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Liu Y, Wang M, Chen F, Zhang Y, Hai W. On-site detection of infectious disease based on CaCO 3-based magnetic micromotor integrated with graphene field effect transistor. Mikrochim Acta 2024; 191:257. [PMID: 38600405 DOI: 10.1007/s00604-024-06345-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/03/2024] [Indexed: 04/12/2024]
Abstract
A new detection platform based on CaCO3-based magnetic micromotor (CaCO3@Fe3O4) integrated with graphene field effect transistor (GFET) was construct and used for on-site SARS-CoV-2 coronavirus pathogen detection. The CaCO3@Fe3O4 micromotor, which was modified with anti-SARS-CoV-2 (labelled antibody, AntiE1), can self-moved in the solution containing hydrochloric acid (HCl) and effective to capture the SARS-CoV-2 coronavirus pathogens. After magnetic field separation, the capture micromotor was detected by GFET, exhibiting a good linear relationship within the range of 1 ag/mL to 100 ng/mL and low detection limit (0.39 ag/mL). Furthermore, the detection platform was also successfully applied to detection of SARS-CoV-2 coronavirus pathogens in soil solution, indicating the potential use in on-site application.
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Affiliation(s)
- Yushuang Liu
- Inner Mongolia Key Laboratory of Carbon Nanomaterials, Nano Innovation Institute (NII), College of Chemistry and Materials Science, Inner Mongolia Minzu University, Tongliao, 028000, People's Republic of China.
- Key Laboratory of Mongolian Medicine Research and Development Engineering, Ministry of Education, Inner Mongolia Minzu University, Tongliao, 028000, People's Republic of China.
| | - Mingxuan Wang
- Inner Mongolia Key Laboratory of Carbon Nanomaterials, Nano Innovation Institute (NII), College of Chemistry and Materials Science, Inner Mongolia Minzu University, Tongliao, 028000, People's Republic of China
| | - Furong Chen
- Inner Mongolia Key Laboratory of Carbon Nanomaterials, Nano Innovation Institute (NII), College of Chemistry and Materials Science, Inner Mongolia Minzu University, Tongliao, 028000, People's Republic of China
| | - Ying Zhang
- Inner Mongolia Key Laboratory of Carbon Nanomaterials, Nano Innovation Institute (NII), College of Chemistry and Materials Science, Inner Mongolia Minzu University, Tongliao, 028000, People's Republic of China
| | - Wenfeng Hai
- Inner Mongolia Key Laboratory of Carbon Nanomaterials, Nano Innovation Institute (NII), College of Chemistry and Materials Science, Inner Mongolia Minzu University, Tongliao, 028000, People's Republic of China
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Coronavirus: a comparative analysis of detection technologies in the wake of emerging variants. Infection 2023; 51:1-19. [PMID: 35471631 PMCID: PMC9038995 DOI: 10.1007/s15010-022-01819-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/30/2022] [Indexed: 01/31/2023]
Abstract
An outbreak of the coronavirus disease caused by a novel pathogen created havoc and continues to affect the entire world. As the pandemic progressed, the scientific community was faced by the limitations of existing diagnostic methods. In this review, we have compared the existing diagnostic techniques such as reverse transcription polymerase chain reaction (RT-PCR), antigen and antibody detection, computed tomography scan, etc. and techniques in the research phase like microarray, artificial intelligence, and detection using novel materials; on the prospect of sample preparation, detection procedure (qualitative/quantitative), detection time, screening efficiency, cost-effectiveness, and ability to detect different variants. A detailed comparison of different techniques showed that RT-PCR is still the most widely used and accepted coronavirus detection method despite certain limitations (single gene targeting- in context to mutations). New methods with similar efficiency that could overcome the limitations of RT-PCR may increase the speed, simplicity, and affordability of diagnosis. In addition to existing devices, we have also discussed diagnostic devices in the research phase showing high potential for clinical use. Our approach would be of enormous benefit in selecting a diagnostic device under a given scenario, which would ultimately help in controlling the current pandemic caused by the coronavirus, which is still far from over with new variants emerging.
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Chong YM, Chan YF, Jamaluddin MFH, Hasan MS, Pang YK, Ponnampalavanar S, Syed Omar SF, Sam IC. Rhinovirus/enterovirus was the most common respiratory virus detected in adults with severe acute respiratory infections pre-COVID-19 in Kuala Lumpur, Malaysia. PLoS One 2022; 17:e0273697. [PMID: 36054088 PMCID: PMC9439195 DOI: 10.1371/journal.pone.0273697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 08/14/2022] [Indexed: 02/01/2023] Open
Abstract
Background Severe acute respiratory infections (SARI) pose a great global burden. The contribution of respiratory viruses to adult SARI is relatively understudied in Asia. We aimed to determine viral aetiology of adult SARI patients in Kuala Lumpur, Malaysia. Methods The prevalence of 20 common (mainly viral) respiratory pathogens, and MERS-CoV, SARS-CoV and 5 bacterial select agents was investigated from May 2017 to October 2019 in 489 SARI adult patients in Kuala Lumpur, Malaysia, using molecular assays (Luminex NxTAG-RPP kit and qPCR assays). Viral metagenomics analysis was performed on 105 negative samples. Results Viral respiratory pathogens were detected by PCR in 279 cases (57.1%), including 10 (2.0%) additional detections by metagenomics analysis. The most detected viruses were rhinovirus/enterovirus (RV/EV) (49.1%) and influenza virus (7.4%). Three melioidosis cases were detected but no SARS-CoV, MERS-CoV or other bacterial select agents. Bacterial/viral co-detections and viral co-detections were found in 44 (9.0%) and 27 (5.5%) cases respectively, mostly involving RV/EV. Independent predictors of critical disease were male gender, chronic lung disease, lack of runny nose and positive blood culture with a significant bacterial pathogen. Asthma and sore throat were associated with increased risk of RV/EV detection, while among RV/EV cases, males and those with neurological disease were at increased risk of critical disease. Conclusions Prior to the COVID-19 pandemic, the high prevalence of respiratory viruses in adults with SARI was mainly attributed to RV/EV. Continued surveillance of respiratory virus trends contributes to effective diagnostic, prevention, and treatment strategies.
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Affiliation(s)
- Yoong Min Chong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yoke Fun Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail: (YFC); (ICS)
| | | | - M. Shahnaz Hasan
- Department of Anesthesiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yong Kek Pang
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | | | - I-Ching Sam
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail: (YFC); (ICS)
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Ejima K, Kim KS, Bento AI, Iwanami S, Fujita Y, Aihara K, Shibuya K, Iwami S. Estimation of timing of infection from longitudinal SARS-CoV-2 viral load data: mathematical modelling study. BMC Infect Dis 2022; 22:656. [PMID: 35902832 PMCID: PMC9331019 DOI: 10.1186/s12879-022-07646-2] [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: 01/25/2022] [Accepted: 07/22/2022] [Indexed: 01/08/2023] Open
Abstract
Background Multiple waves of the COVID-19 epidemic have hit most countries by the end of 2021. Most of those waves are caused by emergence and importation of new variants. To prevent importation of new variants, combination of border control and contact tracing is essential. However, the timing of infection inferred by interview is influenced by recall bias and hinders the contact tracing process. Methods We propose a novel approach to infer the timing of infection, by employing a within-host model to capture viral load dynamics after the onset of symptoms. We applied this approach to ascertain secondary transmission which can trigger outbreaks. As a demonstration, the 12 initial reported cases in Singapore, which were considered as imported because of their recent travel history to Wuhan, were analyzed to assess whether they are truly imported. Results Our approach suggested that 6 cases were infected prior to the arrival in Singapore, whereas other 6 cases might have been secondary local infection. Three among the 6 potential secondary transmission cases revealed that they had contact history to previously confirmed cases. Conclusions Contact trace combined with our approach using viral load data could be the key to mitigate the risk of importation of new variants by identifying cases as early as possible and inferring the timing of infection with high accuracy. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07646-2.
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Affiliation(s)
- Keisuke Ejima
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Bloomington, IN, USA. .,The Tokyo Foundation for Policy Research, Tokyo, Japan.
| | - Kwang Su Kim
- Interdisciplinary Biology Laboratory, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan.,Department of Science system simulation, Pukyong National University, Busan, South Korea
| | - Ana I Bento
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Bloomington, IN, USA
| | - Shoya Iwanami
- Interdisciplinary Biology Laboratory, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Yasuhisa Fujita
- Interdisciplinary Biology Laboratory, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Kazuyuki Aihara
- International Research Center for Neurointelligence, The University of Tokyo, Tokyo, Japan
| | - Kenji Shibuya
- The Tokyo Foundation for Policy Research, Tokyo, Japan
| | - Shingo Iwami
- Interdisciplinary Biology Laboratory, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan. .,Institute of Mathematics for Industry, Kyushu University, Fukuoka, Japan. .,Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan. .,NEXT-Ganken Program, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan. .,Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS), RIKEN, Saitama, Japan. .,Science Groove Inc., Fukuoka, Japan.
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5
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Yin B, Ho WKH, Zhang Q, Li C, Huang Y, Yan J, Yang H, Hao J, Wong SHD, Yang M. Magnetic-Responsive Surface-Enhanced Raman Scattering Platform with Tunable Hot Spot for Ultrasensitive Virus Nucleic Acid Detection. ACS APPLIED MATERIALS & INTERFACES 2022; 14:4714-4724. [PMID: 35081679 DOI: 10.1021/acsami.1c21173] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Surface-enhanced Raman scattering (SERS)-based biosensors are promising tools for virus nucleic acid detection. However, it remains challenging for SERS-based biosensors using a sandwiching strategy to detect long-chain nucleic acids such as nucleocapsid (N) gene of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) because the extension of the coupling distance (CD) between the two tethered metallic nanostructures weakens electric field and SERS signals. Herein, we report a magnetic-responsive substrate consisting of heteoronanostructures that controls the CD for ultrasensitive and highly selective detection of the N gene of SARS-CoV-2. Significantly, our findings show that this platform reversibly shortens the CD and enhances SERS signals with a 10-fold increase in the detection limit from 1 fM to 100 aM, compared to those without magnetic modulation. The optical simulation that emulates the CD shortening process confirms the CD-dependent electric field strength and further supports the experimental results. Our study provides new insights into designing a stimuli-responsive SERS-based platform with tunable hot spots for long-chain nucleic acid detection.
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Affiliation(s)
- Bohan Yin
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
| | - Willis Kwun Hei Ho
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
| | - Qin Zhang
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
| | - Chuanqi Li
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
| | - Yingying Huang
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
| | - Jiaxiang Yan
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
| | - Hongrong Yang
- Department of Bioengineering, College of Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Jianhua Hao
- Department of Applied Physics, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
| | - Siu Hong Dexter Wong
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
| | - Mo Yang
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
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Chen Y, Huang S, Zhou L, Wang X, Yang H, Li W. Coronavirus Disease 2019 (COVID-19): Emerging detection technologies and auxiliary analysis. J Clin Lab Anal 2022; 36:e24152. [PMID: 34894011 PMCID: PMC8761422 DOI: 10.1002/jcla.24152] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 11/09/2021] [Accepted: 11/18/2021] [Indexed: 12/11/2022] Open
Abstract
The ongoing COVID-19 pandemic constitutes a new challenge for public health. Prevention and control of infection have become urgent and serious issues. To meet the clinical demand for higher accuracy of COVID-19 detection, the development of fast and efficient methods represents an important step. The most common methods of COVID-19 diagnosis, relying on real-time fluorescent quantitative PCR(RT-qPCR), computed tomography, and new-generation sequencing technologies, have a series of advantages, especially for early diagnosis and screening. In addition, joint efforts of researchers all over the world have led to the development of other rapid detection methods with high sensitivity, ease of use, cost-effectiveness, or allowing multiplex analysis based on technologies such as dPCR, ELISA, fluorescence immunochromatography assay, and the microfluidic detection chip method. The main goal of this review was to provide a critical discussion on the development and application of these different analytical methods, which based on etiology, serology, and molecular biology, as well as to compare their respective advantages and disadvantages. In addition to these methods, hematology and biochemistry, as well as auxiliary analysis based on pathological anatomy, ultrasonography, and cytokine detection, will help understand COVID-19 pathogenesis. Together, these technologies may promote and open new windows to unravel issues surrounding symptomatic and asymptomatic COVID-19 infections and improve clinical strategies toward reducing mortality.
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Affiliation(s)
- Ying Chen
- School of Medical Technology, Xuzhou Medical University, Xuzhou, China
| | - Shengxiong Huang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Liuyan Zhou
- School of Anesthesiology, Xuzhou Medical University, Xuzhou, China
| | - Xin Wang
- Centralized and Point of Care Solutions & Molecular Diagnostics, Roche Diagnostics (Shanghai) Limited, Shanghai, China
| | - Huan Yang
- School of Medical Technology, Xuzhou Medical University, Xuzhou, China
| | - Wenqing Li
- School of Medical Technology, Xuzhou Medical University, Xuzhou, China
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Ahmad J, Ahmad M, Usman ARA, Al-Wabel MI. Prevalence of human pathogenic viruses in wastewater: A potential transmission risk as well as an effective tool for early outbreak detection for COVID-19. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 298:113486. [PMID: 34391102 PMCID: PMC8352675 DOI: 10.1016/j.jenvman.2021.113486] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 08/01/2021] [Accepted: 08/05/2021] [Indexed: 05/09/2023]
Abstract
Millions of human pathogenic viral particles are shed from infected individuals and introduce into wastewater, subsequently causing waterborne diseases worldwide. These viruses can be transmitted from wastewater to human beings via direct contact and/or ingestion/inhalation of aerosols. Even the advanced wastewater treatment technologies are unable to remove pathogenic viruses from wastewater completely, posing a serious health risk. Recently, coronavirus disease 2019 (COVID-19) has been urged globally due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which has resulted in >4.1 million deaths until July 2021. A rapid human-to-human transmission, uncertainties in effective vaccines, non-specific medical treatments, and unclear symptoms compelled the world into complete lockdown, social distancing, air-travel suspension, and closure of educational institutions, subsequently damaging the global economy and trade. Although, few medical treatments, rapid detection tools, and vaccines have been developed so far to curb the spread of COVID-19; however, several uncertainties exist in their applicability. Further, the acceptance of vaccines among communities is lower owing to the fear of side effects such as blood-clotting and heart inflammation. SARS-CoV-2, an etiologic agent of COVID-19, has frequently been detected in wastewater, depicting a potential transmission risk to healthy individuals. Contrarily, the occurrence of SARS-CoV-2 in wastewater can be used as an early outbreak detection tool via water-based epidemiology. Therefore, the spread of SARS-CoV-2 through fecal-oral pathway can be reduced and any possible outbreak can be evaded by proper wastewater surveillance. In this review, wastewater recycling complications, potential health risks of COVID-19 emergence, and current epidemiological measures to control COVID-19 spread have been discussed. Moreover, the viability of SARS-CoV-2 in various environments and survival in wastewater has been reviewed. Additionally, the necessary actions (vaccination, face mask, social distancing, and hand sanitization) to limit the transmission of SARS-CoV-2 have been recommended. Therefore, wastewater surveillance can serve as a feasible, efficient, and reliable epidemiological measure to lessen the spread of COVID-19.
