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Poydenot F, Lebreton A, Haiech J, Andreotti B. At the crossroads of epidemiology and biology: Bridging the gap between SARS-CoV-2 viral strain properties and epidemic wave characteristics. Biochimie 2023; 213:54-65. [PMID: 36931337 PMCID: PMC10017177 DOI: 10.1016/j.biochi.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 02/08/2023] [Accepted: 03/14/2023] [Indexed: 03/17/2023]
Abstract
The COVID-19 pandemic has given rise to numerous articles from different scientific fields (epidemiology, virology, immunology, airflow physics …) without any effort to link these different insights. In this review, we aim to establish relationships between epidemiological data and the characteristics of the virus strain responsible for the epidemic wave concerned. We have carried out this study on the Wuhan, Alpha, Delta and Omicron strains allowing us to illustrate the evolution of the relationships we have highlighted according to these different viral strains. We addressed the following questions. 1) How can the mean infectious dose (one quantum, by definition in epidemiology) be measured and expressed as an amount of viral RNA molecules (in genome units, GU) or as a number of replicative viral particles (in plaque-forming units, PFU)? 2) How many infectious quanta are exhaled by an infected person per unit of time? 3) How many infectious quanta are exhaled, on average, integrated over the whole contagious period? 4) How do these quantities relate to the epidemic reproduction rate R as measured in epidemiology, and to the viral load, as measured by molecular biological methods? 5) How has the infectious dose evolved with the different strains of SARS-CoV-2? We make use of state-of-the-art modelling, reviewed and explained in the appendix of the article (Supplemental Information, SI), to answer these questions using data from the literature in both epidemiology and virology. We have considered the modification of these relationships according to the vaccination status of the population.
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Affiliation(s)
- Florian Poydenot
- Laboratoire de Physique de l'Ecole Normale Supérieure (LPENS), CNRS UMR 8023, Ecole Normale Supérieure, Université PSL, Sorbonne Université, and Université de Paris, 75005, Paris, France
| | - Alice Lebreton
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France; INRAE, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Jacques Haiech
- CNRS UMR7242 BSC ESBS, 300 Bd Sébastien Brant, CS 10413, 67412, Illkirch cedex, France.
| | - Bruno Andreotti
- Laboratoire de Physique de l'Ecole Normale Supérieure (LPENS), CNRS UMR 8023, Ecole Normale Supérieure, Université PSL, Sorbonne Université, and Université de Paris, 75005, Paris, France
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2
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Haiech J. [Taking into account aerolization during the COVID-19 pandemic]. Med Sci (Paris) 2022; 38:693-697. [PMID: 36094240 DOI: 10.1051/medsci/2022100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Jacques Haiech
- Équipe pédagogique éthique, déontologie et intégrité scientifique (EPEDIS), UFR des sciences fondamentales et biomédicales, campus Saint-Germain- des-Prés, 45 rue des Saints Pères, 75006 Paris, France
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3
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Grudlewska-Buda K, Wiktorczyk-Kapischke N, Wałecka-Zacharska E, Kwiecińska-Piróg J, Buszko K, Leis K, Juszczuk K, Gospodarek-Komkowska E, Skowron K. SARS-CoV-2-Morphology, Transmission and Diagnosis during Pandemic, Review with Element of Meta-Analysis. J Clin Med 2021; 10:1962. [PMID: 34063654 PMCID: PMC8125301 DOI: 10.3390/jcm10091962] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 04/28/2021] [Indexed: 01/08/2023] Open
Abstract
The outbreak of Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2). Thus far, the virus has killed over 2,782,112 people and infected over 126,842,694 in the world (state 27 March 2021), resulting in a pandemic for humans. Based on the present data, SARS-CoV-2 transmission from animals to humans cannot be excluded. If mutations allowing breaking of the species barrier and enhancing transmissibility occurred, next changes in the SARS-CoV-2 genome, leading to easier spreading and greater pathogenicity, could happen. The environment and saliva might play an important role in virus transmission. Therefore, there is a need for strict regimes in terms of personal hygiene, including hand washing and surface disinfection. The presence of viral RNA is not an equivalent of active viral infection. The positive result of the RT-PCR method may represent either viral residues or infectious virus particles. RNA-based tests should not be used in patients after the decline of disease symptoms to confirm convalescence. It has been proposed to use the test based on viral, sub-genomic mRNA, or serological methods to find the immune response to infection. Vertical transmission of SARS-CoV-2 is still a little-known issue. In our review, we have prepared a meta-analysis of the transmission of SARS-CoV-2 from mother to child depending on the type of delivery. Our study indicated that the transmission of the virus from mother to child is rare, and the infection rate is not higher in the case of natural childbirth, breastfeeding, or contact with the mother. We hope that this review and meta-analysis will help to systemize knowledge about SARS-CoV-2 with an emphasis on diagnostic implications and transmission routes, in particular, mother-to-child transmission.
