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Ward C, Brown GD, Oleson JJ. An individual level infectious disease model in the presence of uncertainty from multiple, imperfect diagnostic tests. Biometrics 2023; 79:426-436. [PMID: 34636415 PMCID: PMC8653294 DOI: 10.1111/biom.13579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/29/2021] [Accepted: 10/05/2021] [Indexed: 11/28/2022]
Abstract
Bayesian compartmental infectious disease models yield important inference on disease transmission by appropriately accounting for the dynamics and uncertainty of infection processes. In addition to estimating transition probabilities and reproductive numbers, these statistical models allow researchers to assess the probability of disease risk and quantify the effectiveness of interventions. These infectious disease models rely on data collected from all individuals classified as positive based on various diagnostic tests. In infectious disease testing, however, such procedures produce both false-positives and false-negatives at varying rates depending on the sensitivity and specificity of the diagnostic tests being used. We propose a novel Bayesian spatio-temporal infectious disease modeling framework that accounts for the additional uncertainty in the diagnostic testing and classification process that provides estimates of the important transmission dynamics of interest to researchers. The method is applied to data on the 2006 mumps epidemic in Iowa, in which over 6,000 suspected mumps cases were tested using a buccal or oral swab specimen, a urine specimen, and/or a blood specimen. Although all procedures are believed to have high specificities, the sensitivities can be low and vary depending on the timing of the test as well as the vaccination status of the individual being tested.
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Affiliation(s)
- Caitlin Ward
- Department of BiostatisticsUniversity of IowaIowa CityIowaUSA
| | - Grant D. Brown
- Department of BiostatisticsUniversity of IowaIowa CityIowaUSA
| | - Jacob J. Oleson
- Department of BiostatisticsUniversity of IowaIowa CityIowaUSA
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2
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Ahmed N, Khan D, Oláh J, Popp J. A comparative study of the policy response to COVID-19 in the ASEAN region: A dynamic simulated ARDL approach. PLoS One 2023; 18:e0276973. [PMID: 36701393 PMCID: PMC9879420 DOI: 10.1371/journal.pone.0276973] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 10/18/2022] [Indexed: 01/27/2023] Open
Abstract
The COVID-19 epidemic is the most significant global health disaster of this century and the greatest challenge to humanity since World War II. One of the most important research issues is to determine the effectiveness of measures implemented worldwide to control the spread of the corona virus. A dynamic simulated Autoregressive-Distributed Lag (ARDL) approach was adopted to analyze the policy response to COVID-19 in the ASEAN region using data from February 1, 2020, to November 8, 2021. The results of unit root concluded that the dependent variable is integrated of order one while the independent variables are stationarized at the level or first difference, and the use of a dynamic simulated ARDL technique is appropriate for this paper. The outcomes of the dynamic simulated ARDL model explored that government economic support and debt/contract relief for poor families is substantially important in the fight against COVID-19. The study also explored that closing schools and workplaces, restrictions on gatherings, cancellation of public events, stay at home, closing public transport, restrictions on domestic and international travel are necessary to reduce the spread of COVID-19. Finally, this study explored that public awareness campaigns, testing policy and social distancing significantly decrease the spread of COVID-19. Policy implications such as economic support from the government to help poor families, closing schools and public gatherings during the pandemic, public awareness among the masses, and testing policies must be adopted to reduce the spread of COVID-19. Moreover, the reduction in mortality shows that immunization could be a possible new strategy to combat COVID-19, but the factors responsible for the acceptability of the vaccine must be addressed immediately through public health policies.
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Affiliation(s)
- Nihal Ahmed
- Department of Economics, Kohat University of Science and Technology, Kohat, Pakistan
| | - Dilawar Khan
- Department of Economics, Kohat University of Science and Technology, Kohat, Pakistan
- * E-mail:
| | - Judit Oláh
- Department of Management, Faculty of Applied Sciences, WSB University, Dabrowa Górnicza, Poland
| | - József Popp
- Hungarian National Bank–Research Center, John von Neumann University, Kecskemét, Hungary
- College of Business and Economics, University of Johannesburg, Johannesburg, South Africa
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3
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Castillo-León J, Trebbien R, Castillo JJ, Svendsen WE. Commercially available rapid diagnostic tests for the detection of high priority pathogens: status and challenges. Analyst 2021; 146:3750-3776. [PMID: 34060546 DOI: 10.1039/d0an02286a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ongoing COVID-19 pandemic has shown the importance of having analytical devices that allow a simple, fast, and robust detection of pathogens which cause epidemics and pandemics. The information these devices can collect is crucial for health authorities to make effective decisions to contain the disease's advance. The World Health Organization published a list of primary pathogens that have raised concern as potential causes of future pandemics. Unfortunately, there are no rapid diagnostic tests commercially available and approved by the regulatory bodies to detect most of the pathogens listed by the WHO. This report describes these pathogens, the available detection methods, and highlights areas where more attention is needed to produce rapid diagnostic tests for future pandemic surveillance.
