1
|
Kim Y, Lee E, Kim B, Cho J, Ryu SW, Lee KA. Evaluation of diagnostic performance of SARS-CoV-2 infection using digital droplet polymerase chain reaction in individuals with or without COVID-19 symptoms. Clin Chim Acta 2024; 554:117759. [PMID: 38184140 DOI: 10.1016/j.cca.2023.117759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 09/21/2023] [Accepted: 12/31/2023] [Indexed: 01/08/2024]
Abstract
BACKGROUND Reverse transcription-quantitative PCR (RT-qPCR) is commonly used to diagnose SARS-CoV-2, but it has limited sensitivity in detecting the virus in asymptomatic close contacts and convalescent patients. In this study, we propose the use of reverse transcription-digital droplet PCR (RT-ddPCR) to detect SARS-CoV-2 in clinical samples. METHODS The clinical performance of RT-ddPCR targeting of ORF1ab and N genes was evaluated in parallel with RT-qPCR using 200 respiratory samples collected from close contacts and patients at different phases of infection. RESULTS The limits of detection (LODs) for RT-ddPCR assays were determined using six dilutions of ACCUPLEX SARS-Cov-2 reference material. The LODs of ORF1ab and N genes were 3.7 copies/reaction and 2.2 copies/reaction, respectively. Compared to RT-qPCR, RT-ddPCR increased the positive rate by 12.0% in 142 samples from SARS-CoV-2-infected patients. Additionally, RT-ddPCR detected SARS-CoV-2 in three of 26 specimens from close contacts that tested negative by RT-qPCR, and infection was confirmed using follow-up samples. Finally, RT-ddPCR improved the equivocal results from RT-qPCR in 56.3% (9/16) of convalescent patient samples. CONCLUSIONS Detecting SARS-CoV-2 in samples with low viral loads using RT-qPCR can be challenging. However, our study suggests that RT-ddPCR, with its higher sensitivity and accuracy, is better suited for detecting low viral copies in samples, particularly those from close contacts and convalescent patients.
Collapse
Affiliation(s)
- Yoonjung Kim
- Department of Laboratory Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Eunyoung Lee
- Department of Laboratory Medicine, Armed Forces Capital Hospital, Sungnam, Republic of Korea
| | - Boyeon Kim
- Department of Laboratory Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jinhee Cho
- Department of Laboratory Medicine, Eone Laboratories, Incheon, Republic of Korea
| | - Sook-Won Ryu
- Department of Laboratory Medicine, Kangwon National University, School of Medicine, Kangwondo, Republic of Korea.
| | - Kyung-A Lee
- Department of Laboratory Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea.
| |
Collapse
|
2
|
Shihab SR, Iqbal BN, Arunasalam S, Noordeen F. Quality of the sample-based RNA determines the real-time RT-PCR results in the laboratory diagnosis of COVID-19. Diagn Microbiol Infect Dis 2024; 108:116076. [PMID: 37980858 DOI: 10.1016/j.diagmicrobio.2023.116076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/27/2023] [Accepted: 08/30/2023] [Indexed: 11/21/2023]
Abstract
Effect of the quality of sample-based RNA on COVID-19 real-time RT-PCR results was investigated. The purity of the extracts was dependent on the extraction method (P<0.0001) and affected the test interpretations (P = 0.002). Gross RNA concentration negatively correlated with Ct values (P < 0.0001). The presence of impurities contributed to inconclusive test results.
Collapse
Affiliation(s)
- Sibra Rm Shihab
- Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka; Postgraduate Institute of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Bushran N Iqbal
- Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka
| | - Shiyamalee Arunasalam
- Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka
| | - Faseeha Noordeen
- Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka.
