1
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Minor NR, Ramuta MD, Stauss MR, Harwood OE, Brakefield SF, Alberts A, Vuyk WC, Bobholz MJ, Rosinski JR, Wolf S, Lund M, Mussa M, Beversdorf LJ, Aliota MT, O'Connor SL, O'Connor DH. Metagenomic sequencing detects human respiratory and enteric viruses in air samples collected from congregate settings. Sci Rep 2023; 13:21398. [PMID: 38049453 PMCID: PMC10696062 DOI: 10.1038/s41598-023-48352-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 11/25/2023] [Indexed: 12/06/2023] Open
Abstract
Innovative methods for evaluating virus risk and spread, independent of test-seeking behavior, are needed to improve routine public health surveillance, outbreak response, and pandemic preparedness. Throughout the COVID-19 pandemic, environmental surveillance strategies, including wastewater andair sampling, have been used alongside widespread individual-based SARS-CoV-2 testing programs to provide population-level data. These environmental surveillance strategies have predominantly relied on pathogen-specific detection methods to monitor viruses through space and time. However, this provides a limited picture of the virome present in an environmental sample, leaving us blind to most circulating viruses. In this study, we explore whether pathogen-agnostic deep sequencing can expand the utility of air sampling to detect many human viruses. We show that sequence-independent single-primer amplification sequencing of nucleic acids from air samples can detect common and unexpected human respiratory and enteric viruses, including influenza virus type A and C, respiratory syncytial virus, human coronaviruses, rhinovirus, SARS-CoV-2, rotavirus, mamastrovirus, and astrovirus.
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Affiliation(s)
| | - Mitchell D Ramuta
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 555 Science Drive, Madison, WI, 53711, USA
| | | | - Olivia E Harwood
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 555 Science Drive, Madison, WI, 53711, USA
| | - Savannah F Brakefield
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 555 Science Drive, Madison, WI, 53711, USA
| | - Alexandra Alberts
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 555 Science Drive, Madison, WI, 53711, USA
| | - William C Vuyk
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 555 Science Drive, Madison, WI, 53711, USA
| | - Max J Bobholz
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 555 Science Drive, Madison, WI, 53711, USA
| | - Jenna R Rosinski
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 555 Science Drive, Madison, WI, 53711, USA
| | - Sydney Wolf
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 555 Science Drive, Madison, WI, 53711, USA
| | - Madelyn Lund
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 555 Science Drive, Madison, WI, 53711, USA
| | - Madison Mussa
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 555 Science Drive, Madison, WI, 53711, USA
| | | | - Matthew T Aliota
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Shelby L O'Connor
- Wisconsin National Primate Research Center, Madison, WI, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 555 Science Drive, Madison, WI, 53711, USA
| | - David H O'Connor
- Wisconsin National Primate Research Center, Madison, WI, USA.
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 555 Science Drive, Madison, WI, 53711, USA.
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2
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Minor NR, Ramuta MD, Stauss MR, Harwood OE, Brakefield SF, Alberts A, Vuyk WC, Bobholz MJ, Rosinski JR, Wolf S, Lund M, Mussa M, Beversdorf LJ, Aliota MT, O’Connor SL, O’Connor DH. Metagenomic sequencing detects human respiratory and enteric viruses in air samples collected from congregate settings. medRxiv 2023:2023.05.28.23290648. [PMID: 37398492 PMCID: PMC10312882 DOI: 10.1101/2023.05.28.23290648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Innovative methods for evaluating virus risk and spread, independent of test-seeking behavior, are needed to improve routine public health surveillance, outbreak response, and pandemic preparedness. Throughout the COVID-19 pandemic, environmental surveillance strategies, including wastewater and air sampling, have been used alongside widespread individual-based SARS-CoV-2 testing programs to provide population-level data. These environmental surveillance strategies have predominantly relied on pathogen-specific detection methods to monitor viruses through space and time. However, this provides a limited picture of the virome present in an environmental sample, leaving us blind to most circulating viruses. In this study, we explore whether pathogen-agnostic deep sequencing can expand the utility of air sampling to detect many human viruses. We show that sequence-independent single-primer amplification sequencing of nucleic acids from air samples can detect common and unexpected human respiratory and enteric viruses, including influenza virus type A and C, respiratory syncytial virus, human coronaviruses, rhinovirus, SARS-CoV-2, rotavirus, mamastrovirus, and astrovirus.