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Affiliation(s)
- Jaime Castillo-León
- Bioengineering Department, Technical University of Denmark, Ørsteds Plads, DK-2800 Kgs. Lyngby, Denmark.
| | - Ramona Trebbien
- Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen, Denmark
| | - John J Castillo
- Escuela de Química, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Winnie E Svendsen
- Bioengineering Department, Technical University of Denmark, Ørsteds Plads, DK-2800 Kgs. Lyngby, Denmark.
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4
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Suaifan GARY, Alkhawaja BA, Mohammed AAM. RNA Coronaviruses' Outbreaks: Recent Progress on the SARS-CoV-2 Pandemic Diagnostic Tests, Vaccination and Therapeutics. Mini Rev Med Chem 2021; 22:617-628. [PMID: 33888048 DOI: 10.2174/1389557521666210422113915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 02/18/2021] [Accepted: 02/21/2021] [Indexed: 11/22/2022]
Abstract
Coronaviruses are RNA-infective viruses that could be considered principal players in universal high-profile outbreaks, namely the Severe Acute Respiratory Syndrome (SARS, 2002-2003), the Middle East Respiratory Syndrome (MERS, 2012) and the continuing novel coronavirus disease (COVID-19, 2019) pandemic. RNA coronaviruses infections raise public health concerns with infections' severity ranging from serious pandemics and highly contagious infections to common influenza episodes. With a wide consensus concerning the seminal role of early detection of the infectious agent on the clinical prognosis, recent technological endeavors have facilitated the rapid, sensitive and specific diagnosis of viral infections. Given that the burst of confirmed cases of the novel coronavirus disease 2019 (COVID-19) are climbing steeply, and we are amid this pandemic, this work will center at the respiratory RNA-viruses outbreaks, including the three coronaviruses-related pandemics, emphasizing on the approved diagnostic approaches, outlining therapeutic clinical trials as well as vaccine candidates. Based on the accumulated data and knowledge on the previous RNA-virus outbreaks, this review aspires to link the current intervention measures against SARS-CoV-2 infection with the previous interventions and to provide a roadmap for any possible future measures.
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Affiliation(s)
- Ghadeer A R Y Suaifan
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, Amman 11942, Jordan
| | - Bayan A Alkhawaja
- Faculty of Pharmacy and Medical Sciences, Department of pharmacy, The Department of Pharmaceutical Medicinal Chemistry and Pharmacognosy, The University of Petra, Amman 11196, Jordan
| | - Aya A M Mohammed
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, Amman 11942, Jordan
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5
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Paiva HM, Afonso RJM, Caldeira FMSDLA, Velasquez EDA. A computational tool for trend analysis and forecast of the COVID-19 pandemic. Appl Soft Comput 2021; 105:107289. [PMID: 33723487 PMCID: PMC7944846 DOI: 10.1016/j.asoc.2021.107289] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 02/22/2021] [Accepted: 03/05/2021] [Indexed: 12/24/2022]
Abstract
Purpose: This paper proposes a methodology and a computational tool to study the COVID-19 pandemic throughout the world and to perform a trend analysis to assess its local dynamics. Methods: Mathematical functions are employed to describe the number of cases and demises in each region and to predict their final numbers, as well as the dates of maximum daily occurrences and the local stabilization date. The model parameters are calibrated using a computational methodology for numerical optimization. Trend analyses are run, allowing to assess the effects of public policies. Easy to interpret metrics over the quality of the fitted curves are provided. Country-wise data from the European Centre for Disease Prevention and Control (ECDC) concerning the daily number of cases and demises around the world are used, as well as detailed data from Johns Hopkins University and from the Brasil.io project describing individually the occurrences in United States counties and in Brazilian states and cities, respectively. U. S. and Brazil were chosen for a more detailed analysis because they are the current focus of the pandemic. Results: Illustrative results for different countries, U. S. counties and Brazilian states and cities are presented and discussed. Conclusion: The main contributions of this work lie in (i) a straightforward model of the curves to represent the data, which allows automation of the process without requiring interventions from experts; (ii) an innovative approach for trend analysis, whose results provide important information to support authorities in their decision-making process; and (iii) the developed computational tool, which is freely available and allows the user to quickly update the COVID-19 analyses and forecasts for any country, United States county or Brazilian state or city present in the periodic reports from the authorities.