| |
Collapse
|
3
|
Sparrer MN, Hodges NF, Ragan I, Yamashita T, Reed KJ, Sherman TJ, Mayer T, Maichak C, Adney DR, Carpenter M, Webb TL, Mayo C. SARS-CoV-2 surveillance in a veterinary health system provides insight into transmission risks. J Am Vet Med Assoc 2024; 262:93-99. [PMID: 38103381 PMCID: PMC11234244 DOI: 10.2460/javma.23.05.0229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/12/2023] [Indexed: 12/19/2023]
Abstract
OBJECTIVE To investigate the prevalence and seropositivity of SARS-CoV-2 in companion and exotic animals in a veterinary healthcare system. SAMPLE A total of 341 animals were sampled by a combination of oral and nasal swabs. Serum from whole blood was collected from a subset of animals (86 canines, 25 felines, and 6 exotic animals). METHODS After informed owner consent, convenience samples from client-owned animals and the pets of students and staff members associated with Colorado State University's Veterinary Health System were collected between May 2021 and September 2022. Study samples were collected by trained veterinarians, Veterinary Health System staff, and veterinary students. RESULTS SARS-CoV-2 RNA was detected by reverse transcription PCR in 1.6% (95% CI, 0.5% to 4.6%) of domestic canines and 1.1% (95% CI, 0.2% to 6.1%) of domestic felines. No RNA was detected in any of the exotic animal species tested (n = 66). Plaque reduction neutralization tests indicated that 12.8% (95% CI, 7.3% to 21.5%) of canines and 12.0% (95% CI, 4.2% to 30.0%) of felines had neutralizing antibodies against SARS-CoV-2. CLINICAL RELEVANCE This study provides insight regarding SARS-CoV-2 spillover in domestic companion and exotic animals and contributes to our understanding of transmission risk in the veterinary setting.
Collapse
Affiliation(s)
- McKenzie N Sparrer
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
- 2Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Natasha F Hodges
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Izabela Ragan
- 3Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Tyler Yamashita
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Kirsten J Reed
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Tyler J Sherman
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Treana Mayer
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Courtney Maichak
- 4Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Danielle R Adney
- 5Department of Life Sciences, Lovelace Biomedical, Albuquerque, NM
| | - Molly Carpenter
- 3Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Tracy L Webb
- 2Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Christie Mayo
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| |
Collapse
|
4
|
Zwetsloot PP, Smit WL, Van der Kaaij NP, Szymanski MK, Van der Meer MG, Van Laake LW, Troelstra A, Wegdam-Blans MCA, Oerlemans MIFJ. Pre-Operative SARS-CoV-2 Testing in Asymptomatic Heart Transplantation Recipients. Biomedicines 2023; 11:2103. [PMID: 37626599 PMCID: PMC10452735 DOI: 10.3390/biomedicines11082103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/16/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
INTRODUCTION From the start of the coronavirus disease 2019 (COVID-19) pandemic, international guidelines have recommended pre-operative screening for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) before heart transplantation (HTx). Due to the changing prevalence of COVID-19, the chances of false positive results have increased. Because of increased immunity in the population and evolution of SARS-CoV-2 to current Omicron variants, associated mortality and morbidity have decreased. We set out to investigate the yield and side effects of SARS-CoV-2 screening in our center. METHODS We performed a retrospective cohort study in the University Medical Center Utrecht. The study period was from March 2019 to January 2023. All data from patients who underwent HTx were collected, including all pre-operative and post-operative SARS-CoV-2 tests. Furthermore, all clinical SARS-CoV-2 tests for the indication of potential HTx were screened. RESULTS In the period under study, 51 patients underwent HTx. None of the recipients reported any symptoms of a viral infection. Fifty HTx recipients were screened for SARS-CoV-2. Forty-nine out of fifty patients tested negative. One patient had a false positive result, potentially delaying the HTx procedure. There were no cancelled HTx procedures due to a true positive SARS-CoV-2 test result. CONCLUSION Pre-operative SARS-CoV-2 screening in asymptomatic HTx recipients did not lead to any true positive cases. In 2% of the cases, screening resulted in a false positive test result. With the current Omicron variants, in combination with a low-prevalence situation, we propose to abandon pre-operative SARS-CoV-2 screening and initiate a symptom-driven approach for the general viral testing of patients who are called in for a potential HTx.
Collapse
Affiliation(s)
- Peter-Paul Zwetsloot
- Department of Cardiology, University Medical Centre Utrecht, 3584 CX Utrecht, The Netherlands; (P.-P.Z.); (M.K.S.); (M.G.V.d.M.)
| | - Wouter L. Smit
- Department of Medical Microbiology, University Medical Centre Utrecht, 3584 CX Utrecht, The Netherlands; (W.L.S.); (A.T.); (M.C.A.W.-B.)
| | - Niels P. Van der Kaaij
- Department of Cardiothoracic Surgery, University Medical Centre Utrecht, 3584 CX Utrecht, The Netherlands;
| | - Mariusz K. Szymanski
- Department of Cardiology, University Medical Centre Utrecht, 3584 CX Utrecht, The Netherlands; (P.-P.Z.); (M.K.S.); (M.G.V.d.M.)
