. The samples consisted of any nasopharyngeal sample received at the Douala Gynaeco-Obstetrics and Pediatric Hospital molecular biology laboratory, regardless of its origin. Sociodemographic parameters (age, profession (footballers, travelers, other), matrimonial status, nationality), comorbidity and known status of COVID-19, were recorded at collection sites. The main collection sites were the Deido Health District and the Douala Gynaeco-Obstetric and Pediatric Hospital. We performed testing using AmpliQuick® SARS-CoV-2 and the classic RT-PCR (Da An Gene Co.Ltd) on each sample during the one month period. Analytical performance parameters were determined. To determine the sensitivity of both methods, the Bayesian latent class model was performed on the median with 95% confidence interval, with p≤0.05 as significant level, as well as Kappa (κ) agreement between tests. An ethical clearance was sought and obtained from the University of Douala Institutional Ethics Committee. Results a total of 1813 participants were enrolled, with the predominance of male (68.68%) and the age group 31 to 40 years old (31.33%). Most participants were married (53.46%) with only few with known COVID-19 status (5.47%). One thousand eight hundred and ten (1810) tests were performed by AMPLIQUICK® SARS-CoV-2 while only 1107 could be achieved with the classic RT-PCR. Over the study period, it was noted a drastic reduction in the time necessary to render results with the AMPLIQUICK® SARS-CoV-2 from 24 hours to 3 hours. The AMPLIQUICK® SARS-CoV-2 reduced technician hands-on time and its practicability was noticed based on the prefilled and ready-to-use microplates. A prevalence of 1.93% and 1.45% were obtained for AMPLIQUICK® SARS-CoV-2 and the classic RT-PCR respectively. This difference in the prevalence showed that AMPLIQUICK® SARS-CoV-2 (Sensitivity 83.5% [CI=64.6-95.2]) was more accurate than the classic RT-PCR (67.8% [CI=46.6-84.9]). Conclusion it is time for a change of attitude to scale up the COVID-19 testing ability in Cameroon and the AMPLIQUICK® SARS-CoV-2 is an alternative diagnosis strategy which should help resolve the situation of timely and reliable results.
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Affiliation(s)
- Guy Pascal Ngaba
- Faculty of Medicine and Pharmaceutical Sciences, University of Douala, Douala, Cameroon.,Gynaeco-Obstetrics and Pediatric Hospital Douala, Douala, Cameroon
| | | | | | | | | | - Emile Télesphore Mboudou
- Gynaeco-Obstetrics and Pediatric Hospital Douala, Douala, Cameroon.,Faculty of Medicine and Biomedical Sciences, University of Yaounde I, Yaounde, Cameroon
| | - Francois-Xavier Mbopi-Keou
- Faculty of Medicine and Biomedical Sciences, University of Yaounde I, Yaounde, Cameroon.,The Institute for the Development of Africa (The-IDA), Yaounde, Cameroon
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356
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Silva PJS, Pereira T, Sagastizábal C, Nonato L, Cordova MM, Struchiner CJ. Smart testing and critical care bed sharing for COVID-19 control. PLoS One 2021; 16:e0257235. [PMID: 34613981 PMCID: PMC8494319 DOI: 10.1371/journal.pone.0257235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 08/26/2021] [Indexed: 11/19/2022] Open
Abstract
During the early months of the current COVID-19 pandemic, social distancing measures effectively slowed disease transmission in many countries in Europe and Asia, but the same benefits have not been observed in some developing countries such as Brazil. In part, this is due to a failure to organise systematic testing campaigns at nationwide or even regional levels. To gain effective control of the pandemic, decision-makers in developing countries, particularly those with large populations, must overcome difficulties posed by an unequal distribution of wealth combined with low daily testing capacities. The economic infrastructure of these countries, often concentrated in a few cities, forces workers to travel from commuter cities and rural areas, which induces strong nonlinear effects on disease transmission. In the present study, we develop a smart testing strategy to identify geographic regions where COVID-19 testing could most effectively be deployed to limit further disease transmission. By smart testing we mean the testing protocol that is automatically designed by our optimization platform for a given time period, knowing the available number of tests, the current availability of ICU beds and the initial epidemiological situation. The strategy uses readily available anonymised mobility and demographic data integrated with intensive care unit (ICU) occupancy data and city-specific social distancing measures. Taking into account the heterogeneity of ICU bed occupancy in differing regions and the stages of disease evolution, we use a data-driven study of the Brazilian state of Sao Paulo as an example to show that smart testing strategies can rapidly limit transmission while reducing the need for social distancing measures, even when testing capacity is limited.
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Affiliation(s)
- Paulo J. S. Silva
- Instituto de Matemática, Estatística e Computação Científica, Universidade de Campinas, São Paulo, Brazil
| | - Tiago Pereira
- Instituto de Ciências Matemáticas e Computação, Universidade de São Paulo, São Paulo, Brazil
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Claudia Sagastizábal
- Instituto de Matemática, Estatística e Computação Científica, Universidade de Campinas, São Paulo, Brazil
| | - Luis Nonato
- Instituto de Ciências Matemáticas e Computação, Universidade de São Paulo, São Paulo, Brazil
| | - Marcelo M. Cordova
- Departamento de Engenharia Elétrica, Universidade Federal de Santa Catarina, Florianópolis, Brazil
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357
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Lee JM, Kim CR, Kim S, Min J, Lee MH, Lee S. Mix-and-read, one-minute SARS-CoV-2 diagnostic assay: development of PIFE-based aptasensor. Chem Commun (Camb) 2021; 57:10222-10225. [PMID: 34523638 DOI: 10.1039/d1cc04066a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We developed a one-minute, one-step SARS-CoV-2 antigen assay based on protein-induced fluorescence enhancement of a DNA aptamer. The system showed significant selectivity and sensitivity towards both nucleocapsid protein and SARS-CoV-2 virus lysate, but with marked improvements in speed and manufacturability. We hence propose this platform as a mix-and-read testing strategy for SARS-CoV-2 that can be applied to POC diagnostics in clinical settings, especially in low- and middle-income countries.
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Affiliation(s)
- J Michelle Lee
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,PCL, Inc., Rm 701, Star Valley, 99, Digital-ro-9-gil, Ge-umcheon-gu, Seoul, 08510, Republic of Korea.
| | - Chae Rin Kim
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,PCL, Inc., Rm 701, Star Valley, 99, Digital-ro-9-gil, Ge-umcheon-gu, Seoul, 08510, Republic of Korea.
| | - Sion Kim
- PCL, Inc., Rm 701, Star Valley, 99, Digital-ro-9-gil, Ge-umcheon-gu, Seoul, 08510, Republic of Korea. .,College of LSA, University of Michigan, Ann Arbor, MI, 48104, USA
| | - Junhong Min
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea.
| | - Min-Ho Lee
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea.
| | - SangWook Lee
- PCL, Inc., Rm 701, Star Valley, 99, Digital-ro-9-gil, Ge-umcheon-gu, Seoul, 08510, Republic of Korea. .,e Bio-health Product Research Center, Inje University, Gimhae-si, 50834, Korea
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358
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Cherkaoui D, Huang D, Miller BS, Turbé V, McKendry RA. Harnessing recombinase polymerase amplification for rapid multi-gene detection of SARS-CoV-2 in resource-limited settings. Biosens Bioelectron 2021; 189:113328. [PMID: 34051382 PMCID: PMC8120794 DOI: 10.1016/j.bios.2021.113328] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/26/2021] [Accepted: 05/07/2021] [Indexed: 01/07/2023]
Abstract
The COVID-19 pandemic is challenging diagnostic testing capacity worldwide. The mass testing needed to limit the spread of the virus requires new molecular diagnostic tests to dramatically widen access at the point-of-care in resource-limited settings. Isothermal molecular assays have emerged as a promising technology, given the faster turn-around time and minimal equipment compared to gold standard laboratory PCR methods. However, unlike PCR, they do not typically target multiple SARS-CoV-2 genes, risking sensitivity and specificity. Moreover, they often require multiple steps thus adding complexity and delays. Here we develop a multiplexed, 1-2 step, fast (20-30 min) SARS-CoV-2 molecular test using reverse transcription recombinase polymerase amplification to simultaneously detect two conserved targets - the E and RdRP genes. The agile multi-gene platform offers two complementary detection methods: real-time fluorescence or dipstick. The analytical sensitivity of the fluorescence test was 9.5 (95% CI: 7.0-18) RNA copies per reaction for the E gene and 17 (95% CI: 11-93) RNA copies per reaction for the RdRP gene. The analytical sensitivity for the dipstick method was 130 (95% CI: 82-500) RNA copies per reaction. High specificity was found against common seasonal coronaviruses, SARS-CoV and MERS-CoV model samples. The dipstick readout demonstrated potential for point-of-care testing in decentralised settings, with minimal or equipment-free incubation methods and a user-friendly prototype smartphone application. This rapid, simple, ultrasensitive and multiplexed molecular test offers valuable advantages over gold standard tests and in future could be configurated to detect emerging variants of concern.
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Affiliation(s)
- Dounia Cherkaoui
- London Centre for Nanotechnology, University College London, London, United Kingdom,Division of Medicine, University College London, London, United Kingdom
| | - Da Huang
- London Centre for Nanotechnology, University College London, London, United Kingdom
| | - Benjamin S. Miller
- London Centre for Nanotechnology, University College London, London, United Kingdom
| | - Valérian Turbé
- London Centre for Nanotechnology, University College London, London, United Kingdom
| | - Rachel A. McKendry
- London Centre for Nanotechnology, University College London, London, United Kingdom,Division of Medicine, University College London, London, United Kingdom,Corresponding author. London Centre for Nanotechnology, Univerity College London, 17-19 Gordon Street, London, United Kingdom
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359
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Beauté J, Adlhoch C, Bundle N, Melidou A, Spiteri G. Testing indicators to monitor the COVID-19 pandemic. THE LANCET INFECTIOUS DISEASES 2021; 21:1344-1345. [PMID: 34450053 PMCID: PMC8384351 DOI: 10.1016/s1473-3099(21)00461-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022]
Affiliation(s)
- Julien Beauté
- European Centre for Disease Prevention and Control, Solna 169 73, Sweden.
| | - Cornelia Adlhoch
- European Centre for Disease Prevention and Control, Solna 169 73, Sweden
| | - Nick Bundle
- European Centre for Disease Prevention and Control, Solna 169 73, Sweden
| | - Angeliki Melidou
- European Centre for Disease Prevention and Control, Solna 169 73, Sweden
| | - Gianfranco Spiteri
- European Centre for Disease Prevention and Control, Solna 169 73, Sweden
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360
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Lee Y, Ng M, Daniel K, Wayne E. Rapid growth in the COVID-19 era. MRS BULLETIN 2021; 46:847-853. [PMID: 34608355 PMCID: PMC8480751 DOI: 10.1557/s43577-021-00185-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/18/2021] [Indexed: 05/06/2023]
Abstract
ABSTRACT From Operation Warp Speed to the lipid mRNA vaccine, the COVID-19 pandemic has been a watershed moment for technological development, production, and implementation. The scale and pace of innovation and global collaboration has likely not been experienced since World War II. This article highlights some of the engineering accomplishments that occurred during the pandemic. We provide a broad overview of the technological achievements in vaccine design, antibody engineering, drug repurposing, and rapid diagnostic testing. We also discuss what the future of these technologies and the future of large-scale collaborations might look like moving forward. GRAPHIC ABSTRACT
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Affiliation(s)
- Yerim Lee
- Department of Biomedical Engineering, and Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA USA
| | - Michelle Ng
- Department of Biomedical Engineering, and Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA USA
| | - Kristin Daniel
- Department of Biomedical Engineering, and Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA USA
| | - Elizabeth Wayne
- Department of Biomedical Engineering, and Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA USA
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361
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Pantazopoulos I, Tsikrika S, Kolokytha S, Manos E, Porpodis K. Management of COVID-19 Patients in the Emergency Department. J Pers Med 2021; 11:jpm11100961. [PMID: 34683102 PMCID: PMC8537207 DOI: 10.3390/jpm11100961] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/24/2021] [Accepted: 09/24/2021] [Indexed: 12/15/2022] Open
Abstract
COVID-19 is an emerging disease of global public health concern. As the pandemic overwhelmed emergency departments (EDs), a restructuring of emergency care delivery became necessary in many hospitals. Furthermore, with more than 2000 papers being published each week, keeping up with ever-changing information has proven to be difficult for emergency physicians. The aim of the present review is to provide emergency physician with a summary of the current literature regarding the management of COVID-19 patients in the emergency department.
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Affiliation(s)
- Ioannis Pantazopoulos
- Department of Emergency Medicine, Faculty of Medicine, University of Thessaly, Biopolis, 415 00 Larissa, Greece
- Correspondence: ; Tel.: +30-694-566-1525
| | - Stamatoula Tsikrika
- Emergency Department, Thoracic Diseases COVID-19 Referral Hospital “SOTIRIA”, 115 27 Athens, Greece;
| | - Stavroula Kolokytha
- Department of Emergency Medicine, Sismanoglio Hospital, 151 26 Athens, Greece;
| | - Emmanouil Manos
- Pulmonary Clinic, General Hospital of Lamia, 351 00 Lamia, Greece;
| | - Konstantinos Porpodis
- Respiratory Medicine Department, Aristotle University of Thessaloniki, G Papanikolaou Hospital, 570 10 Thessaloniki, Greece;
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362
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Jindal H, Jain S, Suvvari TK, Kutikuppala LVS, Rackimuthu S, Rocha ICN, Goyal S, Radha. False-Negative RT-PCR Findings and Double Mutant Variant as Factors of an Overwhelming Second Wave of COVID-19 in India: an Emerging Global Health Disaster. SN COMPREHENSIVE CLINICAL MEDICINE 2021; 3:2383-2388. [PMID: 34568761 PMCID: PMC8453462 DOI: 10.1007/s42399-021-01059-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Accepted: 09/01/2021] [Indexed: 12/17/2022]
Abstract
RT-PCR is considered to be the standard gold diagnostic test for detecting COVID-19 causing SARS-CoV-2. Recent reports and recent pieces of evidence from scientific literature, however, tell a different story. There have been speculations of SARS-CoV-2 escaping the RT-PCR because of the series of mutations it has gone through. It is possible that host-dependent RNA editing and high person-to-person transmission have equipped the virus with mutations enabling it to spread faster and even evade the RT-PCR. Added to this is burnout among healthcare workers and technicians handling the RT-PCR machines and sampling. All of these factors may be working in unison to result in the deluge of false-negative cases India is facing during the second COVID-19 wave. The mutant strains are spreading to other parts, posing challenges to the whole world. These circumstances warrant supplementary diagnostic tests such as serological and radiological findings to deal with cases of high clinical suspicion. Even one misdiagnosed COVID-19 patient poses a risk to hundreds of others in the vicinity. Healthcare workers' burnout also has to be dealt with. Erroneous staff should be re-trained.