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Affiliation(s)
- Henrique Mohallem Paiva
- Institute of Science and Technology (ICT), Federal University of Sao Paulo (UNIFESP), Rua Talim, 330, São José dos Campos, SP, Brazil
| | - Rubens Junqueira Magalhães Afonso
- Institute of Flight System Dynamics, Technical University of Munich (TUM), München, Bayern, 85748, Germany.,Department of Electronic Engineering, Aeronautical Institute of Technology (ITA), Praça Marechal Eduardo Gomes, 50, São José dos Campos, SP, Brazil
| | | | - Ester de Andrade Velasquez
- Institute of Science and Technology (ICT), Federal University of Sao Paulo (UNIFESP), Rua Talim, 330, São José dos Campos, SP, Brazil
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Cui Y, Ni S, Shen S. A network-based model to explore the role of testing in the epidemiological control of the COVID-19 pandemic. BMC Infect Dis 2021; 21:58. [PMID: 33435892 PMCID: PMC7803001 DOI: 10.1186/s12879-020-05750-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/27/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Testing is one of the most effective means to manage the COVID-19 pandemic. However, there is an upper bound on daily testing volume because of limited healthcare staff and working hours, as well as different testing methods, such as random testing and contact-tracking testing. In this study, a network-based epidemic transmission model combined with a testing mechanism was proposed to study the role of testing in epidemic control. The aim of this study was to determine how testing affects the spread of epidemics and the daily testing volume needed to control infectious diseases. METHODS We simulated the epidemic spread process on complex networks and introduced testing preferences to describe different testing strategies. Different networks were generated to represent social contact between individuals. An extended susceptible-exposed-infected-recovered (SEIR) epidemic model was adopted to simulate the spread of epidemics in these networks. The model establishes a testing preference of between 0 and 1; the larger the testing preference, the higher the testing priority for people in close contact with confirmed cases. RESULTS The numerical simulations revealed that the higher the priority for testing individuals in close contact with confirmed cases, the smaller the infection scale. In addition, the infection peak decreased with an increase in daily testing volume and increased as the testing start time was delayed. We also discovered that when testing and other measures were adopted, the daily testing volume required to keep the infection scale below 5% was reduced by more than 40% even if other measures only reduced individuals' infection probability by 10%. The proposed model was validated using COVID-19 testing data. CONCLUSIONS Although testing could effectively inhibit the spread of infectious diseases and epidemics, our results indicated that it requires a huge daily testing volume. Thus, it is highly recommended that testing be adopted in combination with measures such as wearing masks and social distancing to better manage infectious diseases. Our research contributes to understanding the role of testing in epidemic control and provides useful suggestions for the government and individuals in responding to epidemics.
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Affiliation(s)
- Yapeng Cui
- Institute of Public Safety Research, Tsinghua University, Beijing, China
- Department of Engineering Physics, Tsinghua University, Beijing, China
- Beijing Key Laboratory of City Integrated Emergency Response Science, Beijing, China
| | - Shunjiang Ni
- Institute of Public Safety Research, Tsinghua University, Beijing, China.
- Department of Engineering Physics, Tsinghua University, Beijing, China.
- Beijing Key Laboratory of City Integrated Emergency Response Science, Beijing, China.
| | - Shifei Shen
- Institute of Public Safety Research, Tsinghua University, Beijing, China
- Department of Engineering Physics, Tsinghua University, Beijing, China
- Beijing Key Laboratory of City Integrated Emergency Response Science, Beijing, China
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7
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Wu Y, Xu W, Zhu Z, Xia X. Laboratory verification of an RT-PCR assay for SARS-CoV-2. J Clin Lab Anal 2020; 34:e23507. [PMID: 32754967 PMCID: PMC7435359 DOI: 10.1002/jcla.23507] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 06/25/2020] [Accepted: 07/07/2020] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Reverse transcription-polymerase chain reaction (RT-PCR) is an extremely common clinical method for detecting pathogens, particularly for emerging infectious diseases such as the new coronavirus disease (COVID-19). Currently, detection of the RNA from the novel coronavirus SARS-CoV-2 is the gold standard for establishing a COVID-19 diagnosis. This study evaluates the characteristic performance of the analytical system in a clinical laboratory. METHODS A commercial SARS-CoV-2 RNA RT-PCR Kit used in a clinical laboratory is assessed based on ISO 15189 verification requirements. A multiple real-time RT-PCR assay for the RdRP, N, and E genes in SARS-CoV-2 is verified. RESULTS The analytical system exhibits good analytical sensitivity (1000 copies/mL) and specificity (100%); however, the values of 86.7% and 100% for analytical accuracy deserved attention, compared with two other types of methods. Overall, the kit is potentially useful for SARS-CoV-2 diagnostic testing and meets the verification requirements. CONCLUSION Compliance with international standards, such as ISO 15189, is valuable for clinical laboratories and for improving laboratory medicine quality and safety. Normalization is essential for obtaining reliable results from the SARS-CoV-2 RNA RT-PCR assay. This study aims to develop an improved SARS-CoV-2 verification framework compared with traditional molecular diagnostic methods, given the urgency of implementing new assays in clinical laboratories.