| | - Manon G. Van der Meer
- Department of Cardiology, University Medical Centre Utrecht, 3584 CX Utrecht, The Netherlands; (P.-P.Z.); (M.K.S.); (M.G.V.d.M.)
| | - Linda W. Van Laake
- Department of Cardiology, University Medical Centre Utrecht, 3584 CX Utrecht, The Netherlands; (P.-P.Z.); (M.K.S.); (M.G.V.d.M.)
| | - Annet Troelstra
- Department of Medical Microbiology, University Medical Centre Utrecht, 3584 CX Utrecht, The Netherlands; (W.L.S.); (A.T.); (M.C.A.W.-B.)
| | - Marjolijn C. A. Wegdam-Blans
- Department of Medical Microbiology, University Medical Centre Utrecht, 3584 CX Utrecht, The Netherlands; (W.L.S.); (A.T.); (M.C.A.W.-B.)
| | - Marish I. F. J. Oerlemans
- Department of Cardiology, University Medical Centre Utrecht, 3584 CX Utrecht, The Netherlands; (P.-P.Z.); (M.K.S.); (M.G.V.d.M.)
| |
Collapse
|
5
|
Different interpretations of inconclusive results of SARS-CoV-2 real-time RT PCR. Diagn Microbiol Infect Dis 2023; 106:115888. [PMID: 36972653 PMCID: PMC9810550 DOI: 10.1016/j.diagmicrobio.2022.115888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/02/2022] [Accepted: 12/30/2022] [Indexed: 01/05/2023]
Abstract
We investigated whether inconclusive results could be interpreted differently depending on the situation. First, data from retesting of the initial samples from subjects without a confirmed COVID-19 history were analyzed. And by analyzing the results of consecutive tests with new specimens after receiving inconclusive results between arrivals and locals for two periods. As a result, 179 of 219 cases (81.7%) showed still inconclusive or weakly positive results. If contamination is well controlled in a general laboratory, the effectiveness of retesting with the same sample is limited. The rate of the subsequently positive patient was significantly higher in locals than in arrivals and periods with a higher positive rate. The inconclusive results could be interpreted differently depending on the epidemiologic background and the positive rate at that time.
Collapse
|
6
|
Maestri S, Grosso V, Alfano M, Lavezzari D, Piubelli C, Bisoffi Z, Rossato M, Delledonne M. STArS (STrain-Amplicon-Seq), a targeted nanopore sequencing workflow for SARS-CoV-2 diagnostics and genotyping. Biol Methods Protoc 2022; 7:bpac020. [PMID: 36046362 PMCID: PMC9422081 DOI: 10.1093/biomethods/bpac020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/12/2022] [Indexed: 11/13/2022] Open
Abstract
Diagnostic tests based on reverse transcription-quantitative polymerase chain reaction (RT-qPCR) are the gold standard approach to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection from clinical specimens. However, unless specifically optimized, this method is usually unable to recognize the specific viral strain responsible of coronavirus disease 2019, a crucial information that is proving increasingly important in relation to virus spread and treatment effectiveness. Even if some RT-qPCR commercial assays are currently being developed for the detection of viral strains, they focus only on single/few genetic variants that may not be sufficient to uniquely identify a specific strain. Therefore, genome sequencing approaches remain the most comprehensive solution for virus genotyping and to recognize viral strains, but their application is much less widespread due to higher costs. Starting from the well-established ARTIC protocol coupled to nanopore sequencing, in this work, we developed STArS (STrain-Amplicon-Seq), a cost/time-effective sequencing-based workflow for both SARS-CoV-2 diagnostics and genotyping. A set of 10 amplicons was initially selected from the ARTIC tiling panel, to cover: (i) all the main biologically relevant genetic variants located on the Spike gene; (ii) a minimal set of variants to uniquely identify the currently circulating strains; (iii) genomic sites usually amplified by RT-qPCR method to identify SARS-CoV-2 presence. PCR-amplified clinical samples (both positive and negative for SARS-CoV-2 presence) were pooled together with a serially diluted exogenous amplicon at known concentration and sequenced on a MinION device. Thanks to a scoring rule, STArS had the capability to accurately classify positive samples in agreement with RT-qPCR results, both at the qualitative and quantitative level. Moreover, the method allowed to effectively genotype strain-specific variants and thus also return the phylogenetic classification of SARS-CoV-2-postive samples. Thanks to the reduced turnaround time and costs, the proposed approach represents a step towards simplifying the clinical application of sequencing for viral genotyping, hopefully aiding in combatting the global pandemic.
