1
|
Liu D, Li H, Li X, Rodriguez GD, Pietz H, Fiel RH, Konadu E, Singh V, Loo F, Rodgers WH. Comparative Analysis of Viral Load and Cytokines during SARS-CoV-2 Infection between Pregnant and Non-Pregnant Women. Int J Mol Sci 2024; 25:7731. [PMID: 39062978 PMCID: PMC11277191 DOI: 10.3390/ijms25147731] [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: 06/19/2024] [Revised: 07/08/2024] [Accepted: 07/13/2024] [Indexed: 07/28/2024] Open
Abstract
To better understand the vulnerabilities of pregnant women during the COVID-19 pandemic, we conducted a comprehensive, retrospective cohort study to assess differences in immune responses to SARS-CoV-2 infection between pregnant and non-pregnant women. Nasopharyngeal swabs and serum specimens from 90 pregnant and 278 age-matched non-pregnant women were collected from 15 March 2020 to 23 July 2021 at NewYork-Presbyterian Queens Hospital in New York City. Multiplex reverse transcription polymerase chain reaction, neutralizing antibody, and cytokine array assays were used to assess the incidence, viral load, antibody titers and profiles, and examine cytokine expression patterns. Our results show a lower incidence of SARS-CoV-2 infection in pregnant women compared with non-pregnant women. Pregnant women infected with SARS-CoV-2 exhibited a substantially lower viral load. In addition, the levels of both anti-spike protein receptor-binding domain IgG neutralizing antibodies and anti-N Protein IgG were elevated in pregnant women. Finally, cytokine profiling revealed differential expression of leptin across cohorts. These findings suggest that pregnancy is associated with distinct immune and virological responses to SARS-CoV-2 infection, characterized by lower infection rates, substantially lower viral loads, and enhanced antibody production. Differential cytokine expression indicates unique immune modulation in pregnant women.
Collapse
Affiliation(s)
- Dakai Liu
- Department of Pathology and Clinical Laboratories, NewYork-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA
| | - Hui Li
- Department of Pathology and Clinical Laboratories, NewYork-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA
| | - Xiaofeng Li
- National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 510182, China
| | - George D. Rodriguez
- NewYork-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA
| | - Harlan Pietz
- NewYork-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA
| | | | - Eric Konadu
- Department of Pathology and Clinical Laboratories, NewYork-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA
| | - Vishnu Singh
- Department of Pathology and Clinical Laboratories, NewYork-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA
| | - Florence Loo
- Department of Pathology and Clinical Laboratories, NewYork-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA
| | - William Harry Rodgers
- Department of Pathology and Clinical Laboratories, NewYork-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA
- Department of Pathology and Laboratory Medicine, Weil Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| |
Collapse
|
2
|
Aravind Kumar N, Aradhana S, Harleen, Vishnuraj MR. SARS-CoV-2 in digital era: Diagnostic techniques and importance of nucleic acid quantification with digital PCRs. Rev Med Virol 2023; 33:e2471. [PMID: 37529971 DOI: 10.1002/rmv.2471] [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: 04/19/2023] [Revised: 07/04/2023] [Accepted: 07/12/2023] [Indexed: 08/03/2023]
Abstract
Studies related to clinical diagnosis and research of SARS-CoV-2 are important in the current pandemic era. Although molecular biology has emphasised the importance of qualitative analysis, quantitative analysis with nucleic acids in relation to SARS-CoV-2 needs to be clearly emphasised, which can provide perspective for viral dynamic studies of SARS-CoV-2. In this regard, the requirement and utilization of digital PCR in COVID-19 research has substantially increased during the pandemic, necessitating the aggregation of its cardinal applications and future scopes. Hence, this meta-review comprehensively addresses and emphasises the importance of nucleic acid quantification of SARS-CoV-2 RNA with digital PCR (dPCR). Various quantitative techniques of clinical significance like immunological, proteomic and nucleic acid-based diagnosis and quantification, have been comparatively discussed. Furthermore, the core part of the article focusses on the working principle and advantages of digital PCR, along with its applications in COVID-19 research. Several important applications like viral load quantitation, environmental surveillance and assay validation have been extensively investigated and discussed. Certain key future scopes of clinical importance, like mortality prediction, viral/variant-symbiosis, and antiviral studies were also identified, suggesting several possible digital PCR applications in COVID-19 research.
Collapse
Affiliation(s)
- N Aravind Kumar
- Meat Species Identification Laboratory, ICAR - National Meat Research Institute, Hyderabad, Telangana, India
| | - S Aradhana
- Department of Biotechnology, School of Bio Sciences & Technology (SBST), Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Harleen
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - M R Vishnuraj
- Meat Species Identification Laboratory, ICAR - National Meat Research Institute, Hyderabad, Telangana, India
| |
Collapse
|
3
|
Smail SW, Babaei E, Amin K. Ct, IL-18 polymorphism, and laboratory biomarkers for predicting chemosensory dysfunctions and mortality in COVID-19. Future Sci OA 2023; 9:FSO838. [PMID: 36999046 PMCID: PMC10005086 DOI: 10.2144/fsoa-2022-0082] [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: 12/05/2022] [Accepted: 02/17/2023] [Indexed: 03/11/2023] Open
Abstract
Aim Patients with COVID-19 often experience chemosensory dysfunction. This research intends to uncover the association of RT-PCR Ct value with chemosensory dysfunctions and SpO2. This study also aims to investigate Ct, SpO2, CRP, D-dimer, and -607 IL-18 T/G polymorphism in order to find out predictors of chemosensory dysfunctions and mortality. Materials & methods This study included 120 COVID-19 patients, of which 54 were mild, 40 were severe and 26 were critical. CRP, D-dimer, RT-PCR, and IL-18 polymorphism were evaluated. Results & conclusion: Low Ct was associated with SpO2 dropping and chemosensory dysfunctions. IL-18 T/G polymorphism did not show an association with COVID-19 mortality; conversely, age, BMI, D-dimer and Ct values did.
Collapse
Affiliation(s)
- Shukur Wasman Smail
- Department of Biology, College of Science, Salahaddin University-Erbil, Iraq
| | - Esmaeil Babaei
- Department of Biology, School of Natural Sciences, University of Tabriz, Tabriz, Iran
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq
| | - Kawa Amin
- College of Medicine, University of Sulaimani, Sulaymaniyah, Iraq
| |
Collapse
|
4
|
Girón Pérez DA, Fonseca-Agüero A, Toledo-Ibarra GA, Gomez-Valdivia JDJ, Díaz-Resendiz KJG, Benitez-Trinidad AB, Razura-Carmona FF, Navidad-Murrieta MS, Covantes-Rosales CE, Giron-Pérez MI. Post-COVID-19 Syndrome in Outpatients and Its Association with Viral Load. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:15145. [PMID: 36429864 PMCID: PMC9690223 DOI: 10.3390/ijerph192215145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/06/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
INTRODUCTION The COVID-19 pandemic is the result of the SARS-CoV-2 virus, which has caused more than 100 million infections and more than 2.5 million deaths worldwide, representing a serious public health problem. The gold method for detecting this virus is qRT-PCR, which is a semiquantitative technique where the viral load can be established through its cycle threshold (Ct). It has also been reported that COVID-19 generates long-term symptoms (post-COVID-19). METHODS After three months, a survey was performed on 70 COVID-19 confirmed patients; subsequently, we divided them into four groups (persistent symptoms, chemo-sensitive, cognitive issues, and changes in habit) in order to determine the correlation between viral load and post-COVID-19 symptoms. RESULTS Data show that fatigue, nervousness, anosmia, and diet changes are common long-term symptoms; in addition, a negative correlation was found between viral load and the number of post-COVID-19 symptoms. CONCLUSION COVID-19 generates long-term symptoms which can cause problems with psychological and social repercussions.
Collapse
Affiliation(s)
- Daniel Alberto Girón Pérez
- Laboratorio Nacional de Investigación Para la Inocuidad Alimentaria (LANIIA) Unidad Nayarit, Universidad Autónoma de Nayarit, Tepic 63000, Mexico
| | - Aimee Fonseca-Agüero
- Laboratorio de Psicofisiología y Conducta, Unidad Académica de Ciencias Sociales, Universidad Autónoma de Nayarit, Tepic 63000, Mexico
| | - Gladys Alejandra Toledo-Ibarra
- Laboratorio Nacional de Investigación Para la Inocuidad Alimentaria (LANIIA) Unidad Nayarit, Universidad Autónoma de Nayarit, Tepic 63000, Mexico
| | - Jaqueline de Jesus Gomez-Valdivia
- Laboratorio de Psicofisiología y Conducta, Unidad Académica de Ciencias Sociales, Universidad Autónoma de Nayarit, Tepic 63000, Mexico
| | | | - Alma Benitez Benitez-Trinidad
- Laboratorio Nacional de Investigación Para la Inocuidad Alimentaria (LANIIA) Unidad Nayarit, Universidad Autónoma de Nayarit, Tepic 63000, Mexico
| | - Francisco Fabian Razura-Carmona
- Laboratorio Nacional de Investigación Para la Inocuidad Alimentaria (LANIIA) Unidad Nayarit, Universidad Autónoma de Nayarit, Tepic 63000, Mexico
| | - Migdalia Sarahy Navidad-Murrieta
- Laboratorio Nacional de Investigación Para la Inocuidad Alimentaria (LANIIA) Unidad Nayarit, Universidad Autónoma de Nayarit, Tepic 63000, Mexico
| | - Carlos Eduardo Covantes-Rosales
- Laboratorio Nacional de Investigación Para la Inocuidad Alimentaria (LANIIA) Unidad Nayarit, Universidad Autónoma de Nayarit, Tepic 63000, Mexico
| | - Manuel Ivan Giron-Pérez
- Laboratorio Nacional de Investigación Para la Inocuidad Alimentaria (LANIIA) Unidad Nayarit, Universidad Autónoma de Nayarit, Tepic 63000, Mexico
| |
Collapse
|
5
|
Dehesh P, Baradaran HR, Eshrati B, Motevalian SA, Salehi M, Donyavi T. The Relationship Between Population-Level SARS-CoV-2 Cycle Threshold Values and Trend of COVID-19 Infection: Longitudinal Study. JMIR Public Health Surveill 2022; 8:e36424. [PMID: 36240022 PMCID: PMC9645421 DOI: 10.2196/36424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/30/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND The distribution of population-level real-time reverse transcription-polymerase chain reaction (RT-PCR) cycle threshold (Ct) values as a proxy of viral load may be a useful indicator for predicting COVID-19 dynamics. OBJECTIVE The aim of this study was to determine the relationship between the daily trend of average Ct values and COVID-19 dynamics, calculated as the daily number of hospitalized patients with COVID-19, daily number of new positive tests, daily number of COVID-19 deaths, and number of hospitalized patients with COVID-19 by age. We further sought to determine the lag between these data series. METHODS The samples included in this study were collected from March 21, 2021, to December 1, 2021. Daily Ct values of all patients who were referred to the Molecular Diagnostic Laboratory of Iran University of Medical Sciences in Tehran, Iran, for RT-PCR tests were recorded. The daily number of positive tests and the number of hospitalized patients by age group were extracted from the COVID-19 patient information registration system in Tehran province, Iran. An autoregressive integrated moving average (ARIMA) model was constructed for the time series of variables. Cross-correlation analysis was then performed to determine the best lag and correlations between the average daily Ct value and other COVID-19 dynamics-related variables. Finally, the best-selected lag of Ct identified through cross-correlation was incorporated as a covariate into the autoregressive integrated moving average with exogenous variables (ARIMAX) model to calculate the coefficients. RESULTS Daily average Ct values showed a significant negative correlation (23-day time delay) with the daily number of newly hospitalized patients (P=.02), 30-day time delay with the daily number of new positive tests (P=.02), and daily number of COVID-19 deaths (P=.02). The daily average Ct value with a 30-day delay could impact the daily number of positive tests for COVID-19 (β=-16.87, P<.001) and the daily number of deaths from COVID-19 (β=-1.52, P=.03). There was a significant association between Ct lag (23 days) and the number of COVID-19 hospitalizations (β=-24.12, P=.005). Cross-correlation analysis showed significant time delays in the average Ct values and daily hospitalized patients between 18-59 years (23-day time delay, P=.02) and in patients over 60 years old (23-day time delay, P<.001). No statistically significant relation was detected in the number of daily hospitalized patients under 5 years old (9-day time delay, P=.27) and aged 5-17 years (13-day time delay, P=.39). CONCLUSIONS It is important for surveillance of COVID-19 to find a good indicator that can predict epidemic surges in the community. Our results suggest that the average daily Ct value with a 30-day delay can predict increases in the number of positive confirmed COVID-19 cases, which may be a useful indicator for the health system.
Collapse
Affiliation(s)
- Paria Dehesh
- Department of Epidemiology, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Reza Baradaran
- Department of Epidemiology, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
- Ageing Clinical and Experimental Research Team, Institute of Applied Health Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Babak Eshrati
- Department of Epidemiology, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
- Preventive Medicine and Public Health Research Center, Tehran, Iran
| | - Seyed Abbas Motevalian
- Department of Epidemiology, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Masoud Salehi
- Department of Biostatistics, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Tahereh Donyavi
- Department of Biotechnology, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
6
|
Mawhorter ME, Nguyen P, Goldsmith M, Owens RG, Baer B, Raman JD. Diagnostic yield and costs associated with a routine pre-operative COVID-19 testing algorithm for asymptomatic patients prior to elective surgery. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL UROLOGY 2022; 10:341-344. [PMID: 36313209 PMCID: PMC9605940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
OBJECTIVES Infection with COVID-19 presents known and unknown perioperative risks to the patient and operative staff. Pre-operative testing protocols have become widespread, yet little is known about the utility of this practice in asymptomatic patients undergoing elective surgery. We describe the impact and cost of a routine testing protocol on elective surgical procedures in a retrospective series at a single institution. METHODS Standardized pre-operative COVID-19 testing in all surgical patients was implemented in May 2020. Health system protocol required testing 3 to 5 days before all elective surgery. Data stratified by surgical specialty were collected over the initial 90-day period and disposition over a period of 6-months was assessed for all positive and indeterminate results. RESULTS Thirty-one (0.41%) positive results amongst 7579 pre-procedural tests, including 3 of 792 (0.38%) for urologic procedures, were noted in asymptomatic patients. Following a positive test, 20 procedures (62.5%) were delayed an average of 49 days, 8 were not performed and 3 proceeded without delay. All 3 urologic procedures were delayed a mean of 59 days. Institutional cost per test ranged from $34-$54. The number needed to test for one positive result was 244 with a cost of $11,573 for each positive result. CONCLUSIONS Institution of a universal pre-operative COVID-19 screening protocol for asymptomatic, unvaccinated patients undergoing elective surgery identified clinically silent infection in 0.4% of cases with a significant associated cost. Risk and symptom-based testing is likely a better strategy for triaging resources.