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Affiliation(s)
| | - Mitchell D. Ramuta
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Olivia E. Harwood
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Savannah F. Brakefield
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Alexandra Alberts
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - William C. Vuyk
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Max J. Bobholz
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Jenna R. Rosinski
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Sydney Wolf
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Madelyn Lund
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Madison Mussa
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Matthew T. Aliota
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Shelby L. O’Connor
- Wisconsin National Primate Research Center, Madison, WI USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - David H. O’Connor
- Wisconsin National Primate Research Center, Madison, WI USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
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3
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Li D, Sun C, Mei X, Yang L. Achieving broad availability of SARS-CoV-2 detections via smartphone-based analysis. Trends Analyt Chem 2023; 158:116878. [PMID: 36506266 PMCID: PMC9728015 DOI: 10.1016/j.trac.2022.116878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022]
Abstract
With the development of COVID-19, widely available tests are in great demand. Naked-eye SARS-CoV-2 test kits have recently been developed as home tests, but their sensitivity and accuracy are sometimes limited. Smartphones can convert various signals into digital information, potentially improving the sensitivity and accuracy of these home tests. Herein, we summarize smartphone-based detections for SARS-CoV-2. Optical detections of non-nucleic acids using various sensors and portable imaging systems, as well as nucleic acid analyses based on LAMP, CRISP, CATCH, and biosensors are discussed. Furthermore, different electrochemical detections were compared. We show results obtained using relatively complex equipment, complicated programming procedures, or custom smartphone apps, and describe methods for obtaining information with only simple setups and free software on smartphones. Then, the combined costs of typical smartphone-based detections are evaluated. Finally, the prospect of improving smartphone-based strategies to achieve broad availability of SARS-CoV-2 detection is proposed.
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Affiliation(s)
- Dan Li
- Jinzhou Medical University, Jinzhou, China
| | - Cai Sun
- AECC Shenyang Liming Aero-Engine Co, Ltd., Shenyang, China
| | - Xifan Mei
- Jinzhou Medical University, Jinzhou, China,Corresponding author
| | - Liqun Yang
- NHC Key Laboratory of Reproductive Health and Medical Genetics (China Medical University), Liaoning Research Institute of Family Planning (The Affiliated Reproductive Hospital of China Medical University), Shenyang, China,Corresponding author
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4
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Yu H, Zhang H, Li J, Zhao Z, Deng M, Ren Z, Li Z, Xue C, Li MG, Chen Z. Rapid and Unamplified Detection of SARS-CoV-2 RNA via CRISPR-Cas13a-Modified Solution-Gated Graphene Transistors. ACS Sens 2022; 7:3923-3932. [PMID: 36472865 PMCID: PMC9745736 DOI: 10.1021/acssensors.2c01990] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022]
Abstract
The disease caused by severe acute respiratory syndrome coronavirus, SARS-CoV-2, is termed COVID-19. Even though COVID-19 has been out for more than two years, it is still causing a global pandemic. Due to the limitations of sample collection, transportation, and kit performance, the traditional reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method has a long detection period and high testing costs. An increased risk of infection is inevitable, since many patients may not be diagnosed in time. The CRISPR-Cas13a system can be designed for RNA identification and knockdown, as a promising platform for nucleic acid detection. Here, we designed a solution-gated graphene transistor (SGGT) biosensor based on the CRISPR-Cas13a system. Using the gene-targeting capacity of CRISPR-Cas13a and gate functionalization via multilayer modification, SARS-CoV-2 nucleic acid sequences can be quickly and precisely identified without the need for amplification or fluorescence tagging. The limit of detection (LOD) in both buffer and serum reached the aM level, and the reaction time was about 10 min. The results of the detection of COVID-19 clinical samples from throat swabs agree with RT-PCR. In addition, the interchangeable gates significantly minimize the cost and time of device fabrication. In a nutshell, our biosensor technology is broadly applicable and will be suitable for point-of-care (POC) testing.