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Affiliation(s)
- Himanshu Jindal
- Ganesh Shankar Vidyarthi Memorial Medical College, Kanpur, India
| | | | | | - LVSimhachalam Kutikuppala
- Konaseema Institute of Medical Sciences and Research Foundation (KIMS&RF), Amalapuram, Andhra Pradesh India
| | | | | | | | - Radha
- Kasturba Medical College, Manipal, India
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363
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Taylor SC, Hurst B, Martiszus I, Hausman MS, Sarwat S, Schapiro JM, Rowell S, Lituev A. Semi-quantitative, high throughput analysis of SARS-CoV-2 neutralizing antibodies: Measuring the level and duration of immune response antibodies post infection/vaccination. Vaccine 2021; 39:5688-5698. [PMID: 34426026 PMCID: PMC8343386 DOI: 10.1016/j.vaccine.2021.07.098] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/24/2021] [Accepted: 07/31/2021] [Indexed: 02/06/2023]
Abstract
The question associated with efficacy and longevity of SARS-CoV-2 protection post-vaccination is paramount. The cPass surrogate virus neutralization test (sVNT) has gained popularity globally as a dual application assay for: 1. Accurate SARS-CoV-2 population surveillance (seroprevalence) analysis and 2. Revealing the presence of antibodies that block and effectively neutralize the interaction between the SARS-CoV-2 receptor binding domain and the host cell ACE2 receptor in recovered or vaccinated individuals. This study describes an approach for accurate quantification of neutralizing antibodies using the cPass sVNT with an automated workflow on the Tecan EVO and Dynex Agility platforms that is applicable to other liquid handling systems. This methodology was used to assess the stability of SARS-CoV-2 neutralizing antibodies between freeze/thaw and refrigerated sample storage conditions. Furthermore, a subset of twenty-five samples from SARS-CoV-2 infected/recovered individuals revealed a 600-fold difference in the neutralizing antibody response where low titers were represented in about half of the samples. Finally, pre- and post-vaccination samples were tested for neutralizing antibodies using the qualitative and semi-quantitative cPass sVNT protocols revealing undetectable or relatively low levels after the first vaccine dose and a decline in levels longitudinally over the months following the second dose. This wide range in neutralizing (blocking) antibodies from both natural infection and vaccination supports a differential immune response that may be attributed to several physiological and genetic factors underlining the potential for measuring SARS-CoV-2 neutralizing antibody titer levels post-vaccination to help ensure robust and prolonged immunity.
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Affiliation(s)
- Sean C Taylor
- GENSCRIPT USA INC., 860 Centennial Ave., Piscataway, NJ 08854, USA.
| | - Beth Hurst
- Cayman Chemical, 1180 E. Ellsworth Road, Ann Arbor, MI 48108, USA
| | - Ian Martiszus
- Cure-Hub, 12655 SW Beaverdam Rd., Beaverton, OR 97005, USA
| | - Marvin S Hausman
- FourthWall Testing LLC, 455 9th Street Suite 128, Winter Garden, FL 34787, USA
| | - Samar Sarwat
- DYNEX Technologies, 14340 Sullyfield Circle, Chantilly, VA 20151-1621, USA
| | | | - Sarah Rowell
- Kaiser Permanente, 1795 A Second Street, Berkeley, CA 94710, USA
| | - Alexander Lituev
- Kaiser Permanente, 1795 A Second Street, Berkeley, CA 94710, USA
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364
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Carmo D, Campiotti I, Rodrigues L, Fantini I, Pinheiro G, Moraes D, Nogueira R, Rittner L, Lotufo R. Rapidly deploying a COVID-19 decision support system in one of the largest Brazilian hospitals. Health Informatics J 2021; 27:14604582211033017. [PMID: 34510949 DOI: 10.1177/14604582211033017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The COVID-19 pandemic generated research interest in automated models to perform classification and segmentation from medical imaging of COVID-19 patients, However, applications in real-world scenarios are still needed. We describe the development and deployment of COVID-19 decision support and segmentation system. A partnership with a Brazilian radiologist consortium, gave us access to 1000s of labeled computed tomography (CT) and X-ray images from São Paulo Hospitals. The system used EfficientNet and EfficientDet networks, state-of-the-art convolutional neural networks for natural images classification and segmentation, in a real-time scalable scenario in communication with a Picture Archiving and Communication System (PACS). Additionally, the system could reject non-related images, using header analysis and classifiers. We achieved CT and X-ray classification accuracies of 0.94 and 0.98, respectively, and Dice coefficient for lung and covid findings segmentations of 0.98 and 0.73, respectively. The median response time was 7 s for X-ray and 4 min for CT.
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Affiliation(s)
- Diedre Carmo
- MICLab, School of Electrical and Computing Engineering, UNICAMP, Campinas, São Paulo, Brazil
| | - Israel Campiotti
- NeuralMind Inteligência Artificial, Campinas, São Paulo, Brasil.,MICLab, School of Electrical and Computing Engineering, UNICAMP, Campinas, São Paulo, Brazil
| | | | | | - Gustavo Pinheiro
- MICLab, School of Electrical and Computing Engineering, UNICAMP, Campinas, São Paulo, Brazil
| | - Daniel Moraes
- NeuralMind Inteligência Artificial, Campinas, São Paulo, Brasil
| | - Rodrigo Nogueira
- NeuralMind Inteligência Artificial, Campinas, São Paulo, Brasil.,MICLab, School of Electrical and Computing Engineering, UNICAMP, Campinas, São Paulo, Brazil
| | - Leticia Rittner
- MICLab, School of Electrical and Computing Engineering, UNICAMP, Campinas, São Paulo, Brazil
| | - Roberto Lotufo
- NeuralMind Inteligência Artificial, Campinas, São Paulo, Brasil.,MICLab, School of Electrical and Computing Engineering, UNICAMP, Campinas, São Paulo, Brazil
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365
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Breedon AME, Saldanha RJ, Salisbury RL, Metzger DE, Werry MP, McPherson CJ, Irvin AP, Davis CM, Bogner CA, Braddock AM, Salter CE, Grigsby CC, Hart CR, Pangburn HA. COVID-19 Seroprevalence and Active Infection in an Asymptomatic Population. Front Med (Lausanne) 2021; 8:749732. [PMID: 34589507 PMCID: PMC8473750 DOI: 10.3389/fmed.2021.749732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/20/2021] [Indexed: 12/15/2022] Open
Abstract
In response to the COVID-19 pandemic, immediate and scalable testing solutions are needed to direct return to full capacity planning in the general public and across the Department of Defense (DoD). To fully understand the extent to which a population has been affected by COVID-19, active monitoring approaches require an estimation of overall seroprevalence in addition to accurate, affordable, and rapid tests to detect current SARS-CoV-2 infection. In this study, researchers in the Air Force Research Laboratory's 711th Human Performance Wing, Airman Systems Directorate evaluated the performance of various testing methods for the detection of SARS-CoV-2 antibodies and viral RNA in asymptomatic adults working at Wright-Patterson Air Force Base and the surrounding area during the period of 23 July 2020-23 Oct 2020. Altogether, there was a seroprevalance of 3.09% and an active infection rate of 0.5% (determined via the testing of saliva samples) amongst individuals tested, both of which were comparable to local and national averages at the time. This work also presents technical and non-technical assessments of various testing strategies as compared to the gold standard approaches (e.g., lateral flow assays vs. ELISA and RT-LAMP vs. RT-PCR) in order to explore orthogonal supply chains and fieldability. Exploration and validation of multiple testing strategies will allow the DoD and other workforces to make informed responses to COVID-19 and future pandemics.
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Affiliation(s)
- Amy M. E. Breedon
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, OH, United States
- UES, Inc., Integrative Health & Performance Sciences Division, Dayton, OH, United States
| | - Roland J. Saldanha
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, OH, United States
| | - Richard L. Salisbury
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, OH, United States
| | - David E. Metzger
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, OH, United States
- UES, Inc., Integrative Health & Performance Sciences Division, Dayton, OH, United States
| | - Michael P. Werry
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, OH, United States
| | - Craig J. McPherson
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, OH, United States
- UES, Inc., Integrative Health & Performance Sciences Division, Dayton, OH, United States
| | - Adam P. Irvin
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, OH, United States
| | - Christina M. Davis
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, OH, United States
- UES, Inc., Integrative Health & Performance Sciences Division, Dayton, OH, United States
| | - Charles A. Bogner
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, OH, United States
| | - Amber M. Braddock
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, OH, United States
- UES, Inc., Integrative Health & Performance Sciences Division, Dayton, OH, United States
| | - Charles E. Salter
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, OH, United States
| | - Claude C. Grigsby
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, OH, United States
| | - Corey R. Hart
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, OH, United States
| | - Heather A. Pangburn
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, OH, United States
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366
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Armendáriz I, Ferrari PA, Fraiman D, Martínez JM, Menzella HG, Ponce Dawson S. Nested pool testing strategy for the diagnosis of infectious diseases. Sci Rep 2021; 11:18108. [PMID: 34518603 PMCID: PMC8438083 DOI: 10.1038/s41598-021-97534-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/17/2021] [Indexed: 11/18/2022] Open
Abstract
The progress of the SARS-CoV-2 pandemic requires the design of large-scale, cost-effective testing programs. Pooling samples provides a solution if the tests are sensitive enough. In this regard, the use of the gold standard, RT-qPCR, raises some concerns. Recently, droplet digital PCR (ddPCR) was shown to be 10-100 times more sensitive than RT-qPCR, making it more suitable for pooling. Furthermore, ddPCR quantifies the RNA content directly, a feature that, as we show, can be used to identify nonviable samples in pools. Cost-effective strategies require the definition of efficient deconvolution and re-testing procedures. In this paper we analyze the practical implementation of an efficient hierarchical pooling strategy for which we have recently derived the optimal, determining the best ways to proceed when there are impediments for the use of the absolute optimum or when multiple pools are tested simultaneously and there are restrictions on the throughput time. We also show how the ddPCR RNA quantification and the nested nature of the strategy can be combined to perform self-consistency tests for a better identification of infected individuals and nonviable samples. The studies are useful to those considering pool testing for the identification of infected individuals.
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Affiliation(s)
- Inés Armendáriz
- Departamento de Matemática & IMAS, FCEN-UBA & CONICET, C1428EGA, Buenos Aires, Argentina
| | - Pablo A Ferrari
- Departamento de Matemática & IMAS, FCEN-UBA & CONICET, C1428EGA, Buenos Aires, Argentina
| | - Daniel Fraiman
- Departamento de Matemática y Ciencias, Universidad de San Andrés & CONICET, B1644BID, Victoria, Argentina
| | - José M Martínez
- Department of Applied Mathematics, IMECC-UNICAMP, Campinas, 13083-859, Brazil
| | - Hugo G Menzella
- Departamento de Tecnología & IPROByQ, FBIOyF-UNR & CONICET, S2002LRK, Rosario, Argentina
| | - Silvina Ponce Dawson
- Departamento de Física & IFIBA, FCEN-UBA & CONICET, C1428EGA, Buenos Aires, Argentina.
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367
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Rodriguez-Mateos P, Ngamsom B, Walter C, Dyer CE, Gitaka J, Iles A, Pamme N. A lab-on-a-chip platform for integrated extraction and detection of SARS-CoV-2 RNA in resource-limited settings. Anal Chim Acta 2021; 1177:338758. [PMID: 34482896 PMCID: PMC8202086 DOI: 10.1016/j.aca.2021.338758] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the unprecedented global pandemic of coronavirus disease-2019 (COVID-19). Efforts are needed to develop rapid and accurate diagnostic tools for extensive testing, allowing for effective containment of the infection via timely identification and isolation of SARS-CoV-2 carriers. Current gold standard nucleic acid tests require many separate steps that need trained personnel to operate specialist instrumentation in laboratory environments, hampering turnaround time and test accessibility, especially in low-resource settings. We devised an integrated on-chip platform coupling RNA extraction based on immiscible filtration assisted by surface tension (IFAST), with RNA amplification and detection via colorimetric reverse-transcription loop mediated isothermal amplification (RT-LAMP), using two sets of primers targeting open reading frame 1a (ORF1a) and nucleoprotein (N) genes of SARS-CoV-2. Results were identified visually, with a colour change from pink to yellow indicating positive amplification, and further confirmed by DNA gel electrophoresis. The specificity of the assay was tested against HCoV-OC43 and H1N1 RNAs. The assay based on use of gene N primers was 100% specific to SARS-CoV-2 with no cross-reactivity to HCoV-OC43 nor H1N1. Proof-of-concept studies on water and artificial sputum containing genomic SARS-CoV-2 RNA showed our IFAST RT-LAMP device to be capable of extracting and detecting 470 SARS-CoV-2 copies mL-1 within 1 h (from sample-in to answer-out). IFAST RT-LAMP is a simple-to-use, integrated, rapid and accurate COVID-19 diagnostic platform, which could provide an attractive means for extensive screening of SARS-CoV-2 infections at point-of-care, especially in resource-constrained settings.