Collapse
Affiliation(s)
- Michael E Mawhorter
- Department of Urology, Penn State Health Milton S. Hershey Medical CenterHershey, PA, USA
| | - Paul Nguyen
- Department of Urology, Penn State Health Milton S. Hershey Medical CenterHershey, PA, USA
| | - Mackenzie Goldsmith
- Department of Urology, Penn State Health Milton S. Hershey Medical CenterHershey, PA, USA
| | - Russell Grant Owens
- Department of Urology, Penn State Health Milton S. Hershey Medical CenterHershey, PA, USA
- Department of Urology, University of IowaIowa, IA, USA
| | - Blake Baer
- Department of Urology, Penn State Health Milton S. Hershey Medical CenterHershey, PA, USA
| | - Jay D Raman
- Department of Urology, Penn State Health Milton S. Hershey Medical CenterHershey, PA, USA
| |
Collapse
|
7
|
Molina-Mora JA, González A, Jiménez-Morgan S, Cordero-Laurent E, Brenes H, Soto-Garita C, Sequeira-Soto J, Duarte-Martínez F. Clinical Profiles at the Time of Diagnosis of SARS-CoV-2 Infection in Costa Rica During the Pre-vaccination Period Using a Machine Learning Approach. PHENOMICS (CHAM, SWITZERLAND) 2022; 2:312-322. [PMID: 35692458 PMCID: PMC9173838 DOI: 10.1007/s43657-022-00058-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/22/2022] [Accepted: 04/27/2022] [Indexed: 04/16/2023]
Abstract
UNLABELLED The clinical manifestations of COVID-19, caused by the SARS-CoV-2, define a large spectrum of symptoms that are mainly dependent on the human host conditions. In Costa Rica, more than 169,000 cases and 2185 deaths were reported during the year 2020, the pre-vaccination period. To describe the clinical presentations at the time of diagnosis of SARS-CoV-2 infection in Costa Rica during the pre-vaccination period, we implemented a symptom-based clustering using machine learning to identify clusters or clinical profiles at the population level among 18,974 records of positive cases. Profiles were compared based on symptoms, risk factors, viral load, and genomic features of the SARS-CoV-2 sequence. A total of 18 symptoms at time of diagnosis of SARS-CoV-2 infection were reported with a frequency > 1%, and those were used to identify seven clinical profiles with a specific composition of clinical manifestations. In the comparison between clusters, a lower viral load was found for the asymptomatic group, while the risk factors and the SARS-CoV-2 genomic features were distributed among all the clusters. No other distribution patterns were found for age, sex, vital status, and hospitalization. In conclusion, during the pre-vaccination time in Costa Rica, the symptoms at the time of diagnosis of SARS-CoV-2 infection were described in clinical profiles. The host co-morbidities and the SARS-CoV-2 genotypes are not specific of a particular profile, rather they are present in all the groups, including asymptomatic cases. In addition, this information can be used for decision-making by the local healthcare institutions (first point of contact with health professionals, case definition, or infrastructure). In further analyses, these results will be compared against the profiles of cases during the vaccination period. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s43657-022-00058-x.
Collapse
Affiliation(s)
- Jose Arturo Molina-Mora
- Centro de Investigación en Enfermedades Tropicales (CIET) and Facultad de Microbiología, Universidad de Costa Rica, San José, 2060 Costa Rica
| | - Alejandra González
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, 30301 Costa Rica
| | | | - Estela Cordero-Laurent
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, 30301 Costa Rica
| | - Hebleen Brenes
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, 30301 Costa Rica
| | - Claudio Soto-Garita
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, 30301 Costa Rica
| | - Jorge Sequeira-Soto
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, 30301 Costa Rica
| | - Francisco Duarte-Martínez
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, 30301 Costa Rica
| |
Collapse
|
8
|
Dufour P, Paridaens H, Senterre JM, Minon JM. Relevance of cycle threshold values in mass screening by reverse-transcription-PCR during COVID-19 pandemic in Belgium: a decision-making support? Future Virol 2022. [PMID: 36172257 PMCID: PMC9491372 DOI: 10.2217/fvl-2022-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 09/06/2022] [Indexed: 11/21/2022]
Abstract
Aim: The Belgium’s strategy against COVID-19 was partly based on mass screening. Here, we reported the results observed in a Belgian mass screening center. Materials & methods: Between October 2020 and February 2021, 32,089 samples were collected analyzed with reverse-transcription PCR (Thermo Fisher Scientific kits and apparatus). Patients were categorized according to their contagiousness (extrapolated from the cycle threshold [Ct] values and the recommendation of Sciensano). Results: We observed association between Ct values and age, with higher Ct observed in extreme age groups (<6 years and >75 years). Conclusion: The analysis of the evolution of the contagiousness of these patients tested twice within a 7-day period showed the relevancy of the recommendation edited by Sciensano. The Belgium’s strategy against COVID-19 was partly based on mass screening performed with reverse-transcription PCR analysis performed on nasopharyngeal samples. Reverse-transcription PCR allows the detection of individuals infected by the virus. In addition, it provides semi quantitative results correlated to the quantity of virus present in the patient, these results are difficult to interpret for the patients and numerous practitioners. In our study, we showed that the interpretation of these results should take into account the age of the patients. We also showed that the semi quantitative result observed in a positive patient is not predictive of the evolution of the viral load (quantity of virus present in the organism) in the 7 following days.
Collapse
Affiliation(s)
- Patrice Dufour
- Department of Laboratory Medicine, Centre Hospitalier Régional de la Citadelle, Liège, 4000, Belgium
| | - Henry Paridaens
- Department of Laboratory Medicine, Centre Hospitalier Régional de la Citadelle, Liège, 4000, Belgium
| | - Jean-Marc Senterre
- Department of Laboratory Medicine, Centre Hospitalier Régional de la Citadelle, Liège, 4000, Belgium
| | - Jean-Marc Minon
- Department of Laboratory Medicine, Centre Hospitalier Régional de la Citadelle, Liège, 4000, Belgium
| |
Collapse
|
9
|
Fujita R, Kurosu H, Norizuki M, Ohishi T, Zamoto-Niikura A, Iwaki M, Mochida K, Takagi H, Harada T, Tsushima K, Matsumoto T, Hanaki KI, Sugai M, Yamagishi T. Potential risk of SARS-CoV-2 infection among people handling linens used by COVID-19 patients before and after washing. Sci Rep 2022; 12:14994. [PMID: 36056067 PMCID: PMC9438874 DOI: 10.1038/s41598-022-18945-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/22/2022] [Indexed: 11/18/2022] Open
Abstract
The risk of SARS-CoV-2 infection when people handle linens is uncertain. We examined the presence of SARS-CoV-2 on linens, in the air, and on personal protective equipment (PPE) to assess potential infection risk among individuals who handle linens used by SARS-CoV-2-infected people. Patients in a hospital and an accommodation facility who tested positive for SARS-CoV-2 participated in this study in 2020. Linen samples before washing or disinfection, rinse water after washing or disinfection, air in the workplace at the hospital and an accommodation facility, and the PPE worn by linen-handling people were tested for SARS-CoV-2 RNA and viable viruses. Among 700 samples from 13 SARS-CoV-2-infected participants and their surrounding environment, SARS-CoV-2 RNA was detected from 14% (52/362) of the linens used by COVID-19 patients (cycle threshold [Ct] value: 33-40). SARS-CoV-2 RNA was detected from 8% (2/26) of rinse water after washing or disinfection, from 15% (16/104) of air samples in the workspace, and from 10% (5/52) of gowns worn by linen-handling people, all with high Ct values (> 36). No SARS-CoV-2 was isolated from any samples. The potential risk of SARS-CoV-2 infection from handling linens used by SARS-CoV-2-infected people exists but appears to below.
Collapse
Affiliation(s)
- Retsu Fujita
- Graduate School of Medicine, International University of Health and Welfare, 4-1-26, Akasaka, Minato-ku, Tokyo, 107-8402, Japan
| | - Hitomi Kurosu
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640, Japan
| | - Masataro Norizuki
- Graduate School of Medicine, International University of Health and Welfare, 4-1-26, Akasaka, Minato-ku, Tokyo, 107-8402, Japan
- Bureau of International Health Cooperation, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku, Tokyo, 162-8655, Japan
| | - Takayuki Ohishi
- Department of Infection Control and Prevention, Saiseikai Yokohama City Eastern Hospital, 3-6-1 Shimosueyoshi, Tsurumiku, Yokohama, Kanagawa, 230-8765, Japan
| | - Aya Zamoto-Niikura
- Management Department of Biosafety , Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640, Japan
| | - Masaaki Iwaki
- Management Department of Biosafety , Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640, Japan
| | - Keiko Mochida
- Management Department of Biosafety , Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640, Japan
| | - Hirotaka Takagi
- Management Department of Biosafety , Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640, Japan
| | - Toshihiko Harada
- Management Department of Biosafety , Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640, Japan
| | - Kenji Tsushima
- International University of Health and Welfare Narita Hospital, 852 Hatakeda, Narita, Chiba, 286-8520, Japan
| | - Tetsuya Matsumoto
- International University of Health and Welfare Narita Hospital, 852 Hatakeda, Narita, Chiba, 286-8520, Japan
| | - Ken-Ichi Hanaki
- Management Department of Biosafety , Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640, Japan
| | - Motoyuki Sugai
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640, Japan
| | - Takuya Yamagishi
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640, Japan.
| |
Collapse
|
10
|
Clinical evaluation of Sofia Rapid Antigen Assay for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among emergency department to hospital admissions. Infect Control Hosp Epidemiol 2022; 43:968-973. [PMID: 34162449 PMCID: PMC8376850 DOI: 10.1017/ice.2021.281] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
OBJECTIVE To determine the utility of the Sofia SARS rapid antigen fluorescent immunoassay (FIA) to guide hospital-bed placement of patients being admitted through the emergency department (ED). DESIGN Cross-sectional analysis of a clinical quality improvement study. SETTING This study was conducted in 2 community hospitals in Maryland from September 21, 2020, to December 3, 2020. In total, 2,887 patients simultaneously received the Sofia SARS rapid antigen FIA and SARS-CoV-2 RT-PCR assays on admission through the ED. METHODS Rapid antigen results and symptom assessment guided initial patient placement while confirmatory RT-PCR was pending. The sensitivity, specificity, positive predictive values, and negative predictive values of the rapid antigen assay were calculated relative to RT-PCR, overall and separately for symptomatic and asymptomatic patients. Assay sensitivity was compared to RT-PCR cycle threshold (Ct) values. Assay turnaround times were compared. Clinical characteristics of RT-PCR-positive patients and potential exposures from false-negative antigen assays were evaluated. RESULTS For all patients, overall agreement was 97.9%; sensitivity was 76.6% (95% confidence interval [CI], 71%-82%), and specificity was 99.7% (95% CI, 99%-100%). We detected no differences in performance between asymptomatic and symptomatic individuals. As RT-PCR Ct increased, the sensitivity of the antigen assay decreased. The mean turnaround time for the antigen assay was 1.2 hours (95% CI, 1.0-1.3) and for RT-PCR it was 20.1 hours (95% CI, 18.9-40.3) (P < .001). No transmission from antigen-negative/RT-PCR-positive patients was identified. CONCLUSIONS Although not a replacement for RT-PCR for detection of all SARS-CoV-2 infections, the Sofia SARS antigen FIA has clinical utility for potential initial timely patient placement.
Collapse
|
11
|
Verma MK, Roychowdhury S, Sahu BD, Mishra A, Sethi KK. CRISPR-based point-of-care diagnostics incorporating Cas9, Cas12, and Cas13 enzymes advanced for SARS-CoV-2 detection. J Biochem Mol Toxicol 2022; 36:e23113. [PMID: 35642647 PMCID: PMC9347549 DOI: 10.1002/jbt.23113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/16/2022] [Accepted: 05/18/2022] [Indexed: 11/24/2022]
Abstract
An outbreak of the novel beta coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) first came to light in December 2019, which has unfolded rapidly and turned out to be a global pandemic. Early prognosis of viral contamination involves speedy intervention, disorder control, and good-sized management of the spread of disease. Reverse transcription-polymerase chain reaction, considered the gold standard test for detecting nucleic acids and pathogen diagnosis, provides high sensitivity and specificity. However, reliance on high-priced equipped kits, associated reagents, and skilled personnel slow down sickness detection. Lately, the improvement of clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated protein)-based diagnostic systems has reshaped molecular diagnosis due to their low cost, simplicity, speed, efficiency, high sensitivity, specificity, and versatility, which is vital for accomplishing point-of-care diagnostics. We reviewed and summarized CRISPR-Cas-based point-of-care diagnostic strategies and research in these paintings while highlighting their characteristics and challenges for identifying SARS-CoV-2.
