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Caffrey M, Jayakumar N, Caffrey V, Anirudhan V, Rong L, Paprotny I. VLP-based model for the study of airborne viral pathogens. Microbiol Spectr 2024; 12:e0001324. [PMID: 38752752 DOI: 10.1128/spectrum.00013-24] [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: 01/03/2024] [Accepted: 04/21/2024] [Indexed: 05/28/2024] Open
Abstract
The recent COVID-19 pandemic has underscored the danger of airborne viral pathogens. The lack of model systems to study airborne pathogens limits the understanding of airborne pathogen distribution as well as potential surveillance and mitigation strategies. In this work, we develop a novel model system to study airborne pathogens using virus-like particles (VLPs). Specifically, we demonstrate the ability to aerosolize VLP and detect and quantify aerosolized VLP RNA by reverse transcription-loop-mediated isothermal amplification in real-time fluorescent and colorimetric assays. Importantly, the VLP model presents many advantages for the study of airborne viral pathogens: (i) similarity in size and surface components; (ii) ease of generation and noninfectious nature enabling the study of biosafety level 3 and biosafety level 4 viruses; (iii) facile characterization of aerosolization parameters; (iv) ability to adapt the system to other viral envelope proteins, including those of newly discovered pathogens and mutant variants; and (v) the ability to introduce viral sequences to develop nucleic acid amplification assays. IMPORTANCE The study and detection of airborne pathogens are hampered by the lack of appropriate model systems. In this work, we demonstrate that noninfectious virus-like particles (VLPs) represent attractive models to study airborne viral pathogens. Specifically, VLPs are readily prepared, are similar in size and composition to infectious viruses, and are amenable to highly sensitive nucleic acid amplification techniques.
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Affiliation(s)
- Michael Caffrey
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Nitin Jayakumar
- Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Veronique Caffrey
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Varada Anirudhan
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Lijun Rong
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Igor Paprotny
- Department of Electrical and Computer Engineering, University of Illinois at Chicago, Chicago, Illinois, USA
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Sousan S, Boatman M, Johansen L, Fan M, Roper RL. Comparing and validating air sampling methods for SARS-CoV-2 detection in HVAC ducts of student dorms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 343:123164. [PMID: 38103710 DOI: 10.1016/j.envpol.2023.123164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/27/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023]
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic demonstrated the threat of airborne pathogenic respiratory viruses such as the airborne Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The ability to detect circulating viruses in a workplace or dormitory setting allows an early warning system that can alert occupants to implement precautions (e.g. masking) and/or trigger individual testing to allow isolation and quarantine measures to halt contagion. This work extends and validates the first successful detection of SARS-CoV-2 virus in dormitory Heating, Ventilation, and Air Conditioning (HVAC) systems and compares different air sampling methods and media types combined with optimized quantitative Reverse-Transcription PCR (qRT-PCR) analysis. The study was performed in two environments; large dormitories of students who underwent periodic testing for COVID-19 (unknown environment) and the HVAC air from a suite with a student who had tested positive for COVID-19 (known dorm). The air sampling methods were performed using Filter Cassettes, BioSampler, AerosolSense Sampler and Button Sampler (with four media types with different pore sizes of 5 μm, 3 μm, 3 μm (gelatin), and 1.2 μm). The SARS-CoV-2 positive air samples were compared with the positive samples collected by individual student campus track tracing methods using PCR testing on saliva and nasopharyngeal samples. The results show a detection rate of 73% in the unknown environment and a 78% detection rate in the known dorm. Our data show that the virus was detectable with all the sampling methods we employed. However, the AerosolSense sampler and BioSampler performed the best at 63% and 61% detection rates, compared to 25% for the Filter Cassettes and 23% for the Button Sampler. Despite the success rate, it is not possible to definitively conclude which method is most sensitive due to the limited number of samples. These results show that with careful sampling and optimized PCR methods, pathogenic respiratory viruses can be detected in large buildings using HVAC return air.