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Affiliation(s)
- Haiyang Yu
- State Key Laboratory of Advanced Technology for
Materials Synthesis and Processing, Wuhan University of
Technology, Wuhan430070, China
- Collaborative Innovation Center for Advanced Organic
Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the
Green Preparation and Application of Functional Materials, Ministry of Education, Hubei
Key Laboratory of Polymer Materials, School of Materials Science and Engineering,
Hubei University, Wuhan430062, China
| | - Huibin Zhang
- Collaborative Innovation Center for Advanced Organic
Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the
Green Preparation and Application of Functional Materials, Ministry of Education, Hubei
Key Laboratory of Polymer Materials, School of Materials Science and Engineering,
Hubei University, Wuhan430062, China
| | - Jinhua Li
- Collaborative Innovation Center for Advanced Organic
Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the
Green Preparation and Application of Functional Materials, Ministry of Education, Hubei
Key Laboratory of Polymer Materials, School of Materials Science and Engineering,
Hubei University, Wuhan430062, China
| | - Zheng Zhao
- State Key Laboratory of Advanced Technology for
Materials Synthesis and Processing, Wuhan University of
Technology, Wuhan430070, China
- Sanya Science and Education Innovation Park
of Wuhan University of Technology, Sanya572000,
China
| | - Minhua Deng
- Collaborative Innovation Center for Advanced Organic
Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the
Green Preparation and Application of Functional Materials, Ministry of Education, Hubei
Key Laboratory of Polymer Materials, School of Materials Science and Engineering,
Hubei University, Wuhan430062, China
| | - Zhanpeng Ren
- Collaborative Innovation Center for Advanced Organic
Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the
Green Preparation and Application of Functional Materials, Ministry of Education, Hubei
Key Laboratory of Polymer Materials, School of Materials Science and Engineering,
Hubei University, Wuhan430062, China
| | - Ziqin Li
- Collaborative Innovation Center for Advanced Organic
Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the
Green Preparation and Application of Functional Materials, Ministry of Education, Hubei
Key Laboratory of Polymer Materials, School of Materials Science and Engineering,
Hubei University, Wuhan430062, China
| | - Chenglong Xue
- Collaborative Innovation Center for Advanced Organic
Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the
Green Preparation and Application of Functional Materials, Ministry of Education, Hubei
Key Laboratory of Polymer Materials, School of Materials Science and Engineering,
Hubei University, Wuhan430062, China
| | - Mitch Guijun Li
- Division of Integrative Systems and Design,
The Hong Kong University of Science and Technology, Clear
Water Bay, Kowloon, Hong Kong SAR999077, China
| | - Zhaowei Chen
- Division of Nephrology, Renmin Hospital
of Wuhan University, Wuhan430060, China
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5
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García-Bernalt Diego J, Fernández-Soto P, Muro A. The Future of Point-of-Care Nucleic Acid Amplification Diagnostics after COVID-19: Time to Walk the Walk. Int J Mol Sci 2022; 23. [PMID: 36430586 DOI: 10.3390/ijms232214110] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 11/18/2022] Open
Abstract
Since the onset of the COVID-19 pandemic, over 610 million cases have been diagnosed and it has caused over 6.5 million deaths worldwide. The crisis has forced the scientific community to develop tools for disease control and management at a pace never seen before. The control of the pandemic heavily relies in the use of fast and accurate diagnostics, that allow testing at a large scale. The gold standard diagnosis of viral infections is the RT-qPCR. Although it provides consistent and reliable results, it is hampered by its limited throughput and technical requirements. Here, we discuss the main approaches to rapid and point-of-care diagnostics based on RT-qPCR and isothermal amplification diagnostics. We describe the main COVID-19 molecular diagnostic tests approved for self-testing at home or for point-of-care testing and compare the available options. We define the influence of specimen selection and processing, the clinical validation, result readout improvement strategies, the combination with CRISPR-based detection and the diagnostic challenge posed by SARS-CoV-2 variants for different isothermal amplification techniques, with a particular focus on LAMP and recombinase polymerase amplification (RPA). Finally, we try to shed light on the effect the improvement in molecular diagnostics during the COVID-19 pandemic could have in the future of other infectious diseases.