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Affiliation(s)
- Yingping Wu
- Department of Clinical LaboratoryFourth Affiliated Hospital of Zhejiang University School of MedicineJinhuaChina
| | - Wei Xu
- Department of Clinical LaboratoryFourth Affiliated Hospital of Zhejiang University School of MedicineJinhuaChina
| | - Zhiqiang Zhu
- Department of Clinical LaboratoryFourth Affiliated Hospital of Zhejiang University School of MedicineJinhuaChina
| | - Xiaoping Xia
- Department of Clinical LaboratoryFourth Affiliated Hospital of Zhejiang University School of MedicineJinhuaChina
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8
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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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9
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Opatz T, Senn‐Bilfinger J, Richert C. Thoughts on What Chemists Can Contribute to Fighting SARS-CoV-2 - A Short Note on Hand Sanitizers, Drug Candidates and Outreach. Angew Chem Int Ed Engl 2020; 59:9236-9240. [PMID: 32329159 PMCID: PMC7264767 DOI: 10.1002/anie.202004721] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Indexed: 11/23/2022]
Abstract
The SARS-CoV-2 outbreak causing the respiratory disease COVID-19 has left many chemists in academia without an obvious option to contribute to fighting the pandemic. Some of our recent experiences indicate that there are ways to overcome this dilemma. A three-pronged approach is proposed.
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Affiliation(s)
- Till Opatz
- Department of ChemistryJohannes Gutenberg-University Mainz55128MainzGermany
| | | | - Clemens Richert
- Institut für Organische ChemieUniversität Stuttgart70569StuttgartGermany
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10
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Opatz T, Senn‐Bilfinger J, Richert C. Thoughts on What Chemists Can Contribute to Fighting SARS‐CoV‐2 – A Short Note on Hand Sanitizers, Drug Candidates and Outreach. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004721] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Till Opatz
- Department of ChemistryJohannes Gutenberg-University Mainz 55128 Mainz Germany
| | | | - Clemens Richert
- Institut für Organische ChemieUniversität Stuttgart 70569 Stuttgart Germany
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11
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Yan Y, Chang L, Wang L. Laboratory testing of SARS-CoV, MERS-CoV, and SARS-CoV-2 (2019-nCoV): Current status, challenges, and countermeasures. Rev Med Virol 2020; 30:e2106. [PMID: 32302058 PMCID: PMC7235496 DOI: 10.1002/rmv.2106] [Citation(s) in RCA: 188] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/20/2020] [Accepted: 03/20/2020] [Indexed: 01/08/2023]
Abstract
Emerging and reemerging infectious diseases are global public concerns. With the outbreak of unknown pneumonia in Wuhan, China in December 2019, a new coronavirus, SARS-CoV-2 has been attracting tremendous attention. Rapid and accurate laboratory testing of SARS-CoV-2 is essential for early discovery, early reporting, early quarantine, early treatment, and cutting off epidemic transmission. The genome structure, transmission, and pathogenesis of SARS-CoV-2 are basically similar to SARS-CoV and MERS-CoV, the other two beta-CoVs of medical importance. During the SARS-CoV and MERS-CoV epidemics, a variety of molecular and serological diagnostic assays were established and should be referred to for SARS-CoV-2. In this review, by summarizing the articles and guidelines about specimen collection, nucleic acid tests (NAT) and serological tests for SARS-CoV, MERS-CoV, and SARS-CoV-2, several suggestions are put forward to improve the laboratory testing of SARS-CoV-2. In summary, for NAT: collecting stool and blood samples at later periods of illness to improve the positive rate if lower respiratory tract specimens are unavailable; increasing template volume to raise the sensitivity of detection; putting samples in reagents containing guanidine salt to inactivate virus as well as protect RNA; setting proper positive, negative and inhibition controls to ensure high-quality results; simultaneously amplifying human RNase P gene to avoid false-negative results. For antibody test, diverse assays targeting different antigens, and collecting paired samples are needed.