Collapse
Affiliation(s)
- Monika K. Verma
- Department of Medicinal ChemistryNational Institute of Pharmaceutical Education and Research (NIPER)—Guwahati, Changsari, KamrupGuwahatiAssamIndia
| | - Sanjana Roychowdhury
- Department of Medicinal ChemistryNational Institute of Pharmaceutical Education and Research (NIPER)—Guwahati, Changsari, KamrupGuwahatiAssamIndia
| | - Bidya Dhar Sahu
- Department of Pharmacology and ToxicologyNational Institute of Pharmaceutical Education and Research (NIPER)—Guwahati, Changsari, KamrupGuwahatiAssamIndia
| | - Awanish Mishra
- Department of Pharmacology and ToxicologyNational Institute of Pharmaceutical Education and Research (NIPER)—Guwahati, Changsari, KamrupGuwahatiAssamIndia
| | - Kalyan K. Sethi
- Department of Medicinal ChemistryNational Institute of Pharmaceutical Education and Research (NIPER)—Guwahati, Changsari, KamrupGuwahatiAssamIndia
| |
Collapse
|
12
|
Pu Y, Weng Y, Wu Y, Gao F, Zheng X, Xiong X, Lv H, Kong Q. Antibody Response to SARS-CoV-2 in the First Batch of COVID-19 Patients in China by a Self-Developed Rapid IgM-IgG Test. Front Cell Infect Microbiol 2022; 12:915751. [PMID: 35719335 PMCID: PMC9204641 DOI: 10.3389/fcimb.2022.915751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 04/28/2022] [Indexed: 12/02/2022] Open
Abstract
It has been over two years since the COVID-19 pandemic began and it is still an unprecedented global challenge. Here, we aim to characterize the antibody profile from a large batch of early COVID-19 cases in China, from January – March 2020. More than 1,000 serum samples from participants in Hubei and Zhejiang province were collected. A series of serum samples were also collected along the disease course from 70 patients in Shanghai and Chongqing for longitudinal analysis. The serologic assay (ALLtest) we developed was confirmed to have high sensitivity (92.58% - 97.55%) and high specificity (92.14% - 96.28%) for the detection of SARS-CoV-2 nucleocapsid-specific antibodies. Confirmed cases found in the Hubei Provincial Center for Disease Control and Prevention (HBCDC), showed a significantly (p = 0.0018) higher positive rate from the ALLtest than RNA test. Then, we further identified the disease course, age, sex, and symptoms that were correlating factors with our ALLtest results. In summary, we confirmed the high reliability of our ALLtest and its important role in COVID-19 diagnosis. The correlating factors we identified will require special attention during future clinical application.
Collapse
Affiliation(s)
- Yiyi Pu
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
| | - Youhong Weng
- Institute of Parasitic Diseases, Hangzhou Medical College, Hangzhou, China
| | - Yahan Wu
- Institute of Parasitic Diseases, Hangzhou Medical College, Hangzhou, China
| | - Fei Gao
- Department of Research and Development, Hangzhou AllTest Biotech Co., Ltd, Hangzhou, China
| | - Xiaojun Zheng
- Department of Research and Development, Hangzhou AllTest Biotech Co., Ltd, Hangzhou, China
| | - Xianqin Xiong
- Department of Research and Development, Hangzhou AllTest Biotech Co., Ltd, Hangzhou, China
| | - Hangjun Lv
- Institute of Parasitic Diseases, Hangzhou Medical College, Hangzhou, China
| | - Qingming Kong
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China.,Institute of Parasitic Diseases, Hangzhou Medical College, Hangzhou, China
| |
Collapse
|
13
|
Ur Rehman M, Sajjad Naqvi S, Ullah R, Arshad N, Ammad M, Ul Ain Q, Razzak A, Yousaf M, Hussain A, Hasan TN. Elucidation of correlation between SARS-CoV-2 RdRp and N gene cycle threshold (Ct) by RT-PCR with age and gender. Clin Chim Acta 2022; 533:42-47. [PMID: 35714938 PMCID: PMC9195597 DOI: 10.1016/j.cca.2022.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/05/2022] [Indexed: 11/05/2022]
Abstract
Background Coronavirus disease 2019 (COVID19) caused by the new severe acute respiratory syndrome coronavirus 2 (SARSCoV2) is a global public health emergency. Age and gender are two important factors related to the risk and outcome of various diseases. Cycle threshold (Ct) value is believed to have relation with age and gender. Objective This study has been conducted to investigates the association between SARS-CoV-2 cycle threshold to age and gender of COVID-19 patients, to investigate whether the population-wide change of SARSCoV2 RTPCR Ct value over time is corelated to the number of new COVID19 cases and to investigate the dynamic of RdRp and N genes. Methods 72,811 individuals from second wave of COVID19, were observed in current study at Pure Health Lab, Mafraq Hospital, Abu Dhabi, UAE. Results 15,201/72,811 (21 %) positivity was observed. COVID-19 were more prevalent in males (59.35%) as compared to female (40.65%). The Positivity rate were significantly higher in Male than in Female cases (p-Value = 0.04). The Ct values for both targets of all the samples were ranged from 4.57 to 29.73. Longitudinal analysis showed significant increased during the study period from starting to end as were hypothesized. Interestingly, both the targets (RdRp and N) were present in age < 1 year. Which may indicate that mutated strains are not prevalent in children’s < 1 year. Conclusion There was no statistically significant difference in viral loads in between age-groups. Males were tending to higher viral load compared to females. The findings have implications for preventive strategies.
Collapse
Affiliation(s)
- Mati Ur Rehman
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates.
| | - Syed Sajjad Naqvi
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates.
| | - Rooh Ullah
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates.
| | - Narmeen Arshad
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates.
| | - Muhammad Ammad
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates.
| | - Qurat Ul Ain
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates.
| | - Anam Razzak
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates.
| | - Muhammad Yousaf
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates.
| | - Arif Hussain
- School of Life Science, Manipal Academy of Higher Education, Dubai, UAE.
| | - Tarique N Hasan
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates; School of Life Science, Manipal Academy of Higher Education, Dubai, UAE.
| |
Collapse
|
14
|
Casati B, Verdi JP, Hempelmann A, Kittel M, Klaebisch AG, Meister B, Welker S, Asthana S, Di Giorgio S, Boskovic P, Man KH, Schopp M, Ginno PA, Radlwimmer B, Stebbins CE, Miethke T, Papavasiliou FN, Pecori R. Rapid, adaptable and sensitive Cas13-based COVID-19 diagnostics using ADESSO. Nat Commun 2022; 13:3308. [PMID: 35676259 PMCID: PMC9176161 DOI: 10.1038/s41467-022-30862-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 05/23/2022] [Indexed: 12/14/2022] Open
Abstract
During the ongoing COVID-19 pandemic, PCR testing and antigen tests have proven critical for helping to stem the spread of its causative agent, SARS-CoV-2. However, these methods suffer from either general applicability and/or sensitivity. Moreover, the emergence of variant strains creates the need for flexibility to correctly and efficiently diagnose the presence of substrains. To address these needs we developed the diagnostic test ADESSO (Accurate Detection of Evolving SARS-CoV-2 through SHERLOCK (Specific High Sensitivity Enzymatic Reporter UnLOCKing) Optimization) which employs Cas13 to diagnose patients in 1 h without sophisticated equipment. Using an extensive panel of clinical samples, we demonstrate that ADESSO correctly identifies infected individuals at a sensitivity and specificity comparable to RT-qPCR on extracted RNA and higher than antigen tests for unextracted samples. Altogether, ADESSO is a fast, sensitive and cheap method that can be applied in a point of care setting to diagnose COVID-19 and can be quickly adjusted to detect new variants.
Collapse
Affiliation(s)
- Beatrice Casati
- Division of Immune Diversity, Department of Immunology and Cancer, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Joseph Peter Verdi
- Division of Immune Diversity, Department of Immunology and Cancer, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Division of Structural Biology of Infection and Immunity, Department of Immunology and Cancer, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
| | - Alexander Hempelmann
- Division of Structural Biology of Infection and Immunity, Department of Immunology and Cancer, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
| | - Maximilian Kittel
- Institute of Clinical Chemistry, Medical Faculty of Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty of Mannheim, University of Heidelberg, Ludolf-Krehl-Str. 13-17, 68167, Mannheim, Germany
| | - Andrea Gutierrez Klaebisch
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty of Mannheim, University of Heidelberg, Ludolf-Krehl-Str. 13-17, 68167, Mannheim, Germany
- Institute of Medical Microbiology and Hygiene, Medical Faculty of Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Bianca Meister
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty of Mannheim, University of Heidelberg, Ludolf-Krehl-Str. 13-17, 68167, Mannheim, Germany
- Institute of Medical Microbiology and Hygiene, Medical Faculty of Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Sybille Welker
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty of Mannheim, University of Heidelberg, Ludolf-Krehl-Str. 13-17, 68167, Mannheim, Germany
- Institute of Medical Microbiology and Hygiene, Medical Faculty of Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Sonal Asthana
- Division of Immune Diversity, Department of Immunology and Cancer, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
| | - Salvatore Di Giorgio
- Division of Immune Diversity, Department of Immunology and Cancer, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
| | - Pavle Boskovic
- Division of Molecular Genetics, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
| | - Ka Hou Man
- Division of Molecular Genetics, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
| | - Meike Schopp
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Paul Adrian Ginno
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Bernhard Radlwimmer
- Division of Molecular Genetics, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
| | - Charles Erec Stebbins
- Division of Structural Biology of Infection and Immunity, Department of Immunology and Cancer, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
| | - Thomas Miethke
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty of Mannheim, University of Heidelberg, Ludolf-Krehl-Str. 13-17, 68167, Mannheim, Germany.
- Institute of Medical Microbiology and Hygiene, Medical Faculty of Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany.
| | - Fotini Nina Papavasiliou
- Division of Immune Diversity, Department of Immunology and Cancer, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany.
| | - Riccardo Pecori
- Division of Immune Diversity, Department of Immunology and Cancer, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany.
| |
Collapse
|
15
|
Petersen J, Jhala D. COVID-19 Cycle Threshold/Cycle Number Testing at a Community Living Center. Fed Pract 2022; 39:254-260. [PMID: 36404943 PMCID: PMC9648608 DOI: 10.12788/fp.0276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
BACKGROUND COVID-19 imposes a special risk to the nursing home population, including community living centers (CLCs) for veterans. Cycle threshold/cycle number (CT/CN) values obtained by serial reverse transcriptase polymerase chain reaction (RT-PCR) testing could yield valuable information about viral load and potential infectiousness. Serial testing for COVID-19 with CT/CN correlates in a nursing home population during an outbreak has not yet been reported in the literature. METHODS A retrospective review of serial RT-PCR testing for COVID-19 during an outbreak at a CLC was performed from March 28 to April 4, 2020, with follow-up of identified patients until November 10, 2020. Testing was performed on the Abbot m2000 or Cepheid platform. RESULTS Of 80 patients tested, 25 (31%) were positive for COVID-19. CT/CN values corresponded to the infection course as expected. CONCLUSIONS Repeat testing for COVID-19 accompanied by CT/CN values could provide clinical and epidemiologic information about the likely stage of the patients' disease course, which may aid public health measures and clinical management.
Collapse
Affiliation(s)
- Jeffrey Petersen
- Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, Pennsylvania
- University of Pennsylvania, Philadelphia
| | - Darshana Jhala
- Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, Pennsylvania
- University of Pennsylvania, Philadelphia
| |
Collapse
|
16
|
Chrzastek K, Tennakoon C, Bialy D, Freimanis G, Flannery J, Shelton H. A random priming amplification method for whole genome sequencing of SARS-CoV-2 virus. BMC Genomics 2022; 23:406. [PMID: 35644636 PMCID: PMC9148844 DOI: 10.1186/s12864-022-08563-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 03/24/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Non-targeted whole genome sequencing is a powerful tool to comprehensively identify constituents of microbial communities in a sample. There is no need to direct the analysis to any identification before sequencing which can decrease the introduction of bias and false negatives results. It also allows the assessment of genetic aberrations in the genome (e.g., single nucleotide variants, deletions, insertions and copy number variants) including in noncoding protein regions. METHODS The performance of four different random priming amplification methods to recover RNA viral genetic material of SARS-CoV-2 were compared in this study. In method 1 (H-P) the reverse transcriptase (RT) step was performed with random hexamers whereas in methods 2-4 RT incorporating an octamer primer with a known tag. In methods 1 and 2 (K-P) sequencing was applied on material derived from the RT-PCR step, whereas in methods 3 (SISPA) and 4 (S-P) an additional amplification was incorporated before sequencing. RESULTS The SISPA method was the most effective and efficient method for non-targeted/random priming whole genome sequencing of SARS-CoV-2 that we tested. The SISPA method described in this study allowed for whole genome assembly of SARS-CoV-2 and influenza A(H1N1)pdm09 in mixed samples. We determined the limit of detection and characterization of SARS-CoV-2 virus which was 103 pfu/ml (Ct, 22.4) for whole genome assembly and 101 pfu/ml (Ct, 30) for metagenomics detection. CONCLUSIONS The SISPA method is predominantly useful for obtaining genome sequences from RNA viruses or investigating complex clinical samples as no prior sequence information is needed. It might be applied to monitor genomic virus changes, virus evolution and can be used for fast metagenomics detection or to assess the general picture of different pathogens within the sample.
Collapse
Affiliation(s)
| | | | - Dagmara Bialy
- The Pirbright Institute, Pirbright, Woking, Surrey, UK
| | | | - John Flannery
- The Pirbright Institute, Pirbright, Woking, Surrey, UK
| | - Holly Shelton
- The Pirbright Institute, Pirbright, Woking, Surrey, UK.
| |
Collapse
|
17
|
Verwilt J, Hellemans J, Sante T, Mestdagh P, Vandesompele J. Evaluation of efficiency and sensitivity of 1D and 2D sample pooling strategies for SARS-CoV-2 RT-qPCR screening purposes. Sci Rep 2022; 12:6603. [PMID: 35459775 PMCID: PMC9033859 DOI: 10.1038/s41598-022-10581-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/06/2022] [Indexed: 11/22/2022] Open
Abstract
To increase the throughput, lower the cost, and save scarce test reagents, laboratories can pool patient samples before SARS-CoV-2 RT-qPCR testing. While different sample pooling methods have been proposed and effectively implemented in some laboratories, no systematic and large-scale evaluations exist using real-life quantitative data gathered throughout the different epidemiological stages. Here, we use anonymous data from 9673 positive cases to model, simulate and compare 1D and 2D pooling strategies. We show that the optimal choice of pooling method and pool size is an intricate decision with a testing population-dependent efficiency-sensitivity trade-off and present an online tool to provide the reader with custom real-time 1D pooling strategy recommendations.
Collapse
Affiliation(s)
- Jasper Verwilt
- OncoRNALab, Cancer Research Institute Ghent, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Center for Medical Genetics, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Jan Hellemans
- Biogazelle, Technologiepark 82, 9052, Zwijnaarde, Belgium
| | - Tom Sante
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Center for Medical Genetics, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Pieter Mestdagh
- OncoRNALab, Cancer Research Institute Ghent, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Center for Medical Genetics, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Biogazelle, Technologiepark 82, 9052, Zwijnaarde, Belgium
| | - Jo Vandesompele
- OncoRNALab, Cancer Research Institute Ghent, Corneel Heymanslaan 10, 9000, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium.
- Center for Medical Genetics, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium.