Collapse
Affiliation(s)
- Simone Maestri
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
| | - Valentina Grosso
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | | | - Denise Lavezzari
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Chiara Piubelli
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, 37024 Verona, Italy
| | - Zeno Bisoffi
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, 37024 Verona, Italy
- Department of Diagnostics and Public Health, University of Verona, 37134, Verona, Italy
| | - Marzia Rossato
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
- Genartis srl, 37126 Verona, Italy
| | - Massimo Delledonne
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
- Genartis srl, 37126 Verona, Italy
| |
Collapse
|
7
|
Moskova M, Zasheva A, Kunchev M, Popivanov I, Dimov D, Vaseva V, Kundurzhiev T, Tsachev I, Baymakova M. Students' Attitudes toward COVID-19 Vaccination: An Inter-University Study from Bulgaria. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:9779. [PMID: 36011415 PMCID: PMC9408712 DOI: 10.3390/ijerph19169779] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/04/2022] [Accepted: 08/07/2022] [Indexed: 06/15/2023]
Abstract
In Bulgaria, vaccination coverage against the SARS-CoV-2 virus is low. The reasons for this fact are many and varied. The aim of the present study was to establish what the attitudes towards the COVID-19 vaccination process are among students from various specialties from several Bulgarian universities. In this research, 600 students participated, divided into two groups: Doctor of Medicine (MD) students (n = 300) and non-MD students, i.e., students of specialties, such as mathematics, engineering, finance and economics, law, human sciences, etc. (n = 300). Each respondent completed a questionnaire which was divided into three parts with closed questions. The mean age of all students was 21.19 ± 1.87 years (95% CI: 20.48−21.90). The female sex dominated among the analyzed participants (sex ratio: female/male = 1/0.85). Nearly 62% (371/600) of individuals declared that they have been COVID-19 vaccinated with at least one dose (p < 0.001). Overall, 33% of the participants sought information on vaccines from video sharing platforms and 36.0% (216/600) from social media platforms. From the conducted multivariable logistic regression the odds of vaccination against COVID-19 were 6.225 times higher in individuals with a positive attitude towards these vaccines than in people with a negative attitude towards them (p < 0.001). We have found that those students who trust the international health organizations had an OR of 2.365 (p = 0.004) to be SARS-CoV-2 vaccinated. We estimated that the odds of vaccination against SARS-CoV-2 among children were 4.794 times higher in parents (students) who had been vaccinated than in non-vaccinated parents (students) (p < 0.001). Our results could support the national public health organizations, the national educational/scientific systems, and the management of Bulgarian universities in making future decisions about the field of COVID-19 control and prevention.
Collapse
Affiliation(s)
- Martina Moskova
- Faculty of Medicine, Medical University, 9002 Varna, Bulgaria
- Faculty of Navigation, Nikola Vaptsarov Naval Academy, 9002 Varna, Bulgaria
| | - Anelia Zasheva
- Department of Infectious Diseases, Military Medical Academy, 1606 Sofia, Bulgaria
| | - Metodi Kunchev
- Department of Virology, Military Medical Academy, 1606 Sofia, Bulgaria
| | - Ivan Popivanov
- Department of Military Medicine, Military Medical Academy, 1606 Sofia, Bulgaria
| | - Dimo Dimov
- Department of Disaster Medicine, Military Medical Academy, 1606 Sofia, Bulgaria
| | - Virsavia Vaseva
- Department of Teaching and Science Activity, Military Medical Academy, 1606 Sofia, Bulgaria
| | - Todor Kundurzhiev
- Department of Occupational Medicine, Faculty of Public Health, Medical University, 1527 Sofia, Bulgaria
| | - Ilia Tsachev
- Department of Microbiology, Infectious and Parasitic Diseases, Faculty of Veterinary Medicine, Trakia University, 6000 Stara Zagora, Bulgaria
| | - Magdalena Baymakova
- Department of Infectious Diseases, Military Medical Academy, 1606 Sofia, Bulgaria
| |
Collapse
|