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Affiliation(s)
- Katarzyna Grudlewska-Buda
- Department of Microbiology, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University in Toruń, 87-094 Bydgoszcz, Poland; (K.G.-B.); (N.W.-K.); (J.K.-P.); (E.G.-K.)
| | - Natalia Wiktorczyk-Kapischke
- Department of Microbiology, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University in Toruń, 87-094 Bydgoszcz, Poland; (K.G.-B.); (N.W.-K.); (J.K.-P.); (E.G.-K.)
| | - Ewa Wałecka-Zacharska
- Department of Food Hygiene and Consumer Health, Wrocław University of Environmental and Life Sciences, 50-375 Wrocław, Poland;
| | - Joanna Kwiecińska-Piróg
- Department of Microbiology, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University in Toruń, 87-094 Bydgoszcz, Poland; (K.G.-B.); (N.W.-K.); (J.K.-P.); (E.G.-K.)
| | - Katarzyna Buszko
- Department of Theoretical Foundations of Biomedical Science and Medical Informatics, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University in Toruń, 87-067 Bydgoszcz, Poland;
| | - Kamil Leis
- Faculty of Medicile, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University in Toruń, 87-067 Bydgoszcz, Poland;
| | - Klaudia Juszczuk
- Clinic of General, Colorectal and Oncological Surgery, Dr. Jana Biziel University Hospital, No. 2 in Bydgoszcz, 75 Ujejskiego St., 85-168 Bydgoszcz, Poland;
| | - Eugenia Gospodarek-Komkowska
- Department of Microbiology, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University in Toruń, 87-094 Bydgoszcz, Poland; (K.G.-B.); (N.W.-K.); (J.K.-P.); (E.G.-K.)
| | - Krzysztof Skowron
- Department of Microbiology, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University in Toruń, 87-094 Bydgoszcz, Poland; (K.G.-B.); (N.W.-K.); (J.K.-P.); (E.G.-K.)
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4
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Hernández‐Huerta MT, Pérez‐Campos Mayoral L, Romero Díaz C, Martínez Cruz M, Mayoral‐Andrade G, Sánchez Navarro LM, Pina‐Canseco MDS, Cruz Parada E, Martínez Cruz R, Pérez‐Campos Mayoral E, Pérez Santiago AD, Vásquez Martínez G, Pérez‐Campos E, Matias‐Cervantes CA. Analysis of SARS-CoV-2 mutations in Mexico, Belize, and isolated regions of Guatemala and its implication in the diagnosis. J Med Virol 2021; 93:2099-2114. [PMID: 33049069 PMCID: PMC7675408 DOI: 10.1002/jmv.26591] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/15/2020] [Accepted: 10/07/2020] [Indexed: 12/24/2022]
Abstract
The genomic sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) worldwide are publicly available and are derived from studies due to the increase in the number of cases. The importance of study of mutations is related to the possible virulence and diagnosis of SARS-CoV-2. To identify circulating mutations present in SARS-CoV-2 genomic sequences in Mexico, Belize, and Guatemala to find out if the same strain spread to the south, and analyze the specificity of the primers used for diagnosis in these samples. Twenty three complete SARS-CoV-2 genomic sequences, available in the GISAID database from May 8 to September 11, 2020 were analyzed and aligned versus the genomic sequence reported in Wuhan, China (NC_045512.2), using Clustal Omega. Open reading frames were translated using the ExPASy Translate Tool and UCSF Chimera (v.1.12) for amino acid substitutions analysis. Finally, the sequences were aligned versus primers used in the diagnosis of COVID-19. One hundred and eighty seven distinct variants were identified, of which 102 are missense, 66 synonymous and 19 noncoding. P4715L and P5828L substitutions in replicase polyprotein were found, as well as D614G in spike protein and L84S in ORF8 in Mexico, Belize, and Guatemala. The primers design by CDC of United States showed a positive E value. The genomic sequences of SARS-CoV-2 in Mexico, Belize, and Guatemala present similar mutations related to a virulent strain of greater infectivity, which could mean a greater capacity for inclusion in the host genome and be related to an increased spread of the virus in these countries, furthermore, its diagnosis would be affected.