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Affiliation(s)
| | - Bongkot Ngamsom
- Department of Chemistry and Biochemistry, University of Hull, UK
| | - Cheryl Walter
- Department of Biomedical Sciences, University of Hull, UK
| | | | - Jesse Gitaka
- Directorate of Research and Innovation, Mount Kenya University, Thika, Republic of Kenya
| | - Alexander Iles
- Department of Chemistry and Biochemistry, University of Hull, UK
| | - Nicole Pamme
- Department of Chemistry and Biochemistry, University of Hull, UK,Corresponding author. Department of Chemistry, Faculty of Science and Engineering, University of Hull, Cottingham Road, Hull, East Riding of Yorkshire, HU6 7RX, UK
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368
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Castro MDM, Caicedo I, Ortiz-Rojas HJ, Castillo CM, Medina AG, Alexander N, Gómez MA, Albornoz LL. Performance verification of the Abbott SARS-CoV-2 test for qualitative detection of IgG in Cali, Colombia. PLoS One 2021; 16:e0256566. [PMID: 34469472 PMCID: PMC8409620 DOI: 10.1371/journal.pone.0256566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/10/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Adequate testing is critically important for control of the SARS-CoV-2 pandemic. Antibody testing is an option for case management and epidemiologic studies, with high specificity and variable sensitivity. However, characteristics of local populations may affect performance of these tests. For this reason, the National Institute of Health (INS) and regulatory agencies in Colombia require verification of diagnostic accuracy of tests introduced to the Colombian market. METHODS We conducted a validation study of the Abbott SARS-CoV-2 test for qualitative detection of IgG using the Abbott Architect i2000SR. Participants and retrospective samples were included from patients with suspected SARS-CoV-2 infection, age ≥18 years, and ≥8 days elapsed since initiation of symptoms. Pre-pandemic plasma samples (taken before October 2019) were used as controls. We estimated the sensitivity, specificity and agreement (kappa) of the Abbott IgG test compared to the gold standard (RT-PCR). RESULTS The overall sensitivity was 83.1% (95% CI: 75.4-100). Sensitivity among patients with ≥14 days since the start of symptoms was 85.7%, reaching 88% in samples collected from patients with COVID-19 symptoms onset >60 days. Specificity was 100% and the kappa index of agreement was 0.804 (95% CI: 0.642-0.965). CONCLUSIONS Our findings show high sensitivity and specificity of the Abbott IgG test in a Colombian population, which meet the criteria set by the Colombian INS to aid in the diagnosis of COVID-19. Data from our patient groups also suggest that IgG response is detectable in a high proportion of individuals (88.1%) during the first two months following onset of symptoms.
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Affiliation(s)
- Maria del Mar Castro
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia
- Universidad Icesi, Cali, Colombia
| | - Isabella Caicedo
- Departamento de Patología y Medicina de Laboratorio, Fundación Valle del Lili, Cali, Colombia
| | | | - Carmen Manuela Castillo
- Departamento de Patología y Medicina de Laboratorio, Fundación Valle del Lili, Cali, Colombia
| | - Adriana Giovanna Medina
- Departamento de Patología y Medicina de Laboratorio, Fundación Valle del Lili, Cali, Colombia
| | - Neal Alexander
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia
- Universidad Icesi, Cali, Colombia
| | - Maria Adelaida Gómez
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia
- Universidad Icesi, Cali, Colombia
| | - Ludwig L. Albornoz
- Departamento de Patología y Medicina de Laboratorio, Fundación Valle del Lili, Cali, Colombia
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369
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Current diagnostic approaches to detect two important betacoronaviruses: Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Pathol Res Pract 2021; 225:153565. [PMID: 34333398 PMCID: PMC8305226 DOI: 10.1016/j.prp.2021.153565] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are two common betacoronaviruses, which are still causing transmission among the human population worldwide. The major difference between the two coronaviruses is that MERS-CoV is now causing sporadic transmission worldwide, whereas SARS-CoV-2 is causing a pandemic outbreak globally. Currently, different guidelines and reports have highlighted several diagnostic methods and approaches which could be used to screen and confirm MERS-CoV and SARS-CoV-2 infections. These methods include clinical evaluation, laboratory diagnosis (nucleic acid-based test, protein-based test, or viral culture), and radiological diagnosis. With the presence of these different diagnostic approaches, it could cause a dilemma to the clinicians and diagnostic laboratories in selecting the best diagnostic strategies to confirm MERS-CoV and SARS-CoV-2 infections. Therefore, this review aims to provide an up-to-date comparison of the advantages and limitations of different diagnostic approaches in detecting MERS-CoV and SARS-CoV-2 infections. This review could provide insights for clinicians and scientists in detecting MERS-CoV and SARS-CoV-2 infections to help combat the transmission of these coronaviruses.
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370
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Hernandez MM, Banu R, Shrestha P, Patel A, Chen F, Cao L, Fabre S, Tan J, Lopez H, Chiu N, Shifrin B, Zapolskaya I, Flores V, Lee PY, Castañeda S, Ramírez JD, Jhang J, Osorio G, Gitman MR, Nowak MD, Reich DL, Cordon‐Cardo C, Sordillo EM, Paniz‐Mondolfi AE. RT-PCR/MALDI-TOF mass spectrometry-based detection of SARS-CoV-2 in saliva specimens. J Med Virol 2021; 93:5481-5486. [PMID: 33963565 PMCID: PMC8242556 DOI: 10.1002/jmv.27069] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/24/2022]
Abstract
As severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections continue, there is a substantial need for cost-effective and large-scale testing that utilizes specimens that can be readily collected from both symptomatic and asymptomatic individuals in various community settings. Although multiple diagnostic methods utilize nasopharyngeal specimens, saliva specimens represent an attractive alternative as they can rapidly and safely be collected from different populations. While saliva has been described as an acceptable clinical matrix for the detection of SARS-CoV-2, evaluations of analytic performance across platforms for this specimen type are limited. Here, we used a novel sensitive RT-PCR/MALDI-TOF mass spectrometry-based assay (Agena MassARRAY®) to detect SARS-CoV-2 in saliva specimens. The platform demonstrated high diagnostic sensitivity and specificity when compared to matched patient upper respiratory specimens. We also evaluated the analytical sensitivity of the platform and determined the limit of detection of the assay to be 1562.5 copies/ml. Furthermore, across the five individual target components of this assay, there was a range in analytic sensitivities for each target with the N2 target being the most sensitive. Overall, this system also demonstrated comparable performance when compared to the detection of SARS-CoV-2 RNA in saliva by the cobas® 6800/8800 SARS-CoV-2 real-time RT-PCR Test (Roche). Together, we demonstrate that saliva represents an appropriate matrix for SARS-CoV-2 detection on the novel Agena system as well as on a conventional real-time RT-PCR assay. We conclude that the MassARRAY® system is a sensitive and reliable platform for SARS-CoV-2 detection in saliva, offering scalable throughput in a large variety of clinical laboratory settings.
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MESH Headings
- Benchmarking
- COVID-19/diagnosis
- COVID-19/virology
- COVID-19 Nucleic Acid Testing/instrumentation
- COVID-19 Nucleic Acid Testing/methods
- COVID-19 Nucleic Acid Testing/standards
- Diagnostic Tests, Routine/instrumentation
- Diagnostic Tests, Routine/methods
- Diagnostic Tests, Routine/standards
- Humans
- Limit of Detection
- Nasopharynx/virology
- RNA, Viral/genetics
- SARS-CoV-2/genetics
- Saliva/virology
- Specimen Handling/standards
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/instrumentation
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/standards
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Affiliation(s)
- Matthew M. Hernandez
- Department of Pathology, Molecular, and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Radhika Banu
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Paras Shrestha
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Armi Patel
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Feng Chen
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Liyong Cao
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Shelcie Fabre
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Jessica Tan
- Department of MicrobiologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- The Graduate School of Biomedical SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Heidi Lopez
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Numthip Chiu
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Biana Shifrin
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Inessa Zapolskaya
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Vanessa Flores
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Pui Yiu Lee
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Sergio Castañeda
- Departamento de Biología, Facultad de Ciencias Naturales, Grupo de Investigaciones Microbiológicas‐UR (GIMUR)Universidad del RosarioBogotáColombia
| | - Juan David Ramírez
- Departamento de Biología, Facultad de Ciencias Naturales, Grupo de Investigaciones Microbiológicas‐UR (GIMUR)Universidad del RosarioBogotáColombia
| | - Jeffrey Jhang
- Department of Pathology, Molecular, and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Giuliana Osorio
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Melissa R. Gitman
- Department of Pathology, Molecular, and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Michael D. Nowak
- Department of Pathology, Molecular, and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - David L. Reich
- Department of Anesthesiology, Perioperative and Pain MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Carlos Cordon‐Cardo
- Department of Pathology, Molecular, and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular, and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Alberto E. Paniz‐Mondolfi
- Department of Pathology, Molecular, and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
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Wang L, Xu T, Stoecker T, Stoecker H, Jiang Y, Zhou K. Machine learning spatio-temporal epidemiological model to evaluate Germany-county-level COVID-19 risk. MACHINE LEARNING: SCIENCE AND TECHNOLOGY 2021. [DOI: 10.1088/2632-2153/ac0314] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Abstract
As the COVID-19 pandemic continues to ravage the world, it is critical to assess the COVID-19 risk timely on multi-scale. To implement it and evaluate the public health policies, we develop a machine learning assisted framework to predict epidemic dynamics from the reported infection data. It contains a county-level spatio-temporal epidemiological model, which combines spatial cellular automata (CA) with time sensitive-undiagnosed-infected-removed (SUIR) model, and is compatible with the existing risk prediction models. The CA-SUIR model shows the multi-scale risk to the public and reveals the transmission modes of coronavirus in different scenarios. Through transfer learning, this new toolbox is used to predict the prevalence of multi-scale COVID-19 in all 412 counties in Germany. A t-day-ahead risk forecast as well as assessment of the non-pharmaceutical intervention policies is presented. We analyzed the situation at Christmas of 2020, and found that the most serious death toll could be 34.5. However, effective policy could control it below 21thousand, which provides a quantitative basis for evaluating the public policies implemented by the government. Such intervening evaluation process would help to improve public health policies and restart the economy appropriately in pandemics.
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372
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Habibzadeh P, Mofatteh M, Silawi M, Ghavami S, Faghihi MA. Molecular diagnostic assays for COVID-19: an overview. Crit Rev Clin Lab Sci 2021; 58:385-398. [PMID: 33595397 PMCID: PMC7898297 DOI: 10.1080/10408363.2021.1884640] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/17/2021] [Accepted: 01/29/2021] [Indexed: 12/26/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has highlighted the cardinal importance of rapid and accurate diagnostic assays. Since the early days of the outbreak, researchers with different scientific backgrounds across the globe have tried to fulfill the urgent need for such assays, with many assays having been approved and with others still undergoing clinical validation. Molecular diagnostic assays are a major group of tests used to diagnose COVID-19. Currently, the detection of SARS-CoV-2 RNA by reverse transcription polymerase chain reaction (RT-PCR) is the most widely used method. Other diagnostic molecular methods, including CRISPR-based assays, isothermal nucleic acid amplification methods, digital PCR, microarray assays, and next generation sequencing (NGS), are promising alternatives. In this review, we summarize the technical and clinical applications of the different COVID-19 molecular diagnostic assays and suggest directions for the implementation of such technologies in future infectious disease outbreaks.
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Affiliation(s)
- Parham Habibzadeh
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Mofatteh
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Mohammad Silawi
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saeid Ghavami
- Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Mohammad Ali Faghihi
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, USA
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373
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Merino-Amador P, González-Donapetry P, Domínguez-Fernández M, González-Romo F, Sánchez-Castellano MÁ, Seoane-Estevez A, Delgado-Iribarren A, García J, Bou G, Cuenca-Estrella M, Oteo-Iglesias J. Clinitest rapid COVID-19 antigen test for the diagnosis of SARS-CoV-2 infection: A multicenter evaluation study. J Clin Virol 2021; 143:104961. [PMID: 34461560 PMCID: PMC8381653 DOI: 10.1016/j.jcv.2021.104961] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 07/01/2021] [Accepted: 07/29/2021] [Indexed: 11/30/2022]
Abstract
Objectives RT-PCR assay is the reference method for diagnosis of COVID-19, but it is also a laborious and time-consuming technic, limiting the availability of testing. Rapid antigen-detection tests are faster and less expensive; however, the reliability of these tests must be validated before they can be used widely. The objective of this study was to determine the performance of the Clinitest Rapid COVID-19 Antigen Test (ClinitestRT) (SIEMENS) for SARS-CoV-2 in nasopharyngeal swab specimens. Methods This prospective multicenter study was carried out in three Spanish university hospitals including individuals with clinical symptoms or epidemiological criteria for COVID-19. Only individuals with ≤7 days from the onset of symptoms or from exposure to a confirmed case of COVID-19 were included. Two nasopharyngeal samples were taken to perform the ClinitestRT, as a point-of-care test, and a diagnostic RT-PCR test. Results Overall sensitivity and specificity for the ClinitestRT among the 450 patients studied were 93.3% (CI 95%: 89.7–96.8) and 99.2% (CI 95%: 97.2–99.8), respectively. Sensitivity in participants with ≤5 days of the clinical course was 93.6% (CI 95%: 89.2–96.3), and in participants who had a CT < 25 for the RT-PCR test was 98.4% (CI 95%: 94.5–99.6). Agreement between techniques was 96.7% (kappa score: 0.93; CI 95%: 0.90–0.97). Conclusions The ClinitestRT provides good clinical performance, with more reliable results for patients with a higher viral load. The results must be interpreted based on the local epidemiological context.
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Affiliation(s)
- Paloma Merino-Amador
- Microbiology Department, Hospital Universitario Clínico San Carlos, Madrid, Spain; Instituto de Investigación Sanitaria Hospital Clínico San Carlos (IdISSC), Madrid, Spain; Department of Medicine, Universidad Complutense School of Medicine, Madrid, Spain
| | | | | | - Fernando González-Romo
- Microbiology Department, Hospital Universitario Clínico San Carlos, Madrid, Spain; Instituto de Investigación Sanitaria Hospital Clínico San Carlos (IdISSC), Madrid, Spain; Department of Medicine, Universidad Complutense School of Medicine, Madrid, Spain
| | | | | | - Alberto Delgado-Iribarren
- Microbiology Department, Hospital Universitario Clínico San Carlos, Madrid, Spain; Instituto de Investigación Sanitaria Hospital Clínico San Carlos (IdISSC), Madrid, Spain; Department of Medicine, Universidad Complutense School of Medicine, Madrid, Spain
| | - Julio García
- Microbiology Department, Hospital Universitario La Paz, Madrid, Spain
| | - Germán Bou
- Microbiology Department, Complejo Hospitalario Universitario de A Coruña, A Coruña, Spain; Spanish Network for Research in Infectious Diseases (REIPI), Spain
| | | | - Jesús Oteo-Iglesias
- Spanish Network for Research in Infectious Diseases (REIPI), Spain; National Centre for Microbiology (CNM), Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain.