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Affiliation(s)
- Jahangir Ahmad
- Soil Sciences Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Munir Ahmad
- Soil Sciences Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Adel R A Usman
- Soil Sciences Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia; Department of Soils and Water, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt
| | - Mohammad I Al-Wabel
- Soil Sciences Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia; Department of Science and Environmental Studies, The Education University of Hong Kong, Hong Kong.
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Chong YM, Chan YF, Jamaluddin MFH, Hasan MS, Pang YK, Ponnampalavanar S, Syed Omar SF, Voon KGL, Sam IC. Detection of respiratory viruses in adults with suspected COVID-19 in Kuala Lumpur, Malaysia. J Clin Virol 2021; 145:105000. [PMID: 34739838 PMCID: PMC8526124 DOI: 10.1016/j.jcv.2021.105000] [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] [Received: 07/27/2021] [Revised: 10/05/2021] [Accepted: 10/16/2021] [Indexed: 12/24/2022]
Abstract
Background Reports of co-circulation of respiratory viruses during the COVID-19 pandemic and co-infections with SARS-CoV-2 vary. However, limited information is available from developing countries. Objectives We aimed to investigate the incidence of respiratory viruses in adult patients with suspected COVID-19 in Kuala Lumpur, Malaysia. Study Design We collected 198 respiratory samples from adult patients hospitalized with suspected COVID-19 in a single teaching hospital in Kuala Lumpur in February-May 2020 and tested combined oro-nasopharyngeal swabs with the NxTAG Respiratory Pathogen Panel (Luminex) and Allplex RV Essential (Seegene) assays. Forty-five negative samples further underwent viral metagenomics analysis. Results Of the 198 samples, 74 (37.4%) had respiratory pathogens, including 56 (28.3%) with SARS-CoV-2 and 18 (9.1%) positive for other respiratory pathogens. There were five (2.5%) SARS-CoV-2 co-infections, all with rhinovirus/enterovirus. Three samples (6.7%; 3/45) had viruses identified by metagenomics, including one case of enterovirus D68 and one of Saffold virus genotype 6 in a patient requiring ICU care. Most of the COVID-19 patients (91.1%; 51/56) had mild symptoms but 5.4% (3/56) died. Conclusion During the early COVID-19 period, common respiratory viruses other than SARS-CoV-2 only accounted for 9.1% of hospitalization cases with ARI and co-infections with SARS-CoV-2 were rare. Continued surveillance is important to understand the impact of COVID-19 and its associated public health control measures on circulation of other respiratory viruses. Metagenomics can identify unexpected or rare pathogens, such as Saffold virus, which is rarely described in adults.
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Affiliation(s)
- Yoong Min Chong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Yoke Fun Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | | | - M Shahnaz Hasan
- Department of Anaesthesiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Yong Kek Pang
- Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | | | | | - Kenny Gah Leong Voon
- Division of Pathology, International Medical University, 57000 Kuala Lumpur, Malaysia
| | - I-Ching Sam
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Medical Microbiology, University of Malaya Medical Centre, 59100 Kuala Lumpur, Malaysia.
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Zandi M, Farahani A, Zakeri A, Akhavan Rezayat S, Mohammadi R, Das U, Dimmock JR, Afzali S, Nakhaei MA, Doroudi A, Erfani Y, Soltani S. Clinical Symptoms and Types of Samples Are Critical Factors for the Molecular Diagnosis of Symptomatic COVID-19 Patients: A Systematic Literature Review. Int J Microbiol 2021; 2021:5528786. [PMID: 34545287 PMCID: PMC8449726 DOI: 10.1155/2021/5528786] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/18/2021] [Accepted: 08/25/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Currently, a novel coronavirus found in 2019 known as SARS-CoV-2 is the etiological agent of the COVID-19 pandemic. Various parameters including clinical manifestations and molecular evaluation can affect the accuracy of diagnosis. This review aims to discuss the various clinical symptoms and molecular evaluation results in COVID-19 patients, to point out the importance of onset symptoms, type, and timing of the sampling, besides the methods that are used for detection of SARS-CoV-2. METHODS A systematic literature review of current articles in the Web of Science, PubMed, Scopus, and EMBASE was conducted according to the PRISMA guideline. RESULTS Of the 12946 patients evaluated in this investigation, 7643 were confirmed to be COVID-19 positive by molecular techniques, particularly the RT-PCR/qPCR combined technique (qRT-PCR). In most of the studies, all of the enrolled cases had 100% positive results for molecular evaluation. Among the COVID-19 patients who were identified as such by positive PCR results, most of them showed fever or cough as the primary clinical signs. Less common symptoms observed in clinically confirmed cases were hemoptysis, bloody sputum, mental disorders, and nasal congestion. The most common clinical samples for PCR-confirmed COVID-19 patients were obtained from throat, oropharyngeal, and nasopharyngeal swabs, while tears and conjunctival secretions seem to be the least common clinical samples for COVID-19 diagnosis among studies. Also, different conserved SARS-CoV-2 gene sequences could be targeted for qRT-PCR detection. The suggested molecular assay being used by most laboratories for the detection of SARS-CoV-2 is qRT-PCR. CONCLUSION There is a worldwide concern on the COVID-19 pandemic and a lack of well-managed global control. Hence, it is crucial to update the molecular diagnostics protocols for handling the situation. This is possible by understanding the available advances in assays for the detection of the SARS-CoV-2 infection. Good sampling procedure and using samples with enough viral loads, also considering the onset symptoms, may reduce the qRT-PCR false-negative results in symptomatic COVID-19 patients. Selection of the most efficient primer-probe for target genes and samples containing enough viral loads to search for the existence of SARS-CoV-2 helps detecting the virus on time using qRT-PCR.
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Affiliation(s)
- Milad Zandi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Farahani
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Armin Zakeri
- Department of Hematology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Sara Akhavan Rezayat
- Department of Health Economics and Management, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ramin Mohammadi
- Drug Discovery and Development Research Group, College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Canada
| | - Umashankar Das
- Drug Discovery and Development Research Group, College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Canada
| | - Jonathan R. Dimmock
- Drug Discovery and Development Research Group, College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Canada
| | - Shervin Afzali
- Department of Cellular and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University G.C., Tehran, Iran
| | - Mohammadvala Ashtar Nakhaei
- Department of Cellular and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University G.C., Tehran, Iran
| | - Alireza Doroudi
- Drug Discovery and Development Research Group, College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Canada
| | - Yousef Erfani
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Tehran University Medical Sciences, Tehran, Iran
| | - Saber Soltani
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
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Buonerba A, Corpuz MVA, Ballesteros F, Choo KH, Hasan SW, Korshin GV, Belgiorno V, Barceló D, Naddeo V. Coronavirus in water media: Analysis, fate, disinfection and epidemiological applications. JOURNAL OF HAZARDOUS MATERIALS 2021; 415:125580. [PMID: 33735767 PMCID: PMC7932854 DOI: 10.1016/j.jhazmat.2021.125580] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 05/03/2023]
Abstract
Considerable attention has been recently given to possible transmission of SARS-CoV-2 via water media. This review addresses this issue and examines the fate of coronaviruses (CoVs) in water systems, with particular attention to the recently available information on the novel SARS-CoV-2. The methods for the determination of viable virus particles and quantification of CoVs and, in particular, of SARS-CoV-2 in water and wastewater are discussed with particular regard to the methods of concentration and to the emerging methods of detection. The analysis of the environmental stability of CoVs, with particular regard of SARS-CoV-2, and the efficacy of the disinfection methods are extensively reviewed as well. This information provides a broad view of the state-of-the-art for researchers involved in the investigation of CoVs in aquatic systems, and poses the basis for further analyses and discussions on the risk associated to the presence of SARS-CoV-2 in water media. The examined data indicates that detection of the virus in wastewater and natural water bodies provides a potentially powerful tool for quantitative microbiological risk assessment (QMRA) and for wastewater-based epidemiology (WBE) for the evaluation of the level of circulation of the virus in a population. Assays of the viable virions in water media provide information on the integrity, capability of replication (in suitable host species) and on the potential infectivity. Challenges and critical issues relevant to the detection of coronaviruses in different water matrixes with both direct and surrogate methods as well as in the implementation of epidemiological tools are presented and critically discussed.
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Affiliation(s)
- Antonio Buonerba
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, Via Giovanni Paolo II, Fisciano, SA, Italy; Inter-University Centre for Prediction and Prevention of Relevant Hazards (Centro Universitario per la Previsione e Prevenzione Grandi Rischi, C.U.G.RI.), Via Giovanni Paolo II, Fisciano, SA, Italy
| | - Mary Vermi Aizza Corpuz
- Environmental Engineering Program, National Graduate School of Engineering, University of the Philippines, 1101 Diliman, Quezon City, Philippines
| | - Florencio Ballesteros
- Environmental Engineering Program, National Graduate School of Engineering, University of the Philippines, 1101 Diliman, Quezon City, Philippines
| | - Kwang-Ho Choo
- Department of Environmental Engineering, Kyungpook National University (KNU), 80 Daehak-ro, Bukgu, Daegu 41566, Republic of Korea
| | - Shadi W Hasan
- Center for Membranes and Advanced Water Technology (CMAT), Department of Chemical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Gregory V Korshin
- Department of Civil and Environmental Engineering, University of Washington, Box 352700, Seattle, WA 98105-2700, United States
| | - Vincenzo Belgiorno
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, Via Giovanni Paolo II, Fisciano, SA, Italy
| | - Damià Barceló
- Catalan Institute for Water Research (ICR-CERCA), H2O Building, Scientific and Technological Park of the University of Girona, Emili Grahit 101, 17003 Girona, Spain
| | - Vincenzo Naddeo
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, Via Giovanni Paolo II, Fisciano, SA, Italy.
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11
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Basavaraju S, Aswathanarayan JB, Basavegowda M, Somanathan B. Coronavirus: occurrence, surveillance, and persistence in wastewater. ENVIRONMENTAL MONITORING AND ASSESSMENT 2021; 193:508. [PMID: 34302225 PMCID: PMC8300075 DOI: 10.1007/s10661-021-09303-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 07/12/2021] [Indexed: 05/02/2023]
Abstract
The coronavirus disease (COVID-19) outbreak reported in China in December 2019 has spread throughout the world. The WHO declared it as a pandemic in March 2020. The pandemic severely affected public health and the global economy. Many studies conducted on the coronavirus have helped us to elucidate its pathogenicity and pathophysiology. However, it is important to study the behavior of the pathogen in the environment to develop effective control measures. While studying the persistence and transmission of viruses in drinking water and wastewater systems, a low concentration of coronavirus and its nucleic acids have been detected in municipal wastewaters. This could be due to their high susceptibilities to degradation in aqueous environments. Epidemiological study on coronaviruses in wastewater will serve two purposes, i.e., in early detection of outbreak and in identifying asymptomatic carriers. In such cases, the epidemiological study will help in early detection of the presence of the virus in the community. Secondly, it will help in knowing if there are asymptomatic carriers, as such people do not show any signs of symptoms but shed the viruses in feces. The present review focuses on the epidemiological surveillance of wastewater for coronaviruses, as in recent years these are increasingly causing global pandemics. In this review we have discussed, the four pertinent areas of coronavirus study: (1) occurrence of coronavirus in wastewater, (2) wastewater based epidemiological surveillance of coronaviruses, (3) epidemiological surveillance tools used for detection of coronaviruses in sewage, and (4) persistence and sustainability of coronaviruses in wastewater.
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Affiliation(s)
| | - Jamuna Bai Aswathanarayan
- Department of Microbiology, Faculty of Life Science, JSS Academy of Higher Education, Mysore, 570015, India.
| | - Madhu Basavegowda
- Department of Community Medicine, JSS Medical College, JSS AHER, Mysore, 570015, India
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12
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Qasem A, Shaw AM, Elkamel E, Naser SA. Coronavirus Disease 2019 (COVID-19) Diagnostic Tools: A Focus on Detection Technologies and Limitations. Curr Issues Mol Biol 2021; 43:728-748. [PMID: 34287238 PMCID: PMC8929116 DOI: 10.3390/cimb43020053] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 12/24/2022] Open
Abstract
The ongoing coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a severe threat to human health and the global economy and has resulted in overwhelming stress on health care systems worldwide. Despite the global health catastrophe, especially in the number of infections and fatalities, the COVID-19 pandemic has also revolutionized research and discovery with remarkable success in diagnostics, treatments, and vaccine development. The use of many diagnostic methods has helped establish public health guidelines to mitigate the spread of COVID-19. However, limited information has been shared about these methods, and there is a need for the scientific community to learn about these technologies, in addition to their sensitivity, specificity, and limitations. This review article is focused on providing insights into the major methods used for SARS-CoV-2 detection. We describe in detail the core principle of each method, including molecular and serological approaches, along with reported claims about the rates of false negatives and false positives, the types of specimens needed, and the level of technology and the time required to perform each test. Although this study will not rank or prioritize these methods, the information will help in the development of guidelines and diagnostic protocols in clinical settings and reference laboratories.
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Affiliation(s)
| | | | | | - Saleh A. Naser
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 4110 Libra Drive, Orlando, FL 32816, USA; (A.Q.); (A.M.S.); (E.E.)
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13
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Liu S, Li Q, Chu X, Zeng M, Liu M, He X, Zou H, Zheng J, Corpe C, Zhang X, Xu J, Wang J. Monitoring Coronavirus Disease 2019: A Review of Available Diagnostic Tools. Front Public Health 2021; 9:672215. [PMID: 34164371 PMCID: PMC8215441 DOI: 10.3389/fpubh.2021.672215] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/23/2021] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) pneumonia is caused by the virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has rapidly become a global public health concern. As the new type of betacoronavirus, SARS-CoV-2 can spread across species and between populations and has a greater risk of transmission than other coronaviruses. To control the spread of SARS-CoV-2, it is vital to have a rapid and effective means of diagnosing asymptomatic SARS-CoV-2-positive individuals and patients with COVID-19, an early isolation protocol for infected individuals, and effective treatments for patients with COVID-19 pneumonia. In this review, we will summarize the novel diagnostic tools that are currently available for coronavirus, including imaging examinations and laboratory medicine by next-generation sequencing (NGS), real-time reverse transcriptase-polymerase chain reaction (rRT-PCR) analysis, immunoassay for COVID-19, cytokine and T cell immunoassays, biochemistry and microbiology laboratory parameters in the blood of the patients with COVID-19, and a field-effect transistor-based biosensor of COVID-19. Specifically, we will discuss the effective detection rate and assay time for the rRT-PCR analysis of SARS-CoV-2 and the sensitivity and specificity of different antibody detection methods, such as colloidal gold and ELISA using specimen sources obtained from the respiratory tract, peripheral serum or plasma, and other bodily fluids. Such diagnostics will help scientists and clinicians develop appropriate strategies to combat COVID-19.