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Affiliation(s)
- Sinan Sousan
- Department of Public Health, Brody School of Medicine, East Carolina University, Greenville, NC, 27834, USA; North Carolina Agromedicine Institute, Greenville, NC, 27834, USA.
| | - Marina Boatman
- Department of Public Health, Brody School of Medicine, East Carolina University, Greenville, NC, 27834, USA; Department of Health Services and Information Management, College of Allied Health, East Carolina University, Greenville, NC, 27834, USA; Department of Microbiology & Immunology, Brody School of Medicine, 5E-106A, East Carolina University, Greenville, NC, 27834, USA
| | - Lauren Johansen
- Department of Public Health, Brody School of Medicine, East Carolina University, Greenville, NC, 27834, USA; Department of Health Education and Promotion, College of Health and Human Performance, East Carolina University, Greenville, NC, 27834, USA; Department of Microbiology & Immunology, Brody School of Medicine, 5E-106A, East Carolina University, Greenville, NC, 27834, USA
| | - Ming Fan
- Department of Microbiology & Immunology, Brody School of Medicine, 5E-106A, East Carolina University, Greenville, NC, 27834, USA
| | - Rachel L Roper
- Department of Microbiology & Immunology, Brody School of Medicine, 5E-106A, East Carolina University, Greenville, NC, 27834, USA
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Caffrey M, Jayakumar N, Caffrey V, Anirudan V, Rong L, Paprotny I. VLP-Based Model for Study of Airborne Viral Pathogens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.574055. [PMID: 38260552 PMCID: PMC10802359 DOI: 10.1101/2024.01.03.574055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The recent COVID-19 pandemic has underscored the danger of airborne viral pathogens. The lack of model systems to study airborne pathogens limits the understanding of airborne pathogen distribution, as well as potential surveillance and mitigation strategies. In this work, we develop a novel model system to study airborne pathogens using virus like particles (VLP). Specifically, we demonstrate the ability to aerosolize VLP and detect and quantify aerosolized VLP RNA by Reverse Transcription-Loop-Mediated Isothermal Amplification (RT-LAMP) in real-time fluorescent and colorimetric assays. Importantly, the VLP model presents many advantages for the study of airborne viral pathogens: (i) similarity in size and surface components; (ii) ease of generation and noninfectious nature enabling study of BSL3 and BSL4 viruses; (iii) facile characterization of aerosolization parameters; (iv) ability to adapt the system to other viral envelope proteins including those of newly discovered pathogens and mutant variants; (v) the ability to introduce viral sequences to develop nucleic acid amplification assays.
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Affiliation(s)
- Michael Caffrey
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607
| | - Nitin Jayakumar
- Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, Chicago, IL 60607
| | - Veronique Caffrey
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607
| | - Varada Anirudan
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612
| | - Lijun Rong
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612
| | - Igor Paprotny
- Department of Electrical and Computer Engineering, University of Illinois at Chicago, Chicago, IL 60607
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Guo J, Lv M, Liu Z, Qin T, Qiu H, Zhang L, Lu J, Hu L, Yang W, Zhou D. Comprehensive performance evaluation of six bioaerosol samplers based on an aerosol wind tunnel. ENVIRONMENT INTERNATIONAL 2024; 183:108402. [PMID: 38150804 DOI: 10.1016/j.envint.2023.108402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 12/29/2023]
Abstract
Choosing a suitable bioaerosol sampler for atmospheric microbial monitoring has been a challenge to researchers interested in environmental microbiology, especially during a pandemic. However, a comprehensive and integrated evaluation method to fully assess bioaerosol sampler performance is still lacking. Herein, we constructed a customized wind tunnel operated at 2-20 km/h wind speed to systematically and efficiently evaluate the performance of six frequently used samplers, where various aerosols, including Arizona test dust, bacterial spores, gram-positive and gram-negative bacteria, phages, and viruses, were generated. After 10 or 60 min of sampling, the physical and biological sampling efficiency and short or long-term sampling capabilities were determined by performing aerodynamic particle size analysis, live microbial culturing, and a qPCR assay. The results showed that AGI-30 and BioSampler impingers have good physical and biological sampling efficiencies for short-term sampling. However, their ability to capture aerosols at low concentrations is restricted. SASS 2300 and BSA-350 wet-wall cyclones had excellent enrichment ratios and high microbial cultivability in both short-term and long-term sampling; however, they were not suitable for quantitative studies of aerosols. Polycarbonate filter samplers showed outstanding performance in physical and long-term sampling but lacked the ability to maintain microbial activity, which can be improved by gelatin filter samplers. However, limitations remain for some fragile microorganisms, such as E. coli phage PhiX174 and coronavirus GX_P2V. In addition, the effects of wind speed and direction should be considered when sampling particles larger than 4 µm. This study provides an improved strategy and guidance for the characterization and selection of a bioaerosol sampler for better measurement and interpretation of collected ambient bioaerosols.