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Affiliation(s)
| | - Laura Pérez‐Campos Mayoral
- Centro de Investigación Facultad de Medicina UNAM‐UABJO, Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de OaxacaOaxacaMexico
| | - Carlos Romero Díaz
- Centro de Investigación Facultad de Medicina UNAM‐UABJO, Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de OaxacaOaxacaMexico
| | | | - Gabriel Mayoral‐Andrade
- Centro de Investigación Facultad de Medicina UNAM‐UABJO, Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de OaxacaOaxacaMexico
| | | | - María Del Socorro Pina‐Canseco
- Centro de Investigación Facultad de Medicina UNAM‐UABJO, Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de OaxacaOaxacaMexico
| | | | - Ruth Martínez Cruz
- Centro de Investigación Facultad de Medicina UNAM‐UABJO, Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de OaxacaOaxacaMexico
| | - Eduardo Pérez‐Campos Mayoral
- Centro de Investigación Facultad de Medicina UNAM‐UABJO, Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de OaxacaOaxacaMexico
| | | | | | - Eduardo Pérez‐Campos
- Centro de Investigación Facultad de Medicina UNAM‐UABJO, Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de OaxacaOaxacaMexico
- Tecnológico Nacional de México/IT de OaxacaOaxacaMexico
- Laboratorio de Patología Clínica “Dr. Eduardo Pérez Ortega”OaxacaMexico
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5
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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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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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7
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Adhikari U, Chabrelie A, Weir M, Boehnke K, McKenzie E, Ikner L, Wang M, Wang Q, Young K, Haas CN, Rose J, Mitchell J. A Case Study Evaluating the Risk of Infection from Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV) in a Hospital Setting Through Bioaerosols. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2019; 39:2608-2624. [PMID: 31524301 PMCID: PMC7169172 DOI: 10.1111/risa.13389] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 05/15/2019] [Accepted: 06/24/2019] [Indexed: 05/03/2023]
Abstract
Middle Eastern respiratory syndrome, an emerging viral infection with a global case fatality rate of 35.5%, caused major outbreaks first in 2012 and 2015, though new cases are continuously reported around the world. Transmission is believed to mainly occur in healthcare settings through aerosolized particles. This study uses Quantitative Microbial Risk Assessment to develop a generalizable model that can assist with interpreting reported outbreak data or predict risk of infection with or without the recommended strategies. The exposure scenario includes a single index patient emitting virus-containing aerosols into the air by coughing, leading to short- and long-range airborne exposures for other patients in the same room, nurses, healthcare workers, and family visitors. Aerosol transport modeling was coupled with Monte Carlo simulation to evaluate the risk of MERS illness for the exposed population. Results from a typical scenario show the daily mean risk of infection to be the highest for the nurses and healthcare workers (8.49 × 10-4 and 7.91 × 10-4 , respectively), and the lowest for family visitors and patients staying in the same room (3.12 × 10-4 and 1.29 × 10-4 , respectively). Sensitivity analysis indicates that more than 90% of the uncertainty in the risk characterization is due to the viral concentration in saliva. Assessment of risk interventions showed that respiratory masks were found to have a greater effect in reducing the risks for all the groups evaluated (>90% risk reduction), while increasing the air exchange was effective for the other patients in the same room only (up to 58% risk reduction).