- Biogazelle, Technologiepark 82, 9052, Zwijnaarde, Belgium.
| |
Collapse
|
18
|
Takahashi H, Ichinose N, Okada Y. False-negative rate of SARS-CoV-2 RT-PCR tests and its relationship to test timing and illness severity: A case series. IDCases 2022; 28:e01496. [PMID: 35402162 PMCID: PMC8982474 DOI: 10.1016/j.idcr.2022.e01496] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 04/01/2022] [Accepted: 04/02/2022] [Indexed: 11/29/2022] Open
Abstract
Objective To determine the false-negative rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse-transcription polymerase chain reaction (RT-PCR) test results, and to describe the characteristics of coronavirus disease 2019 (COVID-19) patients with false-negative results. Methods We validated SARS-CoV-2-positive RT-PCR test results performed in hospitalized patients between February 1 and August 31, 2020 and classified the patients according to disease severity. Results In total, 2038 SARS-CoV-2 RT-PCR tests were performed on 1890 patients. Of these, 145 patients had positive results and were diagnosed with COVID-19. Among the 145 patients with COVID-19, the initial RT-PCR tests were negative in five patients. Of these, three had moderate illness and were initially tested in the early stage of disease, and two had severe illness and were initially tested in the late stage of disease, when RT-PCR testing has lower sensitivity due to viral clearance. Conclusions These findings suggest that false-negative results can be caused by both observer errors and by low viral RNA levels in the later stages of disease, after the infection has cleared. Clinicians should be aware that patients with COVID-19 can have negative RT-PCR test results in the later stages of infection. All SARS-CoV-2 RT-PCR test results of hospitalized COVID-19 patients were reviewed. Of 145 confirmed COVID-19 cases, 5 (3.45%) had a negative first RT-PCR test result. Of the 5 patients, 3 with moderate disease first tested soon after symptom onset. The initial testing was delayed in 2 patients with severe/critical disease. False-negative results can occur in deteriorating patients who have delayed testing.
Collapse
Affiliation(s)
- Hidenori Takahashi
- Department of Infection Control and Prevention, Showa General Hospital, Kodaira, Japan
| | - Naoki Ichinose
- Department of Infection Control and Prevention, Showa General Hospital, Kodaira, Japan
| | - Yasusei Okada
- Department of Critical Care and Emergency Medicine, Showa General Hospital, Kodaira, Japan
| |
Collapse
|
19
|
He Y, Xie T, Tu Q, Tong Y. Importance of sample input volume for accurate SARS-CoV-2 qPCR testing. Anal Chim Acta 2022; 1199:339585. [PMID: 35227385 PMCID: PMC8820412 DOI: 10.1016/j.aca.2022.339585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/30/2022] [Accepted: 02/05/2022] [Indexed: 11/26/2022]
Abstract
Nucleic acid testing is the most widely used detection method for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19) pandemic. Currently, a number of COVID-19 real-time quantitative reverse transcription PCR (qPCR) kits with high sensitivity and specificity are available for SARS-CoV-2 testing. However, these qPCR assays are not always reliable in detecting low viral load samples (Ct-value ≥ 35), resulting in inconclusive or false-negative results. Here, we used a Poisson distribution to illustrate the inconsistent performance of qPCR tests in detecting low viral load samples. From this, we concluded that the false-negative outcomes resulted from the random occurrences of sampling zero target molecules in a single test, and the probability to sample zero target molecules in one test decreased significantly with increasing purified RNA or initial sample input volume. At a given RNA concentration of 0.5 copy/μL, the probability of sampling zero RNA molecules decreased from 36.79% to close to 0.67% after increasing the RNA input volume from 2 to 10 μL. A SARS-CoV-2 qPCR assay with an LOD of 300 copies/mL was used to validate the improved consistency of the qPCR tests. We found that the false-negative qPCR results of clinical COVID-19 samples with a Ct ≥ 35 decreased by 50% after increasing the input of purified RNA from 2 to 10 μL. The consistency, accuracy, and robustness of nucleic acid testing for SARS-CoV-2 samples with low viral loads can be improved by increasing the sample input volume.
Collapse
|
20
|
Mack CD, Wasserman EB, Hostler CJ, Solomon G, Anderson DJ, Walton P, Hawaldar K, Myers E, Best M, Eichner D, Mayer T, Sills A. Effectiveness and Use of
RT‐PCR
Point of Care Testing in a
Large‐Scale COVID
‐19 Surveillance System. Pharmacoepidemiol Drug Saf 2022; 31:511-518. [PMID: 35225407 PMCID: PMC9088538 DOI: 10.1002/pds.5424] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 01/28/2022] [Accepted: 02/25/2022] [Indexed: 12/01/2022]
Abstract
Background Rapid COVID‐19 testing platforms can identify infected individuals at the point of care (POC), allowing immediate isolation of infected individuals and reducing the risk of transmission. While lab‐based nucleic acid amplification testing (NAAT) is often considered the gold standard to detect SARS‐CoV‐2 in the community, results typically take 2–7 days to return, rendering POC testing a critical diagnostic tool for infection control. The National Football League (NFL) and NFL Players Association deployed a new POC testing strategy using a newly available reverse transcriptase polymerase chain reaction (RT‐PCR) rapid test during the 2020 season, and evaluated diagnostic effectiveness compared to other available devices using real‐world population surveillance data. Methods RT‐PCR POC test results were compared to NAAT results from same‐day samples by calculation of positive and negative concordance. Sensitivity analyses were performed for three subgroups: (1) individuals symptomatic at time of positive test; (2) individuals tested during the pilot phase of rollout; and (3) individuals tested daily. Results Among 4989 same‐day POC/NAAT pairs, 4957 (99.4%) were concordant, with 93.1% positive concordance and 99.6% negative concordance. Based on adjudicated case status, the false negative rate was 0.2% and false positive rate was 2.9%. In 43 instances, the immediate turnaround of results by POC allowed isolation of infected individuals 1 day sooner than lab‐based testing. Positive/negative concordance in sensitivity analyses were relatively stable. Conclusion RT‐PCR POC testing provided timely results that were highly concordant with lab‐based NAAT in population surveillance. Expanded use of effective RT‐PCR POC can enable rapid isolation of infected individuals and reduce COVID‐19 infection in the community.
Collapse
Affiliation(s)
| | | | - Christopher J. Hostler
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Duke University School of Medicine Durham NC USA
- Infectious Diseases Section, Durham VA Health Care System Durham NC USA
- Infection Control Education for Major Sports, LLC Chapel Hill NC USA
| | - Gary Solomon
- Player Health and Safety Department National Football League New York City NY USA
| | - Deverick J. Anderson
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Duke University School of Medicine Durham NC USA
- Infection Control Education for Major Sports, LLC Chapel Hill NC USA
| | | | | | - Emily Myers
- Player Health and Safety Department National Football League New York City NY USA
| | - Michele Best
- University of Maryland Medical System Baltimore MD USA
| | - Daniel Eichner
- Sports Medicine Research and Testing Laboratory, University Research Park Salt Lake City UT USA
| | - Thom Mayer
- Duke University School of Medicine Durham NC USA
- National Football League Players Association Washington, D.C. USA
| | - Allen Sills
- Player Health and Safety Department National Football League New York City NY USA
| |
Collapse
|
21
|
Euser S, Aronson S, Manders I, van Lelyveld S, Herpers B, Sinnige J, Kalpoe J, van Gemeren C, Snijders D, Jansen R, Schuurmans Stekhoven S, van Houten M, Lede I, Cohen Stuart J, Slijkerman Megelink F, Kapteijns E, den Boer J, Sanders E, Wagemakers A, Souverein D. SARS-CoV-2 viral-load distribution reveals that viral loads increase with age: a retrospective cross-sectional cohort study. Int J Epidemiol 2022; 50:1795-1803. [PMID: 34999848 PMCID: PMC8499942 DOI: 10.1093/ije/dyab145] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/28/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Describing the SARS-CoV-2 viral-load distribution in different patient groups and age categories. METHODS All results from first nasopharyngeal (NP) and oropharyngeal (OP) swabs from unique patients tested via SARS-CoV-2 reverse transcriptase polymerase chain reaction (RT-PCR) collected between 1 January and 1 December 2020 predominantly in the Public Health Services regions Kennemerland and Hollands Noorden, province of North Holland, the Netherlands, were included in this study. SARS-CoV-2 PCR crossing-point (Cp)-values were used to estimate viral loads. RESULTS In total, 278 455 unique patients were tested, of whom 9.1% (n = 25.374) were SARS-CoV-2-positive. PCRs performed by Public Health Services (n = 211 914), in which sampling and inclusion were uniform, revealed a clear relation between age and SARS-CoV-2 viral load, with especially children aged <12 years showing lower viral loads than adults (β: -0.03, 95% confidence interval: -0.03 to -0.02, p < 0.001), independently of sex and/or symptom duration. Interestingly, the median Cp-values between the >79- and <12-year-old populations differed by more than four PCR cycles, suggesting an ∼16-fold difference in viral load. In addition, the proportion of children aged <12 years with a low load (Cp-value >30) was higher compared with other patients (31.1% vs 17.2%, p-value < 0.001). CONCLUSIONS In patients tested by Public Health Services, SARS-CoV-2 viral load increases with age. Further studies should elucidate whether the lower viral load in children is indeed related to their suggested limited role in SARS-CoV-2 transmission. Moreover, as rapid antigen tests are less sensitive than PCR, these results suggest that SARS-CoV-2 antigen tests have lower sensitivity in children than in adults.
Collapse
Affiliation(s)
- Sjoerd Euser
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Sem Aronson
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
- Department of Internal Medicine, Spaarne Gasthuis, Hoofddorp/Haarlem, The Netherlands
| | - Irene Manders
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
- Department of Infectious Diseases, Public Health Service Kennemerland, Haarlem, The Netherlands
| | - Steven van Lelyveld
- Department of Internal Medicine, Spaarne Gasthuis, Hoofddorp/Haarlem, The Netherlands
| | - Bjorn Herpers
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Jan Sinnige
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Jayant Kalpoe
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | | | - Dominic Snijders
- Department of Pulmonary Disease, Spaarne Gasthuis, Hoofddorp/Haarlem, the Netherlands
| | - Ruud Jansen
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | | | - Marlies van Houten
- Department of Pediatrics, Spaarne Gasthuis, Hoofddorp/Haarlem, the Netherlands
| | - Ivar Lede
- Department of Medical Microbiology, Comicro BV Medical Microbiology, Hoorn, The Netherlands
| | - James Cohen Stuart
- Department of Medical Microbiology, Noordwest Ziekenhuisgroep, Alkmaar, The Netherlands
| | - Fred Slijkerman Megelink
- Department of Infectious Diseases, Public Health Service Hollands Noorden, Alkmaar, The Netherlands
| | - Erik Kapteijns
- Department of Pulmonary Disease, Rode Kruis Ziekenhuis, Beverwijk, The Netherlands
| | - Jeroen den Boer
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Elisabeth Sanders
- Department of Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Alex Wagemakers
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Dennis Souverein
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| |
Collapse
|
22
|
Ford L, Whaley MJ, Shah MM, Salvatore PP, Segaloff HE, Delaney A, Currie DW, Boyle-Estheimer L, O'Hegarty M, Morgan CN, Meece J, Ivacic L, Thornburg NJ, Tamin A, Harcourt JL, Folster JM, Medrzycki M, Jain S, Wong P, Goffard K, Gieryn D, Kahrs J, Langolf K, Zochert T, Tate JE, Hsu CH, Kirking HL. Antigen Test Performance Among Children and Adults at a SARS-CoV-2 Community Testing Site. J Pediatric Infect Dis Soc 2021; 10:1052-1061. [PMID: 34468732 PMCID: PMC8932441 DOI: 10.1093/jpids/piab081] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/18/2021] [Indexed: 01/02/2023]
Abstract
BACKGROUND Performance characteristics of SARS-CoV-2 antigen tests among children are limited despite the need for point-of-care testing in school and childcare settings. We describe children seeking SARS-CoV-2 testing at a community site and compare antigen test performance to real-time reverse transcription-polymerase chain reaction (RT-PCR) and viral culture. METHODS Two anterior nasal specimens were self-collected for BinaxNOW antigen and RT-PCR testing, along with demographics, symptoms, and exposure information from individuals ≥5 years at a community testing site. Viral culture was attempted on residual antigen or RT-PCR-positive specimens. Demographic and clinical characteristics, and the performance of SARS-CoV-2 antigen tests, were compared among children (<18 years) and adults. RESULTS About 1 in 10 included specimens were from children (225/2110); 16.4% (37/225) were RT-PCR-positive. Cycle threshold values were similar among RT-PCR-positive specimens from children and adults (22.5 vs 21.3, P = .46) and among specimens from symptomatic and asymptomatic children (22.5 vs 23.2, P = .39). Sensitivity of antigen test compared to RT-PCR was 73.0% (27/37) among specimens from children and 80.8% (240/297) among specimens from adults; among specimens from children, specificity was 100% (188/188), positive and negative predictive values were 100% (27/27) and 94.9% (188/198), respectively. Virus was isolated from 51.4% (19/37) of RT-PCR-positive pediatric specimens; all 19 had positive antigen test results. CONCLUSIONS With lower sensitivity relative to RT-PCR, antigen tests may not diagnose all positive COVID-19 cases; however, antigen testing identified children with live SARS-CoV-2 virus.
Collapse
Affiliation(s)
- Laura Ford
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA,Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Melissa J. Whaley
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Melisa M. Shah
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA,Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Phillip P. Salvatore
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA,Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Hannah E. Segaloff
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA,Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA,Bureau of Communicable Diseases, Wisconsin Department of Health Services, Madison, Wisconsin, USA
| | - Augustina Delaney
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Dustin W. Currie
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA,Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lauren Boyle-Estheimer
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michelle O'Hegarty
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Clint N. Morgan
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jennifer Meece
- Integrated Research and Development Laboratory, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
| | - Lynn Ivacic
- Integrated Research and Development Laboratory, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
| | - Natalie J. Thornburg
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Azaibi Tamin
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jennifer L. Harcourt
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jennifer M. Folster
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Magdalena Medrzycki
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Shilpi Jain
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Phili Wong
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Douglas Gieryn
- Winnebago County Health Department, Oshkosh, Wisconsin, USA
| | - Juliana Kahrs
- Student Recreation and Wellness, University of Wisconsin-Oshkosh, Oshkosh, Wisconsin, USA
| | - Kimberly Langolf
- Sponsored Programs and Risk and Safety, University of Wisconsin-Oshkosh, Oshkosh, Wisconsin, USA
| | - Tara Zochert
- Sponsored Programs and Risk and Safety, University of Wisconsin-Oshkosh, Oshkosh, Wisconsin, USA
| | - Jacqueline E. Tate
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Christopher H. Hsu
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Hannah L. Kirking
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| |
Collapse
|
23
|
Storms SM, Lowe JF. Active environmental surveillance of SARS-CoV-2 in Midwestern United States meatpacking plants. PLoS One 2021; 16:e0261704. [PMID: 34972125 PMCID: PMC8719691 DOI: 10.1371/journal.pone.0261704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/07/2021] [Indexed: 11/18/2022] Open
Abstract
This pilot project investigated environmental SARS-CoV-2 presence in seven Midwestern meatpacking plants from May 2020 to January 2021. This study investigated social distancing and infection control practices and incorporated environmental sampling of surfaces and air in employee common areas. All plants increased their social distancing efforts, increased the frequency of cleaning and disinfecting worker areas, and screened for symptomatic people to prevent entry into the workplace. 575 samples from common areas were collected and evaluated with RT-qPCR for the presence of SARS-CoV-2. 42/367 surface samples were positive, while no virus was detected in air samples. Case positive data from the counties surrounding each plant showed peak positive SARS-CoV-2 cases from 12-55 days before the virus was detected in the plant, indicating that environmental sampling is likely a lagging indicator of community and plant infection.