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Affiliation(s)
- Shanshan Liu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Qiuyue Li
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Xuntao Chu
- Zhuhai Livzon Diagnostics Inc., Guangdong, China
| | - Minxia Zeng
- Zhuhai Livzon Diagnostics Inc., Guangdong, China
| | - Mingbin Liu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- School of Pharmacy, Gannan Medical University, Jiangxi, China
| | - Xiaomeng He
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Heng Zou
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jianghua Zheng
- Department of Laboratory Medicine, Zhoupu Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Christopher Corpe
- Nutritional Science Department, King's College London, London, United Kingdom
| | - Xiaoyan Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jianqing Xu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jin Wang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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14
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Anand U, Adelodun B, Pivato A, Suresh S, Indari O, Jakhmola S, Jha HC, Jha PK, Tripathi V, Di Maria F. A review of the presence of SARS-CoV-2 RNA in wastewater and airborne particulates and its use for virus spreading surveillance. ENVIRONMENTAL RESEARCH 2021; 196:110929. [PMID: 33640498 PMCID: PMC7906514 DOI: 10.1016/j.envres.2021.110929] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/20/2021] [Accepted: 02/22/2021] [Indexed: 05/08/2023]
Abstract
According to the WHO, on October 16, 2020, the spreading of the SARS-CoV-2, responsible for the COVID-19 pandemic, reached 235 countries and territories, and resulting in more than 39 million confirmed cases and 1.09 million deaths globally. Monitoring of the virus outbreak is one of the main activities pursued to limiting the number of infected people and decreasing the number of deaths that have caused high pressure on the health care, social, and economic systems of different countries. Wastewater based epidemiology (WBE), already adopted for the surveillance of life style and health conditions of communities, shows interesting features for the monitoring of the COVID-19 diffusion. Together with wastewater, the analysis of airborne particles has been recently suggested as another useful tool for detecting the presence of SARS-CoV-2 in given areas. The present review reports the status of research currently performed concerning the monitoring of SARS-CoV-2 spreading by WBE and airborne particles. The former have been more investigated, whereas the latter is still at a very early stage, with a limited number of very recent studies. Nevertheless, the main results highlights in both cases necessitate more research activity for better understating and defining the biomarkers and the related sampling and analysis procedures to be used for this important aim.
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Affiliation(s)
- Uttpal Anand
- Department of Life Sciences, National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Bashir Adelodun
- Department of Agricultural and Biosystems Engineering, University of Ilorin, PMB 1515, Ilorin, Nigeria; Department of Agricultural Civil Engineering, Kyungpook National University, Daegu, Republic of Korea
| | - Alberto Pivato
- DICEA - Department of Civil, Environmental and Architectural Engineering, University of Padova, Via Marzolo 9, 35131, Padova, Italy
| | - S Suresh
- Department of Chemical Engineering, Maulana Azad National Institute of Technology, Bhopal, 462 003, Madhya Pradesh, India
| | - Omkar Indari
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, 453552, Indore, Madhya Pradesh, India
| | - Shweta Jakhmola
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, 453552, Indore, Madhya Pradesh, India
| | - Hem Chandra Jha
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, 453552, Indore, Madhya Pradesh, India
| | - Pawan Kumar Jha
- Centre for Environmental Studies, University of Allahabad, Prayagraj, 211002, Uttar Pradesh, India
| | - Vijay Tripathi
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, 211007, Uttar Pradesh, India.
| | - Francesco Di Maria
- LAR(5) Laboratory - Dipartimento di Ingegneria - University of Perugia, via G. Duranti 93, 06125, Perugia, Italy.
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15
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Chen PZ, Bobrovitz N, Premji Z, Koopmans M, Fisman DN, Gu FX. Heterogeneity in transmissibility and shedding SARS-CoV-2 via droplets and aerosols. eLife 2021; 10:e65774. [PMID: 33861198 PMCID: PMC8139838 DOI: 10.7554/elife.65774] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/15/2021] [Indexed: 01/08/2023] Open
Abstract
Background Which virological factors mediate overdispersion in the transmissibility of emerging viruses remains a long-standing question in infectious disease epidemiology. Methods Here, we use systematic review to develop a comprehensive dataset of respiratory viral loads (rVLs) of SARS-CoV-2, SARS-CoV-1 and influenza A(H1N1)pdm09. We then comparatively meta-analyze the data and model individual infectiousness by shedding viable virus via respiratory droplets and aerosols. Results The analyses indicate heterogeneity in rVL as an intrinsic virological factor facilitating greater overdispersion for SARS-CoV-2 in the COVID-19 pandemic than A(H1N1)pdm09 in the 2009 influenza pandemic. For COVID-19, case heterogeneity remains broad throughout the infectious period, including for pediatric and asymptomatic infections. Hence, many COVID-19 cases inherently present minimal transmission risk, whereas highly infectious individuals shed tens to thousands of SARS-CoV-2 virions/min via droplets and aerosols while breathing, talking and singing. Coughing increases the contagiousness, especially in close contact, of symptomatic cases relative to asymptomatic ones. Infectiousness tends to be elevated between 1 and 5 days post-symptom onset. Conclusions Intrinsic case variation in rVL facilitates overdispersion in the transmissibility of emerging respiratory viruses. Our findings present considerations for disease control in the COVID-19 pandemic as well as future outbreaks of novel viruses. Funding Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant program, NSERC Senior Industrial Research Chair program and the Toronto COVID-19 Action Fund.
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Affiliation(s)
- Paul Z Chen
- Department of Chemical Engineering & Applied Chemistry, University of TorontoTorontoCanada
| | - Niklas Bobrovitz
- Temerty Faculty of Medicine, University of TorontoTorontoCanada
- Department of Critical Care Medicine, Cumming School of Medicine, University of CalgaryCalgaryCanada
- O'Brien Institute of Public Health, University of CalgaryCalgaryCanada
| | - Zahra Premji
- Libraries & Cultural Resources, University of CalgaryCalgaryCanada
| | - Marion Koopmans
- Department of Viroscience, Erasmus University Medical CenterRotterdamNetherlands
| | - David N Fisman
- Division of Epidemiology, Dalla Lana School of Public Health, University of TorontoTorontoCanada
- Division of Infectious Diseases, Temerty Faculty of Medicine, University of TorontoTorontoCanada
| | - Frank X Gu
- Department of Chemical Engineering & Applied Chemistry, University of TorontoTorontoCanada
- Institute of Biomedical Engineering, University of TorontoTorontoCanada
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16
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Hamed I, Shaban N, Nassar M, Cayir D, Love S, Curran MD, Webb S, Yang H, Watson K, Rostron A, Navapurkar V, Mahroof R, Conway Morris A. Paired Nasopharyngeal and Deep Lung Testing for Severe Acute Respiratory Syndrome Coronavirus-2 Reveals a Viral Gradient in Critically Ill Patients: A Multicenter Study. Chest 2021; 159:1387-1390. [PMID: 33069724 PMCID: PMC7557286 DOI: 10.1016/j.chest.2020.10.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/03/2020] [Accepted: 10/11/2020] [Indexed: 12/12/2022] Open
Affiliation(s)
- Islam Hamed
- John Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge, UK
| | - Nesreen Shaban
- John Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge, UK
| | - Marwan Nassar
- John Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge, UK
| | - Dilek Cayir
- John Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge, UK
| | - Sam Love
- John Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge, UK
| | - Martin D Curran
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | | | | | | | - Anthony Rostron
- Sunderland Royal Hospital, Sunderland, UK; Translational and Clinical Research Institute, Newcastle University, Sunderland, UK
| | - Vilas Navapurkar
- John Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge, UK
| | - Razeen Mahroof
- John Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge, UK
| | - Andrew Conway Morris
- John Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge, UK; Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, UK.
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17
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Shi KW, Huang YH, Quon H, Ou-Yang ZL, Wang C, Jiang SC. Quantifying the risk of indoor drainage system in multi-unit apartment building as a transmission route of SARS-CoV-2. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 762:143056. [PMID: 33268249 PMCID: PMC7560110 DOI: 10.1016/j.scitotenv.2020.143056] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/08/2020] [Accepted: 10/10/2020] [Indexed: 05/05/2023]
Abstract
The COVID-19 pandemic has had a profound impact on human society. The isolation of SARS-CoV-2 from patients' feces on human cell line raised concerns of possible transmission through human feces including exposure to aerosols generated by toilet flushing and through the indoor drainage system. Currently, routes of transmission, other than the close contact droplet transmission, are still not well understood. A quantitative microbial risk assessment was conducted to estimate the health risks associated with two aerosol exposure scenarios: 1) toilet flushing, and 2) faulty connection of a floor drain with the building's main sewer pipe. SARS-CoV-2 data were collected from the emerging literature. The infectivity of the virus in feces was estimated based on a range of assumption between viral genome equivalence and infectious unit. The human exposure dose was calculated using Monte Carlo simulation of viral concentrations in aerosols under each scenario and human breathing rates. The probability of COVID-19 illness was generated using the dose-response model for SARS-CoV-1, a close relative of SARS-CoV-2, that was responsible for the SARS outbreak in 2003. The results indicate the median risks of developing COVID-19 for a single day exposure is 1.11 × 10-10 and 3.52 × 10-11 for toilet flushing and faulty drain scenario, respectively. The worst case scenario predicted the high end of COVID-19 risk for the toilet flushing scenario was 5.78 × 10-4 (at 95th percentile). The infectious viral loads in human feces are the most sensitive input parameter and contribute significantly to model uncertainty.
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Affiliation(s)
- Kuang-Wei Shi
- School of Environment, Tsinghua University, Beijing, China
| | - Yen-Hsiang Huang
- Civil and Environmental Engineering, University of California, Irvine, USA
| | - Hunter Quon
- Civil and Environmental Engineering, University of California, Irvine, USA
| | - Zi-Lu Ou-Yang
- School of Environment, Tsinghua University, Beijing, China
| | - Chengwen Wang
- School of Environment, Tsinghua University, Beijing, China.
| | - Sunny C Jiang
- Civil and Environmental Engineering, University of California, Irvine, USA.
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18
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Kim KS, Ejima K, Iwanami S, Fujita Y, Ohashi H, Koizumi Y, Asai Y, Nakaoka S, Watashi K, Aihara K, Thompson RN, Ke R, Perelson AS, Iwami S. A quantitative model used to compare within-host SARS-CoV-2, MERS-CoV, and SARS-CoV dynamics provides insights into the pathogenesis and treatment of SARS-CoV-2. PLoS Biol 2021; 19:e3001128. [PMID: 33750978 PMCID: PMC7984623 DOI: 10.1371/journal.pbio.3001128] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/01/2021] [Indexed: 12/11/2022] Open
Abstract
The scientific community is focused on developing antiviral therapies to mitigate the impacts of the ongoing novel coronavirus disease 2019 (COVID-19) outbreak. This will be facilitated by improved understanding of viral dynamics within infected hosts. Here, using a mathematical model in combination with published viral load data, we compare within-host viral dynamics of SARS-CoV-2 with analogous dynamics of MERS-CoV and SARS-CoV. Our quantitative analyses using a mathematical model revealed that the within-host reproduction number at symptom onset of SARS-CoV-2 was statistically significantly larger than that of MERS-CoV and similar to that of SARS-CoV. In addition, the time from symptom onset to the viral load peak for SARS-CoV-2 infection was shorter than those of MERS-CoV and SARS-CoV. These findings suggest the difficulty of controlling SARS-CoV-2 infection by antivirals. We further used the viral dynamics model to predict the efficacy of potential antiviral drugs that have different modes of action. The efficacy was measured by the reduction in the viral load area under the curve (AUC). Our results indicate that therapies that block de novo infection or virus production are likely to be effective if and only if initiated before the viral load peak (which appears 2-3 days after symptom onset), but therapies that promote cytotoxicity of infected cells are likely to have effects with less sensitivity to the timing of treatment initiation. Furthermore, combining a therapy that promotes cytotoxicity and one that blocks de novo infection or virus production synergistically reduces the AUC with early treatment. Our unique modeling approach provides insights into the pathogenesis of SARS-CoV-2 and may be useful for development of antiviral therapies.
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Affiliation(s)
- Kwang Su Kim
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
| | - Keisuke Ejima
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health–Bloomington, Bloomington, Indiana, United States of America
| | - Shoya Iwanami
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
| | - Yasuhisa Fujita
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
| | - Hirofumi Ohashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshiki Koizumi
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Yusuke Asai
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Shinji Nakaoka
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Koichi Watashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- JST-Mirai, Japan Science and Technology Agency, Saitama, Japan
| | - Kazuyuki Aihara
- International Research Center for Neurointelligence, University of Tokyo Institutes for Advanced Study, University of Tokyo, Tokyo, Japan
| | - Robin N. Thompson
- Mathematics Institute, University of Warwick, Coventry, United Kingdom
- Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, United Kingdom
| | - Ruian Ke
- New Mexico Consortium, Los Alamos, New Mexico, United States of America
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Alan S. Perelson
- New Mexico Consortium, Los Alamos, New Mexico, United States of America
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Shingo Iwami
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
- JST-Mirai, Japan Science and Technology Agency, Saitama, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo, Japan
- Science Groove, Fukuoka, Japan
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19
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Reginelli A, Grassi R, Feragalli B, Belfiore MP, Montanelli A, Patelli G, La Porta M, Urraro F, Fusco R, Granata V, Petrillo A, Giacobbe G, Russo GM, Sacco P, Grassi R, Cappabianca S. Coronavirus Disease 2019 (COVID-19) in Italy: Double Reading of Chest CT Examination. BIOLOGY 2021; 10:biology10020089. [PMID: 33504028 PMCID: PMC7911408 DOI: 10.3390/biology10020089] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 01/22/2021] [Indexed: 12/28/2022]
Abstract
To assess the performance of the second reading of chest compute tomography (CT) examinations by expert radiologists in patients with discordance between the reverse transcription real-time fluorescence polymerase chain reaction (RT-PCR) test for COVID-19 viral pneumonia and the CT report. Three hundred and seventy-eight patients were included in this retrospective study (121 women and 257 men; 71 years median age, with a range of 29-93 years) and subjected to RT-PCR tests for suspicious COVID-19 infection. All patients were subjected to CT examination in order to evaluate the pulmonary disease involvement by COVID-19. CT images were reviewed first by two radiologists who identified COVID-19 typical CT patterns and then reanalyzed by another two radiologists using a CT structured report for COVID-19 diagnosis. Weighted к values were used to evaluate the inter-reader agreement. The median temporal window between RT-PCRs execution and CT scan was zero days with a range of (-9,11) days. The RT-PCR test was positive in 328/378 (86.8%). Discordance between RT-PCR and CT findings for viral pneumonia was revealed in 60 cases. The second reading changed the CT diagnosis in 16/60 (26.7%) cases contributing to an increase the concordance with the RT-PCR. Among these 60 cases, eight were false negative with positive RT-PCR, and 36 were false positive with negative RT-PCR. Sensitivity, specificity, positive predictive value and negative predictive value of CT were respectively of 97.3%, 53.8%, 89.0%, and 88.4%. Double reading of CT scans and expert second readers could increase the diagnostic confidence of radiological interpretation in COVID-19 patients.