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374
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Iitani K, Ramamurthy SS, Ge X, Rao G. Transdermal sensing: in-situ non-invasive techniques for monitoring of human biochemical status. Curr Opin Biotechnol 2021; 71:198-205. [PMID: 34455345 DOI: 10.1016/j.copbio.2021.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/26/2021] [Accepted: 08/04/2021] [Indexed: 12/15/2022]
Abstract
Improving life expectancy necessitates prevention and early diagnosis of any disease state based on active self-monitoring of symptoms and longitudinal biochemical profiling. Non-invasive and continuous measurement of molecular biomarkers that reflect metabolism and health must however be established to realize this plan. Human samples non-invasively obtained via the skin are suitable in this context for in-situ biochemical monitoring. We present a brief classification of transdermal sampling in aqueous and gaseous phases and then introduce a new generation of transdermal monitoring devices for rapid and accurate assessment of important parameters. Finally, we have summarized the diversity of body-wide skin characteristics that have possible effects for transdermal sampling. Because of its passive nature, in-situ biochemical monitoring via transdermal sampling will potentially lead to a greater understanding of important biochemical markers and their temporal variation.
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Affiliation(s)
- Kenta Iitani
- Center for Advanced Sensor Technology (CAST), Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD, 21250 USA; Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University (TWIns), 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Sai Sathish Ramamurthy
- Center for Advanced Sensor Technology (CAST), Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD, 21250 USA; STAR Laboratory, Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Anantapur, Andhra Pradesh 515134, India
| | - Xudong Ge
- Center for Advanced Sensor Technology (CAST), Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD, 21250 USA
| | - Govind Rao
- Center for Advanced Sensor Technology (CAST), Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD, 21250 USA.
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375
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Toropov N, Osborne E, Joshi LT, Davidson J, Morgan C, Page J, Pepperell J, Vollmer F. SARS-CoV-2 Tests: Bridging the Gap between Laboratory Sensors and Clinical Applications. ACS Sens 2021; 6:2815-2837. [PMID: 34392681 PMCID: PMC8386036 DOI: 10.1021/acssensors.1c00612] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/28/2021] [Indexed: 12/15/2022]
Abstract
This review covers emerging biosensors for SARS-CoV-2 detection together with a review of the biochemical and clinical assays that are in use in hospitals and clinical laboratories. We discuss the gap in bridging the current practice of testing laboratories with nucleic acid amplification methods, and the robustness of assays the laboratories seek, and what emerging SARS-CoV-2 sensors have currently addressed in the literature. Together with the established nucleic acid and biochemical tests, we review emerging technology and antibody tests to determine the effectiveness of vaccines on individuals.
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Affiliation(s)
- Nikita Toropov
- Living
Systems Institute, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Eleanor Osborne
- Living
Systems Institute, University of Exeter, Exeter EX4 4QD, United Kingdom
| | | | - James Davidson
- Somerset
Lung Centre, Musgrove Park Hospital, Parkfield Drive, Taunton TA1 5DA, United Kingdom
| | - Caitlin Morgan
- Somerset
Lung Centre, Musgrove Park Hospital, Parkfield Drive, Taunton TA1 5DA, United Kingdom
| | - Joseph Page
- Somerset
Lung Centre, Musgrove Park Hospital, Parkfield Drive, Taunton TA1 5DA, United Kingdom
| | - Justin Pepperell
- Somerset
Lung Centre, Musgrove Park Hospital, Parkfield Drive, Taunton TA1 5DA, United Kingdom
| | - Frank Vollmer
- Living
Systems Institute, University of Exeter, Exeter EX4 4QD, United Kingdom
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376
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A non-enzymatic, isothermal strand displacement and amplification assay for rapid detection of SARS-CoV-2 RNA. Nat Commun 2021; 12:5089. [PMID: 34429424 PMCID: PMC8385016 DOI: 10.1038/s41467-021-25387-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 08/09/2021] [Indexed: 12/24/2022] Open
Abstract
The current nucleic acid signal amplification methods for SARS-CoV-2 RNA detection heavily rely on the functions of biological enzymes which imposes stringent transportation and storage conditions, high cost and global supply shortages. Here, a non-enzymatic whole genome detection method based on a simple isothermal signal amplification approach is developed for rapid detection of SARS-CoV-2 RNA and potentially any types of nucleic acids regardless of their size. The assay, termed non-enzymatic isothermal strand displacement and amplification (NISDA), is able to quantify 10 RNA copies.µL−1. In 164 clinical oropharyngeal RNA samples, NISDA assay is 100 % specific, and it is 96.77% and 100% sensitive when setting up in the laboratory and hospital, respectively. The NISDA assay does not require RNA reverse-transcription step and is fast (<30 min), affordable, highly robust at room temperature (>1 month), isothermal (42 °C) and user-friendly, making it an excellent assay for broad-based testing. The reliance on enzymes in SARS-CoV-2 RNA detection imposes limits on transport and storage conditions. Here the authors use non-enzymatic isothermal amplification to detect RNA with no need for reverse transcription.
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377
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Zayani R, Rezig D, Fares W, Marrakchi M, Essafi M, Raouafi N. Multiplexed Magnetofluorescent Bioplatform for the Sensitive Detection of SARS-CoV-2 Viral RNA without Nucleic Acid Amplification. Anal Chem 2021; 93:11225-11232. [PMID: 34338520 PMCID: PMC8353888 DOI: 10.1021/acs.analchem.1c01950] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/23/2021] [Indexed: 12/26/2022]
Abstract
Rapid and sensitive detection of SARS-CoV-2 virus genetic material is of paramount importance to mitigate the COVID-19 pandemic outbreak and lower the death toll. Herein, we report the design of a magnetofluorescent bioplatform for the direct and specific detection of the viral RNA of SARS-CoV-2 in the total RNA extracted from nasopharyngeal swabs of COVID-19-positive patients. A higher fluorescence response was achieved using two capture probes tethered to magnetic beads using a biotin/streptavidin linkage, targeting two specific sites in the ORF1a and S genes. Two horseradish peroxidase (HRP)-conjugated reporter sequences, complementary to the loci of the S and N genes, were used to reveal the presence of the viral RNA through the oxidation of o-phenylenediamine to fluorescent 2,3-diaminophenazine. Under optimal conditions, the bioplatform showed high selectivity and sensitivity and was able to detect as low as 0.01 ng of viral RNA (1 × 103 copies/μL) with a linear dynamic range varying from 0.01 to 3.0 ng (1 × 103 to 9 × 107 copies/μL). The bioplatform was also able to discriminate the SARS-CoV-2 RNA from those of other related viruses such as hepatitis C, West Nile, measles, and non-polio viruses. Furthermore, the developed biosensor was validated in 46 clinical samples (36 COVID-19-positive patients and 10 COVID-19-negative subjects, as assessed with the gold standard RT-qPCR method). Both sensitivity and specificity of the developed method reached 100%. Finally, making such a simple and specific method available in the field, at a primary point of care, can better help the detection of SARS-CoV-2 infection in low-resource settings.
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Affiliation(s)
- Riham Zayani
- Sensors
and Biosensors Group, Laboratory of Analytical Chemistry & Electrochemistry
(LR99ES15), Faculty of Science, University
of Tunis El Manar, 2092 Tunis, Tunisia
| | - Dorra Rezig
- Laboratory
of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and
Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University of Tunis El Manar, 1068 Tunis, Tunisia
- Research
Laboratory “Virus, Vectors and Hosts: One Health Approach and
Technological Innovation for a Better Health”, LR20IPT02, Pasteur Institute of Tunis, 1006 Tunis, Tunisia
| | - Wasfi Fares
- Laboratory
of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and
Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University of Tunis El Manar, 1068 Tunis, Tunisia
- Research
Laboratory “Virus, Vectors and Hosts: One Health Approach and
Technological Innovation for a Better Health”, LR20IPT02, Pasteur Institute of Tunis, 1006 Tunis, Tunisia
| | - Mouna Marrakchi
- Sensors
and Biosensors Group, Laboratory of Analytical Chemistry & Electrochemistry
(LR99ES15), Faculty of Science, University
of Tunis El Manar, 2092 Tunis, Tunisia
| | - Makram Essafi
- Laboratory
Transmission, Control and Immunobiology of Infections (LTCII, LR11
IPT02), Pasteur Institute of Tunis, 1002 Tunis, Tunisia
| | - Noureddine Raouafi
- Sensors
and Biosensors Group, Laboratory of Analytical Chemistry & Electrochemistry
(LR99ES15), Faculty of Science, University
of Tunis El Manar, 2092 Tunis, Tunisia
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Mushtaq MZ, Shakoor S, Kanji A, Shaheen N, Nasir A, Ansar Z, Ahmed I, Mahmood SF, Hasan R, Hasan Z. Discrepancy between PCR based SARS-CoV-2 tests suggests the need to re-evaluate diagnostic assays. BMC Res Notes 2021; 14:316. [PMID: 34404471 PMCID: PMC8369441 DOI: 10.1186/s13104-021-05722-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE We investigated the discrepancy between clinical and PCR-based diagnosis of COVID-19. We compared results of ten patients with mild to severe COVID-19. Respiratory samples from all cases were tested on the Roche SARS-CoV-2 (Cobas) assay, Filmarray RP2.1 (bioMereiux) and TaqPath™ COVID19 (Thermofisher) PCR assays. RESULTS Laboratory records of ten patients with mild to severe COVID-19 were examined. Initially, respiratory samples from the patients were tested as negative on the SARS-CoV-2 Roche® assay. Further investigation using the BIOFIRE® Filmarray RP2.1 assay identified SARS-CoV-2 as the pathogen in all ten cases. To investigate possible discrepancies between PCR assays, additional testing was conducted using the TaqPath™ COVID19 PCR. Eight of ten samples were positive for SARS-CoV-2 on the TaqPath assay. Further, Spike gene target failures (SGTF) were identified in three of these eight cases. Discrepancy between the three PCR assays could be due to variation in PCR efficiencies of the amplification reactions or, variation at primer binding sites. Strains with SGTF indicate the presence of new SARS-CoV-2 variant strains. Regular modification of gene targets in diagnostic assays may be necessary to maintain robustness and accuracy of SARS-CoV-2 diagnostic assays to avoid reduced case detection, under-surveillance, and missed opportunities for control.
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Affiliation(s)
| | - Sadia Shakoor
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan.,Department of Pediatrics and Child Health, Division of Women and Child Health, Aga Khan University, Karachi, Pakistan
| | - Akbar Kanji
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Najma Shaheen
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Asghar Nasir
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Zeeshan Ansar
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Imran Ahmed
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | | | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan.
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Molina P, Torres Arias M. Herramientas biotecnológicas en el diagnóstico, prevención y tratamiento frente a pandemias. BIONATURA 2021. [DOI: 10.21931/rb/2021.06.03.33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Las pandemias son consideradas como un problema emergente de salud pública a nivel mundial, las cuales además de caracterizarse por tasas altas de morbilidad y mortalidad, ocasionan conflictos en los aspectos sociales, económicos y políticos. Las herramientas biotecnológicas, por su parte, han ido evolucionando conforme al avance tecnológico-científico, lo que ha permitido optimizar métodos de diagnóstico con alta sensibilidad y especificidad, además de mejorar el desarrollo de productos biológicos para la prevención y terapia de enfermedades. El objetivo de esta revisión es identificar la actualización de las herramientas biotecnológicas en el diagnóstico, tratamiento terapéutico y profiláctico frente a los patógenos causantes de las enfermedades pandémicas a lo largo de la historia, mediante la recopilación de información científica. Con este estudio se logró establecer que las herramientas y productos de origen biotecnológico han constituido un papel fundamental en el control de pandemias a través de la innovación constante que ha permitido alcanzar resultados eficientes tanto en diagnóstico como en el tratamiento.
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Affiliation(s)
- Pamela Molina
- Departamento de Ciencias de la Vida y Agricultura, Carrera de Ingeniería en Biotecnología, Universidad de las Fuerzas Armadas ESPE
| | - Marbel Torres Arias
- Departamento de Ciencias de la Vida y Agricultura, Carrera de Ingeniería en Biotecnología, Universidad de las Fuerzas Armadas ESPE Laboratorio de Inmunología y Virología, CENCINAT, GISAH, Universidad de las Fuerzas Armadas ESPE] Av. General Rumiñahui S/N y Ambato, PO BOX 171-5-231B, Sangolquí, Pichincha, Ecuador
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de Paula Eduardo F, Bezinelli LM, de Araujo CAR, Moraes JVV, Birbrair A, Pinho JRR, Hamerschlak N, Al-Hashimi I, Heller D. Self-collected unstimulated saliva, oral swab, and nasopharyngeal swab specimens in the detection of SARS-CoV-2. Clin Oral Investig 2021; 26:1561-1567. [PMID: 34387730 PMCID: PMC8360804 DOI: 10.1007/s00784-021-04129-7] [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: 01/22/2021] [Accepted: 08/03/2021] [Indexed: 11/25/2022]
Abstract
OBJECTIVES The presence of SARS-CoV-2 virus in the saliva of patients infected with COVID-19 has been confirmed by several studies. However, the use of saliva for the diagnosis of COVID-19 remains limited, because of the discrepancies in the results, which might be due to using different saliva sampling methods. The purpose of this study was to compare the consistency of SARS-CoV-2 detection using two different saliva sampling methods (oral swab and unstimulated saliva) to that of the standard nasopharyngeal swab. METHODS Fifty-five subjects were recruited from a pool of COVID-19 inpatient at the Hospital Israelita Albert Einstein (HIAE), Brazil. Nasopharyngeal swab, oral swab, and self-collected unstimulated saliva samples were examined for SARS-CoV-2 using RT-PCR. RESULTS Self-collected unstimulated saliva demonstrated 87.3% agreement in the detection of SARS-CoV-2 virus as compared with the nasopharyngeal swab, while oral swab displayed 65.9% agreement when compared to nasopharyngeal swab and 73% when compared to self-collected unstimulated saliva. CONCLUSION Unstimulated self-collected saliva samples have shown a higher agreement with the nasopharyngeal swab samples for SARS-COV-2 detection than that obtained when using oral swab samples. CLINICAL RELEVANCE This study compares the accuracy of COVID-19 test using different saliva sampling methods to that of nasopharyngeal swab. Given the need for a simple self-applied test that can be performed at home, our findings support the efficacy of self-collected unstimulated saliva samples in the diagnosis of SARS-CoV-2 infection, alleviating the demands for swab supplies, personal protective equipment, and healthcare personnel.