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Affiliation(s)
- Ying Yan
- National Center for Clinical Laboratories, Beijing Hospital, National Center of GerontologyInstitute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Le Chang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of GerontologyInstitute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Lunan Wang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of GerontologyInstitute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
- Graduate School, Peking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
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12
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Noell K, Kolls JK. Further Defining the Human Virome using NGS: Identification of Redondoviridae. Cell Host Microbe 2019; 25:634-635. [PMID: 31071291 PMCID: PMC6849504 DOI: 10.1016/j.chom.2019.04.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this issue of Cell Host & Microbe, Abbas et al. (2019) uncover a previously undefined family of single-stranded DNA viruses, Redondoviridae, in human ororespiratory sites. The presence of Redondoviridae associates with critical illness such as respiratory failure and periodontitis, illustrating the power of metagenomics to define the human virome.
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Affiliation(s)
- Kristin Noell
- Departments of Pediatrics & Medicine, Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, LA, USA
| | - Jay K Kolls
- Departments of Pediatrics & Medicine, Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, LA, USA.
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13
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Vijay R, Hashem AM. Qualitative and Quantitative Determination of MERS-CoV S1-Specific Antibodies Using ELISA. Methods Mol Biol 2019; 2099:127-133. [PMID: 31883093 PMCID: PMC7122216 DOI: 10.1007/978-1-0716-0211-9_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Indirect enzyme-linked immunosorbent assay (ELISA) enables detection and quantification of antigen-specific antibodies in biological samples such as human or animal sera. Most current MERS-CoV serological assays such as neutralization, immunofluorescence, or protein microarray rely on handling of live MERS-CoV in high containment laboratories, highly trained personnel as well as the need for expensive and special equipment and reagents representing a hurdle for most laboratories especially when resources are limited. In this chapter, we describe a validated and optimized indirect ELISA protocol based on recombinant S1 subunit (amino acids 1-725) of MERS-CoV for qualitative and quantitative determination of MERS-CoV-binding antibodies.
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Affiliation(s)
- Rahul Vijay
- grid.214572.70000 0004 1936 8294Department of Microbiology and Immunology, University of Iowa, Iowa City, IA USA
| | - Anwar M Hashem
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia. .,Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.
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14
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Rampling T, Page M, Horby P. International Biological Reference Preparations for Epidemic Infectious Diseases. Emerg Infect Dis 2019; 25:205-211. [PMID: 30666925 PMCID: PMC6346470 DOI: 10.3201/eid2502.180798] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Recent years have seen unprecedented investment in research and development for countermeasures for high-threat pathogens, including specific and ambitious objectives for development of diagnostics, therapeutics, and vaccines. The inadequate availability of biological reference materials for these pathogens poses a genuine obstacle in pursuit of these objectives, and the lack of a comprehensive and equitable framework for developing reference materials is a weakness. We outline the need for internationally standardized biological materials for high-threat pathogens as a core element of global health security. We also outline the key components of a framework for addressing this deficiency.
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15
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Kelly-Cirino C, Mazzola LT, Chua A, Oxenford CJ, Van Kerkhove MD. An updated roadmap for MERS-CoV research and product development: focus on diagnostics. BMJ Glob Health 2019; 4:e001105. [PMID: 30815285 PMCID: PMC6361340 DOI: 10.1136/bmjgh-2018-001105] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/13/2018] [Accepted: 10/23/2018] [Indexed: 01/12/2023] Open
Abstract
Diagnostics play a central role in the early detection and control of outbreaks and can enable a more nuanced understanding of the disease kinetics and risk factors for the Middle East respiratory syndrome-coronavirus (MERS-CoV), one of the high-priority pathogens identified by the WHO. In this review we identified sources for molecular and serological diagnostic tests used in MERS-CoV detection, case management and outbreak investigations, as well as surveillance for humans and animals (camels), and summarised the performance of currently available tests, diagnostic needs, and associated challenges for diagnostic test development and implementation. A more detailed understanding of the kinetics of infection of MERS-CoV is needed in order to optimise the use of existing assays. Notably, MERS-CoV point-of-care tests are needed in order to optimise supportive care and to minimise transmission risk. However, for new test development, sourcing clinical material continues to be a major challenge to achieving assay validation. Harmonisation and standardisation of laboratory methods are essential for surveillance and for a rapid and effective international response to emerging diseases. Routine external quality assessment, along with well-characterised and up-to-date proficiency panels, would provide insight into MERS-CoV diagnostic performance worldwide. A defined set of Target Product Profiles for diagnostic technologies will be developed by WHO to address these gaps in MERS-CoV outbreak management.