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Affiliation(s)
- Alfonso Reginelli
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80121 Naples, Italy; (A.R.); (R.G.); (M.P.B.); (F.U.); (G.G.); (G.M.R.); (R.G.); (S.C.)
| | - Roberta Grassi
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80121 Naples, Italy; (A.R.); (R.G.); (M.P.B.); (F.U.); (G.G.); (G.M.R.); (R.G.); (S.C.)
| | - Beatrice Feragalli
- Oral and Biotechnological Sciences—Radiology Unit “G. D’Annunzio”, Department of Medical, University of Chieti-Pescara, 66100 Chieti, Italy;
| | - Maria Paola Belfiore
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80121 Naples, Italy; (A.R.); (R.G.); (M.P.B.); (F.U.); (G.G.); (G.M.R.); (R.G.); (S.C.)
| | | | | | | | - Fabrizio Urraro
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80121 Naples, Italy; (A.R.); (R.G.); (M.P.B.); (F.U.); (G.G.); (G.M.R.); (R.G.); (S.C.)
| | - Roberta Fusco
- Radiology Division, Istituto Nazionale Tumori IRCCS Fondazione Pascale—IRCCS di Napoli, 80131 Naples, Italy; (V.G.); (A.P.)
- Correspondence: ; Tel.: +39-081-590-3714
| | - Vincenza Granata
- Radiology Division, Istituto Nazionale Tumori IRCCS Fondazione Pascale—IRCCS di Napoli, 80131 Naples, Italy; (V.G.); (A.P.)
| | - Antonella Petrillo
- Radiology Division, Istituto Nazionale Tumori IRCCS Fondazione Pascale—IRCCS di Napoli, 80131 Naples, Italy; (V.G.); (A.P.)
| | - Giuliana Giacobbe
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80121 Naples, Italy; (A.R.); (R.G.); (M.P.B.); (F.U.); (G.G.); (G.M.R.); (R.G.); (S.C.)
| | - Gaetano Maria Russo
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80121 Naples, Italy; (A.R.); (R.G.); (M.P.B.); (F.U.); (G.G.); (G.M.R.); (R.G.); (S.C.)
| | - Palmino Sacco
- Diagnostic Imaging Unit, Department of Radiological Sciences, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy;
| | - Roberto Grassi
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80121 Naples, Italy; (A.R.); (R.G.); (M.P.B.); (F.U.); (G.G.); (G.M.R.); (R.G.); (S.C.)
- Foundation SIRM, 20122 Milan, Italy
| | - Salvatore Cappabianca
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80121 Naples, Italy; (A.R.); (R.G.); (M.P.B.); (F.U.); (G.G.); (G.M.R.); (R.G.); (S.C.)
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20
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Cleary B, Hay JA, Blumenstiel B, Harden M, Cipicchio M, Bezney J, Simonton B, Hong D, Senghore M, Sesay AK, Gabriel S, Regev A, Mina MJ. Using viral load and epidemic dynamics to optimize pooled testing in resource constrained settings. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2020.05.01.20086801. [PMID: 32511487 PMCID: PMC7273255 DOI: 10.1101/2020.05.01.20086801] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Extensive virological testing is central to SARS-CoV-2 containment, but many settings face severe limitations on testing. Group testing offers a way to increase throughput by testing pools of combined samples; however, most proposed designs have not yet addressed key concerns over sensitivity loss and implementation feasibility. Here, we combine a mathematical model of epidemic spread and empirically derived viral kinetics for SARS-CoV-2 infections to identify pooling designs that are robust to changes in prevalence, and to ratify losses in sensitivity against the time course of individual infections. Using this framework, we show that prevalence can be accurately estimated across four orders of magnitude using only a few dozen pooled tests without the need for individual identification. We then exhaustively evaluate the ability of different pooling designs to maximize the number of detected infections under various resource constraints, finding that simple pooling designs can identify up to 20 times as many positives compared to individual testing with a given budget. We illustrate how pooling affects sensitivity and overall detection capacity during an epidemic and on each day post infection, finding that sensitivity loss is mainly attributed to individuals sampled at the end of infection when detection for public health containment has minimal benefit. Crucially, we confirm that our theoretical results can be accurately translated into practice using pooled human nasopharyngeal specimens. Our results show that accounting for variation in sampled viral loads provides a nuanced picture of how pooling affects sensitivity to detect epidemiologically relevant infections. Using simple, practical group testing designs can vastly increase surveillance capabilities in resource-limited settings.
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Affiliation(s)
- Brian Cleary
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - James A. Hay
- Centre for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard School of Public Health
| | | | - Maegan Harden
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | | | - Jon Bezney
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | | | - David Hong
- Wharton Statistics, University of Pennsylvania, Philadelphia, PA, USA
| | - Madikay Senghore
- Centre for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Abdul K. Sesay
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Stacey Gabriel
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142 USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Michael J. Mina
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Centre for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard School of Public Health
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School
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21
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Wei J, Guo S, Long E, Zhang L, Shu B, Guo L. Why does the spread of COVID-19 vary greatly in different countries? Revealing the efficacy of face masks in epidemic prevention. Epidemiol Infect 2021; 149:e24. [PMID: 33441205 PMCID: PMC7844184 DOI: 10.1017/s0950268821000108] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 11/05/2022] Open
Abstract
The severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) is highly contagious, and the coronavirus disease 2019 (COVID-19) pandemic caused by it has forced many countries to adopt 'lockdown' measures to prevent the spread of the epidemic through social isolation of citizens. Some countries proposed universal mask wearing as a protection measure of public health to strengthen national prevention efforts and to limit the wider spread of the epidemic. In order to reveal the epidemic prevention efficacy of masks, this paper systematically evaluates the experimental studies of various masks and filter materials, summarises the general characteristics of the filtration efficiency of isolation masks with particle size, and reveals the actual efficacy of masks by combining the volume distribution characteristics of human exhaled droplets with different particle sizes and the SARS-CoV-2 virus load of nasopharynx and throat swabs from patients. The existing measured data show that the filtration efficiency of all kinds of masks for large particles and extra-large droplets is close to 100%. From the perspective of filtering the total number of pathogens discharged in the environment and protecting vulnerable individuals from breathing live viruses, the mask has a higher protective effect. If considering the weighted average filtration efficiency with different particle sizes, the filtration efficiencies of the N95 mask and the ordinary mask are 99.4% and 98.5%, respectively. The mask can avoid releasing active viruses to the environment from the source of infection, thus maximising the protection of vulnerable individuals by reducing the probability of inhaling a virus. Therefore, if the whole society strictly implements the policy of publicly wearing masks, the risk of large-scale spread of the epidemic can be greatly reduced. Compared with the overall cost of social isolation, limited personal freedoms and forced suspension of economic activities, the inconvenience for citizens caused by wearing masks is perfectly acceptable.
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Affiliation(s)
- Jincheng Wei
- MOE Key Laboratory of Deep Earth Science and Engineering, College of Architecture and Environment, Sichuan University, Chengdu, China
| | - Shurui Guo
- MOE Key Laboratory of Deep Earth Science and Engineering, College of Architecture and Environment, Sichuan University, Chengdu, China
| | - Enshen Long
- MOE Key Laboratory of Deep Earth Science and Engineering, College of Architecture and Environment, Sichuan University, Chengdu, China
| | - Li Zhang
- Department of Solid Waste Treatment Technology, Sichuan Environmental Protection Key Laboratory of Pollution Control for Heavy Metals, Sichuan Academy of Environmental Sciences, Chengdu, China
| | - Bizhen Shu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, West China Second Hospital of Sichuan University, Chengdu, China
| | - Lei Guo
- MOE Key Laboratory of Deep Earth Science and Engineering, College of Architecture and Environment, Sichuan University, Chengdu, China
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22
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Yang B, Li W, Wang J, Tian Z, Cheng X, Zhang Y, Qiu R, Hou S, Guo H. Estimation of the potential spread risk of COVID-19: Occurrence assessment along the Yangtze, Han, and Fu River basins in Hubei, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 746:141353. [PMID: 32763612 PMCID: PMC7388013 DOI: 10.1016/j.scitotenv.2020.141353] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/27/2020] [Accepted: 07/27/2020] [Indexed: 05/09/2023]
Abstract
Given that the novel coronavirus was detected in stool and urine from diagnosed patients, the potential risk of its transmission through the water environment might not be ignored. In the current study, to investigate the spread possibility of COVID-19 via the environmental media, three typical rivers (Yangtze, Han, and Fu River) and watershed cities in Hubei province of China were selected, and a more comprehensive risk assessment analysis method was built with a risk index proposed. Results showed that the risk index in the Yangtze River Basin is about 10-12, compared to 10-10 and 10-8 in the Han and Fu River Basins, and the risk index is gradually reduced from Wuhan city to the surrounding cities. The safety radius and safety time period for the Yangtze, Han, and Fu River are 8 km/14 h, 20 km/30 h and 36 km/36 h, respectively. The linear relationship between the risk potential calculated by the QMRA model and the multiple linear regression proved that the built index model is statistically significant. By comparing the theoretical removal rates for the novel coronavirus, our study proposed an effective method to estimate the potential spread risk of COVID-19 in the typical river basins.
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Affiliation(s)
- Bo Yang
- MOE Key Laboratory of Deep Earth Science and Engineering, College of Architecture and Environment, Sichuan University, Chengdu 610065, China
| | - Wei Li
- MOE Key Laboratory of Deep Earth Science and Engineering, College of Architecture and Environment, Sichuan University, Chengdu 610065, China
| | - Jingquan Wang
- MOE Key Laboratory of Deep Earth Science and Engineering, College of Architecture and Environment, Sichuan University, Chengdu 610065, China
| | - Zixin Tian
- MOE Key Laboratory of Deep Earth Science and Engineering, College of Architecture and Environment, Sichuan University, Chengdu 610065, China
| | - Xin Cheng
- MOE Key Laboratory of Deep Earth Science and Engineering, College of Architecture and Environment, Sichuan University, Chengdu 610065, China; Department of Chemical and Environmental Engineering, Yale University, New Haven, CT 06511, United States
| | - Yongli Zhang
- MOE Key Laboratory of Deep Earth Science and Engineering, College of Architecture and Environment, Sichuan University, Chengdu 610065, China
| | - Rui Qiu
- Business School, Sichuan University, Chengdu 610064, China
| | - Shuhua Hou
- Business School, Sichuan University, Chengdu 610064, China
| | - Hongguang Guo
- MOE Key Laboratory of Deep Earth Science and Engineering, College of Architecture and Environment, Sichuan University, Chengdu 610065, China.
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23
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Rattan A, Ahmad H. WITHDRAWN: Can quantitative RT-PCR for SARS-coV-2 help in better management of patients and control of coronavirus disease 2019 pandemic. Indian J Med Microbiol 2020:S0255-0857(20)30019-0. [PMID: 33487476 PMCID: PMC7667399 DOI: 10.1016/j.ijmmb.2020.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
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Affiliation(s)
- Ashok Rattan
- All India Institute of Medical Sciences, Delhi, India; Pathkind Labs, Gurgaon, Haryana, India
| | - Hafiz Ahmad
- Department of Medical Microbiology and Immunology, RAK College of Medical Sciences, RAK Medical and Health Sciences University, United Arab Emirates; RAK Hospital, Ras Al Khaimah, United Arab Emirates
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24
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Choi WS, Jeong JH, Nicolas HDG, Oh S, Antigua KJC, Park JH, Kim B, Yoon SW, Shin KS, Choi YK, Baek YH, Song MS. Peptide Nucleic Acid (PNA)-Enhanced Specificity of a Dual-Target Real-Time Quantitative Polymerase Chain Reaction (RT-qPCR) Assay for the Detection and Differentiation of SARS-CoV-2 from Related Viruses. Diagnostics (Basel) 2020; 10:diagnostics10100775. [PMID: 33007999 PMCID: PMC7601008 DOI: 10.3390/diagnostics10100775] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/24/2020] [Accepted: 09/29/2020] [Indexed: 12/02/2022] Open
Abstract
The threat posed by coronaviruses to human health has necessitated the development of a highly specific and sensitive viral detection method that could differentiate between the currently circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other SARS-related coronaviruses (SARSr-CoVs). In this study, we developed a peptide nucleic acid (PNA)-based real-time quantitative polymerase chain reaction (RT-qPCR) assay targeting the N gene to efficiently discriminate SARS-CoV-2 from other SARSr-CoVs in human clinical samples. Without compromising the sensitivity, this method significantly enhanced the specificity of SARS-CoV-2 detection by 100-fold as compared to conventional RT-qPCR. In addition, we designed an RT-qPCR method for the sensitive and universal detection of ORF3ab-E genes of SARSr-CoV with a limit of detection (LOD) of 3.3 RNA copies per microliter. Thus, the developed assay serves as a confirmative dual-target detection method. Our PNA-mediated dual-target RT-qPCR assay can detect clinical SARS-CoV-2 samples in the range of 18.10–35.19 Ct values with an 82.6–100% detection rate. Furthermore, our assay showed no cross-reactions with other coronaviruses such as human coronaviruses (229E, NL63, and OC43) and Middle East respiratory syndrome coronavirus, influenza viruses (Type B, H1N1, H3N2, HPAI H5Nx, and H7N9), and other respiratory disease-causing viruses (MPV, RSV A, RSV B, PIV, AdV, and HRV). We, thus, developed a PNA-based RT-qPCR assay that differentiates emerging pathogens such as SARS-CoV-2 from closely related viruses such as SARSr-CoV and allows diagnosis of infections related to already identified or new coronavirus strains.
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Affiliation(s)
- Won-Suk Choi
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju 28644, Korea; (W.-S.C.); (J.H.J.); (H.D.G.N.); (S.O.); (K.J.C.A.); (J.-H.P.); (B.K.); (Y.K.C.)
| | - Ju Hwan Jeong
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju 28644, Korea; (W.-S.C.); (J.H.J.); (H.D.G.N.); (S.O.); (K.J.C.A.); (J.-H.P.); (B.K.); (Y.K.C.)
| | - Halcyon Dawn G. Nicolas
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju 28644, Korea; (W.-S.C.); (J.H.J.); (H.D.G.N.); (S.O.); (K.J.C.A.); (J.-H.P.); (B.K.); (Y.K.C.)
| | - Sol Oh
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju 28644, Korea; (W.-S.C.); (J.H.J.); (H.D.G.N.); (S.O.); (K.J.C.A.); (J.-H.P.); (B.K.); (Y.K.C.)
| | - Khristine Joy C. Antigua
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju 28644, Korea; (W.-S.C.); (J.H.J.); (H.D.G.N.); (S.O.); (K.J.C.A.); (J.-H.P.); (B.K.); (Y.K.C.)
| | - Ji-Hyun Park
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju 28644, Korea; (W.-S.C.); (J.H.J.); (H.D.G.N.); (S.O.); (K.J.C.A.); (J.-H.P.); (B.K.); (Y.K.C.)
| | - Beomkyu Kim
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju 28644, Korea; (W.-S.C.); (J.H.J.); (H.D.G.N.); (S.O.); (K.J.C.A.); (J.-H.P.); (B.K.); (Y.K.C.)
| | - Sun-Woo Yoon
- Infectious Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea;
| | - Kyeong Seob Shin
- Department of Laboratory Medicine, Chungbuk National University College of Medicine, Cheongju 28644, Korea;
| | - Young Ki Choi
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju 28644, Korea; (W.-S.C.); (J.H.J.); (H.D.G.N.); (S.O.); (K.J.C.A.); (J.-H.P.); (B.K.); (Y.K.C.)
| | - Yun Hee Baek
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju 28644, Korea; (W.-S.C.); (J.H.J.); (H.D.G.N.); (S.O.); (K.J.C.A.); (J.-H.P.); (B.K.); (Y.K.C.)