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Affiliation(s)
| | | | - Carlos Ariel Rodrigues de Araujo
- Post Graduate Program in Dentistry, Universidade Cruzeiro Do Sul, Rua Galvão Bueno, 868, São Paulo, São Paulo, 01506-000, Brazil
| | - João Vitor Vanderlan Moraes
- Faculdade Israelita de Ciencias da Saúde Albert Einstein, Hospital Israelita Albert Einstein, São Paulo, 05652-900, Brazil
| | - Alexander Birbrair
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, Brazil.,Department of Radiology, Columbia University Medical Center, New York, NY, USA
| | | | | | | | - Debora Heller
- Hospital Israelita Albert Einstein, São Paulo, 05652-900, Brazil. .,Post Graduate Program in Dentistry, Universidade Cruzeiro Do Sul, Rua Galvão Bueno, 868, São Paulo, São Paulo, 01506-000, Brazil. .,Department of Periodontology, School of Dentistry, University of Texas Health Science Center At San Antonio, San Antonio, TX, 78229, USA.
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Fontana C, Favaro M, Minelli S, Bossa MC, Altieri A. Co-infections observed in SARS-CoV-2 positive patients using a rapid diagnostic test. Sci Rep 2021; 11:16355. [PMID: 34381118 PMCID: PMC8357960 DOI: 10.1038/s41598-021-95772-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/26/2021] [Indexed: 12/23/2022] Open
Abstract
Rapid diagnostic tests are tools of paramount impact both for improving patient care and in antimicrobial management programs. Particularly in the case of respiratory infections, it is of great importance to quickly confirm/exclude the involvement of pathogens, be they bacteria or viruses, while obtaining information about the presence/absence of a genetic target of resistance to modulate antibiotic therapy. In this paper, we present our experiences with the use of the Biofire® FilmArray® Pneumonia Panel Plus (FAPP; bioMérieux; Marcy l'Etoile, France) to assess coinfection in COVID-19 patients. A total of 152 respiratory samples from consecutive patients were examined, and 93 (61%) were found to be FAPP positive, with the detection of bacteria and/or viruses. The patients were 93 males and 59 females with an average age of 65 years who were admitted to our hospital due to moderate/severe acute respiratory symptoms. Among the positive samples were 52 from sputum (SPU) and 41 from bronchoalveolar lavage (BAL). The most representative species was S. aureus (most isolates were mecA positive; 30/44, 62%), followed by gram-negative pathogens such as P. aeruginosa, K. pneumoniae, and A. baumannii. Evidence of a virus was rare. Cultures performed from BAL and SPU samples gave poor results. Most of the discrepant negative cultures were those in which FAPP detected pathogens with a microbial count ≤ 105 CFU/mL. H. influenzae was one of the most common pathogens lost by the conventional method. Despite the potential limitations of FAPP, which detects a defined number of pathogens, its advantages of rapid detection combined with predictive information regarding the antimicrobial resistance of pathogens through the detection of some relevant markers of resistance could be very useful for establishing empirical targeted therapy for the treatment of patients with respiratory failure. In the COVID era, we understand the importance of using antibiotics wisely to curb the phenomenon of antibiotic resistance.
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Affiliation(s)
- Carla Fontana
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133, Rome, Italy.
- Microbiology and Virology Lab, Tor Vergata University Hospital, V.le Oxford, 81 00133, Rome, Italy.
| | - Marco Favaro
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133, Rome, Italy
| | - Silvia Minelli
- Microbiology and Virology Lab, Tor Vergata University Hospital, V.le Oxford, 81 00133, Rome, Italy
| | - Maria Cristina Bossa
- Microbiology and Virology Lab, Tor Vergata University Hospital, V.le Oxford, 81 00133, Rome, Italy
| | - Anna Altieri
- Microbiology and Virology Lab, Tor Vergata University Hospital, V.le Oxford, 81 00133, Rome, Italy
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382
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Krumkamp R, Kreuels B, Jaeger VK, May J, Mikolajczyk R, Karch A. Negative SARS-CoV-2 PCR or rapid antigen test result and the subsequent risk of being infectious: a mathematical simulation study. BMC Med Res Methodol 2021; 21:165. [PMID: 34376152 PMCID: PMC8353420 DOI: 10.1186/s12874-021-01361-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/08/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND A considerable proportion of SARS-CoV-2 transmission occurs from asymptomatic and pre-symptomatic cases. Therefore, different polymerase chain reaction (PCR)- or rapid antigen test (RAT)-based approaches are being discussed and applied to identify infectious individuals that would have otherwise gone undetected. In this article, we provide a framework to estimate the time-dependent risk of being infectious after a negative SARS-CoV-2 test, and we simulate the number of expected infectious individuals over time in populations who initially tested negative. METHODS A Monte Carlo approach is used to simulate asymptomatic infections over a 10-days period in populations of 1000 individuals following a negative SARS-CoV-2 test. Parameters representing the application of PCR tests or RATs are utilized, and SARS-CoV-2 cumulative 7-day incidences between 25 and 200 per 100,000 people are considered. Simulation results are compared to case numbers predicted via a mathematical equation. RESULTS The simulations showed a continuous increase in infectious individuals over time in populations of individuals who initially tested SARS-CoV-2 negative. The interplay between false negative rates of PCR tests or RATs, and the time that has passed since testing determines the number of infectious individuals. The simulated and the mathematically predicted number of infectious individuals were comparable. However, Monte Carlo simulations highlight that, due to random variation, theoretically observed infectious individuals can considerably exceed predicted case numbers even shortly after a test was conducted. CONCLUSIONS This study demonstrates that the number of infectious individuals in a screened group of asymptomatic people can be effectively reduced, and this effect can be described mathematically. However, the false negative rate of a test, the time since the negative test and the underlying SARS-CoV-2 incidence are critical parameters in determining the observed subsequent number of cases in tested population groups.
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Affiliation(s)
- Ralf Krumkamp
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg - Lübeck - Borstel – Riems, Hamburg, Germany
| | - Benno Kreuels
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
- Department of Medicine, College of Medicine, P. O. Box 278, Zomba Blantyre, Malawi
| | - Veronika K. Jaeger
- Institute of Epidemiology and Social Medicine, University of Muenster, Albert-Schweitzer-Campus 1, 48149 Münster, Germany
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg - Lübeck - Borstel – Riems, Hamburg, Germany
- Tropical Medicine II, University Medical Centre Hamburg-Eppendorf, 20151 Hamburg, Germany
| | - Rafael Mikolajczyk
- Institute for Medical Epidemiology, Biometrics and Informatics, Interdisciplinary Center for Health Sciences, Martin Luther University Halle-Wittenberg, Magdeburger Straße 8, 06112 Halle, Germany
| | - André Karch
- Institute of Epidemiology and Social Medicine, University of Muenster, Albert-Schweitzer-Campus 1, 48149 Münster, Germany
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383
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Biyani R, Sharma K, Kojima K, Biyani M, Sharma V, Kumawat T, Juma KM, Yanagihara I, Fujiwara S, Kodama E, Takamura Y, Takagi M, Yasukawa K, Biyani M. Development of robust isothermal RNA amplification assay for lab-free testing of RNA viruses. Sci Rep 2021; 11:15997. [PMID: 34362977 PMCID: PMC8346491 DOI: 10.1038/s41598-021-95411-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 07/26/2021] [Indexed: 11/30/2022] Open
Abstract
Simple tests of infectiousness that return results in minutes and directly from samples even with low viral loads could be a potential game-changer in the fight against COVID-19. Here, we describe an improved isothermal nucleic acid amplification assay, termed the RICCA (RNA Isothermal Co-assisted and Coupled Amplification) reaction, that consists of a simple one-pot format of ‘sample-in and result-out’ with a primary focus on the detection of low copy numbers of RNA virus directly from saliva without the need for laboratory processing. We demonstrate our assay by detecting 16S rRNA directly from E. coli cells with a sensitivity as low as 8 CFU/μL and RNA fragments from a synthetic template of SARS-CoV-2 with a sensitivity as low as 1740 copies/μL. We further demonstrate the applicability of our assay for real-time testing at the point of care by designing a closed format for paper-based lateral flow assay and detecting heat-inactivated SARS-COV-2 virus in human saliva at concentrations ranging from 28,000 to 2.8 copies/μL with a total assay time of 15–30 min.
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Affiliation(s)
- Radhika Biyani
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan
| | - Kirti Sharma
- BioSeeds Corporation, JAIST Venture Business Laboratory, Ishikawa Create Labo, Asahidai 2-13, Nomi City, Ishikawa, 923-1211, Japan
| | - Kenji Kojima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Madhu Biyani
- BioSeeds Corporation, JAIST Venture Business Laboratory, Ishikawa Create Labo, Asahidai 2-13, Nomi City, Ishikawa, 923-1211, Japan.,Biyani BioSolutions Pvt. Ltd., Biyani Group of Colleges Venture Business Laboratory, R-4, Sector 3, Vidhyadhar Nagar, Jaipur, 302039, India
| | - Vishnu Sharma
- Biyani BioSolutions Pvt. Ltd., Biyani Group of Colleges Venture Business Laboratory, R-4, Sector 3, Vidhyadhar Nagar, Jaipur, 302039, India
| | - Tarun Kumawat
- Biyani BioSolutions Pvt. Ltd., Biyani Group of Colleges Venture Business Laboratory, R-4, Sector 3, Vidhyadhar Nagar, Jaipur, 302039, India
| | - Kevin Maafu Juma
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Itaru Yanagihara
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, 840 Murodocho, Izumi, Osaka, 594-1101, Japan
| | - Shinsuke Fujiwara
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo, 669-1337, Japan
| | - Eiichi Kodama
- Division of Infectious Diseases, International Research Institute of Disaster Science, Tohoku University, 2-1 Seiryocho Aoba-ku, Sendai, Miyagi, 980-8575, Japan
| | - Yuzuru Takamura
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan
| | - Masahiro Takagi
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Manish Biyani
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan. .,BioSeeds Corporation, JAIST Venture Business Laboratory, Ishikawa Create Labo, Asahidai 2-13, Nomi City, Ishikawa, 923-1211, Japan. .,Biyani BioSolutions Pvt. Ltd., Biyani Group of Colleges Venture Business Laboratory, R-4, Sector 3, Vidhyadhar Nagar, Jaipur, 302039, India.
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384
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Efficiency of pooled surveillance testing in academic labs to detect and inhibit COVID-19 outbreaks. Bioanalysis 2021; 13:1177-1182. [PMID: 34355577 PMCID: PMC8438944 DOI: 10.4155/bio-2021-0054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Robust surveillance testing is a key strategic plan to prevent COVID-19 outbreaks and slow the spread of the SARS-CoV-2 pandemic; however, limited resources, facilities and time often impair the implementation of a widespread surveillance effort. To mitigate these resource limitations, we employed a strategy of pooling samples, reducing reagent cost and processing time. Through utilizing academic faculty and labs, successful pooled surveillance testing was conducted throughout Fall 2020 semester to detect positive SARS-CoV-2 infections in a population of 4400 students. During the semester, over 25,000 individual COVID status evaluations were made by pooling eight individual samples into one quantitative reverse transcription polymerase chain reaction. This pooled surveillance strategy was highly effective at detecting infection and significantly reduced financial burden and cost by $3.6 million.
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385
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Stüder F, Petit JL, Engelen S, Mendoza-Parra MA. Real-time SARS-CoV-2 diagnostic and variants tracking over multiple candidates using nanopore DNA sequencing. Sci Rep 2021; 11:15869. [PMID: 34354202 PMCID: PMC8342707 DOI: 10.1038/s41598-021-95563-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/21/2021] [Indexed: 11/16/2022] Open
Abstract
Since December 2019, a novel coronavirus responsible for a severe acute respiratory syndrome (SARS-CoV-2) is accountable for a major pandemic situation. The emergence of the B.1.1.7 strain, as a highly transmissible variant has accelerated the world-wide interest in tracking SARS-CoV-2 variants' occurrence. Similarly, other extremely infectious variants, were described and further others are expected to be discovered due to the long period of time on which the pandemic situation is lasting. All described SARS-CoV-2 variants present several mutations within the gene encoding the Spike protein, involved in host receptor recognition and entry into the cell. Hence, instead of sequencing the whole viral genome for variants' tracking, herein we propose to focus on the SPIKE region to increase the number of candidate samples to screen at once; an essential aspect to accelerate diagnostics, but also variants' emergence/progression surveillance. This proof of concept study accomplishes both at once, population-scale diagnostics and variants' tracking. This strategy relies on (1) the use of the portable MinION DNA sequencer; (2) a DNA barcoding and a SPIKE gene-centered variant's tracking, increasing the number of candidates per assay; and (3) a real-time diagnostics and variant's tracking monitoring thanks to our software RETIVAD. This strategy represents an optimal solution for addressing the current needs on SARS-CoV-2 progression surveillance, notably due to its affordable implementation, allowing its implantation even in remote places over the world.
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Affiliation(s)
- François Stüder
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ of Évry, Paris-Saclay University, 91057, Evry, France
| | - Jean-Louis Petit
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ of Évry, Paris-Saclay University, 91057, Evry, France
| | - Stefan Engelen
- Genoscope, Institut de Biologie François-Jacob, Commissariat À L'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Marco Antonio Mendoza-Parra
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ of Évry, Paris-Saclay University, 91057, Evry, France.