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Affiliation(s)
| | | | - Arlene Chua
- Department of Information, Evidence and Research, WHO, Geneva, Switzerland.,Medecins Sans Frontières, Geneva, Switzerland
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16
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Hashem AM, Al-Amri SS, Al-Subhi TL, Siddiq LA, Hassan AM, Alawi MM, Alhabbab RY, Hindawi SI, Mohammed OB, Amor NS, Alagaili AN, Mirza AA, Azhar EI. Development and validation of different indirect ELISAs for MERS-CoV serological testing. J Immunol Methods 2019; 466:41-46. [PMID: 31883093 PMCID: PMC7094657 DOI: 10.1016/j.jim.2019.01.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 01/12/2019] [Accepted: 01/14/2019] [Indexed: 11/25/2022]
Abstract
Since 2012, MERS-CoV has caused up to 2220 cases and 790 deaths in 27 countries with Saudi Arabia being the most affected country with ~83.1% of the cases and ~38.8% local death rate. Current serological assays such as microneutralization (MN), plaque reduction neutralization, immunofluorescence, protein microarray or pseudoparticle neutralization assays rely on handling of live MERS-CoV in high containment laboratories or need for expensive and special equipment and reagents and highly trained personnel which represent a technical hurdle for most laboratories in resource-limited MERS-CoV endemic countries. Here, we developed, compared and evaluated three different indirect ELISAs based on MERS-CoV nucleocapsid protein (N), spike (S) ectodomain (amino acids 1–1297) and S1 subunit (amino acids 1–725) and compared them with MN assay. The developed ELISAs were evaluated using large number of confirmed seropositive (79 samples) and seronegative (274 samples) MERS-CoV human serum samples. Both rS1- and rS-ELISAs maintained high sensitivity and specificity (≥90%) across a wider range of OD values compared to rN-ELISA. Moreover, rS1- and rS-based ELISAs showed better agreement and correlation with MN assay in contrast to rN-ELISA. Collectively, our data demonstrate that rS1-ELISA and rS-ELISA are more reliable than rN-ELISA and represent a suitable choice for seroepidemiological testing and surveillance in MERS-CoV endemic regions.
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Affiliation(s)
- Anwar M Hashem
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Sawsan S Al-Amri
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Tagreed L Al-Subhi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Loai A Siddiq
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed M Hassan
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Maha M Alawi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia; Infection Control & Environmental Health Unit, Faculty of Medicine, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Rowa Y Alhabbab
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Salwa I Hindawi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Blood Transfusion Services, King Abdulaziz University Hospital, Jeddah, Saudi Arabia; Department of Hematology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Osama B Mohammed
- KSU Mammals Research Chair, Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Nabil S Amor
- KSU Mammals Research Chair, Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdulaziz N Alagaili
- KSU Mammals Research Chair, Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed A Mirza
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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17
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Al-Omari A, Rabaan AA, Salih S, Al-Tawfiq JA, Memish ZA. MERS coronavirus outbreak: Implications for emerging viral infections. Diagn Microbiol Infect Dis 2018; 93:265-285. [PMID: 30413355 PMCID: PMC7127703 DOI: 10.1016/j.diagmicrobio.2018.10.011] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 09/28/2018] [Accepted: 10/11/2018] [Indexed: 02/08/2023]
Abstract
In September 2012, a novel coronavirus was isolated from a patient who died in Saudi Arabia after presenting with acute respiratory distress and acute kidney injury. Analysis revealed the disease to be due to a novel virus which was named Middle East Respiratory Coronavirus (MERS-CoV). There have been several MERS-CoV hospital outbreaks in KSA, continuing to the present day, and the disease has a mortality rate in excess of 35%. Since 2012, the World Health Organization has been informed of 2220 laboratory-confirmed cases resulting in at least 790 deaths. Cases have since arisen in 27 countries, including an outbreak in the Republic of Korea in 2015 in which 36 people died, but more than 80% of cases have occurred in Saudi Arabia.. Human-to-human transmission of MERS-CoV, particularly in healthcare settings, initially caused a ‘media panic’, however human-to-human transmission appears to require close contact and thus far the virus has not achieved epidemic potential. Zoonotic transmission is of significant importance and evidence is growing implicating the dromedary camel as the major animal host in spread of disease to humans. MERS-CoV is now included on the WHO list of priority blueprint diseases for which there which is an urgent need for accelerated research and development as they have the potential to cause a public health emergency while there is an absence of efficacious drugs and/or vaccines. In this review we highlight epidemiological, clinical, and infection control aspects of MERS-CoV as informed by the Saudi experience. Attention is given to recommended treatments and progress towards vaccine development. 2220 laboratory-confirmed cases of MERS-CoV resulting in at least 790 deaths since 2012 MERS-CoV is on the WHO list of priority blueprint diseases Zoonotic and human-to-human transmission modes need further clarification. No specific therapy has yet been approved. There is a need for well-controlled clinical trials on potential direct therapies.