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Affiliation(s)
- Umesh Adhikari
- Department of Biosystems and Agricultural EngineeringMichigan State UniversityEast LansingMIUSA
| | - Alexandre Chabrelie
- Department of Biosystems and Agricultural EngineeringMichigan State UniversityEast LansingMIUSA
| | - Mark Weir
- Division of Environmental Health Sciences, College of Public HealthThe Ohio State UniversityColumbusOHUSA
| | - Kevin Boehnke
- Department of Anesthesiology & the Chronic Pain and Fatigue Research CenterUniversity of MichiganAnn ArborMIUSA
| | - Erica McKenzie
- Department of Civil and Environmental EngineeringTemple UniversityPhiladelphiaPAUSA
| | - Luisa Ikner
- Department of Soil, Water and Environmental ScienceUniversity of ArizonaTucsonAZUSA
| | - Meng Wang
- Department of Civil & Environmental EngineeringUniversity of South FloridaTampaFLUSA
| | - Qing Wang
- Department of Animal and Food SciencesUniversity of DelawareNewarkDEUSA
| | - Kyana Young
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMIUSA
| | - Charles N. Haas
- Department of Civil, Architectural and Environmental EngineeringDrexel UniversityPhiladelphiaPAUSA
| | - Joan Rose
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMIUSA
| | - Jade Mitchell
- Department of Biosystems and Agricultural EngineeringMichigan State UniversityEast LansingMIUSA
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Suresh MR, Bhatnagar PK, Das D. Molecular targets for diagnostics and therapeutics of severe acute respiratory syndrome (SARS-CoV). JOURNAL OF PHARMACY AND PHARMACEUTICAL SCIENCES 2008; 11:1s-13s. [PMID: 19203466 DOI: 10.18433/j3j019] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
PURPOSE The large number of deaths in a short period of time due to the spread of severe acute respiratory syndrome (SARS) infection led to the unparalleled collaborative efforts world wide to determine and characterize the new coronavirus (SARS-CoV). The full genome sequence was determined within weeks of the first outbreak by the Canadian group with international collaboration. As per the World Health Organization (WHO), the continual lack of a rapid laboratory test to aid the early diagnosis of suspected cases of SARS makes this area a priority for future research. To prevent deaths in the future, early diagnosis and therapy of this infectious disease is of paramount importance. METHODS This review describes the specific molecular targets for diagnostics and therapeutics of viral infection. RESULTS The three major diagnostic methods available for SARS includes viral RNA detection by reverse transcription polymerase chain reaction (RT-PCR), virus induced antibodies by immunofluorescence assay (IFA) or by enzyme linked immunosorbant assay (ELISA) of nucleocapsid protein (NP). The spike glycoprotein of SARS-CoV is the major inducer of neutralizing antibodies. The receptor binding domain (RBD) in the S1 region of the spike glycoprotein contains multiple conformational epitopes that induces highly potent neutralizing antibodies. The genetically engineered attenuated form of the virus or viral vector vaccine encoding for the SARS-CoV spike glycoprotein has been shown to elicit protective immunity in vaccinated animals. CONCLUSION NP is the preferred target for routine detection of SARS-CoV infection by ELISA which is an economical method compared to other methods. The RBD of the spike glycoprotein is both a functional domain for cell receptor binding and also a major neutralizing determinant of SARS-CoV. The progress in evaluating a therapeutic or vaccine would depend on the avail ability of clinically relevant animal model.
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Affiliation(s)
- Mavanur R Suresh
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada.
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Yu M, Stevens V, Berry JD, Crameri G, McEachern J, Tu C, Shi Z, Liang G, Weingartl H, Cardosa J, Eaton BT, Wang LF. Determination and application of immunodominant regions of SARS coronavirus spike and nucleocapsid proteins recognized by sera from different animal species. J Immunol Methods 2007; 331:1-12. [PMID: 18191140 PMCID: PMC7094251 DOI: 10.1016/j.jim.2007.11.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Revised: 11/03/2007] [Accepted: 11/14/2007] [Indexed: 02/08/2023]
Abstract
Knowledge of immunodominant regions in major viral antigens is important for rational design of effective vaccines and diagnostic tests. Although there have been many reports of such work done for SARS–CoV, these were mainly focused on the immune responses of humans and mice. In this study, we aim to search for and compare immunodominant regions of the spike (S) and nucleocapsid (N) proteins which are recognized by sera from different animal species, including mouse, rat, rabbit, civet, pig and horse. Twelve overlapping recombinant protein fragments were produced in Escherichia coli, six each for the S and N proteins, which covered the entire coding region of the two proteins. Using a membrane-strip based Western blot approach, the reactivity of each antigen fragment against a panel of animal sera was determined. Immunodominant regions containing linear epitopes, which reacted with sera from all the species tested, were identified for both proteins. The S3 fragment (aa 402–622) and the N4 fragment (aa 220–336) were the most immunodominant among the six S and N fragments, respectively. Antibodies raised against the S3 fragment were able to block the binding of a panel of S-specific monoclonal antibodies (mAb) to SARS–CoV in ELISA, further demonstrating the immunodominance of this region. Based on these findings, one-step competition ELISAs were established which were able to detect SARS–CoV antibodies from human and at least seven different animal species. Considering that a large number of animal species are known to be susceptible to SARS–CoV, these assays will be a useful tool to trace the origin and transmission of SARS–CoV and to minimise the risk of animal-to-human transmission.