- Correspondence: (Y.H.B.); (M.-S.S.)
| | - Min-Suk Song
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju 28644, Korea; (W.-S.C.); (J.H.J.); (H.D.G.N.); (S.O.); (K.J.C.A.); (J.-H.P.); (B.K.); (Y.K.C.)
- Correspondence: (Y.H.B.); (M.-S.S.)
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25
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Wang Y, Lee Y, Yang T, Sun J, Shen C, Cheng C. Current diagnostic tools for coronaviruses-From laboratory diagnosis to POC diagnosis for COVID-19. Bioeng Transl Med 2020; 5:e10177. [PMID: 32838038 PMCID: PMC7435577 DOI: 10.1002/btm2.10177] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/28/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022] Open
Abstract
The Coronavirus-2019 (COVID-19) pandemic has put tremendous strain on healthcare systems worldwide. It is challenging for clinicians to differentiate COVID-19 from other acute respiratory tract infections via clinical symptoms because those who are infected display a wide range of symptoms. An effective, point-of-care (POC) diagnostic tool could mitigate healthcare system strain, protect healthcare professionals, and support quarantine efforts. We believe that a POC tool can be developed that would be rapid, easy to use, and inexpensive. It could be used in the home, in resource-limited areas, and even in clinical settings. In this article, we summarize the current state of COVID-19 diagnostic methods and make a case for an all-in-one, highly sensitive POC assay that integrates antibody detection, protein detection, and serum cytokine detection to diagnose COVID-19 infection. We believe this article will provide insights into the current state of diagnostics for COVID-19, and promote additional research and tool development that could be exceptionally impactful.
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Affiliation(s)
- Yung‐Chih Wang
- Division of Infectious Diseases and Tropical Medicine, Department of Internal MedicineTri‐Service General Hospital, National Defense Medical CenterTaipeiTaiwan
| | - Yi‐Tzu Lee
- Department of Emergency MedicineTaipei Veterans General HospitalTaipeiTaiwan
- Faculty of Medicine, School of MedicineNational Yang‐Ming UniversityTaipeiTaiwan
| | - Ting Yang
- Institute of Biomedical EngineeringNational Tsing Hua UniversityHsinchuTaiwan
| | - Jun‐Ren Sun
- Institute of Preventive MedicineNational Defense Medical CenterTaipeiTaiwan
| | - Ching‐Fen Shen
- Department of PediatricsNational Cheng Kung University Hospital, College of Medicine, National Cheng Kung UniversityTainanTaiwan
| | - Chao‐Min Cheng
- Institute of Biomedical EngineeringNational Tsing Hua UniversityHsinchuTaiwan
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26
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Bilal M, Nazir MS, Rasheed T, Parra-Saldivar R, Iqbal HMN. Water matrices as potential source of SARS-CoV-2 transmission - An overview from environmental perspective. CASE STUDIES IN CHEMICAL AND ENVIRONMENTAL ENGINEERING 2020; 2:100023. [PMID: 38620691 PMCID: PMC7347329 DOI: 10.1016/j.cscee.2020.100023] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 02/08/2023]
Abstract
Evidently, the emergence of novel coronavirus disease (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has rapidly blowout across the world. Since, the presence of coronaviruses, including SARS-CoV-2 in the fecal specimens and anal swabs of some infected patients, has raised emerging concern with the likelihood of fecal-based spread must be inspected and clarified. Therefore, herein, an effort has been made to spotlight the current scenarios and possible solutions to better understand the risks associated with the wastewater matrices as a potential source of SARS-CoV-2 transmission in the environment. The information reviewed here constitutes a paramount intellectual basis to sustenance ongoing research to tackle the SARS-CoV-2 issue. Thus, this overview indicates the most accessible frontiers related to the detection, quantification, and possible transmission of SARS-CoV-2 in the environment through water routes. The regulatory authorities and policymakers must assure the society via dissemination of evidence-based guidelines that the water matrices, including groundwater and drinking water resources are safe. Finally, we have identified and enlisted a number of pressing questions concerning the ongoing SARS-CoV-2 transmission or COVID-19 emergence issue that must be carefully answered to put further and deeper insight into SARS-CoV-2/COVID-19 in future studies.
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Affiliation(s)
- Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | | | - Tahir Rasheed
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Roberto Parra-Saldivar
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, N.L., CP 64849, Mexico
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, N.L., CP 64849, Mexico
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27
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Melenotte C, Silvin A, Goubet AG, Lahmar I, Dubuisson A, Zumla A, Raoult D, Merad M, Gachot B, Hénon C, Solary E, Fontenay M, André F, Maeurer M, Ippolito G, Piacentini M, Wang FS, Ginhoux F, Marabelle A, Kroemer G, Derosa L, Zitvogel L. Immune responses during COVID-19 infection. Oncoimmunology 2020; 9:1807836. [PMID: 32939324 PMCID: PMC7480812 DOI: 10.1080/2162402x.2020.1807836] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/05/2020] [Accepted: 08/05/2020] [Indexed: 02/09/2023] Open
Abstract
Over the past 16 years, three coronaviruses (CoVs), severe acute respiratory syndrome CoV (SARS-CoV) in 2002, Middle East respiratory syndrome CoV (MERS-CoV) in 2012 and 2015, and SARS-CoV-2 in 2020, have been causing severe and fatal human epidemics. The unpredictability of coronavirus disease-19 (COVID-19) poses a major burden on health care and economic systems across the world. This is caused by the paucity of in-depth knowledge of the risk factors for severe COVID-19, insufficient diagnostic tools for the detection of SARS-CoV-2, as well as the absence of specific and effective drug treatments. While protective humoral and cellular immune responses are usually mounted against these betacoronaviruses, immune responses to SARS-CoV2 sometimes derail towards inflammatory tissue damage, leading to rapid admissions to intensive care units. The lack of knowledge on mechanisms that tilt the balance between these two opposite outcomes poses major threats to many ongoing clinical trials dealing with immunostimulatory or immunoregulatory therapeutics. This review will discuss innate and cognate immune responses underlying protective or deleterious immune reactions against these pathogenic coronaviruses.
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Affiliation(s)
- Cléa Melenotte
- Immunology, Gustave Roussy, Villejuif, France
- Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Infectious Diseases, Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
- Infectious Diseases, IHU-Méditerranée Infection, Marseille, France
| | | | - Anne-Gaëlle Goubet
- Immunology, Gustave Roussy, Villejuif, France
- Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Immunology, Institut National de la Santé Et de la Recherche Médicale (INSERM), U1015 Equipe Labellisée—Ligue Nationale contre le Cancer, Villejuif, France
- Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France
| | - Imran Lahmar
- Immunology, Gustave Roussy, Villejuif, France
- Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Immunology, Institut National de la Santé Et de la Recherche Médicale (INSERM), U1015 Equipe Labellisée—Ligue Nationale contre le Cancer, Villejuif, France
- Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France
| | - Agathe Dubuisson
- Immunology, Gustave Roussy, Villejuif, France
- Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Immunology, Institut National de la Santé Et de la Recherche Médicale (INSERM), U1015 Equipe Labellisée—Ligue Nationale contre le Cancer, Villejuif, France
- Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France
| | - Alimuddin Zumla
- Department of Infection, Division of Infection and Immunity, University College London, National Institute for Health Research Biomedical Research Centre, University College London Hospitals NHS Foundation Trust, London, UK
| | - Didier Raoult
- Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Infectious Diseases, Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
| | - Mansouria Merad
- Service de Urgences et de Permanence des Soins, Gustave Roussy Cancer Campus Grand Paris, Villejuif, France
| | | | | | - Eric Solary
- Immunology, Gustave Roussy, Villejuif, France
| | - Michaela Fontenay
- INSERM U1016, Centre National Recherche Scientifique (CNRS) UMR8104, Institut Cochin, Université de Paris, Paris, France
| | | | - Markus Maeurer
- Immunosurgery, Immunotherapy Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
- Med Clinic, University of Mainz, Mayence, Germany
| | - Giuseppe Ippolito
- Dipartimento di Epidemiologia Ricerca Pre-Clinica e Diagnostica Avanzata, National Institute for Infectious Diseases “Lazzaro Spallanzani” I.R.C.C.S., Rome, Italy
| | - Mauro Piacentini
- Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
- Infectious Diseases Department, National Institute for Infectious Disease IRCCS “Lazzaro Spallanzani”, Rome, Italy
| | - Fu-Sheng Wang
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Florent Ginhoux
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore
| | - Aurélien Marabelle
- Infectious Diseases, Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
- Pôle de Biologie,Pathologie – PUI – Hygiène, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
- Karolinska Institute, Department of Women’s and Children’s Health, Karolinska University Hospital, Stockholm, Sweden
- Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China
| | - Lisa Derosa
- Immunology, Gustave Roussy, Villejuif, France
- Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Immunology, Institut National de la Santé Et de la Recherche Médicale (INSERM), U1015 Equipe Labellisée—Ligue Nationale contre le Cancer, Villejuif, France
- Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France
| | - Laurence Zitvogel
- Immunology, Gustave Roussy, Villejuif, France
- Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Immunology, Institut National de la Santé Et de la Recherche Médicale (INSERM), U1015 Equipe Labellisée—Ligue Nationale contre le Cancer, Villejuif, France
- Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France
- Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China
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28
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Choe PG, Park WB, Choi SJ, Kang CK, Koh Y, Kim NJ, Oh MD. Prolonged (6-Month) Shedding of Middle East Respiratory Syndrome Coronavirus RNA in the Sputum of a Lymphoma Patient. Open Forum Infect Dis 2020; 7:ofaa292. [PMID: 32782912 PMCID: PMC7408226 DOI: 10.1093/ofid/ofaa292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/16/2020] [Indexed: 01/03/2023] Open
Abstract
During the 2015 Korea Middle East Respiratory Syndrome coronavirus (MERS-CoV) outbreak, a lymphoma patient developed MERS pneumonia. His pneumonia improved by 45 days after illness onset, but the polymerase chain reaction tests remained (+) for 6 months. However, replication-competent virus was detected by 60 days after illness onset.
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Affiliation(s)
- Pyoeng Gyun Choe
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Laboratory of Infection & Immunity, Seoul National University Hospital Biomedical Research Institute, Seoul, Republic of Korea
| | - Wan Beom Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Laboratory of Infection & Immunity, Seoul National University Hospital Biomedical Research Institute, Seoul, Republic of Korea
| | - Su-Jin Choi
- Laboratory of Infection & Immunity, Seoul National University Hospital Biomedical Research Institute, Seoul, Republic of Korea
| | - Chang Kyung Kang
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yongil Koh
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Nam Joong Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Myoung-Don Oh
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
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29
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Carducci A, Federigi I, Liu D, Thompson JR, Verani M. Making Waves: Coronavirus detection, presence and persistence in the water environment: State of the art and knowledge needs for public health. WATER RESEARCH 2020; 179:115907. [PMID: 32389891 PMCID: PMC7199000 DOI: 10.1016/j.watres.2020.115907] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/25/2020] [Accepted: 05/01/2020] [Indexed: 05/18/2023]
Abstract
The main route of transmission of the human coronaviruses (HCoVs), and presumably also of the new pandemic SARS-CoV-2, is via droplets and close contacts, however their fecal elimination also suggests the possible spread via water. A scientific literature search was thus carried out to highlight the current state of the art and knowledge gaps regarding coronavirus in water. Since 1978 only 22 studies have met the inclusion criteria, and considered heterogeneous purposes, detection methods and types of water. In vitro experiments have addressed the recovery efficiency of analytical methods, survival in different types of water and the removal efficiency of water treatments. Field studies have monitored coronaviruses in surface waters, sewage, slurry, and biosolids. Overall, at the lab scale, HCoVs or surrogates can survive for several days at 4 °C, however their persistence is lower compared with non-enveloped viruses and is strongly influenced by temperature and organic or microbial pollution. HCoVs have rarely been detected in field investigations, however may be due to the low recovery efficiency of the analytical methods. The scarcity of information on HCoV in the environment suggests that research is needed to understand the fate of these viruses in the water cycle.
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Affiliation(s)
| | - Ileana Federigi
- Department of Biology, University of Pisa, Pisa, 56127, Italy.
| | - Dasheng Liu
- Ecological Society of Shandong, Jinan, 250012, China
| | - Julian R Thompson
- UCL Department of Geography, University College London, London, WC1E 6BT, United Kingdom
| | - Marco Verani
- Department of Biology, University of Pisa, Pisa, 56127, Italy
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30
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Rattan A, Ahmad H. Can quantitative RT-PCR for SARS-CoV-2 help in better management of patients and control of coronavirus disease 2019 pandemic. Indian J Med Microbiol 2020; 38:284-287. [PMID: 33154236 PMCID: PMC7709651 DOI: 10.4103/ijmm.ijmm_20_380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/24/2020] [Accepted: 10/17/2020] [Indexed: 12/23/2022]
Abstract
The emergence of SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19), represents a public health emergency of unprecedented proportion. The global containment efforts have been focused on testing, tracing of contacts and treatment (isolation) of those found COVID-19 positive. Since the whole genome sequences of a number of strains of this novel RNA virus were available in the public domain by early January 2020, a number of real-time polymerase chain reaction (RT-PCR) protocols were designed and used for diagnosis of this infection. Most RT-PCRs are designed for qualitative COVID-19 reporting (SARS-CoV-2 detected or not detected), but have been used for semi-quantitative estimation of viral load based on cycle threshold value. Our manuscript discusses the utility of quantitative PCR testing for COVID-19 and its patient management benefits.