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6
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Ramuta MD, Newman CM, Brakefield SF, Stauss MR, Wiseman RW, Kita-Yarbro A, O'Connor EJ, Dahal N, Lim A, Poulsen KP, Safdar N, Marx JA, Accola MA, Rehrauer WM, Zimmer JA, Khubbar M, Beversdorf LJ, Boehm EC, Castañeda D, Rushford C, Gregory DA, Yao JD, Bhattacharyya S, Johnson MC, Aliota MT, Friedrich TC, O'Connor DH, O'Connor SL. SARS-CoV-2 and other respiratory pathogens are detected in continuous air samples from congregate settings. Nat Commun 2022; 13:4717. [PMID: 35953484 DOI: 10.1038/s41467-022-32406-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
Two years after the emergence of SARS-CoV-2, there is still a need for better ways to assess the risk of transmission in congregate spaces. We deployed active air samplers to monitor the presence of SARS-CoV-2 in real-world settings across communities in the Upper Midwestern states of Wisconsin and Minnesota. Over 29 weeks, we collected 527 air samples from 15 congregate settings. We detected 106 samples that were positive for SARS-CoV-2 viral RNA, demonstrating that SARS-CoV-2 can be detected in continuous air samples collected from a variety of real-world settings. We expanded the utility of air surveillance to test for 40 other respiratory pathogens. Surveillance data revealed differences in timing and location of SARS-CoV-2 and influenza A virus detection. In addition, we obtained SARS-CoV-2 genome sequences from air samples to identify variant lineages. Collectively, this shows air sampling is a scalable, high throughput surveillance tool that could be used in conjunction with other methods for detecting respiratory pathogens in congregate settings.
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7
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Hyman LB, Christopher CR, Romero PA. Competitive SNP-LAMP probes for rapid and robust single-nucleotide polymorphism detection. Cell Rep Methods 2022; 2:100242. [PMID: 35880021 PMCID: PMC9308130 DOI: 10.1016/j.crmeth.2022.100242] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 02/28/2022] [Accepted: 06/02/2022] [Indexed: 12/01/2022]
Abstract
In this work, we developed a simple and robust assay to rapidly detect SNPs in nucleic acid samples. Our approach combines loop-mediated isothermal amplification (LAMP)-based target amplification with fluorescent probes to detect SNPs with high specificity. A competitive "sink" strand preferentially binds to non-SNP amplicons and shifts the free energy landscape to favor specific activation by SNP products. We demonstrated the broad utility and reliability of our SNP-LAMP method by detecting three distinct SNPs across the human genome. We also designed an assay to rapidly detect highly transmissible severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants from crude biological samples. This work demonstrates that competitive SNP-LAMP is a powerful and universal method that could be applied in point-of-care settings to detect any target SNP with high specificity and sensitivity. We additionally developed a publicly available web application for researchers to design SNP-LAMP probes for any target sequence of interest.