Collapse
Affiliation(s)
- Suzanna M. Storms
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois, Urbana, Illinois, United States of America
| | - James F. Lowe
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois, Urbana, Illinois, United States of America
| |
Collapse
|
24
|
Evans D, Cowen S, Kammel M, O'Sullivan DM, Stewart G, Grunert HP, Moran-Gilad J, Verwilt J, In J, Vandesompele J, Harris K, Hong KH, Storey N, Hingley-Wilson S, Dühring U, Bae YK, Foy CA, Braybrook J, Zeichhardt H, Huggett JF. The Dangers of Using Cq to Quantify Nucleic Acid in Biological Samples: A Lesson From COVID-19. Clin Chem 2021; 68:153-162. [PMID: 34633030 DOI: 10.1093/clinchem/hvab219] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/20/2021] [Indexed: 01/01/2023]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA quantities, measured by reverse transcription quantitative PCR (RT-qPCR), have been proposed to stratify clinical risk or determine analytical performance targets. We investigated reproducibility and how setting diagnostic cutoffs altered the clinical sensitivity of coronavirus disease 2019 (COVID-19) testing. METHODS Quantitative SARS-CoV-2 RNA distributions [quantification cycle (Cq) and copies/mL] from more than 6000 patients from 3 clinical laboratories in United Kingdom, Belgium, and the Republic of Korea were analyzed. Impact of Cq cutoffs on clinical sensitivity was assessed. The June/July 2020 INSTAND external quality assessment scheme SARS-CoV-2 materials were used to estimate laboratory reported copies/mL and to estimate the variation in copies/mL for a given Cq. RESULTS When the WHO-suggested Cq cutoff of 25 was applied, the clinical sensitivity dropped to about 16%. Clinical sensitivity also dropped to about 27% when a simulated limit of detection of 106 copies/mL was applied. The interlaboratory variation for a given Cq value was >1000 fold in copies/mL (99% CI). CONCLUSION While RT-qPCR has been instrumental in the response to COVID-19, we recommend Cq (cycle threshold or crossing point) values not be used to set clinical cutoffs or diagnostic performance targets due to poor interlaboratory reproducibility; calibrated copy-based units (used elsewhere in virology) offer more reproducible alternatives. We also report a phenomenon where diagnostic performance may change relative to the effective reproduction number. Our findings indicate that the disparities between patient populations across time are an important consideration when evaluating or deploying diagnostic tests. This is especially relevant to the emergency situation of an evolving pandemic.
Collapse
Affiliation(s)
- Daniel Evans
- National Measurement Laboratory, LGC, Teddington, Middlesex, UK
- Department of Microbial Sciences, School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford, UK
| | - Simon Cowen
- National Measurement Laboratory, LGC, Teddington, Middlesex, UK
| | - Martin Kammel
- Gesellschaft zur Foerderung der Qualitaetssicherung in Medizinischen Laboratorien e. V. (INSTAND), Düsseldorf, Germany
- IQVD GmbH, Institut fuer Qualitaetssicherung in der Virusdiagnostik, Berlin, Germany
| | | | - Graham Stewart
- Department of Microbial Sciences, School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford, UK
| | | | - Jacob Moran-Gilad
- Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Jasper Verwilt
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Jiwon In
- Seoul Medical Center, Seoul, Republic of Korea
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Biogazelle, Zwijnaarde, Belgium
| | - Kathryn Harris
- Department of Virology, NHS East and South East London Pathology Partnership, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Ki Ho Hong
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Republic of Korea
| | - Nathaniel Storey
- Department of Microbiology, Virology and Infection Prevention and Control, Level 4 Camelia Botnar Laboratories, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Suzie Hingley-Wilson
- Department of Microbial Sciences, School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford, UK
| | - Ulf Dühring
- GBD Gesellschaft fuer Biotechnologische Diagnostik mbH, Berlin, Germany
| | - Young-Kyung Bae
- Center for Bioanalysis, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea
| | - Carole A Foy
- National Measurement Laboratory, LGC, Teddington, Middlesex, UK
| | | | - Heinz Zeichhardt
- Gesellschaft zur Foerderung der Qualitaetssicherung in Medizinischen Laboratorien e. V. (INSTAND), Düsseldorf, Germany
- IQVD GmbH, Institut fuer Qualitaetssicherung in der Virusdiagnostik, Berlin, Germany
- GBD Gesellschaft fuer Biotechnologische Diagnostik mbH, Berlin, Germany
| | - Jim F Huggett
- National Measurement Laboratory, LGC, Teddington, Middlesex, UK
- Department of Microbial Sciences, School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford, UK
| |
Collapse
|
25
|
Alcántara R, Peñaranda K, Mendoza-Rojas G, Nakamoto JA, Dueñas E, Alvarez D, Adaui V, Milón P. UnCovid: A versatile, low-cost, and open-source protocol for SARS-CoV-2 RNA detection. STAR Protoc 2021; 2:100878. [PMID: 34604812 PMCID: PMC8463329 DOI: 10.1016/j.xpro.2021.100878] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Here, we describe a detailed step-by-step protocol to detect SARS-CoV-2 RNA using RT-PCR-mediated amplification and CRISPR/Cas-based visualization. The optimized assay uses basic molecular biology equipment such as conventional thermocyclers and transilluminators for qualitative detection. Alternatively, a fluorescence plate reader can be used for quantitative measurements. The protocol detects two regions of the SARS-CoV-2 genome in addition to the human RNaseP sample control. Aiming to reach remote regions, this work was developed to use the portable molecular workstation from BentoLab. For complete details on the use and execution of this protocol, please refer to Alcántara et al., 2021.
Collapse
Affiliation(s)
- Roberto Alcántara
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Katherin Peñaranda
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Gabriel Mendoza-Rojas
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Jose A. Nakamoto
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Eva Dueñas
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Daniela Alvarez
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Vanessa Adaui
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Pohl Milón
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| |
Collapse
|
26
|
Xu J, Suo W, Goulev Y, Sun L, Kerr L, Paulsson J, Zhang Y, Lao T. Handheld Microfluidic Filtration Platform Enables Rapid, Low-Cost, and Robust Self-Testing of SARS-CoV-2 Virus. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2104009. [PMID: 34845827 PMCID: PMC8725168 DOI: 10.1002/smll.202104009] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 10/27/2021] [Indexed: 05/17/2023]
Abstract
Here, a novel microfluidic test kit combining ultrahigh throughput hydrodynamic filtration and sandwich immunoassay is reported. Specifically, nano and microbeads coated with two different, noncompetitive antibodies, are used to capture the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid (N) proteins simultaneously, forming larger complexes. Microfluidic filtration discards free nanobeads but retains antigen-bridged complexes in the observation zone, where a display of red color indicates the presence of antigen in the sample. This testing platform exhibits high throughput separation (<30 s) and enrichment of antigen that exceeds the traditional lateral flow assays or microfluidic assays, with a low limit of detection (LoD) < 100 copies mL-1 . In two rounds of clinical trials conducted in December 2020 and August 2021, the assays demonstrate high sensitivities of 95.4% and 100%, respectively, which proves this microfluidic test kit is capable of detecting SARS-CoV-2 virus variants evolved over significant periods of time. Furthermore, the mass-produced chip can be fabricated at a cost of $0.98/test and the robust design allows the chip to be reused for over 50 times. All of these features make the microfluidic test kit particularly suitable for areas with inadequate medical infrastructure and a shortage of laboratory resources.
Collapse
Affiliation(s)
- Jiang Xu
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Wenhao Suo
- Department of Pathology, The First Affiliated Hospital of Xiamen University, 55 Zhenhai Road, Xiamen, 361003, China
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Youlian Goulev
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Lei Sun
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Liam Kerr
- Department of Mechanical Engineering, Center for Intelligent Machines, McGill University, Montreal, QC, H3A0C3, Canada
| | - Johan Paulsson
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Taotao Lao
- Boston Molecules Inc., 564 Main Street, Waltham, MA 02452, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02114, USA
| |
Collapse
|
27
|
Orf GS, Forberg K, Meyer TV, Mowerman I, Mohaimani A, Faron ML, Jennings C, Landay AL, Goldstein DY, Fox AS, Berg MG, Cloherty GA. SNP and Phylogenetic Characterization of Low Viral Load SARS-CoV-2 Specimens by Target Enrichment. FRONTIERS IN VIROLOGY 2021. [DOI: 10.3389/fviro.2021.765974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Background: Surveillance of SARS-CoV-2 across the globe has enabled detection of new variants and informed the public health response. With highly sensitive methods like qPCR widely adopted for diagnosis, the ability to sequence and characterize specimens with low titers needs to keep pace.Methods: Nucleic acids extracted from nasopharyngeal swabs collected from four sites in the United States in early 2020 were converted to NGS libraries to sequence SARS-CoV-2 genomes using metagenomic and xGen target enrichment approaches. Single nucleotide polymorphism (SNP) analysis and phylogeny were used to determine clade assignments and geographic origins of strains.Results: SARS-CoV-2-specific xGen enrichment enabled full genome coverage for 87 specimens with Ct values <29, corresponding to viral loads of >10,000 cp/ml. For samples with viral loads between 103 and 106 cp/ml, the median genome coverage for xGen was 99.1%, sequence depth was 605X, and the “on-target” rate was 57 ± 21%, compared to 13%, 2X and 0.001 ± 0.016%, respectively, for metagenomic sequencing alone. Phylogenetic analysis revealed the presence of most clades that existed at the time of the study, though clade GH dominated in the Midwest.Conclusions: Even as vaccines are being widely distributed, a high case load of SARS-CoV-2 infection persists around the world. Viral genetic surveillance has succeeded in warning the public of new variants in circulation and ensured that diagnostic tools remain resilient to a steadily increasing number of mutations. Target capture offers a means of characterizing low viral load samples which would normally pose a challenge for metagenomic sequencing.
Collapse
|
28
|
Alcántara R, Peñaranda K, Mendoza-Rojas G, Nakamoto JA, Martins-Luna J, del Valle-Mendoza J, Adaui V, Milón P. Unlocking SARS-CoV-2 detection in low- and middle-income countries. CELL REPORTS METHODS 2021; 1:100093. [PMID: 34697612 PMCID: PMC8529268 DOI: 10.1016/j.crmeth.2021.100093] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/31/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
Low- and middle-income countries (LMICs) are significantly affected by SARS-CoV-2, partially due to their limited capacity for local production and implementation of molecular testing. Here, we provide detailed methods and validation of a molecular toolkit that can be readily produced and deployed using laboratory equipment available in LMICs. Our results show that lab-scale production of enzymes and nucleic acids can supply over 50,000 tests per production batch. The optimized one-step RT-PCR coupled to CRISPR-Cas12a-mediated detection showed a limit of detection of 102 ge/μL in a turnaround time of 2 h. The clinical validation indicated an overall sensitivity of 80%-88%, while for middle and high viral load samples (Cq ≤ 31) the sensitivity was 92%-100%. The specificity was 96%-100% regardless of viral load. Furthermore, we show that the toolkit can be used with the mobile laboratory Bento Lab, potentially enabling LMICs to implement detection services in unattended remote regions.
Collapse
Affiliation(s)
- Roberto Alcántara
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Katherin Peñaranda
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Gabriel Mendoza-Rojas
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Jose A. Nakamoto
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Johanna Martins-Luna
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
- Laboratorio de Biología Molecular, Instituto de Investigación Nutricional, Lima, Peru
| | - Juana del Valle-Mendoza
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
- Laboratorio de Biología Molecular, Instituto de Investigación Nutricional, Lima, Peru
| | - Vanessa Adaui
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Pohl Milón
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| |
Collapse
|
29
|
Taziki Balajelini MH, Rajabi A, Mohammadi M, Nikoo HR, Tabarraei A, Mansouri M, Hosseini SM. Virus load and incidence of olfactory, gustatory, respiratory, gastrointestinal disorders in COVID-19 patients: A retrospective cohort study. Clin Otolaryngol 2021; 46:1331-1338. [PMID: 34358409 PMCID: PMC8444685 DOI: 10.1111/coa.13844] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/07/2021] [Accepted: 07/27/2021] [Indexed: 12/23/2022]
Abstract
OBJECTIVES This study investigated the relationship between viral load and the incidence of olfactory and gustatory dysfunction (OD and GD), the incidence of respiratory and gastrointestinal symptoms and the recovery of OD and GD in COVID-19 patients. DESIGN A retrospective cohort study. SETTING AND PARTICIPANTS This study was conducted on 599 outpatients' cases in Golestan province between February and June 2020. MAIN OUTCOME MEASURES The incidence, severity (complete or partial) and recovery time of OD and GD and their associations with cycle threshold (CT) values of SARS-CoV-2 polymerase chain reaction were assessed. RESULTS The mean age of patients was 38.27 ± 13.62 years. The incidence of general symptoms included myalgia 70.1%, headache 51.8%, fever 47.7% and dyspnoea 21.4%. 41.9% of patients had gastrointestinal symptoms, including abdominal pain 26.5%, diarrhoea 25.2%, nausea 20.5% and vomiting 12.9%. 12.2% of patients had comorbidity. The trimester recovery rates of OD and GD were 93.94% and 94.74% respectively. The mean recovery time of OD and GD was 14.56 ± 13.37 and 13.8 ± 3.77 days respectively. The mean CT value in all patients was 27.45 ± 4.55. There were significant associations between the mean of CT value with headache (p = 0.04), GD (p = 0.002) and OD (p = 0.001). CONCLUSIONS The finding of this study indicates a possible association between viral load with incidence of OD and GD in COVID-19 patient's cases and assures the recovery of OD/GD in these patients.