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Affiliation(s)
- Ashok Rattan
- Advisor - Quality, Research and Development, Pathkind Labs, Gurgaon, Haryana, India
| | - Hafiz Ahmad
- Department of Medical Microbiology and Immunology, RAK College of Medical Sciences, RAK Medical and Health Sciences University, Ras Al Khaimah, UAE
- Molecular Microbiology and COVID Lab In-Charge, RAK Hospital, Ras Al Khaimah, UAE
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31
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Vammen K, Guillen SM. Water Resources of Nicaragua and COVID-19: Between panic and apathy? BRAZ J BIOL 2020; 80:690-696. [PMID: 32555975 DOI: 10.1590/1519-6984.237891] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 05/19/2020] [Indexed: 11/22/2022] Open
Affiliation(s)
- K Vammen
- Institute of Interdisciplinary Research in Natural Sciences, University of Central America - UCA Managua, Managua, Nicaragua
| | - S M Guillen
- Honorary Member of the Academy of Science of Nicaragua, Managua, Nicaragua
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32
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Sims N, Kasprzyk-Hordern B. Future perspectives of wastewater-based epidemiology: Monitoring infectious disease spread and resistance to the community level. ENVIRONMENT INTERNATIONAL 2020; 139:105689. [PMID: 32283358 PMCID: PMC7128895 DOI: 10.1016/j.envint.2020.105689] [Citation(s) in RCA: 295] [Impact Index Per Article: 73.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/05/2020] [Accepted: 03/24/2020] [Indexed: 05/17/2023]
Abstract
Infectious diseases are acknowledged as one of the most critical threats to global public health today. Climate change, unprecedented population growth with accelerated rates of antimicrobial resistance, have resulted in both the emergence of novel pathogenic organisms and the re-emergence of infections that were once controlled. The consequences have led to an increased vulnerability to infectious diseases globally. The ability to rapidly monitor the spread of diseases is key for prevention, intervention and control, however several limitations exist for current surveillance systems and the capacity to cope with the rapid population growth and environmental changes. Wastewater-Based Epidemiology (WBE) is a new epidemiology tool that has potential to act as a complementary approach for current infectious disease surveillance systems and an early warning system for disease outbreaks. WBE postulates that through the analysis of population pooled wastewater, infectious disease and resistance spread, the emergence of new disease outbreak to the community level can be monitored comprehensively and in real-time. This manuscript provides critical overview of current infectious disease surveillance status, as well as it introduces WBE and its recent advancements. It also provides recommendations for further development required for WBE application as an effective tool for infectious disease surveillance.
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Affiliation(s)
- Natalie Sims
- Department of Chemistry, University of Bath, Bath BA2 7AY, UK; Centre for Doctoral Training in Sustainable Chemical Technologies, University of Bath, Bath BA2 7AY, UK
| | - Barbara Kasprzyk-Hordern
- Department of Chemistry, University of Bath, Bath BA2 7AY, UK; Centre for Doctoral Training in Sustainable Chemical Technologies, University of Bath, Bath BA2 7AY, UK.
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33
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Wölfel R, Corman VM, Guggemos W, Seilmaier M, Zange S, Müller MA, Niemeyer D, Jones TC, Vollmar P, Rothe C, Hoelscher M, Bleicker T, Brünink S, Schneider J, Ehmann R, Zwirglmaier K, Drosten C, Wendtner C. Virological assessment of hospitalized patients with COVID-2019. Nature 2020. [PMID: 32096611 DOI: 10.1038/s41586-020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is an acute infection of the respiratory tract that emerged in late 20191,2. Initial outbreaks in China involved 13.8% of cases with severe courses, and 6.1% of cases with critical courses3. This severe presentation may result from the virus using a virus receptor that is expressed predominantly in the lung2,4; the same receptor tropism is thought to have determined the pathogenicity-but also aided in the control-of severe acute respiratory syndrome (SARS) in 20035. However, there are reports of cases of COVID-19 in which the patient shows mild upper respiratory tract symptoms, which suggests the potential for pre- or oligosymptomatic transmission6-8. There is an urgent need for information on virus replication, immunity and infectivity in specific sites of the body. Here we report a detailed virological analysis of nine cases of COVID-19 that provides proof of active virus replication in tissues of the upper respiratory tract. Pharyngeal virus shedding was very high during the first week of symptoms, with a peak at 7.11 × 108 RNA copies per throat swab on day 4. Infectious virus was readily isolated from samples derived from the throat or lung, but not from stool samples-in spite of high concentrations of virus RNA. Blood and urine samples never yielded virus. Active replication in the throat was confirmed by the presence of viral replicative RNA intermediates in the throat samples. We consistently detected sequence-distinct virus populations in throat and lung samples from one patient, proving independent replication. The shedding of viral RNA from sputum outlasted the end of symptoms. Seroconversion occurred after 7 days in 50% of patients (and by day 14 in all patients), but was not followed by a rapid decline in viral load. COVID-19 can present as a mild illness of the upper respiratory tract. The confirmation of active virus replication in the upper respiratory tract has implications for the containment of COVID-19.
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Affiliation(s)
- Roman Wölfel
- Bundeswehr Institute of Microbiology, Munich, Germany
| | | | | | | | - Sabine Zange
- Bundeswehr Institute of Microbiology, Munich, Germany
| | | | | | - Terry C Jones
- Charité Universitätsmedizin Berlin, Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | | | | | | | | | | | | | - Rosina Ehmann
- Bundeswehr Institute of Microbiology, Munich, Germany
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Wölfel R, Corman VM, Guggemos W, Seilmaier M, Zange S, Müller MA, Niemeyer D, Jones TC, Vollmar P, Rothe C, Hoelscher M, Bleicker T, Brünink S, Schneider J, Ehmann R, Zwirglmaier K, Drosten C, Wendtner C. Virological assessment of hospitalized patients with COVID-2019. Nature 2020. [PMID: 32235945 DOI: 10.1038/s41586-020-2196x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is an acute infection of the respiratory tract that emerged in late 20191,2. Initial outbreaks in China involved 13.8% of cases with severe courses, and 6.1% of cases with critical courses3. This severe presentation may result from the virus using a virus receptor that is expressed predominantly in the lung2,4; the same receptor tropism is thought to have determined the pathogenicity-but also aided in the control-of severe acute respiratory syndrome (SARS) in 20035. However, there are reports of cases of COVID-19 in which the patient shows mild upper respiratory tract symptoms, which suggests the potential for pre- or oligosymptomatic transmission6-8. There is an urgent need for information on virus replication, immunity and infectivity in specific sites of the body. Here we report a detailed virological analysis of nine cases of COVID-19 that provides proof of active virus replication in tissues of the upper respiratory tract. Pharyngeal virus shedding was very high during the first week of symptoms, with a peak at 7.11 × 108 RNA copies per throat swab on day 4. Infectious virus was readily isolated from samples derived from the throat or lung, but not from stool samples-in spite of high concentrations of virus RNA. Blood and urine samples never yielded virus. Active replication in the throat was confirmed by the presence of viral replicative RNA intermediates in the throat samples. We consistently detected sequence-distinct virus populations in throat and lung samples from one patient, proving independent replication. The shedding of viral RNA from sputum outlasted the end of symptoms. Seroconversion occurred after 7 days in 50% of patients (and by day 14 in all patients), but was not followed by a rapid decline in viral load. COVID-19 can present as a mild illness of the upper respiratory tract. The confirmation of active virus replication in the upper respiratory tract has implications for the containment of COVID-19.
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Affiliation(s)
- Roman Wölfel
- Bundeswehr Institute of Microbiology, Munich, Germany
| | | | | | | | - Sabine Zange
- Bundeswehr Institute of Microbiology, Munich, Germany
| | | | | | - Terry C Jones
- Charité Universitätsmedizin Berlin, Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | | | | | | | | | | | | | - Rosina Ehmann
- Bundeswehr Institute of Microbiology, Munich, Germany
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35
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Wölfel R, Corman VM, Guggemos W, Seilmaier M, Zange S, Müller MA, Niemeyer D, Jones TC, Vollmar P, Rothe C, Hoelscher M, Bleicker T, Brünink S, Schneider J, Ehmann R, Zwirglmaier K, Drosten C, Wendtner C. Virological assessment of hospitalized patients with COVID-2019. Nature 2020; 581:465-469. [PMID: 32235945 DOI: 10.1101/2020.03.05.20030502] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 03/24/2020] [Indexed: 05/18/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is an acute infection of the respiratory tract that emerged in late 20191,2. Initial outbreaks in China involved 13.8% of cases with severe courses, and 6.1% of cases with critical courses3. This severe presentation may result from the virus using a virus receptor that is expressed predominantly in the lung2,4; the same receptor tropism is thought to have determined the pathogenicity-but also aided in the control-of severe acute respiratory syndrome (SARS) in 20035. However, there are reports of cases of COVID-19 in which the patient shows mild upper respiratory tract symptoms, which suggests the potential for pre- or oligosymptomatic transmission6-8. There is an urgent need for information on virus replication, immunity and infectivity in specific sites of the body. Here we report a detailed virological analysis of nine cases of COVID-19 that provides proof of active virus replication in tissues of the upper respiratory tract. Pharyngeal virus shedding was very high during the first week of symptoms, with a peak at 7.11 × 108 RNA copies per throat swab on day 4. Infectious virus was readily isolated from samples derived from the throat or lung, but not from stool samples-in spite of high concentrations of virus RNA. Blood and urine samples never yielded virus. Active replication in the throat was confirmed by the presence of viral replicative RNA intermediates in the throat samples. We consistently detected sequence-distinct virus populations in throat and lung samples from one patient, proving independent replication. The shedding of viral RNA from sputum outlasted the end of symptoms. Seroconversion occurred after 7 days in 50% of patients (and by day 14 in all patients), but was not followed by a rapid decline in viral load. COVID-19 can present as a mild illness of the upper respiratory tract. The confirmation of active virus replication in the upper respiratory tract has implications for the containment of COVID-19.
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Affiliation(s)
- Roman Wölfel
- Bundeswehr Institute of Microbiology, Munich, Germany
| | | | | | | | - Sabine Zange
- Bundeswehr Institute of Microbiology, Munich, Germany
| | | | | | - Terry C Jones
- Charité Universitätsmedizin Berlin, Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | | | | | | | | | | | | | - Rosina Ehmann
- Bundeswehr Institute of Microbiology, Munich, Germany
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Gandhi M, Havlir D. The Time for Universal Masking of the Public for Coronavirus Disease 2019 Is Now. Open Forum Infect Dis 2020; 7:ofaa131. [PMID: 32346544 PMCID: PMC7179801 DOI: 10.1093/ofid/ofaa131] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 12/20/2022] Open
Abstract
In this perspective, we recommend universal masking of the US public during coronavirus disease 2019 due to the high contagiousness of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), viral shedding of viable SARS-CoV-2 from asymptomatic individuals, and the likely contribution of masking to core distancing public health strategies for curbing transmission.
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Affiliation(s)
- Monica Gandhi
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco (UCSF), San Francisco, California, USA
| | - Diane Havlir
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco (UCSF), San Francisco, California, USA
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37
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Wölfel R, Corman VM, Guggemos W, Seilmaier M, Zange S, Müller MA, Niemeyer D, Jones TC, Vollmar P, Rothe C, Hoelscher M, Bleicker T, Brünink S, Schneider J, Ehmann R, Zwirglmaier K, Drosten C, Wendtner C. Virological assessment of hospitalized patients with COVID-2019. Nature 2020; 581:465-469. [DOI: 10.1038/s41586-020-2196-x] [Citation(s) in RCA: 4769] [Impact Index Per Article: 1192.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 03/24/2020] [Indexed: 02/06/2023]
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38
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Lescure FX, Bouadma L, Nguyen D, Parisey M, Wicky PH, Behillil S, Gaymard A, Bouscambert-Duchamp M, Donati F, Le Hingrat Q, Enouf V, Houhou-Fidouh N, Valette M, Mailles A, Lucet JC, Mentre F, Duval X, Descamps D, Malvy D, Timsit JF, Lina B, van-der-Werf S, Yazdanpanah Y. Clinical and virological data of the first cases of COVID-19 in Europe: a case series. THE LANCET. INFECTIOUS DISEASES 2020; 20:697-706. [PMID: 32224310 PMCID: PMC7156120 DOI: 10.1016/s1473-3099(20)30200-0] [Citation(s) in RCA: 750] [Impact Index Per Article: 187.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 02/07/2023]
Abstract
Background On Dec 31, 2019, China reported a cluster of cases of pneumonia in people at Wuhan, Hubei Province. The responsible pathogen is a novel coronavirus, named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We report the relevant features of the first cases in Europe of confirmed infection, named coronavirus disease 2019 (COVID-19), with the first patient diagnosed with the disease on Jan 24, 2020. Methods In this case series, we followed five patients admitted to Bichat-Claude Bernard University Hospital (Paris, France) and Pellegrin University Hospital (Bordeaux, France) and diagnosed with COVID-19 by semi-quantitative RT-PCR on nasopharyngeal swabs. We assessed patterns of clinical disease and viral load from different samples (nasopharyngeal and blood, urine, and stool samples), which were obtained once daily for 3 days from hospital admission, and once every 2 or 3 days until patient discharge. All samples were refrigerated and shipped to laboratories in the National Reference Center for Respiratory Viruses (The Institut Pasteur, Paris, and Hospices Civils de Lyon, Lyon, France), where RNA extraction, real-time RT-PCR, and virus isolation and titration procedures were done. Findings The patients were three men (aged 31 years, 48 years, and 80 years) and two women (aged 30 years and 46 years), all of Chinese origin, who had travelled to France from China around mid-January, 2020. Three different clinical evolutions are described: (1) two paucisymptomatic women diagnosed within a day of exhibiting symptoms, with high nasopharyngeal titres of SARS-CoV-2 within the first 24 h of the illness onset (5·2 and 7·4 log10 copies per 1000 cells, respectively) and viral RNA detection in stools; (2) a two-step disease progression in two young men, with a secondary worsening around 10 days after disease onset despite a decreasing viral load in nasopharyngeal samples; and (3) an 80-year-old man with a rapid evolution towards multiple organ failure and a persistent high viral load in lower and upper respiratory tract with systemic virus dissemination and virus detection in plasma. The 80-year-old patient died on day 14 of illness (Feb 14, 2020); all other patients had recovered and been discharged by Feb 19, 2020. Interpretation We illustrated three different clinical and biological types of evolution in five patients infected with SARS-CoV-2 with detailed and comprehensive viral sampling strategy. We believe that these findings will contribute to a better understanding of the natural history of the disease and will contribute to advances in the implementation of more efficient infection control strategies. Funding REACTing (Research & Action Emerging Infectious Diseases).