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386
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Taghioff SM, Slavin BR, Holton T, Singh D. Examining the potential benefits of the influenza vaccine against SARS-CoV-2: A retrospective cohort analysis of 74,754 patients. PLoS One 2021; 16:e0255541. [PMID: 34343191 PMCID: PMC8330918 DOI: 10.1371/journal.pone.0255541] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/17/2021] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION Recently, several single center studies have suggested a protective effect of the influenza vaccine against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). This study utilizes a continuously updated Electronic Medical Record (EMR) network to assess the possible benefits of influenza vaccination mitigating critical adverse outcomes in SARS-CoV-2 positive patients from 56 healthcare organizations (HCOs). METHODS The de-identified records of 73,346,583 patients were retrospectively screened. Two cohorts of 37,377 patients, having either received or not received influenza vaccination six months-two weeks prior to SARS-CoV-2 positive diagnosis, were created using Common Procedural Terminology (CPT) and logical observation identifiers names and codes (LOINC) codes. Adverse outcomes within 30, 60, 90, and 120 days of positive SARS-CoV-2 diagnosis were compared between cohorts. Outcomes were assessed with stringent propensity score matching including age, race, ethnicity, gender, hypertension, diabetes, hyperlipidemia, chronic obstructive pulmonary disease (COPD), obesity, heart disease, and lifestyle habits such as smoking. RESULTS SARS-CoV-2-positive patients who received the influenza vaccine experienced decreased sepsis (p<0.01, Risk Ratio: 1.361-1.450, 95% CI:1.123-1.699, NNT:286) and stroke (p<0.02, RR: 1.451-1.580, 95% CI:1.075-2.034, NNT:625) across all time points. ICU admissions were lower in SARS-CoV-2-positive patients receiving the influenza vaccine at 30, 90, and 120 days (p<0.03, RR: 1.174-1.200, 95% CI:1.003-1.385, NNT:435), while approaching significance at 60 days (p = 0.0509, RR: 1.156, 95% CI:0.999-1.338). Patients who received the influenza vaccine experienced fewer DVTs 60-120 days after positive SARS-CoV-2 diagnosis (p<0.02, RR:1.41-1.530, 95% CI:1.082-2.076, NNT:1000) and experienced fewer emergency department (ED) visits 90-120 days post SARS-CoV-2-positive diagnosis (p<0.01, RR:1.204-1.580, 95% CI: 1.050-1.476, NNT:176). CONCLUSION Our analysis outlines the potential protective effect of influenza vaccination in SARS-CoV-2-positive patients against adverse outcomes within 30, 60, 90, and 120 days of a positive diagnosis. Significant findings favoring influenza vaccination mitigating the risks of sepsis, stroke, deep vein thrombosis (DVT), emergency department (ED) & Intensive Care Unit (ICU) admissions suggest a potential protective effect that could benefit populations without readily available access to SARS-CoV-2 vaccination. Thus further investigation with future prospective studies is warranted.
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Affiliation(s)
- Susan M. Taghioff
- Division of Plastic & Reconstructive Surgery, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Benjamin R. Slavin
- Division of Plastic & Reconstructive Surgery, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Tripp Holton
- Anne Arundel Medical Center, Annapolis, Maryland, United States of America
| | - Devinder Singh
- Division of Plastic & Reconstructive Surgery, University of Miami Miller School of Medicine, Miami, Florida, United States of America
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387
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Evaluating tests for diagnosing COVID-19 in the absence of a reliable reference standard: pitfalls and potential solutions. J Clin Epidemiol 2021; 138:182-188. [PMID: 34358639 PMCID: PMC8330140 DOI: 10.1016/j.jclinepi.2021.07.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/22/2021] [Accepted: 07/29/2021] [Indexed: 01/12/2023]
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388
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Benoit P, Labbé AC, Lalancette L, Gagnon S, Bonneau E, Lavallée C, Roger M, Fafard J, Dumaresq J, Beauchemin S, Coutlée F. Comparison of SARS-CoV-2 detection with the Cobas® 6800/8800 system on gargle samples using two sample processing methods with combined oropharyngeal/nasopharyngeal swab. J Med Virol 2021; 93:6837-6840. [PMID: 34324212 PMCID: PMC8426914 DOI: 10.1002/jmv.27245] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 07/27/2021] [Indexed: 01/30/2023]
Abstract
Background Gargle samples have been proposed as a noninvasive method for detection of SARS‐CoV‐2 RNA. The clinical performance of gargle specimens diluted in Cobas® PCR Media and in Cobas® Omni Lysis Reagent was compared to oropharyngeal/nasopharyngeal swab (ONPS) for the detection of SARS‐CoV‐2 RNA. Study Design Participants were recruited prospectively in two COVID‐19 screening clinics. In addition to the ONPS, participants gargled with 5 ml of natural spring water split in the laboratory as follows: 1 ml was added to 4.3 ml of polymerase chain reaction (PCR) media and 400 μl was added to 200 μl of lysis buffer. Testing was performed with the Cobas® SARS‐CoV‐2 test on the Cobas® 6800 or 8800 platforms. Results Overall, 134/647 (20.7%) participants were considered infected because the ONPS or at least one gargle test was positive. ONPS had, respectively, a sensitivity of 96.3% (95% confidence interval [CI]: 91.3–98.5); both gargle processing methods were slightly less but equally sensitive (90.3% [95% CI: 83.9–94.3]). When ONPS and gargle specimens were both positive, the mean cycle threshold (Ct) was significantly higher for gargles, suggesting lower viral loads. Conclusion Gargle specimens directly added in PCR Media provide a similar clinical sensitivity to chemical lysis, both having a slightly, not significantly, lower sensitivity to ONPS.
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Affiliation(s)
- Patrick Benoit
- Département de microbiologie, Infectiologie et Immunologie, Université de Montréal, Québec, Canada
| | - Annie-Claude Labbé
- Département de microbiologie, Infectiologie et Immunologie, Université de Montréal, Québec, Canada.,Service d'infectiologie, Département de médecine, Hôpital Maisonneuve-Rosemont-CIUSSS de l'Est-de-l'Île-de-Montréal, Montréal, Québec, Canada
| | - Linda Lalancette
- Département de Microbiologie et d'Infectiologie, Centre Hospitalier de St-Eustache, St-Eustache, Québec, Canada
| | - Simon Gagnon
- Service de biologie moléculaire, Département clinique de Médecine de laboratoire, Centre Hospitalier de l'Université de Montréal, Montréal, Québec, Canada
| | - Eric Bonneau
- Département de Microbiologie et d'Infectiologie, Centre Hospitalier de St-Eustache, St-Eustache, Québec, Canada
| | - Christian Lavallée
- Département de microbiologie, Infectiologie et Immunologie, Université de Montréal, Québec, Canada.,Service d'infectiologie, Département de médecine, Hôpital Maisonneuve-Rosemont-CIUSSS de l'Est-de-l'Île-de-Montréal, Montréal, Québec, Canada
| | - Michel Roger
- Département de microbiologie, Infectiologie et Immunologie, Université de Montréal, Québec, Canada.,Service de biologie moléculaire, Département clinique de Médecine de laboratoire, Centre Hospitalier de l'Université de Montréal, Montréal, Québec, Canada.,Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Ste-Anne-de-Bellevue, Québec, Canada
| | - Judith Fafard
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Ste-Anne-de-Bellevue, Québec, Canada
| | - Jeannot Dumaresq
- Département de Microbiologie et d'Infectiologie, CISSS de Chaudière-Appalaches, Lévis, Québec, Canada
| | - Stéphanie Beauchemin
- Service d'infectiologie, Département de médecine, Hôpital Maisonneuve-Rosemont-CIUSSS de l'Est-de-l'Île-de-Montréal, Montréal, Québec, Canada
| | - François Coutlée
- Département de microbiologie, Infectiologie et Immunologie, Université de Montréal, Québec, Canada.,Service de biologie moléculaire, Département clinique de Médecine de laboratoire, Centre Hospitalier de l'Université de Montréal, Montréal, Québec, Canada
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389
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Rapid and Convenient Quantitative Analysis of SARS-CoV-2 RNA in Serous Saliva with a Direct PCR Method. EPIDEMIOLGIA (BASEL, SWITZERLAND) 2021; 2:305-314. [PMID: 36417227 PMCID: PMC9620949 DOI: 10.3390/epidemiologia2030023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/05/2021] [Accepted: 07/16/2021] [Indexed: 12/14/2022]
Abstract
Sensitive and accurate detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), frequently performed using direct polymerase chain reaction (PCR), is essential for restricting the spread of coronavirus disease 2019 (COVID-19). However, studies evaluating accurate detection are still required. This study evaluated the quantitativeness and sensitivity of the Ampdirect™ 2019-nCoV detection kit, a direct PCR method. Using saliva with or without Tris-buffered saline (TBS) dilution, linearity, and limits of the N1 and N2 regions of SARS-CoV-2 genomic RNA were assessed using EDX SARS-CoV-2 RNA standard dissolved in RNase-free water (RFW). Fluorescence intensities in non-diluted saliva were higher than those in TBS-diluted samples. Linear regression analysis of detected quantification cycle values and spiked standard RNA concentrations showed that the coefficient of determination of the N1 and N2 genes was 0.972 and 0.615 in RFW and 0.947 and 0.660 in saliva, respectively. N1- and N2-positive detection rates in saliva were 46% (6/13 tests) and 0% (0/12 tests) at one copy/reaction, respectively. These results indicate good quantitativeness and sensitivity for N1 but not for N2. Therefore, our findings reveal that the Ampdirect™ 2019-nCoV system, especially targeting the N1 gene, enables rapid and convenient quantification of SARS-CoV-2 RNA in saliva at one copy/reaction.
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390
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Schuit E, Veldhuijzen IK, Venekamp RP, van den Bijllaardt W, Pas SD, Lodder EB, Molenkamp R, GeurtsvanKessel CH, Velzing J, Huisman RC, Brouwer L, Boelsums TL, Sips GJ, Benschop KSM, Hooft L, van de Wijgert JHHM, van den Hof S, Moons KGM. Diagnostic accuracy of rapid antigen tests in asymptomatic and presymptomatic close contacts of individuals with confirmed SARS-CoV-2 infection: cross sectional study. BMJ 2021; 374:n1676. [PMID: 34315770 PMCID: PMC8314145 DOI: 10.1136/bmj.n1676] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/30/2021] [Indexed: 01/14/2023]
Abstract
OBJECTIVE To assess the diagnostic test accuracy of two rapid antigen tests in asymptomatic and presymptomatic close contacts of people with SARS-CoV-2 infection on day 5 after exposure. DESIGN Prospective cross sectional study. SETTING Four public health service covid-19 test sites in the Netherlands. PARTICIPANTS 4274 consecutively included close contacts (identified through test-and-trace programme or contact tracing app) aged 16 years or older and asymptomatic for covid-19 when requesting a test. MAIN OUTCOME MEASURES Sensitivity, specificity, and positive and negative predictive values of Veritor System (Beckton Dickinson) and Biosensor (Roche Diagnostics) rapid antigen tests, with reverse-transcriptase polymerase chain reaction (RT-PCR) testing as reference standard. The viral load cut-off above which 95% of people with a positive RT-PCR test result were virus culture positive was used as a proxy of infectiousness. RESULTS Of 2678 participants tested with Veritor, 233 (8.7%) had a RT-PCR confirmed SARS-CoV-2 infection of whom 149 were also detected by the rapid antigen test (sensitivity 63.9%, 95% confidence interval 57.4% to 70.1%). Of 1596 participants tested with Biosensor, 132 (8.3%) had a RT-PCR confirmed SARS-CoV-2 infection of whom 83 were detected by the rapid antigen test (sensitivity 62.9%, 54.0% to 71.1%). In those who were still asymptomatic at the time of sampling, sensitivity was 58.7% (51.1% to 66.0%) for Veritor (n=2317) and 59.4% (49.2% to 69.1%) for Biosensor (n=1414), and in those who developed symptoms were 84.2% (68.7% to 94.0%; n=219) for Veritor and 73.3% (54.1% to 87.7%; n=158) for Biosensor. When a viral load cut-off was applied for infectiouness (≥5.2 log10 SARS-CoV-2 E gene copies/mL), the overall sensitivity was 90.1% (84.2% to 94.4%) for Veritor and 86.8% (78.1% to 93.0%) for Biosensor, and 88.1% (80.5% to 93.5%) for Veritor and 85.1% (74.3% to 92.6%) for Biosensor, among those who remained asymptomatic throughout. Specificities were >99%, and positive and negative predictive values were >90% and >95%, for both rapid antigen tests in all analyses. CONCLUSIONS The sensitivities of both rapid antigen tests in asymptomatic and presymptomatic close contacts tested on day 5 onwards after close contact with an index case were more than 60%, increasing to more than 85% after a viral load cut-off was applied as a proxy for infectiousness.