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Affiliation(s)
- Jianshu Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China; Department of Environmental Health, School of Public Health and the Key Laboratory of Public Health Safety, Fudan University, Shanghai, China
| | - Meng Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhijian Liu
- Department of Power Engineering, North China Electric Power University, Baoding, Hebei, China
| | - Tongtong Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hongying Qiu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lili Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jianchun Lu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lingfei Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wenhui Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
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Luong Nguyen LB, Goupil de Bouillé J, Menant L, Noret M, Dumas A, Salmona M, Le Goff J, Delaugerre C, Crépey P, Zeggagh J. A randomised controlled trial to study the transmission of SARS-CoV-2 and other respiratory viruses during indoor clubbing events (ANRS0066s ITOC study). Clin Infect Dis 2023; 77:ciad603. [PMID: 37795682 PMCID: PMC10724450 DOI: 10.1093/cid/ciad603] [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: 03/11/2023] [Revised: 07/05/2023] [Accepted: 10/04/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND In the context of the circulation of the SARS-CoV-2 B.1.617.2 (Delta) variant, vaccination re-authorised mass indoor gatherings. The "Indoor Transmission of COVID-19" (ITOC) trial (ClinicalTrials.gov, NCT05311865) aimed to assess the risk of transmission of SARS-CoV-2 and other respiratory viruses during an indoor clubbing event among participants fully-vaccinated against COVID-19. METHODS ITOC, a randomised, controlled trial in the Paris region (France), enrolled healthy volunteers aged 18-49 years, fully-vaccinated against COVID-19, with no co-morbidities or symptoms, randomised 1:1 to be interventional group "attendees" or control "non-attendees". The intervention, a 7-hour indoor event in a nightclub at full capacity, with no masking, prior SARS-CoV-2 test result or social distancing required. The primary-outcome measure was the numbers of RT-PCR-determined SARS-CoV-2-positive subjects on self-collected saliva 7 days post-gathering in the per-protocol population. Secondary endpoints focused on 20 other respiratory viruses. RESULTS Healthy participants (n = 1,216) randomised 2:1 by blocks up to 10, 815 attendees and 401 non-attendees, yielding 529 and 287 subjects, respectively, with day-7 saliva samples. One day-7 sample from each group was positive. Looking at all respiratory viruses together, the clubbing event was associated with an increased risk of infection of 1.59 [95% CI 1.04-2.61]. CONCLUSIONS In the context of low Delta-VOC circulation, no evidence of SARS-CoV-2 transmission among asymptomatic and vaccinated participants was found, but the risk of other respiratory virus transmission was higher.
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Affiliation(s)
- Liem Binh Luong Nguyen
- CIC Cochin Pasteur, Hôpital Cochin Port-Royal, AP-HP, Université de Paris Cité, Paris, France
| | - Jeanne Goupil de Bouillé
- Service de Maladies Infectieuses et Tropicales, Hôpital Avicenne, AP-HP, Bobigny, France
- LEPS Laboratoire Éducations et Promotion de Santé, Université Paris 13, Bobigny, France
| | - Lola Menant
- Université de Rennes, EHESP, CNRS, Inserm, Arènes—UMR 6051, RSMS—U 1309, Rennes, France
| | - Marion Noret
- Réseau National de Recherche Clinique en Infectiologie (RENARCI), Service de Maladies Infectieuses et Tropicales, Hôpital Saint-Louis, AP-HP, Paris, France
| | - Audrey Dumas
- ANRS∣Emerging Infectious Diseases, Paris, France
| | - Maud Salmona
- Service de Virologie, Hôpital Saint-Louis, AP-HP, Université de Paris Cité, Paris, France
| | - Jérôme Le Goff
- Service de Virologie, Hôpital Saint-Louis, AP-HP, Université de Paris Cité, Paris, France
| | - Constance Delaugerre
- Service de Virologie, Hôpital Saint-Louis, AP-HP, Université de Paris Cité, Paris, France
| | - Pascal Crépey
- Université de Rennes, EHESP, CNRS, Inserm, Arènes—UMR 6051, RSMS—U 1309, Rennes, France
| | - Jeremy Zeggagh
- Service de Maladies Infectieuses et Tropicales, Hôpital Saint-Louis, AP-HP, Paris, France
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Raymenants J, Geenen C, Budts L, Thibaut J, Thijssen M, De Mulder H, Gorissen S, Craessaerts B, Laenen L, Beuselinck K, Ombelet S, Keyaerts E, André E. Indoor air surveillance and factors associated with respiratory pathogen detection in community settings in Belgium. Nat Commun 2023; 14:1332. [PMID: 36898982 PMCID: PMC10005919 DOI: 10.1038/s41467-023-36986-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/27/2023] [Indexed: 03/12/2023] Open
Abstract