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Affiliation(s)
- Francois-Xavier Lescure
- Department of Infectious and Tropical Diseases, Assistance Publique-Hôpitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France; Infections Antimicrobials Modelling Evolution (IAME) UMR 1137, University of Paris, Paris, France
| | - Lila Bouadma
- Medical and Infectious Diseases Intensive Care Unit, Assistance Publique-Hôpitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France; Infections Antimicrobials Modelling Evolution (IAME) UMR 1137, University of Paris, Paris, France
| | - Duc Nguyen
- Department of Infectious Diseases and Tropical Medicine, University Hospital of Bordeaux, Bordeaux, France; INSERM U1219, University of Bordeaux, Bordeaux, France
| | - Marion Parisey
- Department of Infectious and Tropical Diseases, Assistance Publique-Hôpitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France
| | - Paul-Henri Wicky
- Medical and Infectious Diseases Intensive Care Unit, Assistance Publique-Hôpitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France; Infections Antimicrobials Modelling Evolution (IAME) UMR 1137, University of Paris, Paris, France
| | - Sylvie Behillil
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, CNRS-UMR 3569, The Institut Pasteur, Paris, France
| | - Alexandre Gaymard
- National Reference Center for Respiratory Viruses, Department of Virology, Infective Agents Institute, North Hospital Network, Lyon, France; Virpath Laboratory, International Center of Research in Infectiology, INSERM U1111, CNRS-UMR 5308, École Normale Supérieure de Lyon, Université Claude Bernard Lyon, Lyon University, Lyon, France
| | - Maude Bouscambert-Duchamp
- National Reference Center for Respiratory Viruses, Department of Virology, Infective Agents Institute, North Hospital Network, Lyon, France; Virpath Laboratory, International Center of Research in Infectiology, INSERM U1111, CNRS-UMR 5308, École Normale Supérieure de Lyon, Université Claude Bernard Lyon, Lyon University, Lyon, France
| | - Flora Donati
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, CNRS-UMR 3569, The Institut Pasteur, Paris, France
| | - Quentin Le Hingrat
- Department of Virology, Assistance Publique-Hôpitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France; Infections Antimicrobials Modelling Evolution (IAME) UMR 1137, University of Paris, Paris, France
| | - Vincent Enouf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, CNRS-UMR 3569, The Institut Pasteur, Paris, France; Mutualized Platform of Microbiology, Pasteur International Bioresources Network, The Institut Pasteur, Paris, France
| | - Nadhira Houhou-Fidouh
- Department of Virology, Assistance Publique-Hôpitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France
| | - Martine Valette
- National Reference Center for Respiratory Viruses, Department of Virology, Infective Agents Institute, North Hospital Network, Lyon, France; Virpath Laboratory, International Center of Research in Infectiology, INSERM U1111, CNRS-UMR 5308, École Normale Supérieure de Lyon, Université Claude Bernard Lyon, Lyon University, Lyon, France
| | | | - Jean-Christophe Lucet
- Infection Control Unit, Assistance Publique-Hôpitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France; Infections Antimicrobials Modelling Evolution (IAME) UMR 1137, University of Paris, Paris, France
| | - France Mentre
- Department of Epidemiology, Biostatistics and Clinical Research, Assistance Publique-Hôpitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France; Infections Antimicrobials Modelling Evolution (IAME) UMR 1137, University of Paris, Paris, France
| | - Xavier Duval
- Center for Clinical Investigation, Assistance Publique-Hôpitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France; Infections Antimicrobials Modelling Evolution (IAME) UMR 1137, University of Paris, Paris, France
| | - Diane Descamps
- Department of Virology, Assistance Publique-Hôpitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France; Infections Antimicrobials Modelling Evolution (IAME) UMR 1137, University of Paris, Paris, France
| | - Denis Malvy
- Department of Infectious Diseases and Tropical Medicine, University Hospital of Bordeaux, Bordeaux, France; INSERM U1219, University of Bordeaux, Bordeaux, France
| | - Jean-François Timsit
- Medical and Infectious Diseases Intensive Care Unit, Assistance Publique-Hôpitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France; Infections Antimicrobials Modelling Evolution (IAME) UMR 1137, University of Paris, Paris, France
| | - Bruno Lina
- National Reference Center for Respiratory Viruses, Department of Virology, Infective Agents Institute, North Hospital Network, Lyon, France; Virpath Laboratory, International Center of Research in Infectiology, INSERM U1111, CNRS-UMR 5308, École Normale Supérieure de Lyon, Université Claude Bernard Lyon, Lyon University, Lyon, France
| | - Sylvie van-der-Werf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, CNRS-UMR 3569, The Institut Pasteur, Paris, France
| | - Yazdan Yazdanpanah
- Department of Infectious and Tropical Diseases, Assistance Publique-Hôpitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France; Infections Antimicrobials Modelling Evolution (IAME) UMR 1137, University of Paris, Paris, France.
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Al-Tawfiq JA. Viral loads of SARS-CoV, MERS-CoV and SARS-CoV-2 in respiratory specimens: What have we learned? Travel Med Infect Dis 2020; 34:101629. [PMID: 32179122 PMCID: PMC7206223 DOI: 10.1016/j.tmaid.2020.101629] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/09/2020] [Accepted: 03/12/2020] [Indexed: 01/29/2023]
Affiliation(s)
- Jaffar A Al-Tawfiq
- Specialty Internal Medicine, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia; Quality and Patient Safety Department, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia; Indiana University School of Medicine, IN, USA; Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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40
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Abstract
The immense global burden of infectious disease outbreaks and the need to establish prediction and prevention systems have been recognized by the World Health Organization (WHO), the National Institutes of Health (NIH), the United States Agency of International Development (USAID), the Bill and Melinda Gates Foundation, and the international scientific community. Despite multiple efforts, this infectious burden is still increasing. For example, it has been reported that between 1.5 and 12 million people die each year from waterborne diseases and diarrheal diseases are listed within the top 15 leading causes of death worldwide. Rapid population growth, climate change, natural disasters, immigration, globalization, and the corresponding sanitation and waste management challenges are expected to intensify the problem in the years to come.
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Wu W, Fan H, Lian X, Zhou J, Zhang T. Aligner-mediated cleavage-triggered exponential amplification for sensitive detection of nucleic acids. Talanta 2018; 185:141-145. [PMID: 29759180 DOI: 10.1016/j.talanta.2018.03.067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/14/2018] [Accepted: 03/22/2018] [Indexed: 10/17/2022]
Abstract
Exponential amplification reaction (EXPAR), as a simple and high sensitive method, holds great promise in nucleic acids detection. One major challenge in EXPAR is the generation of trigger DNA with a definite 3'-end, which now relies on fingerprinting technology. However, the requirement of different endonucleases for varying target sequences and two head-to-head recognition sites in double stranded DNA, as well as the confinement of trigger DNA's 3'-end to be near/within the recognition site, usually subject EXPAR to compromised universality and/or repeated matching of reaction conditions. Herein, we report a simple and universal method for high sensitive detection of nucleic acids, termed aligner-mediated cleavage-triggered exponential amplification (AMCEA). The aligner-mediated cleavage (AMC) needs only one nicking endonuclease and can make a break at any site of choice in a programmable way. Thus, the 3'-end of target DNA can be easily redefined as required, a key step for initiating the amplification reaction. This capability endows the proposed AMCEA with excellent universality and simplicity. Moreover, it is sensitive and specific, with a detection limit at amol level, a broad dynamic range of 5~6 orders of magnitude and the ability to distinguish single nucleotide mutation. Experiments performed with human serum indicate that AMCEA is compatible with the complex biological sample, and thus has the potentials for practical applications.
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Affiliation(s)
- Wanghua Wu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, PR China
| | - Hongliang Fan
- Department of Environmental Medicine, Institute of Hygiene, Zhejiang Academy of Medical Sciences, Hangzhou 310013, PR China
| | - Xiang Lian
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, PR China
| | - Jianguang Zhou
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, PR China
| | - Tao Zhang
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, PR China.
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Aleanizy FS, Mohmed N, Alqahtani FY, El Hadi Mohamed RA. Outbreak of Middle East respiratory syndrome coronavirus in Saudi Arabia: a retrospective study. BMC Infect Dis 2017; 17:23. [PMID: 28056850 PMCID: PMC5217314 DOI: 10.1186/s12879-016-2137-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 12/17/2016] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The Middle East respiratory syndrome (MERS) is proposed to be a zoonotic disease. Dromedary camels have been implicated due to reports that some confirmed cases were exposed to camels. Risk factors for MERS coronavirus (MERS-CoV) infections in humans are incompletely understood. This study aimed to describe the demographic characteristics, mortality rate, clinical manifestations and comorbidities with confirmed cases of MERS-CoV. METHODS Retrospective chart review were performed to identify all laboratory-confirmed cases of MERS-CoV in Saudi Arabia who reported to the Ministry of Health (MOH) of Saudi Arabia and WHO between April 23, 2014 and August 31, 2015. Patients' charts were also reviewed for demographic information, mortality, comorbidities, clinical presentations, health care facility and presented with descriptive and comparative statistics using non parametric binomial test and Chi-square test. RESULTS Confirmed cases of male patients (61.1%) exceeded those of female patients (38.9%). Infections among Saudi patients (62.6%) exceeded those among non-Saudi patients (37.4%; P = 0.001). The majority of the patients were aged 21-40 years (37.4%) or 41-60 years (35.8%); 43 (22.6%) were aged >61 years, and (8) 4.2% were aged 0-20 years. There was a difference in mortality between confirmed MERS-CoV cases (63.7% alive versus 36.3% dead cases, respectively). Furthermore, fever with cough and shortness of breath (SOB) (n = 39; 20.5%), fever with cough (n = 29; 15.3%), fever (n = 18; 9.5%), and fever with SOB (n = 13; 6.8%), were the most common clinical manifestations associated with confirmed MERS-CoV cases. CONCLUSION MERS-CoV is considered an epidemic in Saudi Arabia. The results of the present study showed that the frequency of cases is higher among men than women, in Saudi patients than non-Saudi, and those between 21 to 60 years are most affected. Further studies are required to improve the surveillance associated with MERS-CoV to get definite and clear answers and better understanding of the MERS-CoV outbreak as well the source, and route of infection transmission in Saudi Arabia.
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Affiliation(s)
- Fadilah Sfouq Aleanizy
- College of Pharmacy, Department of Pharmaceutics, King Saud University, 22452, Riyadh, 11495 Saudi Arabia
| | - Nahla Mohmed
- College of Medicine, Princess Nourah Bint Abdulrahman University, Riyadh, 12484 Saudi Arabia
| | - Fulwah Y. Alqahtani
- College of Pharmacy, Department of Pharmaceutics, King Saud University, 22452, Riyadh, 11495 Saudi Arabia
| | - Rania Ali El Hadi Mohamed
- College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, 12484 Saudi Arabia
- Scientific research, Federal Ministry of Health, Khartoum, 303 Sudan
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Woo PCY, Lau SKP, Choi GKY, Huang Y, Wernery R, Joseph S, Wong EYM, Elizabeth SK, Patteril NAG, Li T, Wernery U, Yuen KY. Equine rhinitis B viruses in horse fecal samples from the Middle East. Virol J 2016; 13:94. [PMID: 27267372 PMCID: PMC4897857 DOI: 10.1186/s12985-016-0547-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 05/24/2016] [Indexed: 12/03/2022] Open
Abstract
Background Among all known picornaviruses, only two species, equine rhinitis A virus and equine rhinitis B virus (ERBV) are known to infect horses, causing respiratory infections. No reports have described the detection of ERBV in fecal samples of horses and no complete genome sequences of ERBV3 are available. Methods We performed a molecular epidemiology study to detect ERBVs in horses from Dubai and Hong Kong. Complete genome sequencing of the ERBVs as well as viral loads and genome, phylogenetic and evolutionary analysis were performed on the positive samples. Results ERBV was detected in four (13.8 %) of the 29 fecal samples in horses from Dubai, with viral loads 8.28 × 103 to 5.83 × 104 copies per ml, but none of the 47 fecal samples in horses from Hong Kong by RT-PCR. Complete genome sequencing and phylogenetic analysis showed that three of the four strains were ERBV3 and one was ERBV2. The major difference between the genomes of ERBV3 and those of ERBV1 and ERBV2 lied in the amino acid sequences of their VP1 proteins. The Ka/Ks ratios of all the coding regions in the ERBV3 genomes were all <0.1, suggesting that ERBV3 were stably evolving in horses. Using the uncorrelated lognormal distributed relaxed clock model on VP1 gene, the date of the most recent common ancestor (MRCA) of ERBV3 was estimated to be 1785 (HPDs, 1176 to 1937) and the MRCA dates of ERBV1 and ERBV2 were estimated to be 1848 (HPDs, 1466 to 1949) respectively. Conclusions Both acid stable (ERBV3) and acid labile (ERBV2) ERBVs could be found in fecal samples of horses. Detection of ERBVs in fecal samples would have implications for their transmission and potential role in gastrointestinal diseases as well as fecal sampling as an alternative method of identifying infected horses.
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Affiliation(s)
- Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China. .,Department of Microbiology, The University of Hong Kong, Hong Kong, China. .,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China. .,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China.
| | - Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.,Department of Microbiology, The University of Hong Kong, Hong Kong, China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Garnet K Y Choi
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Yi Huang
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Renate Wernery
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Sunitha Joseph
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Emily Y M Wong
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | | | | | - Tong Li
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Ulrich Wernery
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates.
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.,Department of Microbiology, The University of Hong Kong, Hong Kong, China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
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Ye Y, Ellenberg RM, Graham KE, Wigginton KR. Survivability, Partitioning, and Recovery of Enveloped Viruses in Untreated Municipal Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:5077-85. [PMID: 27111122 PMCID: PMC7099725 DOI: 10.1021/acs.est.6b00876] [Citation(s) in RCA: 378] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/19/2016] [Accepted: 04/25/2016] [Indexed: 05/17/2023]
Abstract
Many of the devastating pandemics and outbreaks of the 20th and 21st centuries have involved enveloped viruses, including influenza, HIV, SARS, MERS, and Ebola. However, little is known about the presence and fate of enveloped viruses in municipal wastewater. Here, we compared the survival and partitioning behavior of two model enveloped viruses (MHV and ϕ6) and two nonenveloped bacteriophages (MS2 and T3) in raw wastewater samples. We showed that MHV and ϕ6 remained infective on the time scale of days. Up to 26% of the two enveloped viruses adsorbed to the solid fraction of wastewater compared to 6% of the two nonenveloped viruses. Based on this partitioning behavior, we assessed and optimized methods for recovering enveloped viruses from wastewater. Our optimized ultrafiltration method resulted in mean recoveries (±SD) of 25.1% (±3.6%) and 18.2% (±9.5%) for the enveloped MHV and ϕ6, respectively, and mean recoveries of 55.6% (±16.7%) and 85.5% (±24.5%) for the nonenveloped MS2 and T3, respectively. A maximum of 3.7% of MHV and 2% of MS2 could be recovered from the solids. These results shed light on the environmental fate of an important group of viruses and the presented methods will enable future research on enveloped viruses in water environments.
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Affiliation(s)
- Yinyin Ye
- Department of Civil and Environmental Engineering,
University of Michigan, Ann Arbor,
Michigan 48109-2125, United States
| | - Robert M. Ellenberg
- Department of Civil and Environmental Engineering,
University of Michigan, Ann Arbor,
Michigan 48109-2125, United States
| | - Katherine E. Graham
- Department of Civil and Environmental Engineering,
University of Michigan, Ann Arbor,
Michigan 48109-2125, United States
| | - Krista R. Wigginton
- Department of Civil and Environmental Engineering,
University of Michigan, Ann Arbor,
Michigan 48109-2125, United States
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45
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Ye Y, Ellenberg RM, Graham KE, Wigginton KR. Survivability, Partitioning, and Recovery of Enveloped Viruses in Untreated Municipal Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:5077-5085. [PMID: 27111122 DOI: 10.1021/acs.est.6b00876.s001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Many of the devastating pandemics and outbreaks of the 20th and 21st centuries have involved enveloped viruses, including influenza, HIV, SARS, MERS, and Ebola. However, little is known about the presence and fate of enveloped viruses in municipal wastewater. Here, we compared the survival and partitioning behavior of two model enveloped viruses (MHV and ϕ6) and two nonenveloped bacteriophages (MS2 and T3) in raw wastewater samples. We showed that MHV and ϕ6 remained infective on the time scale of days. Up to 26% of the two enveloped viruses adsorbed to the solid fraction of wastewater compared to 6% of the two nonenveloped viruses. Based on this partitioning behavior, we assessed and optimized methods for recovering enveloped viruses from wastewater. Our optimized ultrafiltration method resulted in mean recoveries (±SD) of 25.1% (±3.6%) and 18.2% (±9.5%) for the enveloped MHV and ϕ6, respectively, and mean recoveries of 55.6% (±16.7%) and 85.5% (±24.5%) for the nonenveloped MS2 and T3, respectively. A maximum of 3.7% of MHV and 2% of MS2 could be recovered from the solids. These results shed light on the environmental fate of an important group of viruses and the presented methods will enable future research on enveloped viruses in water environments.