Collapse
Affiliation(s)
| | - Abdolhalim Rajabi
- Department of Health Management and Social Development Research CenterFaculty of HealthGolestan University of Medical SciencesGorganIran
| | - Masoud Mohammadi
- Department of Golestan Research Centre of Gastroenterology and HepatologyGolestan University of Medical SciencesGorganIran
| | - Hadi Razavi Nikoo
- Department of MicrobiologySchool of MedicineInfectious Diseases Research CenterGolestan University of Medical SciencesGorganIran
| | - Alijan Tabarraei
- Department of MicrobiologySchool of MedicineInfectious Diseases Research CenterGolestan University of Medical SciencesGorganIran
| | - Mohsen Mansouri
- Department of Statistics and Information Technology ManagementGolestan University of Medical SciencesGorganIran
| | - Seyed Mehran Hosseini
- Department of PhysiologySchool of MedicineNeuroscience Research CenterGolestan University of Medical SciencesGorganIran
| |
Collapse
|
30
|
Herman DS, Rhoads DD, Schulz WL, Durant TJS. Artificial Intelligence and Mapping a New Direction in Laboratory Medicine: A Review. Clin Chem 2021; 67:1466-1482. [PMID: 34557917 DOI: 10.1093/clinchem/hvab165] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/26/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND Modern artificial intelligence (AI) and machine learning (ML) methods are now capable of completing tasks with performance characteristics that are comparable to those of expert human operators. As a result, many areas throughout healthcare are incorporating these technologies, including in vitro diagnostics and, more broadly, laboratory medicine. However, there are limited literature reviews of the landscape, likely future, and challenges of the application of AI/ML in laboratory medicine. CONTENT In this review, we begin with a brief introduction to AI and its subfield of ML. The ensuing sections describe ML systems that are currently in clinical laboratory practice or are being proposed for such use in recent literature, ML systems that use laboratory data outside the clinical laboratory, challenges to the adoption of ML, and future opportunities for ML in laboratory medicine. SUMMARY AI and ML have and will continue to influence the practice and scope of laboratory medicine dramatically. This has been made possible by advancements in modern computing and the widespread digitization of health information. These technologies are being rapidly developed and described, but in comparison, their implementation thus far has been modest. To spur the implementation of reliable and sophisticated ML-based technologies, we need to establish best practices further and improve our information system and communication infrastructure. The participation of the clinical laboratory community is essential to ensure that laboratory data are sufficiently available and incorporated conscientiously into robust, safe, and clinically effective ML-supported clinical diagnostics.
Collapse
Affiliation(s)
- Daniel S Herman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel D Rhoads
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH, USA.,Department of Pathology, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Wade L Schulz
- Department of Laboratory Medicine, Yale University, New Haven, CT, USA
| | - Thomas J S Durant
- Department of Laboratory Medicine, Yale University, New Haven, CT, USA
| |
Collapse
|
31
|
Koblížek M, Hávová D, Kopejtka K, Tomasch J, Bišová K. Distribution of cycle threshold values in RT-qPCR tests during the autumn 2020 peak of the COVID-19 pandemic in the Czech Republic. Access Microbiol 2021; 3:000263. [PMID: 34712908 PMCID: PMC8549392 DOI: 10.1099/acmi.0.000263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/01/2021] [Indexed: 11/18/2022] Open
Abstract
Reverse-transcription quantitative PCR (RT-qPCR) is currently the most sensitive method to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19). We analysed 1927 samples collected in a local public hospital during the autumn 2020 peak of the pandemic in the Czech Republic. The tests were performed using the Seegene Allplex 2019-nCov assay, which simultaneously detects three SARS-CoV-2 genes. In all samples analysed, 44.5 % were negative for all three genes, and 37.6 % were undoubtedly positive, with all three viral genes being amplified. A high degree of correlation between Ct values among the genes confirmed the internal consistency of testing. Most of the positive samples were detected between the 15th and 35th cycles. We also registered a small number of samples with only one (13.2 %) or two (4.7 %) amplified genes, which may have originated from either freshly infected or already recovering patients. In addition, we did not detect any potentially false-positive samples from low-prevalence settings. Our results document that PCR testing represents a reliable and robust method for routine diagnostic detection of SARS-CoV-2.
Collapse
Affiliation(s)
- Michal Koblížek
- Institute of Microbiology of the Czech Acad. Sci., Centre Algatech, 37981 Třeboň, Czechia
| | - Daniela Hávová
- Institute of Microbiology of the Czech Acad. Sci., Centre Algatech, 37981 Třeboň, Czechia
| | - Karel Kopejtka
- Institute of Microbiology of the Czech Acad. Sci., Centre Algatech, 37981 Třeboň, Czechia
| | - Jürgen Tomasch
- Institute of Microbiology of the Czech Acad. Sci., Centre Algatech, 37981 Třeboň, Czechia
| | - Kateřina Bišová
- Institute of Microbiology of the Czech Acad. Sci., Centre Algatech, 37981 Třeboň, Czechia
| |
Collapse
|
32
|
A Real-World Comparison of SARS-CoV-2 Rapid Antigen vs. Polymerase Chain Reaction Testing in Florida. J Clin Microbiol 2021; 59:e0110721. [PMID: 34346715 PMCID: PMC8451433 DOI: 10.1128/jcm.01107-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Background The reported sensitivity of rapid, antigen-based diagnostics for SARS-CoV-2 infection varies. Few studies have evaluated rapid antigen tests in real-world settings or among large populations. Methods Beginning October 2020, Florida offered individuals presenting for SARS-CoV-2 testing polymerase chain reaction (PCR) testing if they tested positive by the Abbott BinaxNOWTM COVID-19 Ag Card, were symptomatic, or required or requested PCR testing. We compared test results among individuals who received both types of tests at four publicly-accessible testing sites across Florida. We calculated the positive percent agreement (PPA) between the two test types by symptom status. Subsequently, we evaluated the PPA among individuals regardless of symptoms with lower cycle threshold values (<30). Results Overall, 18,457 individuals were tested via both methods, of which 3,153 (17.1%) were positive by PCR. The PPA for the Abbott BinaxNOWTM COVID-19 Ag Card using the PCR comparator was 49.2% (95% CI 47.4%-50.9%). That performance was moderately improved among symptomatic individuals (51.9%; 95% CI 49.7%-54.0%). When restricted to positive PCR tests with a cycle threshold value <30, regardless of symptom status, the PPA was 75.3% (95% CI 72.8%-77.6%). Conclusion The PPA of the Abbott BinaxNOWTM COVID-19 Ag Card with PCR was lower than among previous reports. Our findings may reflect the performance of the BinaxNOWTM antigen test in real-world settings.
Collapse
|
33
|
Duan X, Wang X, Xie Y, Yu P, Zhuang T, Zhang Y, Fang L, Ping Y, Liu W, Tao Z. High concentrations of hypochlorous acid-based disinfectant in the environment reduced the load of SARS-CoV-2 in nucleic acid amplification testing. Electrophoresis 2021; 42:1411-1418. [PMID: 34142386 PMCID: PMC8426966 DOI: 10.1002/elps.202000387] [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: 12/28/2020] [Revised: 05/10/2021] [Accepted: 06/15/2021] [Indexed: 11/07/2022]
Abstract
During the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) pandemic, chlorine-containing disinfectants have been widely used in nucleic acid amplification testing laboratories. Whether the use of disinfectants affect the results of viral nucleic acid amplification is unknown. We examined the impact of different hypochlorous acid (HOCl) concentrations on the quantitative results of SARS-CoV-2 by real-time reverse-transcription polymerase chain reaction (RT-PCR). We also explored the mechanisms and models of action of chlorine-containing disinfectants that affected the detection of SARS-CoV-2. The results showed that different HOCl concentrations and different action times had an impact on the SARS-CoV-2 results. High concentrations of ambient HOCl have a greater impact than low concentrations, and this effect will increase with the extension of the action time and with the increase in ambient humidity. Compared with the enzymes or the extracted RNA required for RT-PCR, the impact of HOCl on the SARS-CoV-2 detection is more likely to be caused by damage to primers and probes in the PCR system. The false negative result still existed after changing the ambient disinfectant to ethanol but not peracetic acid. The use of HOCl in the environment will have an unpredictable impact on the nucleic acid test results of SARS-CoV-2. In order to reduce the possibility of false negative of SARS-CoV-2 nucleic acid test and prevent the spread of epidemic disease, environmental disinfectants should be used at the beginning and end of the experiment rather than during the experimental operation.
Collapse
Affiliation(s)
- Xiuzhi Duan
- Department of Laboratory MedicineThe Second Affiliated Hospital of Zhejiang University School of MedicineHangzhouP. R. China
| | - Xuchu Wang
- Department of Laboratory MedicineThe Second Affiliated Hospital of Zhejiang University School of MedicineHangzhouP. R. China
| | - Yiyi Xie
- Department of Laboratory MedicineThe Second Affiliated Hospital of Zhejiang University School of MedicineHangzhouP. R. China
| | - Pan Yu
- Department of Laboratory MedicineThe Second Affiliated Hospital of Zhejiang University School of MedicineHangzhouP. R. China
| | - Tingting Zhuang
- Department of Laboratory MedicineThe Second Affiliated Hospital of Zhejiang University School of MedicineHangzhouP. R. China
| | - Yingzhi Zhang
- Department of Laboratory MedicineThe Second Affiliated Hospital of Zhejiang University School of MedicineHangzhouP. R. China
| | - Liuyu Fang
- Department of Laboratory MedicineThe Second Affiliated Hospital of Zhejiang University School of MedicineHangzhouP. R. China
| | - Ying Ping
- Department of Laboratory MedicineThe Second Affiliated Hospital of Zhejiang University School of MedicineHangzhouP. R. China
| | - Weiwei Liu
- Department of Laboratory MedicineThe Second Affiliated Hospital of Zhejiang University School of MedicineHangzhouP. R. China
| | - Zhihua Tao
- Department of Laboratory MedicineThe Second Affiliated Hospital of Zhejiang University School of MedicineHangzhouP. R. China
| |
Collapse
|
34
|
Mack CD, Osterholm M, Wasserman EB, Petruski-Ivleva N, Anderson DJ, Myers E, Singh N, Walton P, Solomon G, Hostler C, Mancell J, Sills A. Optimizing SARS-CoV-2 Surveillance in the United States: Insights From the National Football League Occupational Health Program. Ann Intern Med 2021; 174:1081-1089. [PMID: 34125571 PMCID: PMC8252091 DOI: 10.7326/m21-0319] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Evidence to understand effective strategies for surveillance and early detection of SARS-CoV-2 is limited. OBJECTIVE To describe the results of a rigorous, large-scale COVID-19 testing and monitoring program. DESIGN The U.S. National Football League (NFL) and the NFL Players Association (NFLPA) instituted a large-scale COVID-19 monitoring program involving daily testing using 2 reverse transcription polymerase chain reaction (RT-PCR) platforms (Roche cobas and Thermo Fisher QuantStudio), a transcription-mediated amplification platform (Hologic Panther), and an antigen point-of-care (aPOC) test (Quidel Sofia). SETTING 32 NFL clubs in 24 states during the 2020 NFL season. PARTICIPANTS NFL players and staff. MEASUREMENTS SARS-CoV-2 test results were described in the context of medically adjudicated status. Cycle threshold (Ct) values are reported when available. RESULTS A total of 632 370 tests administered across 11 668 persons identified 270 (2.4%) COVID-19 cases from 1 August to 14 November 2020. Positive predictive values ranged from 73.0% to 82.0% across the RT-PCR platforms. High Ct values (33 to 37) often indicated early infection. For the first positive result, the median Ct value was 32.77 (interquartile range, 30.02 to 34.72) and 22% of Ct values were above 35. Among adjudicated COVID-19 cases tested with aPOC, 42.3% had a negative result. Positive concordance between aPOC test result and adjudicated case status increased as viral load increased. LIMITATIONS Platforms varied by laboratory, and test variability may reflect procedural differences. CONCLUSION Routine RT-PCR testing allowed early detection of infection. Cycle threshold values provided a useful guidepost for understanding results, with high values often indicating early infection. Antigen POC testing was unable to reliably rule out COVID-19 early in infection. PRIMARY FUNDING SOURCE The NFL and the NFLPA.
Collapse
Affiliation(s)
| | | | | | | | - Deverick J Anderson
- Duke University School of Medicine, Durham, North Carolina, and Infection Control Education for Major Sports, Chapel Hill, North Carolina (D.J.A.)
| | - Emily Myers
- National Football League, New York, New York (E.M., G.S., A.S.)
| | - Navdeep Singh
- Eden Medical Center, Castro Valley, California (N.S.)
| | - Patti Walton
- Williamson Medical Center, Franklin, Tennessee (P.W.)
| | - Gary Solomon
- National Football League, New York, New York (E.M., G.S., A.S.)
| | - Christopher Hostler
- Duke University School of Medicine and Durham VA Health Care System, Durham, North Carolina, and Infection Control Education for Major Sports, Chapel Hill, North Carolina (C.H.)
| | - Jimmie Mancell
- University of Tennessee Health Science Center, Memphis, Tennessee (J.M.)
| | - Allen Sills
- National Football League, New York, New York (E.M., G.S., A.S.)
| |
Collapse
|
35
|
Raju S, Anderson NW, Robinson E, Squires C, Wallace MA, Zhang R, Burnham CAD, Parikh BA. Comparison of Six SARS-CoV-2 Molecular Methods and Correlation with the Cycle Threshold Distribution in Clinical Specimens. J Appl Lab Med 2021; 6:1452-1462. [PMID: 34289054 PMCID: PMC8436400 DOI: 10.1093/jalm/jfab086] [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: 04/26/2021] [Accepted: 07/06/2021] [Indexed: 11/14/2022]
Abstract
Background The detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
in patient samples is of critical importance in the management of patients
and monitoring transmission in the population. However, data on the
analytical performance characteristics for detection of SARS-CoV-2 in
clinical specimens between individual targets within the same platform, and
among different analytical platforms, are limited. Methods Here we evaluated the performance of 6 different sample-to-answer SARS-CoV-2
detection methods—Roche cobas 6800, Cepheid GeneXpert, Diasorin
Simplexa, Luminex Aries emergency use authorization (EUA), Luminex Aries
research use only (RUO), and bioMérieux BioFire—in clinical
specimens with a range of viral loads. Results The positive percentage agreement between the Roche cobas 6800 and GeneXpert
was 100%, Diasorin 95%, Aries EUA 74%, Aries RUO
83%, and BioFire 97%. Notably, in samples with cycle threshold
(Ct) values below 30 for the E gene on the Roche cobas 6800
platform, we found 100% positive agreement among all platforms. Given
these results, we examined the distribution of over 10 000 Ct values of all
positive specimens from individuals at our institution on the Roche cobas
platform. Nearly 60% of specimens from asymptomatic individuals had a
PCR Ct value >30 as measured using the cobas 6800 assay
E gene. Conclusions Our results demonstrate performance characteristics between different
platforms by Ct value and provide data regarding the distribution of viral
RNA present in positive specimens.