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Affiliation(s)
- Leland B. Hyman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Philip A. Romero
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
- The University of Wisconsin Carbone Cancer Center, Madison, WI, USA
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8
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Tobik ER, Kitfield-Vernon LB, Thomas RJ, Steel SA, Tan SH, Allicock OM, Choate BL, Akbarzada S, Wyllie AL. Saliva as a sample type for SARS-CoV-2 detection: implementation successes and opportunities around the globe. Expert Rev Mol Diagn 2022; 22:519-535. [PMID: 35763281 DOI: 10.1080/14737159.2022.2094250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Symptomatic testing and asymptomatic screening for SARS-CoV-2 continue to be essential tools for mitigating virus transmission. Though COVID-19 diagnostics initially defaulted to oropharyngeal or nasopharyngeal sampling, the worldwide urgency to expand testing efforts spurred innovative approaches and increased diversity of detection methods. Strengthening innovation and facilitating widespread testing remains critical for global health, especially as additional variants emerge and other mitigation strategies are recalibrated. AREAS COVERED A growing body of evidence reflects the need to expand testing efforts and further investigate the efficiency, sensitivity, and acceptability of saliva samples for SARS-CoV-2 detection. Countries have made pandemic response decisions based on resources, costs, procedures, and regional acceptability - the adoption and integration of saliva-based testing among them. Saliva has demonstrated high sensitivity and specificity while being less invasive relative to nasopharyngeal swabs, securing saliva's position as a more acceptable sample type. EXPERT OPINION Despite the accessibility and utility of saliva sampling, global implementation remains low compared to swab-based approaches. In some cases, countries have validated saliva-based methods but face challenges with testing implementation or expansion. Here, we review the localities that have demonstrated success with saliva-based SARS-CoV-2 testing approaches and can serve as models for transforming concepts into globally-implemented best practices.
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Affiliation(s)
- Emily R Tobik
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Lily B Kitfield-Vernon
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Russell J Thomas
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Sydney A Steel
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Steph H Tan
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.,Department of Health Policy and Management, Yale School of Public Health, New Haven, Connecticut, USA
| | - Orchid M Allicock
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Brittany L Choate
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Sumaira Akbarzada
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
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9
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Ramuta MD, Newman CM, Brakefield SF, Stauss MR, Wiseman RW, Kita-Yarbro A, O'Connor EJ, Dahal N, Lim A, Poulsen KP, Safdar N, Marx JA, Accola MA, Rehrauer WM, Zimmer JA, Khubbar M, Beversdorf LJ, Boehm EC, Castañeda D, Rushford C, Gregory DA, Yao JD, Bhattacharyya S, Johnson MC, Aliota MT, Friedrich TC, O'Connor DH, O'Connor SL. SARS-CoV-2 and other respiratory pathogens are detected in continuous air samples from congregate settings. medRxiv 2022. [PMID: 35378751 PMCID: PMC8978944 DOI: 10.1101/2022.03.29.22272716] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Two years after the emergence of SARS-CoV-2, there is still a need for better ways to assess the risk of transmission in congregate spaces. We deployed active air samplers to monitor the presence of SARS-CoV-2 in real-world settings across communities in the Upper Midwestern states of Wisconsin and Minnesota. Over 29 weeks, we collected 527 air samples from 15 congregate settings and detected 106 SARS-CoV-2 positive samples, demonstrating SARS-CoV-2 can be detected in air collected from daily and weekly sampling intervals. We expanded the utility of air surveillance to test for 40 other respiratory pathogens. Surveillance data revealed differences in timing and location of SARS-CoV-2 and influenza A virus detection in the community. In addition, we obtained SARS-CoV-2 genome sequences from air samples to identify variant lineages. Collectively, this shows air surveillance is a scalable, cost-effective, and high throughput alternative to individual testing for detecting respiratory pathogens in congregate settings.