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Affiliation(s)
- Ewoud Schuit
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Cochrane Netherlands, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Irene K Veldhuijzen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Roderick P Venekamp
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | | | - Suzan D Pas
- Microvida Laboratory for Medical Microbiology, Amphia Hospital, Breda, Netherlands
- Microvida Laboratory for Medical Microbiology. Bravis Hospital, Roosendaal, Netherlands
| | | | | | | | - Jans Velzing
- Department of Viroscience, Erasmus MC, Rotterdam, Netherlands
| | - Robin C Huisman
- Department of Viroscience, Erasmus MC, Rotterdam, Netherlands
| | - Lieke Brouwer
- Public Health Service Rotterdam-Rijnmond, Rotterdam, Netherlands
| | - Timo L Boelsums
- Public Health Service Rotterdam-Rijnmond, Rotterdam, Netherlands
| | - Gregorius J Sips
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
- Public Health Service Rotterdam-Rijnmond, Rotterdam, Netherlands
| | - Kimberly S M Benschop
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Lotty Hooft
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Cochrane Netherlands, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Janneke H H M van de Wijgert
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Susan van den Hof
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Karel G M Moons
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Cochrane Netherlands, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
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391
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Manolea C, Capitanescu A, Borș R, Rugescu I, Bechir M, Mehedintu C, Varlas V. The prevalence of SARS-CoV-2 antibodies in triage-negative patients and staff of a fertility setting from lockdown release throughout 2020. Hum Reprod Open 2021; 2021:hoab028. [PMID: 34322605 PMCID: PMC8313405 DOI: 10.1093/hropen/hoab028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 06/10/2021] [Indexed: 12/13/2022] Open
Abstract
STUDY QUESTION What is the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in triage-negative patients undergoing ART and fertility care providers after lockdown release and throughout 2020? SUMMARY ANSWER Out of the triage-negative patients whose blood samples were assessed for SARS-CoV-2 antibodies over 6 months, 5.2% yielded positive results with a significantly higher rate in health care workers (HCWs) and a significant month-by-month increase in those with evidence of antibodies. WHAT IS KNOWN ALREADY Patients of reproductive age are more prone to asymptomatic or minimal forms of coronavirus disease 2019 (COVID-19) as compared to older age groups, and the identification of those with active infection and those already exposed (and probably immunized) is important for safety and cost-effective use of testing resources in the fertility setting. Data on the prevalence of SARS-CoV-2 in ART patients are limited and encompass short time frames; current rates are unknown. There is also no consensus on the optimal way of screening triage-negative ART patients in moderate/high-risk areas. STUDY DESIGN SIZE DURATION A prospective longitudinal unicentric study on triage negative ART patients (n = 516) and clinical staff (n = 30) was carried out. We analyzed 705 serological tests for SARS-CoV-2 sampled between 17 May 2020 (the first working day after lockdown release) up to 1 December 2020, to assess the positivity rates for SARS-CoV-2 antibodies. PARTICIPANTS/MATERIALS SETTING METHODS We collected data on the serological status for IgM and IgG antibodies against SARS-CoV-2 in 516 triage-negative men (n = 123) and women (n = 393) undergoing ART at a private fertility center and 30 HCWs that were at work during the study period. Antibodies were detected with a capture chemiluminescence assay (CLIA) targeting the highly Immunogenic S1 and S2 domains on the virus spike protein. We also analyzed the molecular test results of the cases exhibiting a positive serology. MAIN RESULTS AND THE ROLE OF CHANCE The data showed that 5.2% of the triage-negative ART patients had a positive serological result for SARS-CoV-2, with an overall conversion rate of 2.1% for IgG and 4.6% for IgM. There was no significant difference in seroprevalence between sexes. The small cohort (n = 30) of HCWs had a markedly increased seroprevalence (12.9% for Ig M and 22.6% for IgG). The highest seropositivity in our cohort was recorded in November (16.2%). The IgM positivity rates revealed significant monthly increments, paralleling official prevalence rates based on nasopharyngeal swabs. No positive molecular tests were identified in cases exhibiting a solitary positive IgG result. We show that despite a 6-fold increase in the number of ART patients with a positive serology between May and December 2020, most of our patients remain unexposed to the virus. The study was undertaken in a high-risk area for COVID-19, with a 20-times increase in the active cases across the study period. LIMITATIONS REASONS FOR CAUTION The geographical restriction, alongside the lack of running a second, differently-targeted immunoassay (orthogonal testing), could limit the generalizability and translation of our results to other fertility settings or other immunoassays. WIDER IMPLICATIONS OF THE FINDINGS The low positivity rates for IgG against the SARS-CoV-2 spike protein seen at the end of 2020 imply that most of the fertility patients are still at risk for SARS-CoV-2 infection. Until mass vaccination and other measures effectively diminish the pandemic, risk mitigation strategies must be maintained in the fertility units in the foreseeable future. Patients with a solitary IgG+ status are most likely 'non-infectious' and can elude further testing without giving up the strict use of universal protective measures. With increasing seroprevalences owing to infection or vaccination, and with the consecutive increase in test performance, it is possible that serological screening of ART patients might be more cost-effective than PCR testing, especially for the many patients with repeat treatments/procedures in a time-frame of months. STUDY FUNDING/COMPETING INTERESTS This research received no external funding. All authors declare having no conflict of interest with regard to this trial.
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Affiliation(s)
- Corina Manolea
- Department of Obstetrics and Gynecology, ‘Carol Davila’ University of Medicine and Pharmacy, Bucharest, Romania
- Department of Assisted Reproduction, Columna Medical Center, Bucharest, Romania
| | - Andrei Capitanescu
- Hemodialysis Unit, ‘Marie Curie’ Pediatric Clinical Emergency Hospital, Bucharest, Romania
| | - Roxana Borș
- Department of Obstetrics and Gynaecology, Filantropia Clinical Hospital, Bucharest, Romania
| | - Ioana Rugescu
- Department of Cells, National Transplant Agency, Bucharest, Romania
| | - Melihan Bechir
- Department of Assisted Reproduction, Columna Medical Center, Bucharest, Romania
- Dept of Obstetrics and Gynecology, Infertility Center, Regina Maria Medical Network, Bucharest, Romania
| | - Claudia Mehedintu
- Department of Obstetrics and Gynecology, ‘Carol Davila’ University of Medicine and Pharmacy, Bucharest, Romania
- Department of Obstetrics and Gynecology, Nicolae Malaxa Clinical Hospital, Bucharest, Romania
| | - Valentin Varlas
- Department of Obstetrics and Gynecology, ‘Carol Davila’ University of Medicine and Pharmacy, Bucharest, Romania
- Department of Obstetrics and Gynaecology, Filantropia Clinical Hospital, Bucharest, Romania
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392
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Reich N, Lowe CF, Puddicombe D, Matic N, Greiner J, Simons J, Leung V, Chu T, Naik H, Myles N, Burns L, Romney MG, Ritchie G, Champagne S, Dooley K, Sekirov I, Stefanovic A. Repeat virological and serological profiles in hospitalized patients initially tested by nasopharyngeal RT-PCR for SARS-CoV-2. J Med Virol 2021; 93:6808-6812. [PMID: 34297350 PMCID: PMC8426995 DOI: 10.1002/jmv.27227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/13/2021] [Accepted: 07/21/2021] [Indexed: 01/08/2023]
Abstract
Real‐time polymerase chain reaction (PCR) for SARS‐CoV‐2 is the mainstay of COVID‐19 diagnosis, yet there are conflicting reports on its diagnostic performance. Wide ranges of false‐negative PCR tests have been reported depending on clinical presentation, the timing of testing, specimens tested, testing method, and reference standard used. We aimed to estimate the frequency of discordance between initial nasopharyngeal (NP) PCR and repeat NP sampling PCR and serology in acutely ill patients admitted to the hospital. Panel diagnosis of COVID‐19 infection is further utilized in discordance analysis. Included in the study were 160 patients initially tested by NP PCR with repeat NP sampling PCR and/or serology performed. The percent agreement between initial and repeat PCR was 96.7%, while the percent agreement between initial PCR and serology was 98.9%. There were 5 (3.1%) cases with discordance on repeat testing. After discordance analysis, 2 (1.4%) true cases tested negative on initial PCR. Using available diagnostic methods, discordance on repeat NP sampling PCR and/or serology is a rare occurrence.
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Affiliation(s)
- Noah Reich
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, Providence Health Care, St. Paul's Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - David Puddicombe
- Perinatal Services BC, Provincial Health Service Authority, Vancouver, British Columbia, Canada
| | - Nancy Matic
- Division of Medical Microbiology and Virology, Providence Health Care, St. Paul's Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jesse Greiner
- Division of General Internal Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Janet Simons
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Victor Leung
- Division of Medical Microbiology and Virology, Providence Health Care, St. Paul's Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Terry Chu
- Division of General Internal Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hiten Naik
- Division of General Internal Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nick Myles
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Laura Burns
- Division of General Internal Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, Providence Health Care, St. Paul's Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gordon Ritchie
- Division of Medical Microbiology and Virology, Providence Health Care, St. Paul's Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sylvie Champagne
- Division of Medical Microbiology and Virology, Providence Health Care, St. Paul's Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kent Dooley
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada, Life Labs, Vancouver, British Columbia, Canada
| | - Inna Sekirov
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia Center for Disease Control, Vancouver, British Columbia, Canada
| | - Aleksandra Stefanovic
- Division of Medical Microbiology and Virology, Providence Health Care, St. Paul's Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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393
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of COVID-19. Testing for SARS-CoV-2 infection is a critical element of the public health response to COVID-19. Point-of-care (POC) tests can drive patient management decisions for infectious diseases, including COVID-19. POC tests are available for the diagnosis of SARS-CoV-2 infections and include those that detect SARS-CoV-2 antigens as well as amplified RNA sequences. We provide a review of SARS-CoV-2 POC tests including their performance, settings for which they might be used, their impact and future directions. Further optimization and validation, new technologies as well as studies to determine clinical and epidemiological impact of SARS-CoV-2 POC tests are needed.
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394
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Evaluation of sixteen ELISA SARS-CoV-2 serological tests. J Clin Virol 2021; 142:104931. [PMID: 34365228 PMCID: PMC8295192 DOI: 10.1016/j.jcv.2021.104931] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 07/04/2021] [Accepted: 07/14/2021] [Indexed: 01/12/2023]
Abstract
Background In response to the current COVID-19 pandemic, multiple companies marketed serological tests. Rigorous, independent and comparative performances of these assays on defined clinical specimens are needed. Methods In a first preliminary phase, we investigated 16 IgG, IgM, IgA and pan Ig serological ELISA using a panel of 180 sera, comprising 97 sera from patients with a positive RT-PCR, and 83 negative sera sampled before November 1, 2019. In a second phase and to complete the evaluation on the full panel (100 positive and 300 negative), tests that passed pre-defined exclusion criteria of 90% sensitivity and 97% specificity were further evaluated on 220 additional sera chosen to assess possible cross-reactivity with other human viral infections. Results Among the 16 tests evaluated in the preliminary phase, two were excluded due to insufficient sensitivity at 15 days post-symptom onset and one was excluded due to poor specificity. Of the 13 tests evaluated using the full panel comprised of a diverse pool of sera including those reactive against known respiratory viruses, no systematic cross-reactivity was observed. However, heterogeneities across tests were found. Consistent with kinetics of antibody expression, maximal sensitivity was found two weeks post-symptom onset. Conclusion In this independent evaluation, we compared the performance of 16 SARS-CoV-2 serological tests using well-characterized sera and found 13 tests with more than 90% sensitivity at 15 days post-symptom onset and 97% specificity across a diverse range of negative samples.
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395
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Optimization and Standardization of Human Saliva Collection for MALDI-TOF MS. Diagnostics (Basel) 2021; 11:diagnostics11081304. [PMID: 34441239 PMCID: PMC8392517 DOI: 10.3390/diagnostics11081304] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/16/2021] [Accepted: 07/16/2021] [Indexed: 12/14/2022] Open
Abstract
SARS-CoV-2 outbreak led to unprecedented innovative scientific research to preclude the virus dissemination and limit its impact on life expectancy. Waiting for the collective immunity by vaccination, mass-testing, and isolation of positive cases remain essential. The development of a diagnosis method requiring a simple and non-invasive sampling with a quick and low-cost approach is on demand. We hypothesized that the combination of saliva specimens with MALDI-TOF MS profiling analyses could be the winning duo. Before characterizing MS saliva signatures associated with SARS-CoV-2 infection, optimization and standardization of sample collection, preparation and storage up to MS analyses appeared compulsory. In this view, successive experiments were performed on saliva from healthy healthcare workers. Specimen sampling with a roll cotton of Salivette® devices appeared the most appropriate collection mode. Saliva protein precipitation with organic buffers did not improved MS spectra profiles compared to a direct loading of samples mixed with acetonitrile/formic acid buffer onto MS plate. The assessment of sample storage conditions and duration revealed that saliva should be stored on ice until MS analysis, which should occur on the day of sampling. Kinetic collection of saliva highlighted reproducibility of saliva MS profiles over four successive days and also at two-week intervals. The intra-individual stability of saliva MS profiles should be a key factor in the future investigation for biomarkers associated with SARS-CoV-2 infection. However, the singularity of MS profiles between individuals will require the development of sophisticated bio-statistical analyses such as machine learning approaches. MALDI-TOF MS profiling of saliva could be a promising PCR-free tool for SARS-CoV-2 screening.
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396
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Lessons learned from the COVID-19 pandemic and its impact on bioanalysis and drug development. Bioanalysis 2021; 13:1205-1211. [PMID: 34275332 PMCID: PMC8288281 DOI: 10.4155/bio-2021-0120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The COVID-19 pandemic challenged pharmaceutical and bioanalytical communities at large, in the development of vaccines and therapeutics as well as supporting ongoing drug development efforts. Existing processes were challenged to manage loss of staffing at facilities along with added workloads for COVID related study support including conducting preclinical testing, initiating clinical trials, conducting bioanalysis and interactions with regulatory agencies, all in an ultra-rapid timeframes. A key factor of success was creative rethinking of processes and removing barriers – some of which hitherto had been considered immovable. This article describes how bioanalysis was crippled at the onset of the pandemic but how innovative and highly collaborative efforts across teams within and outside of both pharma, bioanalytical labs and regulatory agencies worked together remarkably well.
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397
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Aisyah DN, Mayadewi CA, Igusti G, Manikam L, Adisasmito W, Kozlakidis Z. Laboratory Readiness and Response for SARS-Cov-2 in Indonesia. Front Public Health 2021; 9:705031. [PMID: 34350153 PMCID: PMC8326463 DOI: 10.3389/fpubh.2021.705031] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/18/2021] [Indexed: 11/13/2022] Open
Abstract
The laboratory diagnosis of SARS-CoV-2 infection comprises the informational cornerstone in the effort to contain the infections. Therefore, the ability to leverage laboratories' capacity in diagnostic testing and to increase the number of people being tested are critical. This paper reviews the readiness of Indonesian laboratories during the early months of the pandemic. It discusses the success of cross-sectoral collaboration among previously siloed national and sub-national government institutions, international development agencies, and private sector stakeholders. This collaboration managed to scale-up the COVID-19 referral laboratory network from one Ministry of Health NIHRD laboratory in the capital to 685 laboratories across 34 provinces. However, this rapid growth within 12 months since the first Indonesian case was discovered remained insufficient to cater for the constantly surging testing demands within the world's fourth most populous country. Reflecting on how other countries built their current pandemic preparedness from past emergencies, this paper highlights challenges and opportunities in workforce shortage, logistic distribution, and complex administration that need to be addressed.