Collapse
Affiliation(s)
- Saravanan Raju
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Neil W Anderson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Elizabeth Robinson
- Barnes-Jewish Hospital Department of Laboratories, St. Louis, Missouri, USA
| | - Crystal Squires
- Barnes-Jewish Hospital Department of Laboratories, St. Louis, Missouri, USA
| | - Meghan A Wallace
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Ray Zhang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Bijal A Parikh
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| |
Collapse
|
36
|
Kost GJ. The Impact of Increasing Disease Prevalence, False Omissions, and Diagnostic Uncertainty on Coronavirus Disease 2019 (COVID-19) Test Performance. Arch Pathol Lab Med 2021; 145:797-813. [PMID: 33684204 DOI: 10.5858/arpa.2020-0716-sa] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Coronavirus disease 2019 (COVID-19) test performance depends on predictive values in settings of increasing disease prevalence. Geospatially distributed diagnostics with minimal uncertainty facilitate efficient point-of-need strategies. OBJECTIVES.— To use original mathematics to interpret COVID-19 test metrics; assess US Food and Drug Administration Emergency Use Authorizations and Health Canada targets; compare predictive values for multiplex, antigen, polymerase chain reaction kit, point-of-care antibody, and home tests; enhance test performance; and improve decision-making. DESIGN.— PubMed/newsprint-generated articles documenting prevalence. Mathematica and open access software helped perform recursive calculations, graph multivariate relationships, and visualize performance by comparing predictive value geometric mean-squared patterns. RESULTS.— Tiered sensitivity/specificity comprised: T1, 90%, 95%; T2, 95%, 97.5%; and T3, 100%, ≥99%. Tier 1 false negatives exceeded true negatives at >90.5% prevalence; false positives exceeded true positives at <5.3% prevalence. High-sensitivity/specificity tests reduced false negatives and false positives, yielding superior predictive values. Recursive testing improved predictive values. Visual logistics facilitated test comparisons. Antigen test quality fell off as prevalence increased. Multiplex severe acute respiratory syndrome (SARS)-CoV-2)*influenza A/B*respiratory syncytial virus testing performed reasonably well compared with tier 3. Tier 3 performance with a tier 2 confidence band lower limit will generate excellent performance and reliability. CONCLUSIONS.— The overriding principle is to select the best combined performance and reliability pattern for the prevalence bracket. Some public health professionals recommend repetitive testing to compensate for low sensitivity. More logically, improved COVID-19 assays with less uncertainty conserve resources. Multiplex differentiation of COVID-19 from influenza A/B-respiratory syncytial virus represents an effective strategy if seasonal flu surges next year.
Collapse
Affiliation(s)
- Gerald J Kost
- From the Department of Pathology and Laboratory Medicine, POCT•CTR, School of Medicine, University of California, Davis
| |
Collapse
|
37
|
Newsom K, Zhang Y, Chamala S, Martinez K, Clare-Salzler M, Starostik P. The Hologic Aptima SARS-CoV-2 assay enables high ratio pooling saving reagents and improving turnaround time. J Clin Lab Anal 2021; 35:e23888. [PMID: 34213803 PMCID: PMC8418467 DOI: 10.1002/jcla.23888] [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: 05/03/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND The Hologic Aptima™ TMA SARS-CoV-2 assay was employed to test pooled nasopharyngeal (NP) samples to evaluate the performance of pooled sample testing and characterize variables influencing results. METHODS Results on 1033 previously tested NP samples were retrieved to characterize the relative light units (RLU) of SARS-CoV-2-positive samples in the tested population. The pooling strategy of combining 10 SARS-CoV-2 samples into one pool (10/1) was used in this study. The results were compared with neat sample testing using the same Aptima™ TMA SARS-CoV-2 assay and also the CDC RT-PCR and the Cepheid SARS-CoV-2 assays. RESULTS The Aptima assay compares favorably with both CDC RT-PCR and the Cepheid SARS-CoV-2 assays. Once samples are pooled 10 to 1 as in our experiments, the resulting signal strength of the assay suffers. A divide opens between pools assembled from strong-positive versus only weak-positive samples. Pools of the former can be reliably detected with positive percent agreement (PPA) of 95.2%, while pools of the latter are frequently misclassified as negative with PPA of 40%. When the weak-positive samples with kRLU value lower than 1012 constitute 3.4% of the total sample profile, the assay PPA approaches 93.4% suggesting that 10/1 pooled sample testing by the Aptima assay is an effective screening tool for SARS-CoV-2. CONCLUSION Performing pooled testing, one should monitor the weak positives with kRLU lower than 1012 or quantification cycle (Cq) value higher than 35 on an ongoing basis and adjust pooling approaches to avoid reporting false negatives.
Collapse
Affiliation(s)
- Kimberly Newsom
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Yuan Zhang
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Srikar Chamala
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Katherine Martinez
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Michael Clare-Salzler
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Petr Starostik
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| |
Collapse
|
38
|
Marcolungo L, Beltrami C, Degli Esposti C, Lopatriello G, Piubelli C, Mori A, Pomari E, Deiana M, Scarso S, Bisoffi Z, Grosso V, Cosentino E, Maestri S, Lavezzari D, Iadarola B, Paterno M, Segala E, Giovannone B, Gallinaro M, Rossato M, Delledonne M. ACoRE: Accurate SARS-CoV-2 genome reconstruction for the characterization of intra-host and inter-host viral diversity in clinical samples and for the evaluation of re-infections. Genomics 2021; 113:1628-1638. [PMID: 33839270 PMCID: PMC8028595 DOI: 10.1016/j.ygeno.2021.04.008] [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: 02/05/2021] [Revised: 03/26/2021] [Accepted: 04/06/2021] [Indexed: 01/04/2023]
Abstract
Sequencing the SARS-CoV-2 genome from clinical samples can be challenging, especially in specimens with low viral titer. Here we report Accurate SARS-CoV-2 genome Reconstruction (ACoRE), an amplicon-based viral genome sequencing workflow for the complete and accurate reconstruction of SARS-CoV-2 sequences from clinical samples, including suboptimal ones that would usually be excluded even if unique and irreplaceable. The protocol was optimized to improve flexibility and the combination of technical replicates was established as the central strategy to achieve accurate analysis of low-titer/suboptimal samples. We demonstrated the utility of the approach by achieving complete genome reconstruction and the identification of false-positive variants in >170 clinical samples, thus avoiding the generation of inaccurate and/or incomplete sequences. Most importantly, ACoRE was crucial to identify the correct viral strain responsible of a relapse case, that would be otherwise mis-classified as a re-infection due to missing or incorrect variant identification by a standard workflow.
Collapse
Affiliation(s)
- Luca Marcolungo
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Cristina Beltrami
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Chiara Degli Esposti
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Giulia Lopatriello
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Chiara Piubelli
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Antonio Mori
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Elena Pomari
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Michela Deiana
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Salvatore Scarso
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Zeno Bisoffi
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy,Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy
| | - Valentina Grosso
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Emanuela Cosentino
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Simone Maestri
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Denise Lavezzari
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Barbara Iadarola
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Marta Paterno
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Elena Segala
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Barbara Giovannone
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Martina Gallinaro
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Marzia Rossato
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy,Genartis srl, via IV Novembre 24, 37126 Verona, Italy
| | - Massimo Delledonne
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy,Genartis srl, via IV Novembre 24, 37126 Verona, Italy,Corresponding author at: Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| |
Collapse
|
39
|
Buchan BW, Gerstbrein D, Cruz A, Hoff J, Sievert E, Ledeboer NA, Faron ML. Evaluation of a High-Definition PCR Assay for the Detection of SARS-CoV-2 in Extracted and Nonextracted Respiratory Specimens Collected in Various Transport Media. Am J Clin Pathol 2021; 156:24-33. [PMID: 33940605 PMCID: PMC8135719 DOI: 10.1093/ajcp/aqab060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Objectives We conducted an analytic and clinical comparison of a novel high-definition polymerase chain reaction PCR (HDPCR) assay to traditional real-time PCR (RT-PCR) for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in upper respiratory specimens. Methods Analytic performance of RT-PCR, HDPCR, and extraction-free HDPCR was established through replicate testing of a serially diluted clinical specimen containing SARS-CoV-2. A clinical comparison of all 3 assays was conducted using 351 prospectively collected upper respiratory swab specimens obtained from symptomatic and asymptomatic individuals collected in various transport media. Results RT-PCR and HDPCR assays using extracted nucleic acid demonstrated similar analytic limits of detection (LoD) and clinical performance, with 100% positive and negative agreement. Extraction-free HDPCR demonstrated a 1.5 to 2.0 log10 increase in LoD based on cycle threshold values. However, clinical performance of extraction-free HDPCR remained high, demonstrating 97.8% positive and 99.6% negative agreement with RT-PCR. An overall increase in “invalid” and “presumptive” results was observed when using the extraction-free method, but this was highly variable based on transport medium used. Conclusions HDPCR performs similar to RT-PCR for the detection of SARS-CoV-2. The use of an extraction-free HDPCR protocol maintained high clinical performance despite reduced analytic LoD, with the benefit of reduced hands-on time and cost of reagents associated with nucleic acid extraction.
Collapse
Affiliation(s)
- Blake W Buchan
- Department of Pathology, The Medical College of Wisconsin, Milwaukee, WI, USA
| | - Derek Gerstbrein
- Department of Pathology, The Medical College of Wisconsin, Milwaukee, WI, USA
| | - Amorina Cruz
- Department of Pathology, The Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jess Hoff
- Wisconsin Diagnostic Laboratories, Milwaukee, WI, USA
| | - Emily Sievert
- Wisconsin Diagnostic Laboratories, Milwaukee, WI, USA
| | - Nathan A Ledeboer
- Department of Pathology, The Medical College of Wisconsin, Milwaukee, WI, USA
| | - Matthew L Faron
- Department of Pathology, The Medical College of Wisconsin, Milwaukee, WI, USA
| |
Collapse
|
40
|
Combination of rRT-PCR and Anti-Nucleocapsid/Anti-Spike Antibodies to Characterize Specimens with Very Low Viral SARs-CoV-2 Load: A Real-Life Experience. Microorganisms 2021; 9:microorganisms9061263. [PMID: 34200837 PMCID: PMC8230444 DOI: 10.3390/microorganisms9061263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/28/2021] [Accepted: 06/08/2021] [Indexed: 11/17/2022] Open
Abstract
The objective of the present study was to evaluate the true positivity among people, whose results of initial testing of nasopharyngeal swabs (NPS) showed a very low viral load of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Seventy-seven people detected with low viral loads of SARs-CoV-2 in nasopharyngeal samples (Ct ≥ 35) were enrolled in the study. For this purpose, a second NPS was collected for rRT-PCR (real-time reverse transcription polymerase chain reaction) combined with a pair of serum samples for detection of anti-nucleocapsid (anti-N) and anti-spike (anti-S) antibodies. In 8 people, subsequent examinations indicated an increase in viral loads, thereafter, followed by an increase of anti-N and anti-S antibodies, findings compatible with an early stage of COVID-19 infection. In 9 people, who already had increased anti-N antibodies, subsequent examination showed a decrease or absence of viral load and an increase in antibodies, indicative of a late stage of COVID-19 infection. In 60 people, subsequent examination showed absence of infection (as indicated by absence of viral load and antibodies). We propose that the combination of a second NPS and one serum-specimen, both taken three days after the first NPS, helps significantly to avoid false-positive results.
Collapse
|
41
|
Aging correlates with lower threshold cycle values for RdRP/RdRP+S genes during molecular detection of SARS-CoV-2. Exp Gerontol 2021; 150:111361. [PMID: 33878423 PMCID: PMC8053219 DOI: 10.1016/j.exger.2021.111361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/10/2021] [Accepted: 04/16/2021] [Indexed: 11/20/2022]
Abstract
RT-qPCR is the most reliable molecular method for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we analyzed results of RT-qPCR obtained for 3044 patients diagnosed as SARS-CoV-2-positive using four different molecular tests utilizing five RNA sequences. The analysis showed that patients' age inversely correlates with threshold cycle (Ct) values for RdRP gene (LightMix® Modular Wuhan CoV RdRP-gene by Roche Diagnostics) and RdRP+S genes (MutaPLEX® Coronavirus RT-PCR kit by Immundiagnostic). At the same time, there was no correlation between age and Ct values for E, N, and ORF1ab genes. When patients were grouped by age, mean Ct values for RdRP gene in older patients were significantly lower compared with younger individuals. Collectively, our report indicates that older SARS-CoV-2-infected individuals exhibit higher viremia at diagnosis than younger patients, which may reflect impaired functioning of their immune response and predispose to more severe disease and worse prognosis.