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10
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Arbaciauskaite S, Babakhani P, Sandetskaya N, Vitkus D, Jancoriene L, Karosiene D, Karciauskaite D, Zablockiene B, Kuhlmeier D. Self-Sampled Gargle Water Direct RT-LAMP as a Screening Method for the Detection of SARS-CoV-2 Infections. Diagnostics (Basel) 2022; 12:diagnostics12040775. [PMID: 35453823 PMCID: PMC9030430 DOI: 10.3390/diagnostics12040775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/17/2022] [Accepted: 03/19/2022] [Indexed: 11/16/2022] Open
Abstract
We assessed the viability of self-sampled gargle water direct RT-LAMP (LAMP) for detecting SARS-CoV-2 infections by estimating its sensitivity with respect to the gold standard indirect RT-PCR of paired oro-nasopharyngeal swab samples. We also assessed the impact of symptom onset to test time (STT)—i.e., symptom days at sampling, on LAMP. In addition, we appraised the viability of gargle water self-sampling versus oro-nasopharyngeal swab sampling, by comparing paired indirect RT-PCR results. 202 oro-nasopharyngeal swab and paired self-sampled gargle water samples were collected from hospital patients with COVID-19 associated symptoms. LAMP, indirect and direct RT-PCR were performed on all gargle water samples, and indirect RT-PCR was performed on all oro-nasopharyngeal samples. LAMP presented a sensitivity of 80.8% (95% CI: 70.8–90.8%) for sample pairs with sub-25 Ct oro-nasopharyngeal indirect RT-PCR results, and 77.6% (66.2–89.1%) sensitivity for sub-30 Ct samples with STT ≤ 7 days. STT, independently of Ct value, correlated negatively with LAMP performance. 80.7% agreement was observed between gargle water and oro-nasopharyngeal indirect RT-PCR results. In conclusion, LAMP presents an acceptable sensitivity for low Ct and low STT samples. Gargle water may be considered as a viable sampling method, and LAMP as a screening method, especially for symptomatic persons with low STT values.
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Affiliation(s)
- Skaiste Arbaciauskaite
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, Perlickstraße 1, 04103 Leipzig, Germany; (N.S.); (D.K.)
- Institute of Cell Biology and Neurobiology, Charité—Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- Correspondence:
| | - Pouya Babakhani
- Department of Computer Science, University of Bath, Claverton Down, Bath BA2 7AY, UK;
| | - Natalia Sandetskaya
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, Perlickstraße 1, 04103 Leipzig, Germany; (N.S.); (D.K.)
| | - Dalius Vitkus
- Institute of Biomedical Sciences, Vilnius University Faculty of Medicine, M.K. Ciurlionio 21, LT-03101 Vilnius, Lithuania; (D.V.); (D.K.)
- Centre of Laboratory Medicine, Vilnius University Hospital Santaros Klinikos, Santariskiu 14, LT-08406 Vilnius, Lithuania;
| | - Ligita Jancoriene
- Clinic of Infectious Diseases and Dermatovenerology, Institute of Clinical Medicine, Vilnius University Faculty of Medicine, M.K. Ciurlionio 21, LT-03101 Vilnius, Lithuania; (L.J.); (B.Z.)
- Center of Infectious Diseases, Vilnius University Hospital Santaros Klinikos, Santariskiu 14, LT-08406 Vilnius, Lithuania
| | - Dovile Karosiene
- Centre of Laboratory Medicine, Vilnius University Hospital Santaros Klinikos, Santariskiu 14, LT-08406 Vilnius, Lithuania;
| | - Dovile Karciauskaite
- Institute of Biomedical Sciences, Vilnius University Faculty of Medicine, M.K. Ciurlionio 21, LT-03101 Vilnius, Lithuania; (D.V.); (D.K.)
- Centre of Laboratory Medicine, Vilnius University Hospital Santaros Klinikos, Santariskiu 14, LT-08406 Vilnius, Lithuania;
| | - Birute Zablockiene
- Clinic of Infectious Diseases and Dermatovenerology, Institute of Clinical Medicine, Vilnius University Faculty of Medicine, M.K. Ciurlionio 21, LT-03101 Vilnius, Lithuania; (L.J.); (B.Z.)
- Center of Infectious Diseases, Vilnius University Hospital Santaros Klinikos, Santariskiu 14, LT-08406 Vilnius, Lithuania
| | - Dirk Kuhlmeier
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, Perlickstraße 1, 04103 Leipzig, Germany; (N.S.); (D.K.)
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