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Affiliation(s)
- Dewi N. Aisyah
- Department of Epidemiology and Public Health, Institute of Epidemiology and Health Care, University College London, London, United Kingdom
- Indonesia One Health University Network, Depok, Indonesia
| | | | - Gayatri Igusti
- Aceso Global Health Consultants Limited, London, United Kingdom
| | - Logan Manikam
- Department of Epidemiology and Public Health, Institute of Epidemiology and Health Care, University College London, London, United Kingdom
- Aceso Global Health Consultants Limited, London, United Kingdom
| | - Wiku Adisasmito
- Indonesia One Health University Network, Depok, Indonesia
- Faculty of Public Health, Universitas Indonesia, Depok, Indonesia
| | - Zisis Kozlakidis
- International Agency for Research on Cancer World Health Organization, Lyon, France
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398
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López-Hernández Y, Monárrez-Espino J, Oostdam ASHV, Delgado JEC, Zhang L, Zheng J, Valdez JJO, Mandal R, González FDLO, Moreno JCB, Trejo-Medinilla FM, López JA, Moreno JAE, Wishart DS. Targeted metabolomics identifies high performing diagnostic and prognostic biomarkers for COVID-19. Sci Rep 2021; 11:14732. [PMID: 34282210 PMCID: PMC8290000 DOI: 10.1038/s41598-021-94171-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/06/2021] [Indexed: 12/14/2022] Open
Abstract
Research exploring the development and outcome of COVID-19 infections has led to the need to find better diagnostic and prognostic biomarkers. This cross-sectional study used targeted metabolomics to identify potential COVID-19 biomarkers that predicted the course of the illness by assessing 110 endogenous plasma metabolites from individuals admitted to a local hospital for diagnosis/treatment. Patients were classified into four groups (≈ 40 each) according to standard polymerase chain reaction (PCR) COVID-19 testing and disease course: PCR-/controls (i.e., non-COVID controls), PCR+/not-hospitalized, PCR+/hospitalized, and PCR+/intubated. Blood samples were collected within 2 days of admission/PCR testing. Metabolite concentration data, demographic data and clinical data were used to propose biomarkers and develop optimal regression models for the diagnosis and prognosis of COVID-19. The area under the receiver operating characteristic curve (AUC; 95% CI) was used to assess each models' predictive value. A panel that included the kynurenine: tryptophan ratio, lysoPC a C26:0, and pyruvic acid discriminated non-COVID controls from PCR+/not-hospitalized (AUC = 0.947; 95% CI 0.931-0.962). A second panel consisting of C10:2, butyric acid, and pyruvic acid distinguished PCR+/not-hospitalized from PCR+/hospitalized and PCR+/intubated (AUC = 0.975; 95% CI 0.968-0.983). Only lysoPC a C28:0 differentiated PCR+/hospitalized from PCR+/intubated patients (AUC = 0.770; 95% CI 0.736-0.803). If additional studies with targeted metabolomics confirm the diagnostic value of these plasma biomarkers, such panels could eventually be of clinical use in medical practice.
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Affiliation(s)
- Yamilé López-Hernández
- Cátedras-CONACyT, Consejo Nacional de Ciencia y Tecnologia, 03940, México, México.
- Autonomous University of Zacatecas, 98000, Zacatecas, Mexico.
| | - Joel Monárrez-Espino
- Christus Muguerza Hospital Chihuahua-University of Monterrey, 31000, Chihuahua, Mexico.
| | | | - Julio Enrique Castañeda Delgado
- Cátedras-CONACyT, Consejo Nacional de Ciencia y Tecnologia, 03940, México, México
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, 98000, Zacatecas, México
| | - Lun Zhang
- The Metabolomics Innovation Center, University of Alberta, Edmonton, AB, T6G1C9, Canada
| | - Jiamin Zheng
- The Metabolomics Innovation Center, University of Alberta, Edmonton, AB, T6G1C9, Canada
| | - Juan José Oropeza Valdez
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, 98000, Zacatecas, México
| | - Rupasri Mandal
- The Metabolomics Innovation Center, University of Alberta, Edmonton, AB, T6G1C9, Canada
| | - Fátima de Lourdes Ochoa González
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, 98000, Zacatecas, México
- Doctorado en Ciencias Básicas, Universidad Autónoma de Zacatecas, Zacatecas, México
| | - Juan Carlos Borrego Moreno
- Departmento de Epidemiología, Hospital General de Zona #1 "Emilio Varela Luján", Instituto Mexicano del Seguro Social, 98000, Zacatecas, México
| | - Flor M Trejo-Medinilla
- Autonomous University of Zacatecas, 98000, Zacatecas, Mexico
- Doctorado en Ciencias Básicas, Universidad Autónoma de Zacatecas, Zacatecas, México
| | - Jesús Adrián López
- MicroRNAs Laboratory, Academic Unit for Biological Sciences, Autonomous University of Zacatecas, 98000, Zacatecas, Mexico
| | - José Antonio Enciso Moreno
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, 98000, Zacatecas, México
| | - David S Wishart
- The Metabolomics Innovation Center, University of Alberta, Edmonton, AB, T6G1C9, Canada
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399
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Mak GCK, Lau SSY, Wong KKY, Chow NLS, Lau CS, Ng KHL, Lam ETK, Chan RCW, Tsang DNC. Evaluation of automated antigen detection test for detection of SARS-CoV-2. Diagn Microbiol Infect Dis 2021; 101:115490. [PMID: 34399380 PMCID: PMC8284070 DOI: 10.1016/j.diagmicrobio.2021.115490] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/07/2021] [Accepted: 07/10/2021] [Indexed: 11/28/2022]
Abstract
RT-PCR is the gold standard to detect SARS-CoV-2, however, its capacity is limited. We evaluated an automated antigen detection (AAD) test, Elecsys SARS-CoV-2 Antigen (Roche, Germany), for detecting SARS-CoV-2. We compared the limit of detection (LOD) between AAD test, rapid antigen detection (RAD) test; SARS-CoV-2 Rapid Antigen Test (SD Biosensor, Korea), and in-house RT-PCR test. LOD results showed that the AAD test was 100 fold more sensitive than the RAD test, while the sensitivity of the AAD test was comparable to the RT-PCR test. The AAD test detected between 85.7% and 88.6% of RT-PCR-positive specimens collected from COVID-19 patients, false negative results were observed for specimens with Ct values >30. Although clinical sensitivity for the AAD test was not superior or comparable to the RT-PCR test in the present study, the AAD test may be an alternative to RT-PCR test in terms of turn-around time and throughput.
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Affiliation(s)
- Gannon C K Mak
- Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Department of Health, Hong Kong Special Administrative Region, Hong Kong, China.
| | - Stephen S Y Lau
- Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Department of Health, Hong Kong Special Administrative Region, Hong Kong, China
| | - Kitty K Y Wong
- Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Department of Health, Hong Kong Special Administrative Region, Hong Kong, China
| | - Nancy L S Chow
- Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Department of Health, Hong Kong Special Administrative Region, Hong Kong, China
| | - C S Lau
- Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Department of Health, Hong Kong Special Administrative Region, Hong Kong, China
| | - Ken H L Ng
- Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Department of Health, Hong Kong Special Administrative Region, Hong Kong, China
| | - Edman T K Lam
- Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Department of Health, Hong Kong Special Administrative Region, Hong Kong, China
| | - Rickjason C W Chan
- Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Department of Health, Hong Kong Special Administrative Region, Hong Kong, China
| | - Dominic N C Tsang
- Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Department of Health, Hong Kong Special Administrative Region, Hong Kong, China
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400
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van Belkum A, Almeida C, Bardiaux B, Barrass SV, Butcher SJ, Çaykara T, Chowdhury S, Datar R, Eastwood I, Goldman A, Goyal M, Happonen L, Izadi-Pruneyre N, Jacobsen T, Johnson PH, Kempf VAJ, Kiessling A, Bueno JL, Malik A, Malmström J, Meuskens I, Milner PA, Nilges M, Pamme N, Peyman SA, Rodrigues LR, Rodriguez-Mateos P, Sande MG, Silva CJ, Stasiak AC, Stehle T, Thibau A, Vaca DJ, Linke D. Host-Pathogen Adhesion as the Basis of Innovative Diagnostics for Emerging Pathogens. Diagnostics (Basel) 2021; 11:diagnostics11071259. [PMID: 34359341 PMCID: PMC8305138 DOI: 10.3390/diagnostics11071259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/19/2021] [Accepted: 06/21/2021] [Indexed: 12/18/2022] Open
Abstract
Infectious diseases are an existential health threat, potentiated by emerging and re-emerging viruses and increasing bacterial antibiotic resistance. Targeted treatment of infectious diseases requires precision diagnostics, especially in cases where broad-range therapeutics such as antibiotics fail. There is thus an increasing need for new approaches to develop sensitive and specific in vitro diagnostic (IVD) tests. Basic science and translational research are needed to identify key microbial molecules as diagnostic targets, to identify relevant host counterparts, and to use this knowledge in developing or improving IVD. In this regard, an overlooked feature is the capacity of pathogens to adhere specifically to host cells and tissues. The molecular entities relevant for pathogen–surface interaction are the so-called adhesins. Adhesins vary from protein compounds to (poly-)saccharides or lipid structures that interact with eukaryotic host cell matrix molecules and receptors. Such interactions co-define the specificity and sensitivity of a diagnostic test. Currently, adhesin-receptor binding is typically used in the pre-analytical phase of IVD tests, focusing on pathogen enrichment. Further exploration of adhesin–ligand interaction, supported by present high-throughput “omics” technologies, might stimulate a new generation of broadly applicable pathogen detection and characterization tools. This review describes recent results of novel structure-defining technologies allowing for detailed molecular analysis of adhesins, their receptors and complexes. Since the host ligands evolve slowly, the corresponding adhesin interaction is under selective pressure to maintain a constant receptor binding domain. IVD should exploit such conserved binding sites and, in particular, use the human ligand to enrich the pathogen. We provide an inventory of methods based on adhesion factors and pathogen attachment mechanisms, which can also be of relevance to currently emerging pathogens, including SARS-CoV-2, the causative agent of COVID-19.
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Affiliation(s)
- Alex van Belkum
- BioMérieux, Open Innovation & Partnerships, 38390 La Balme Les Grottes, France;
- Correspondence: (A.v.B.); (D.L.)
| | | | - Benjamin Bardiaux
- Institut Pasteur, Structural Biology and Chemistry, 75724 Paris, France; (B.B.); (N.I.-P.); (T.J.); (M.N.)
| | - Sarah V. Barrass
- Department of Biological Sciences, University of Helsinki, 00014 Helsinki, Finland; (S.V.B.); (S.J.B.); (A.G.)
| | - Sarah J. Butcher
- Department of Biological Sciences, University of Helsinki, 00014 Helsinki, Finland; (S.V.B.); (S.J.B.); (A.G.)
| | - Tuğçe Çaykara
- Centre for Nanotechnology and Smart Materials, 4760-034 Vila Nova de Famalicão, Portugal; (T.Ç.); (C.J.S.)
| | - Sounak Chowdhury
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, 22242 Lund, Sweden; (S.C.); (L.H.); (J.M.)
| | - Rucha Datar
- BioMérieux, Microbiology R&D, 38390 La Balme Les Grottes, France;
| | | | - Adrian Goldman
- Department of Biological Sciences, University of Helsinki, 00014 Helsinki, Finland; (S.V.B.); (S.J.B.); (A.G.)
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Manisha Goyal
- BioMérieux, Open Innovation & Partnerships, 38390 La Balme Les Grottes, France;
| | - Lotta Happonen
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, 22242 Lund, Sweden; (S.C.); (L.H.); (J.M.)
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Structural Biology and Chemistry, 75724 Paris, France; (B.B.); (N.I.-P.); (T.J.); (M.N.)
| | - Theis Jacobsen
- Institut Pasteur, Structural Biology and Chemistry, 75724 Paris, France; (B.B.); (N.I.-P.); (T.J.); (M.N.)
| | - Pirjo H. Johnson
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Volkhard A. J. Kempf
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe-University, 60596 Frankfurt am Main, Germany; (V.A.J.K.); (A.T.); (D.J.V.)
| | - Andreas Kiessling
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Juan Leva Bueno
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Anchal Malik
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Johan Malmström
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, 22242 Lund, Sweden; (S.C.); (L.H.); (J.M.)
| | - Ina Meuskens
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway;
| | - Paul A. Milner
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Michael Nilges
- Institut Pasteur, Structural Biology and Chemistry, 75724 Paris, France; (B.B.); (N.I.-P.); (T.J.); (M.N.)
| | - Nicole Pamme
- School of Mathematics and Physical Sciences, University of Hull, Hull HU6 7RX, UK; (N.P.); (P.R.-M.)
| | - Sally A. Peyman
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Ligia R. Rodrigues
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (L.R.R.); (M.G.S.)
| | - Pablo Rodriguez-Mateos
- School of Mathematics and Physical Sciences, University of Hull, Hull HU6 7RX, UK; (N.P.); (P.R.-M.)
| | - Maria G. Sande
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (L.R.R.); (M.G.S.)
| | - Carla Joana Silva
- Centre for Nanotechnology and Smart Materials, 4760-034 Vila Nova de Famalicão, Portugal; (T.Ç.); (C.J.S.)
| | - Aleksandra Cecylia Stasiak
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany; (A.C.S.); (T.S.)
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany; (A.C.S.); (T.S.)
| | - Arno Thibau
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe-University, 60596 Frankfurt am Main, Germany; (V.A.J.K.); (A.T.); (D.J.V.)
| | - Diana J. Vaca
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe-University, 60596 Frankfurt am Main, Germany; (V.A.J.K.); (A.T.); (D.J.V.)
| | - Dirk Linke
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway;
- Correspondence: (A.v.B.); (D.L.)
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