Collapse
|
42
|
Prasad NK, Lake R, Englum BR, Turner DJ, Siddiqui T, Mayorga-Carlin M, Sorkin JD, Lal BK. Increased complications in patients who test COVID-19 positive after elective surgery and implications for pre and postoperative screening. Am J Surg 2021; 223:380-387. [PMID: 33894979 PMCID: PMC8045424 DOI: 10.1016/j.amjsurg.2021.04.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/30/2021] [Accepted: 04/08/2021] [Indexed: 12/14/2022]
Abstract
Background The COVID-19 pandemic has necessitated the adoption of protocols to minimize risk of periprocedural complications associated with SARS-CoV-2 infection. This typically involves a preoperative symptom screen and nasal swab RT-PCR test for viral RNA. Asymptomatic patients with a negative COVID-19 test are cleared for surgery. However, little is known about the rate of postoperative COVID-19 positivity among elective surgical patients, risk factors for this group and rate of complications. Methods This prospective multicenter study included all patients undergoing elective surgery at 170 Veterans Health Administration (VA) hospitals across the United States. Patients were divided into groups based on first positive COVID-19 test within 30 days after surgery (COVID[-/+]), before surgery (COVID[+/−]) or negative throughout (COVID[−/−]). The cumulative incidence, risk factors for and complications of COVID[-/+], were estimated using univariate analysis, exact matching, and multivariable regression. Results Between March 1 and December 1, 2020 90,093 patients underwent elective surgery. Of these, 60,853 met inclusion criteria, of which 310 (0.5%) were in the COVID[-/+] group. Adjusted multivariable logistic regression identified female sex, end stage renal disease, chronic obstructive pulmonary disease, congestive heart failure, cancer, cirrhosis, and undergoing neurosurgical procedures as risk factors for being in the COVID[-/+] group. After matching on current procedural terminology code and month of procedure, multivariable Poisson regression estimated the complication rate ratio for the COVID[-/+] group vs. COVID[−/−] to be 8.4 (C.I. 4.9–14.4) for pulmonary complications, 3.0 (2.2, 4.1) for major complications, and 2.6 (1.9, 3.4) for any complication. Discussion Despite preoperative COVID-19 screening, there remains a risk of COVID infection within 30 days after elective surgery. This risk is increased for patients with a high comorbidity burden and those undergoing neurosurgical procedures. Higher intensity preoperative screening and closer postoperative monitoring is warranted in such patients because they have a significantly elevated risk of postoperative complications.
Collapse
Affiliation(s)
- Nikhil K Prasad
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD, USA; Surgery Service, Veterans Affairs Medical Center, Baltimore, MD, USA
| | - Rachel Lake
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD, USA; Surgery Service, Veterans Affairs Medical Center, Baltimore, MD, USA
| | - Brian R Englum
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Douglas J Turner
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD, USA; Surgery Service, Veterans Affairs Medical Center, Baltimore, MD, USA
| | - Tariq Siddiqui
- Surgery Service, Veterans Affairs Medical Center, Baltimore, MD, USA
| | - Minerva Mayorga-Carlin
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD, USA; Surgery Service, Veterans Affairs Medical Center, Baltimore, MD, USA
| | - John D Sorkin
- Geriatrics Research, Education, and Clinical Center, Veterans Affairs Medical Center, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Brajesh K Lal
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD, USA; Surgery Service, Veterans Affairs Medical Center, Baltimore, MD, USA.
| |
Collapse
|
43
|
Hemani G, Thomas AC, Walker JG, Trickey A, Nixon E, Ellis D, Kwiatkowska R, Relton C, Danon L, Christensen H, Brooks-Pollock E. Modelling pooling strategies for SARS-CoV-2 testing in a university setting. Wellcome Open Res 2021. [DOI: 10.12688/wellcomeopenres.16639.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Background: Pre-symptomatic and asymptomatic transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are important elements in the coronavirus disease 2019 (COVID-19) pandemic, and there remains a reliance on testing to manage the spread of the disease. In the UK, many universities opened for blended learning for the 2020-2021 academic year, with a mixture of face to face and online teaching. Methods: In this study we present a simulation framework to evaluate the effectiveness of different mass testing strategies within a university setting, across a range of transmission scenarios. Results: The sensitivity of 5x pooled RT-qPCR tests appears to be higher than testing using the lateral flow device with relatively little loss compared to single RT-qPCR tests, and is improved by pooling by social cluster. The range of strategies that we evaluated give comparable results for estimating prevalence. Conclusions: Pooling tests by known social structures, such as student households can substantially improve the cost effectiveness of RT-qPCR tests. We also note that routine recording of quantitative RT-qPCR results would facilitate future modelling studies.
Collapse
|
44
|
Abstract
We report the performance of a variety of commercially available SARS-CoV-2 PCR kits, used in several different sites across Ireland to determine if Ct values across platforms are comparable. We also investigate whether a Ct value, a surrogate for calculated viral loads in the absence of viral culture of > 34 can be used to exclude SARS-CoV-2 infection and its complications. We found a variation in Ct values from different assays for the same calculated viral load; this should be taken into consideration for result interpretation.
Collapse
Affiliation(s)
- Anne Carroll
- Public Health Laboratory-Health Service Executive-Dublin, Ireland
| | - Eleanor McNamara
- Public Health Laboratory-Health Service Executive-Dublin, Ireland
| |
Collapse
|
45
|
Kim N, Kwon A, Roh EY, Yoon JH, Han MS, Park SW, Park H, Shin S. Effects of Storage Temperature and Media/Buffer for SARS-CoV-2 Nucleic Acid Detection. Am J Clin Pathol 2021; 155:280-285. [PMID: 33067995 PMCID: PMC7665474 DOI: 10.1093/ajcp/aqaa207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVES The increase in the number of patients with coronavirus disease 2019 (COVID-19) has delayed real-time reverse transcription-quantitative polymerase chain reaction (RT-qPCR), requiring proper shipping and storage conditions, especially in hot weather. This study aims to assess how some conditions, such as storage period, temperature, media or buffer, and sample types, affect the results of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RT-qPCR. METHODS SARS-CoV-2-positive specimens were collected from Boramae Medical Center for 2 months (from May to June 2020) and stored in different media or buffers at different temperatures. RESULTS As a result of examining confirmed patient samples, RT-qPCR results were not significantly affected by 2°C to 8°C storage until after 7 days. When stored at 20°C to 22°C or above 35°C, the results were affected negatively even after 1 day. Higher storage temperatures resulted in a lower probability of detecting viral nucleic acids because of degradation. Samples stored in pH-controlled media or buffer were more stable than those stored in nonbuffer states. CONCLUSIONS These results emphasize the importance of storage temperature and media or buffer and performing RT-qPCR for SARS-CoV-2 nucleic acid detection as soon as possible after sample collection.
Collapse
Affiliation(s)
- Namhee Kim
- Department of Laboratory Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
- Infection Control Office, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Ahrin Kwon
- Department of Laboratory Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Eun Youn Roh
- Department of Laboratory Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Jong Hyun Yoon
- Department of Laboratory Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Mi Seon Han
- Infection Control Office, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
- Department of Pediatrics, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Sang-Won Park
- Infection Control Office, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
- Department of Internal Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Hyunwoong Park
- Department of Laboratory Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Sue Shin
- Department of Laboratory Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
- Infection Control Office, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| |
Collapse
|
46
|
Awang H, Hamzah FH, Ahmad MH, Mahmood MF, Wahab A, Embong K, Yunus NA. Polymerase chain reaction cycle threshold value as prerequisite for reporting of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. Infect Dis (Lond) 2021; 53:390-392. [PMID: 33512265 DOI: 10.1080/23744235.2021.1876913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Hafizuddin Awang
- Setiu District Health Office, Bandar Permaisuri, Setiu, Malaysia
| | | | | | | | - Azmani Wahab
- Terengganu State Health Department, Wisma Persekutuan, Kuala Terengganu, Malaysia
| | - Kasemani Embong
- Terengganu State Health Department, Wisma Persekutuan, Kuala Terengganu, Malaysia
| | - Nor Azimi Yunus
- Terengganu State Health Department, Wisma Persekutuan, Kuala Terengganu, Malaysia
| |
Collapse
|
47
|
Silva J, Lucas C, Sundaram M, Israelow B, Wong P, Klein J, Tokuyama M, Lu P, Venkataraman A, Liu F, Mao T, Oh JE, Park A, Casanovas-Massana A, Vogels CBF, Muenker MC, Zell J, Fournier JB, Campbell M, Chiorazzi M, Fuentes ER, Petrone ME, Kalinich CC, Ott IM, Watkins A, Moore AJ, Nakahata M, Farhadian S, Cruz CD, Ko AI, Schulz WL, Ring A, Ma S, Omer S, Wyllie AL, Iwasaki A. Saliva viral load is a dynamic unifying correlate of COVID-19 severity and mortality. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.01.04.21249236. [PMID: 33442706 PMCID: PMC7805468 DOI: 10.1101/2021.01.04.21249236] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
While several clinical and immunological parameters correlate with disease severity and mortality in SARS-CoV-2 infection, work remains in identifying unifying correlates of coronavirus disease 2019 (COVID-19) that can be used to guide clinical practice. Here, we examine saliva and nasopharyngeal (NP) viral load over time and correlate them with patient demographics, and cellular and immune profiling. We found that saliva viral load was significantly higher in those with COVID-19 risk factors; that it correlated with increasing levels of disease severity and showed a superior ability over nasopharyngeal viral load as a predictor of mortality over time (AUC=0.90). A comprehensive analysis of immune factors and cell subsets revealed strong predictors of high and low saliva viral load, which were associated with increased disease severity or better overall outcomes, respectively. Saliva viral load was positively associated with many known COVID-19 inflammatory markers such as IL-6, IL-18, IL-10, and CXCL10, as well as type 1 immune response cytokines. Higher saliva viral loads strongly correlated with the progressive depletion of platelets, lymphocytes, and effector T cell subsets including circulating follicular CD4 T cells (cTfh). Anti-spike (S) and anti-receptor binding domain (RBD) IgG levels were negatively correlated with saliva viral load showing a strong temporal association that could help distinguish severity and mortality in COVID-19. Finally, patients with fatal COVID-19 exhibited higher viral loads, which correlated with the depletion of cTfh cells, and lower production of anti-RBD and anti-S IgG levels. Together these results demonstrated that viral load - as measured by saliva but not nasopharyngeal - is a dynamic unifying correlate of disease presentation, severity, and mortality over time.
Collapse
Affiliation(s)
- Julio Silva
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Carolina Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Maria Sundaram
- ICES, Toronto, ON, Canada
- University of Toronto Dalla Lana School of Public Health, Toronto, ON, Canada
| | - Benjamin Israelow
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Patrick Wong
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Jon Klein
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Maria Tokuyama
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Peiwen Lu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Arvind Venkataraman
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Feimei Liu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Tianyang Mao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Ji Eun Oh
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Annsea Park
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chantal B. F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - M. Catherine Muenker
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Joseph Zell
- Department of Medicine, Section of Pulmonary and Critical Care Medicine; Yale University School of Medicine, New Haven, CT, USA
| | - John B. Fournier
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Melissa Campbell
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Michael Chiorazzi
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Edwin Ruiz Fuentes
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chaney C. Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Isabel M. Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Annie Watkins
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Adam J. Moore
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Maura Nakahata
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | - Shelli Farhadian
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Charles Dela Cruz
- Department of Medicine, Section of Pulmonary and Critical Care Medicine; Yale University School of Medicine, New Haven, CT, USA
| | - Albert I. Ko
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Wade L. Schulz
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, CT, USA
| | - Aaron Ring
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Shuangge Ma
- Department of Biostatistics, Yale University, New Haven, Connecticut, USA
| | - Saad Omer
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Yale Institute for Global Health, Yale University, New Haven, CT, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| |
Collapse
|
48
|
Affiliation(s)
- Rajesh T Gandhi
- From Massachusetts General Hospital and Harvard Medical School, Boston (R.T.G.); the Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle (J.B.L.); and the Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, and Grady Health System, Atlanta (C.R.)
| | - John B Lynch
- From Massachusetts General Hospital and Harvard Medical School, Boston (R.T.G.); the Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle (J.B.L.); and the Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, and Grady Health System, Atlanta (C.R.)
| | - Carlos Del Rio
- From Massachusetts General Hospital and Harvard Medical School, Boston (R.T.G.); the Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle (J.B.L.); and the Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, and Grady Health System, Atlanta (C.R.)
| |
Collapse
|
49
|
Arumugam A, Faron ML, Yu P, Markham C, Wu M, Wong S. A Rapid SARS-CoV-2 RT-PCR Assay for Low Resource Settings. Diagnostics (Basel) 2020; 10:E739. [PMID: 32987722 PMCID: PMC7598596 DOI: 10.3390/diagnostics10100739] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/18/2020] [Accepted: 09/23/2020] [Indexed: 12/18/2022] Open
Abstract
Quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay is the gold standard recommended to test for acute SARS-CoV-2 infection. However, it generally requires expensive equipment such as RNA isolation instruments and real-time PCR thermal cyclers. As a pandemic, COVID-19 has spread indiscriminately, and many low resource settings and developing countries do not have the means for fast and accurate COVID-19 detection to control the outbreak. Additionally, long assay times, in part caused by slow sample preparation steps, have created a large backlog when testing patient samples suspected of COVID-19. With many PCR-based molecular assays including an extraction step, this can take a significant amount of time and labor, especially if the extraction is performed manually. Using COVID-19 clinical specimens, we have collected evidence that the RT-qPCR assay can feasibly be performed directly on patient sample material in virus transport medium (VTM) without an RNA extraction step, while still producing sensitive test results. If RNA extraction steps can be omitted without significantly affecting clinical sensitivity, the turn-around time of COVID-19 tests, and the backlog we currently experience can be reduced drastically. Furthermore, our data suggest that rapid RT-PCR can be implemented for sensitive and specific molecular diagnosis of COVID-19 in locations where sophisticated laboratory instruments are not available. Our USD 300 set up achieved rapid RT-PCR using thin-walled PCR tubes and a water bath setup using sous vide immersion heaters, a Raspberry Pi computer, and a single servo motor that can process up to 96 samples at a time. Using COVID-19 positive clinical specimens, we demonstrated that RT-PCR assays can be performed in as little as 12 min using untreated samples, heat-inactivated samples, or extracted RNA templates with our low-cost water bath setup. These findings can help rapid COVID-19 testing to become more accessible and attainable across the globe.
Collapse
Affiliation(s)
- Arunkumar Arumugam
- AI Biosciences, Inc., College Station, TX 77845, USA; (A.A.); (P.Y.); (C.M.); (M.W.)
| | | | - Peter Yu
- AI Biosciences, Inc., College Station, TX 77845, USA; (A.A.); (P.Y.); (C.M.); (M.W.)
| | - Cole Markham
- AI Biosciences, Inc., College Station, TX 77845, USA; (A.A.); (P.Y.); (C.M.); (M.W.)
| | - Michelle Wu
- AI Biosciences, Inc., College Station, TX 77845, USA; (A.A.); (P.Y.); (C.M.); (M.W.)
| | - Season Wong
- AI Biosciences, Inc., College Station, TX 77845, USA; (A.A.); (P.Y.); (C.M.); (M.W.)
| |
Collapse
|