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Affiliation(s)
- Awad Al-Omari
- Critical Care and Infection Control Department, Dr. Sulaiman Al-Habib Medical Group, and Al-Faisal University, Riyadh, Saudi Arabia
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia.
| | - Samer Salih
- Internal Medicine Department, Dr.Sulaiman Al-Habib Medical Group, Riyadh, Saudi Arabia
| | - Jaffar A Al-Tawfiq
- Medical Department, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Ziad A Memish
- College of Medicine, Al-Faisal University, Riyadh, Saudi Arabia
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18
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Radwańska MJ, Jaskółowski M, Davydova E, Derewenda U, Miyake T, Engel DA, Kossiakoff AA, Derewenda ZS. The structure of the C-terminal domain of the nucleoprotein from the Bundibugyo strain of the Ebola virus in complex with a pan-specific synthetic Fab. Acta Crystallogr D Struct Biol 2018; 74:681-689. [PMID: 29968677 PMCID: PMC6038385 DOI: 10.1107/s2059798318007878] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/28/2018] [Indexed: 11/10/2022] Open
Abstract
The vast majority of platforms for the detection of viral or bacterial antigens rely on immunoassays, typically ELISA or sandwich ELISA, that are contingent on the availability of suitable monoclonal antibodies (mAbs). This is a major bottleneck, since the generation and production of mAbs is time-consuming and expensive. Synthetic antibody fragments (sFabs) generated by phage-display selection offer an alternative with many advantages over Fabs obtained from natural antibodies using hybridoma technology. Unlike mAbs, sFabs are generated using phage display, allowing selection for binding to specific strains or for pan-specificity, for identification of structural epitopes or unique protein conformations and even for complexes. Further, they can easily be produced in Escherichia coli in large quantities and engineered for purposes of detection technologies and other applications. Here, the use of phage-display selection to generate a pan-specific Fab (MJ20), based on a Herceptin Fab scaffold, with the ability to bind selectively and with high affinity to the C-terminal domains of the nucleoproteins (NPs) from all five known strains of the Ebola virus is reported. The high-resolution crystal structure of the complex of MJ20 with the antigen from the Bundibugyo strain of the Ebola virus reveals the basis for pan-specificity and illustrates how the phage-display technology can be used to manufacture suitable Fabs for use in diagnostic or therapeutic applications.
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Affiliation(s)
- Malwina J. Radwańska
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Mateusz Jaskółowski
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, Chicago, IL 60637, USA
| | - Elena Davydova
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, Chicago, IL 60637, USA
| | - Urszula Derewenda
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Tsuyoshi Miyake
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Daniel A. Engel
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Anthony A. Kossiakoff
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, Chicago, IL 60637, USA
| | - Zygmunt S. Derewenda
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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19
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Trivedi S, Miao C, Al‐Abdallat MM, Haddadin A, Alqasrawi S, Iblan I, Nsour MA, Alsanouri T, Ali SS, Rha B, Gerber SI, Payne DC, Tamin A, Thornburg NJ. Inclusion of MERS-spike protein ELISA in algorithm to determine serologic evidence of MERS-CoV infection. J Med Virol 2018; 90:367-371. [PMID: 28906003 PMCID: PMC6158782 DOI: 10.1002/jmv.24948] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 09/04/2017] [Indexed: 11/06/2022]
Abstract
The Centers for Disease Control and Prevention (CDC) algorithm for detecting presence of serum antibodies against Middle East Respiratory Syndrome coronavirus (MERS-CoV) in subjects with potential infections with the virus has included screening by indirect ELISA against recombinant nucleocapsid (N) protein and confirmation by immunofluorescent staining of infected monolayers and/or microneutralization titration. Other international groups include indirect ELISA assays using the spike (S) protein, as part of their serological determinations. In the current study, we describe development and validation of an indirect MERS-CoV S ELISA to be used as part of our serological determination for evidence of previous exposure to the virus.