Currently, the real-life impact of indoor climate, human behaviour, ventilation and air filtration on respiratory pathogen detection and concentration are poorly understood. This hinders the interpretability of bioaerosol quantification in indoor air to surveil respiratory pathogens and transmission risk. We tested 341 indoor air samples from 21 community settings in Belgium for 29 respiratory pathogens using qPCR. On average, 3.9 pathogens were positive per sample and 85.3% of samples tested positive for at least one. Pathogen detection and concentration varied significantly by pathogen, month, and age group in generalised linear (mixed) models and generalised estimating equations. High CO2 and low natural ventilation were independent risk factors for detection. The odds ratio for detection was 1.09 (95% CI 1.03-1.15) per 100 parts per million (ppm) increase in CO2, and 0.88 (95% CI 0.80-0.97) per stepwise increase in natural ventilation (on a Likert scale). CO2 concentration and portable air filtration were independently associated with pathogen concentration. Each 100ppm increase in CO2 was associated with a qPCR Ct value decrease of 0.08 (95% CI -0.12 to -0.04), and portable air filtration with a 0.58 (95% CI 0.25-0.91) increase. The effects of occupancy, sampling duration, mask wearing, vocalisation, temperature, humidity and mechanical ventilation were not significant. Our results support the importance of ventilation and air filtration to reduce transmission.
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Affiliation(s)
- Joren Raymenants
- Laboratory of Clinical Microbiology, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
- Department of General Internal Medicine, University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium.
| | - Caspar Geenen
- Laboratory of Clinical Microbiology, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Lore Budts
- Department of Laboratory Medicine, National Reference Center of Respiratory Pathogens, University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Jonathan Thibaut
- Laboratory of Clinical Microbiology, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Marijn Thijssen
- Laboratory of Clinical and Epidemiological Virology (Rega Institute), KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Hannelore De Mulder
- Laboratory of Clinical Microbiology, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Sarah Gorissen
- Laboratory of Clinical Microbiology, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Bastiaan Craessaerts
- Department of Laboratory Medicine, National Reference Center of Respiratory Pathogens, University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Lies Laenen
- Laboratory of Clinical Microbiology, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
- Department of Laboratory Medicine, National Reference Center of Respiratory Pathogens, University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Kurt Beuselinck
- Department of Laboratory Medicine, National Reference Center of Respiratory Pathogens, University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Sien Ombelet
- Department of Laboratory Medicine, National Reference Center of Respiratory Pathogens, University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Els Keyaerts
- Department of Laboratory Medicine, National Reference Center of Respiratory Pathogens, University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Emmanuel André
- Laboratory of Clinical Microbiology, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
- Department of Laboratory Medicine, National Reference Center of Respiratory Pathogens, University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium
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7
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Tan KS, Ang AXY, Tay DJW, Somani J, Ng AJY, Peng LL, Chu JJH, Tambyah PA, Allen DM. Detection of hospital environmental contamination during SARS-CoV-2 Omicron predominance using a highly sensitive air sampling device. Front Public Health 2023; 10:1067575. [PMID: 36703815 PMCID: PMC9873263 DOI: 10.3389/fpubh.2022.1067575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/23/2022] [Indexed: 01/11/2023] Open
Abstract
Background and objectives The high transmissibility of SARS-CoV-2 has exposed weaknesses in our infection control and detection measures, particularly in healthcare settings. Aerial sampling has evolved from passive impact filters to active sampling using negative pressure to expose culture substrate for virus detection. We evaluated the effectiveness of an active air sampling device as a potential surveillance system in detecting hospital pathogens, for augmenting containment measures to prevent nosocomial transmission, using SARS-CoV-2 as a surrogate. Methods We conducted air sampling in a hospital environment using the AerosolSenseTM air sampling device and compared it with surface swabs for their capacity to detect SARS-CoV-2. Results When combined with RT-qPCR detection, we found the device provided consistent SARS-CoV-2 detection, compared to surface sampling, in as little as 2 h of sampling time. The device also showed that it can identify minute quantities of SARS-CoV-2 in designated "clean areas" and through a N95 mask, indicating good surveillance capacity and sensitivity of the device in hospital settings. Conclusion Active air sampling was shown to be a sensitive surveillance system in healthcare settings. Findings from this study can also be applied in an organism agnostic manner for surveillance in the hospital, improving our ability to contain and prevent nosocomial outbreaks.