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Affiliation(s)
- Yinyin Ye
- Department of Civil and Environmental Engineering, University of Michigan , Ann Arbor, Michigan 48109-2125, United States
| | - Robert M Ellenberg
- Department of Civil and Environmental Engineering, University of Michigan , Ann Arbor, Michigan 48109-2125, United States
| | - Katherine E Graham
- Department of Civil and Environmental Engineering, University of Michigan , Ann Arbor, Michigan 48109-2125, United States
| | - Krista R Wigginton
- Department of Civil and Environmental Engineering, University of Michigan , Ann Arbor, Michigan 48109-2125, United States
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46
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Ye Y, Ellenberg RM, Graham KE, Wigginton KR. Survivability, Partitioning, and Recovery of Enveloped Viruses in Untreated Municipal Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016. [PMID: 27111122 DOI: 10.1021/acs.est.6b0087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Many of the devastating pandemics and outbreaks of the 20th and 21st centuries have involved enveloped viruses, including influenza, HIV, SARS, MERS, and Ebola. However, little is known about the presence and fate of enveloped viruses in municipal wastewater. Here, we compared the survival and partitioning behavior of two model enveloped viruses (MHV and ϕ6) and two nonenveloped bacteriophages (MS2 and T3) in raw wastewater samples. We showed that MHV and ϕ6 remained infective on the time scale of days. Up to 26% of the two enveloped viruses adsorbed to the solid fraction of wastewater compared to 6% of the two nonenveloped viruses. Based on this partitioning behavior, we assessed and optimized methods for recovering enveloped viruses from wastewater. Our optimized ultrafiltration method resulted in mean recoveries (±SD) of 25.1% (±3.6%) and 18.2% (±9.5%) for the enveloped MHV and ϕ6, respectively, and mean recoveries of 55.6% (±16.7%) and 85.5% (±24.5%) for the nonenveloped MS2 and T3, respectively. A maximum of 3.7% of MHV and 2% of MS2 could be recovered from the solids. These results shed light on the environmental fate of an important group of viruses and the presented methods will enable future research on enveloped viruses in water environments.
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Affiliation(s)
- Yinyin Ye
- Department of Civil and Environmental Engineering, University of Michigan , Ann Arbor, Michigan 48109-2125, United States
| | - Robert M Ellenberg
- Department of Civil and Environmental Engineering, University of Michigan , Ann Arbor, Michigan 48109-2125, United States
| | - Katherine E Graham
- Department of Civil and Environmental Engineering, University of Michigan , Ann Arbor, Michigan 48109-2125, United States
| | - Krista R Wigginton
- Department of Civil and Environmental Engineering, University of Michigan , Ann Arbor, Michigan 48109-2125, United States
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47
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Corman VM, Albarrak AM, Omrani AS, Albarrak MM, Farah ME, Almasri M, Muth D, Sieberg A, Meyer B, Assiri AM, Binger T, Steinhagen K, Lattwein E, Al-Tawfiq J, Müller MA, Drosten C, Memish ZA. Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection. Clin Infect Dis 2015; 62:477-483. [PMID: 26565003 PMCID: PMC7108065 DOI: 10.1093/cid/civ951] [Citation(s) in RCA: 263] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/29/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The Middle East respiratory syndrome (MERS) coronavirus causes isolated cases and outbreaks of severe respiratory disease. Essential features of the natural history of disease are poorly understood. METHODS We studied 37 adult patients infected with MERS coronavirus for viral load in the lower and upper respiratory tracts (LRT and URT, respectively), blood, stool, and urine. Antibodies and serum neutralizing activities were determined over the course of disease. RESULTS One hundred ninety-nine LRT samples collected during the 3 weeks following diagnosis yielded virus RNA in 93% of tests. Average (maximum) viral loads were 5 × 10(6) (6 × 10(10)) copies/mL. Viral loads (positive detection frequencies) in 84 URT samples were 1.9 × 10(4) copies/mL (47.6%). Thirty-three percent of all 108 serum samples tested yielded viral RNA. Only 14.6% of stool and 2.4% of urine samples yielded viral RNA. All seroconversions occurred during the first 2 weeks after diagnosis, which corresponds to the second and third week after symptom onset. Immunoglobulin M detection provided no advantage in sensitivity over immunoglobulin G (IgG) detection. All surviving patients, but only slightly more than half of all fatal cases, produced IgG and neutralizing antibodies. The levels of IgG and neutralizing antibodies were weakly and inversely correlated with LRT viral loads. Presence of antibodies did not lead to the elimination of virus from LRT. CONCLUSIONS The timing and intensity of respiratory viral shedding in patients with MERS closely matches that of those with severe acute respiratory syndrome. Blood viral RNA does not seem to be infectious. Extrapulmonary loci of virus replication seem possible. Neutralizing antibodies do not suffice to clear the infection.
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Affiliation(s)
- Victor M Corman
- Institute of Virology, University of Bonn Medical Centre.,German Centre for Infection Research, Partner Site Bonn-Cologne, Bonn, Germany
| | | | | | | | - Mohamed Elamin Farah
- Central Military Laboratory and Blood Bank, Microbiology Division, Prince Sultan Military City
| | | | - Doreen Muth
- Institute of Virology, University of Bonn Medical Centre.,German Centre for Infection Research, Partner Site Bonn-Cologne, Bonn, Germany
| | - Andrea Sieberg
- Institute of Virology, University of Bonn Medical Centre
| | - Benjamin Meyer
- Institute of Virology, University of Bonn Medical Centre
| | | | - Tabea Binger
- Institute of Virology, University of Bonn Medical Centre
| | | | | | - Jaffar Al-Tawfiq
- Johns Hopkins Aramco Healthcare, Dhahran.,Indiana University School of Medicine, Indianapolis
| | | | - Christian Drosten
- Institute of Virology, University of Bonn Medical Centre.,German Centre for Infection Research, Partner Site Bonn-Cologne, Bonn, Germany
| | - Ziad A Memish
- Ministry of Health, Riyadh, Kingdom of Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Kingdom of Saudi Arabia
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48
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Yip MS, Leung NHL, Cheung CY, Li PH, Lee HHY, Daëron M, Peiris JSM, Bruzzone R, Jaume M. Antibody-dependent infection of human macrophages by severe acute respiratory syndrome coronavirus. Virol J 2014; 11:82. [PMID: 24885320 PMCID: PMC4018502 DOI: 10.1186/1743-422x-11-82] [Citation(s) in RCA: 181] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 04/22/2014] [Indexed: 12/24/2022] Open
Abstract
Background Public health risks associated to infection by human coronaviruses remain considerable and vaccination is a key option for preventing the resurgence of severe acute respiratory syndrome coronavirus (SARS-CoV). We have previously reported that antibodies elicited by a SARS-CoV vaccine candidate based on recombinant, full-length SARS-CoV Spike-protein trimers, trigger infection of immune cell lines. These observations prompted us to investigate the molecular mechanisms and responses to antibody-mediated infection in human macrophages. Methods We have used primary human immune cells to evaluate their susceptibility to infection by SARS-CoV in the presence of anti-Spike antibodies. Fluorescence microscopy and real-time quantitative reverse transcriptase polymerase chain reaction (RT-PCR) were utilized to assess occurrence and consequences of infection. To gain insight into the underlying molecular mechanism, we performed mutational analysis with a series of truncated and chimeric constructs of fragment crystallizable γ receptors (FcγR), which bind antibody-coated pathogens. Results We show here that anti-Spike immune serum increased infection of human monocyte-derived macrophages by replication-competent SARS-CoV as well as Spike-pseudotyped lentiviral particles (SARS-CoVpp). Macrophages infected with SARS-CoV, however, did not support productive replication of the virus. Purified anti-viral IgGs, but not other soluble factor(s) from heat-inactivated mouse immune serum, were sufficient to enhance infection. Antibody-mediated infection was dependent on signaling-competent members of the human FcγRII family, which were shown to confer susceptibility to otherwise naïve ST486 cells, as binding of immune complexes to cell surface FcγRII was necessary but not sufficient to trigger antibody-dependent enhancement (ADE) of infection. Furthermore, only FcγRII with intact cytoplasmic signaling domains were competent to sustain ADE of SARS-CoVpp infection, thus providing additional information on the role of downstream signaling by FcγRII. Conclusions These results demonstrate that human macrophages can be infected by SARS-CoV as a result of IgG-mediated ADE and indicate that this infection route requires signaling pathways activated downstream of binding to FcγRII receptors.
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Affiliation(s)
| | | | | | | | | | | | | | - Roberto Bruzzone
- HKU-Pasteur Research Pole and Center of Influenza Research, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR.
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49
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Real-time reverse transcription-PCR assay panel for Middle East respiratory syndrome coronavirus. J Clin Microbiol 2013; 52:67-75. [PMID: 24153118 DOI: 10.1128/jcm.02533-13] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A new human coronavirus (CoV), subsequently named Middle East respiratory syndrome (MERS)-CoV, was first reported in Saudi Arabia in September 2012. In response, we developed two real-time reverse transcription-PCR (rRT-PCR) assays targeting the MERS-CoV nucleocapsid (N) gene and evaluated these assays as a panel with a previously published assay targeting the region upstream of the MERS-CoV envelope gene (upE) for the detection and confirmation of MERS-CoV infection. All assays detected ≤10 copies/reaction of quantified RNA transcripts, with a linear dynamic range of 8 log units and 1.3 × 10(-3) 50% tissue culture infective doses (TCID50)/ml of cultured MERS-CoV per reaction. All assays performed comparably with respiratory, serum, and stool specimens spiked with cultured virus. No false-positive amplifications were obtained with other human coronaviruses or common respiratory viral pathogens or with 336 diverse clinical specimens from non-MERS-CoV cases; specimens from two confirmed MERS-CoV cases were positive with all assay signatures. In June 2012, the U.S. Food and Drug Administration authorized emergency use of the rRT-PCR assay panel as an in vitro diagnostic test for MERS-CoV. A kit consisting of the three assay signatures and a positive control was assembled and distributed to public health laboratories in the United States and internationally to support MERS-CoV surveillance and public health responses.
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50
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Lau SKP, Lau CCY, Chan KH, Li CPY, Chen H, Jin DY, Chan JFW, Woo PCY, Yuen KY. Delayed induction of proinflammatory cytokines and suppression of innate antiviral response by the novel Middle East respiratory syndrome coronavirus: implications for pathogenesis and treatment. J Gen Virol 2013; 94:2679-2690. [PMID: 24077366 DOI: 10.1099/vir.0.055533-0] [Citation(s) in RCA: 287] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The high mortality associated with the novel Middle East respiratory syndrome coronavirus (MERS-CoV) has raised questions about the possible role of a cytokine storm in its pathogenesis. Although recent studies showed that MERS-CoV infection is associated with an attenuated IFN response, no induction of inflammatory cytokines was demonstrated during the early phase of infection. To study both early and late cytokine responses associated with MERS-CoV infection, we measured the mRNA levels of eight cytokine genes [TNF-α, IL-1β, IL-6, IL-8, IFN-β, monocyte chemotactic protein-1, transforming growth factor-β and IFN-γ-induced protein (IP)-10] in cell lysates of polarized airway epithelial Calu-3 cells infected with MERS-CoV or severe acute respiratory syndrome (SARS)-CoV up to 30 h post-infection. Among the eight cytokine genes, IL-1β, IL-6 and IL-8 induced by MERS-CoV were markedly higher than those induced by SARS-CoV at 30 h, whilst TNF-α, IFN-β and IP-10 induced by SARS-CoV were markedly higher than those induced by MERS-CoV at 24 and 30 h in infected Calu-3 cells. The activation of IL-8 and attenuated IFN-β response by MERS-CoV were also confirmed by protein measurements in the culture supernatant when compared with SARS-CoV and Sendai virus. To further confirm the attenuated antiviral response, cytokine response was compared with human HCoV-229E in embryonal lung fibroblast HFL cells, which also revealed higher IFN-β and IP-10 levels induced by HCoV-229E than MERS-CoV at 24 and 30 h. Whilst our data supported recent findings that MERS-CoV elicits attenuated innate immunity, this represents the first report to demonstrate delayed proinflammatory cytokine induction by MERS-CoV. Our results provide insights into the pathogenesis and treatment of MERS-CoV infections.
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Affiliation(s)
- Susanna K P Lau
- Department of Microbiology, University of Hong Kong, Hong Kong, P.R. China.,State Key Laboratory of Emerging Infectious Diseases, University of Hong Kong, Hong Kong, P.R. China.,Carol Yu Centre for Infection, University of Hong Kong, Hong Kong, P.R. China.,Research Centre of Infection and Immunology, University of Hong Kong, Hong Kong, P.R. China
| | - Candy C Y Lau
- Department of Microbiology, University of Hong Kong, Hong Kong, P.R. China
| | - Kwok-Hung Chan
- Department of Microbiology, University of Hong Kong, Hong Kong, P.R. China
| | - Clara P Y Li
- Department of Microbiology, University of Hong Kong, Hong Kong, P.R. China
| | - Honglin Chen
- Research Centre of Infection and Immunology, University of Hong Kong, Hong Kong, P.R. China.,Carol Yu Centre for Infection, University of Hong Kong, Hong Kong, P.R. China.,State Key Laboratory of Emerging Infectious Diseases, University of Hong Kong, Hong Kong, P.R. China.,Department of Microbiology, University of Hong Kong, Hong Kong, P.R. China
| | - Dong-Yan Jin
- Department of Biochemistry, University of Hong Kong, Hong Kong, P.R. China
| | - Jasper F W Chan
- Department of Microbiology, University of Hong Kong, Hong Kong, P.R. China
| | - Patrick C Y Woo
- Carol Yu Centre for Infection, University of Hong Kong, Hong Kong, P.R. China.,Department of Microbiology, University of Hong Kong, Hong Kong, P.R. China.,State Key Laboratory of Emerging Infectious Diseases, University of Hong Kong, Hong Kong, P.R. China.,Research Centre of Infection and Immunology, University of Hong Kong, Hong Kong, P.R. China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, University of Hong Kong, Hong Kong, P.R. China.,Department of Microbiology, University of Hong Kong, Hong Kong, P.R. China.,Research Centre of Infection and Immunology, University of Hong Kong, Hong Kong, P.R. China.,Carol Yu Centre for Infection, University of Hong Kong, Hong Kong, P.R. China
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