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Affiliation(s)
| | - Congrong Miao
- Respiratory Viruses Branch, Div. of Viral DiseasesNatl. Ctr. for Immunization and Respiratory Diseases, CDCAtlantaGeorgia
| | | | | | | | - Ibrahim Iblan
- Jordan Field Epidemiology Training ProgramAmmanJordan
| | | | | | | | - Brian Rha
- Respiratory Viruses Branch, Div. of Viral DiseasesNatl. Ctr. for Immunization and Respiratory Diseases, CDCAtlantaGeorgia
| | - Susan I. Gerber
- Respiratory Viruses Branch, Div. of Viral DiseasesNatl. Ctr. for Immunization and Respiratory Diseases, CDCAtlantaGeorgia
| | - Daniel C. Payne
- Respiratory Viruses Branch, Div. of Viral DiseasesNatl. Ctr. for Immunization and Respiratory Diseases, CDCAtlantaGeorgia
| | - Azaibi Tamin
- Respiratory Viruses Branch, Div. of Viral DiseasesNatl. Ctr. for Immunization and Respiratory Diseases, CDCAtlantaGeorgia
| | - Natalie J. Thornburg
- Respiratory Viruses Branch, Div. of Viral DiseasesNatl. Ctr. for Immunization and Respiratory Diseases, CDCAtlantaGeorgia
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20
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An Opportunistic Pathogen Afforded Ample Opportunities: Middle East Respiratory Syndrome Coronavirus. Viruses 2017; 9:v9120369. [PMID: 29207494 PMCID: PMC5744144 DOI: 10.3390/v9120369] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 11/28/2017] [Accepted: 12/01/2017] [Indexed: 01/10/2023] Open
Abstract
The human coronaviruses (CoV) include HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1, some of which have been known for decades. The severe acute respiratory syndrome (SARS) CoV briefly emerged into the human population but was controlled. In 2012, another novel severely human pathogenic CoV—the Middle East Respiratory Syndrome (MERS)-CoV—was identified in the Kingdom of Saudi Arabia; 80% of over 2000 human cases have been recorded over five years. Targeted research remains key to developing control strategies for MERS-CoV, a cause of mild illness in its camel reservoir. A new therapeutic toolbox being developed in response to MERS is also teaching us more about how CoVs cause disease. Travel-related cases continue to challenge the world’s surveillance and response capabilities, and more data are needed to understand unexplained primary transmission. Signs of genetic change have been recorded, but it remains unclear whether there is any impact on clinical disease. How camels came to carry the virus remains academic to the control of MERS. To date, human-to-human transmission has been inefficient, but virus surveillance, characterisation, and reporting are key to responding to any future change. MERS-CoV is not currently a pandemic threat; it is spread mainly with the aid of human habit and error.
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21
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Xiong Y, Ford NR, Hecht KA, Roesijadi G, Squier TC. Hydrogel Tethering Enhances Interdomain Stabilization of Single-Chain Antibodies. Bioconjug Chem 2017; 28:2804-2814. [DOI: 10.1021/acs.bioconjchem.7b00512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yijia Xiong
- Department
of Basic Medical Sciences, Western University of Health Sciences, Lebanon, Oregon 97355, United States
| | - Nicole R. Ford
- Marine
Biotechnology, Pacific Northwest National Laboratory, Sequim, Washington 98382, United States
| | - Karen A. Hecht
- Marine
Biotechnology, Pacific Northwest National Laboratory, Sequim, Washington 98382, United States
| | - Guritno Roesijadi
- Marine
Biotechnology, Pacific Northwest National Laboratory, Sequim, Washington 98382, United States
- Department
of Microbiology, Oregon State University, Corvallis, Oregon 97331, United States
| | - Thomas C. Squier
- Department
of Basic Medical Sciences, Western University of Health Sciences, Lebanon, Oregon 97355, United States
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22
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Yin Y, Wunderink RG. MERS, SARS and other coronaviruses as causes of pneumonia. Respirology 2017; 23:130-137. [PMID: 29052924 PMCID: PMC7169239 DOI: 10.1111/resp.13196] [Citation(s) in RCA: 633] [Impact Index Per Article: 90.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 08/28/2017] [Accepted: 09/17/2017] [Indexed: 11/29/2022]
Abstract
Human coronaviruses (HCoVs) have been considered to be relatively harmless respiratory pathogens in the past. However, after the outbreak of the severe acute respiratory syndrome (SARS) and emergence of the Middle East respiratory syndrome (MERS), HCoVs have received worldwide attention as important pathogens in respiratory tract infection. This review focuses on the epidemiology, pathogenesis and clinical characteristics among SARS-coronaviruses (CoV), MERS-CoV and other HCoV infections.
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Affiliation(s)
- Yudong Yin
- Department of Infectious Diseases and Clinical Microbiology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Richard G Wunderink
- Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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