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Affiliation(s)
- Kai Sen Tan
- Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,Infectious Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,*Correspondence: Kai Sen Tan ✉
| | - Alicia Xin Yu Ang
- Department of Medicine, Division of Infectious Diseases, National University Hospital, Singapore, Singapore
| | - Douglas Jie Wen Tay
- Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,Infectious Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jyoti Somani
- Department of Medicine, Division of Infectious Diseases, National University Hospital, Singapore, Singapore
| | - Alexander Jet Yue Ng
- Department of Emergency Medicine, National University Hospital, Singapore, Singapore
| | - Li Lee Peng
- Department of Emergency Medicine, National University Hospital, Singapore, Singapore
| | - Justin Jang Hann Chu
- Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,Infectious Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,Collaborative and Translation Unit for Hand, Foot and Mouth Disease (HFMD), Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Paul Anantharajah Tambyah
- Infectious Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,Department of Medicine, Division of Infectious Diseases, National University Hospital, Singapore, Singapore
| | - David Michael Allen
- Infectious Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,Department of Medicine, Division of Infectious Diseases, National University Hospital, Singapore, Singapore,David Michael Allen ✉
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SARS-CoV-2 and other respiratory pathogens are detected in continuous air samples from congregate settings. Nat Commun 2022; 13:4717. [PMID: 35953484 PMCID: PMC9366802 DOI: 10.1038/s41467-022-32406-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [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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9
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Mshamu S, Mmbando A, Meta J, Bradley J, Bøjstrup TC, Day NPJ, Mukaka M, Okumu F, Olotu A, Pell C, Deen J, Knudsen J, Lindsay SW, von Seidlein L. Assessing the impact of a novel house design on the incidence of malaria in children in rural Africa: study protocol for a household-cluster randomized controlled superiority trial. Trials 2022; 23:519. [PMID: 35725486 PMCID: PMC9207857 DOI: 10.1186/s13063-022-06461-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 06/09/2022] [Indexed: 11/10/2022] Open
Abstract
Background Traditional rural housing in hot, humid regions of sub-Saharan Africa usually consists of single-level, poorly ventilated dwellings. Houses are mostly poorly screened against malaria mosquitoes and limited airflow discourages the use of bednets resulting in high indoor transmission. This study aims to determine whether living in a novel design house with elevated bedrooms and permeable screened walls reduces malaria, respiratory tract infections, and diarrhoea among children in rural Tanzania. Methods/study design This is a household-randomized, controlled study in 60 villages in Mtwara, Tanzania. A total of 550 households are randomly selected, 110 of which are allocated a novel design house and 440 households continue to reside in traditional houses. A dynamic cohort of about 1650 children under 13 years will be enrolled and followed for 3 years, approximately 330 living in novel design houses and 1320 in traditional rural houses. The primary endpoint is the incidence of malaria; secondary endpoints are incidences of acute respiratory tract infections and diarrhoea diseases detected by passive and active surveillance. Exposure to malaria vectors will be assessed using light traps in all study houses. Structural, economic, and social science studies will assess the durability, cost-effectiveness, and acceptability of the new houses compared with traditional housing. Environmental data will be collected indoors and outdoors in study homes to assess the differences between house typologies. Discussion This is the first randomized controlled trial to assess the protective efficacy of a new house design targeting malaria in sub-Saharan Africa. The findings of this study could influence the future construction of homes in hot and humid zones of Africa. Trial registration ClinicalTrials.govNCT04529434. Registered on August 27, 2020
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Affiliation(s)
- Salum Mshamu
- CSK Research Solutions, Mtwara, Tanzania.,Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Arnold Mmbando
- Ifakara Health Institute, Ifakara, Tanzania.,Department of Biosciences, Durham University, Durham, UK
| | - Judith Meta
- University of Amsterdam, Amsterdam, Netherlands
| | - John Bradley
- MRC International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Nicholas P J Day
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Mavuto Mukaka
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | | | - Ally Olotu
- Ifakara Health Institute, Ifakara, Tanzania
| | | | | | - Jakob Knudsen
- The Royal Danish Academy of Fine Arts, Copenhagen, Denmark
| | | | - Lorenz von Seidlein
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK. .,Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand.
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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 : THE PREPRINT SERVER FOR HEALTH SCIENCES 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] [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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