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Affiliation(s)
- Meng Yu
- CSIRO Livestock Industries, Australian Animal Health Laboratory, Geelong, Victoria, Australia
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10
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Abstract
Background: The detection of multiple viruses is important for pathogenic diagnosis and disease control. Microarray detection is a good method, but requires complex procedures for multiple virus detection. Methods: We developed a novel PCR assay, the microarray-in-a-tube system, which integrates multiple PCR processes and DNA microarrays for multiple virus detection. A 5 × 5 oligonucleotide microarray for detecting 4 respiratory tract viruses (severe acute respiratory syndrome–associated coronavirus, influenza A virus, influenza B virus, and enterovirus) with inner controls was arranged on the inner surface of a specially designed Eppendorf cap with a flat, optically transparent window. Results: We were able to perform all detection processes in the encapsulated system without opening the cap. The 4 viruses were successfully amplified by one-step reverse transcription–PCR in the encapsulated tube. After the PCR process, the microarray-in-a-tube was inverted, and the fluorescence-labeled PCR products were directly hybridized on the microarray. Hybridization signals were obtained with an ordinary fluorescent microscope. The sensitivity of the system for virus detection reached 102 copies/μL. With the help of inner controls, the system provided reliable results without false negatives and false positives. Conclusions: The microarray-in-a-tube system is a rapid, labor-saving tool for multiple virus detection with several advantages, such as convenience, prevention of cross-contamination of the PCR products, and potential for multiple-gene detection.
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Affiliation(s)
- Quanjun Liu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, People’s Republic of China
| | - Yunfei Bai
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, People’s Republic of China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, People’s Republic of China
| | - Shixin Zhou
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, People’s Republic of China
| | - Tian Wen
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, People’s Republic of China
| | - Zuhong Lu
- Address correspondence to this author at: State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, People’s Republic of China. Fax 086-25-83793779; e-mail
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11
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Yip SP, To SST, Leung PHM, Cheung TS, Cheng PKC, Lim WWL. Use of dual TaqMan probes to increase the sensitivity of 1-step quantitative reverse transcription-PCR: application to the detection of SARS coronavirus. Clin Chem 2006; 51:1885-8. [PMID: 16189379 PMCID: PMC7108148 DOI: 10.1373/clinchem.2005.054106] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Shea Ping Yip
- Department of Health Technology & Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China.
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12
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Mahony JB, Richardson S. Molecular diagnosis of severe acute respiratory syndrome: the state of the art. J Mol Diagn 2005; 7:551-9. [PMID: 16258152 PMCID: PMC1867551 DOI: 10.1016/s1525-1578(10)60587-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2005] [Indexed: 12/24/2022] Open
Abstract
Severe acute respiratory syndrome (SARS) first appeared in Guangdong Province, China, in November 2002. Although virus isolation and serology were useful early in the SARS outbreak for diagnosing new cases, these tests are not generally useful because virus culture requires a BSL-3 laboratory and seroconversion is often delayed until 2 to 3 weeks after infection. The first qualitative reverse transcriptase-polymerase chain reaction tests for SARS-coronavirus (CoV) were sensitive and capable of detecting 1 to 10 genome equivalents. These assays were quickly supplemented with quantitative real-time assays that helped elucidate the natural history of SARS, particularly the initial presence of low viral loads in the upper respiratory tract and high viral loads in the lower respiratory tract. The unique natural history of SARS-CoV infection dictates the testing of both respiratory and nonrespiratory specimens, the testing of multiple specimens from the same patient, and sending out positives to be confirmed by a reference laboratory. Commercially available reverse transcriptase-polymerase chain reaction tests for SARS have recently appeared; however, meaningful evaluations of these assays have not yet been performed and their true performance has not been determined. These and other issues related to diagnosis of SARS-CoV infection are discussed in this review.
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Affiliation(s)
- James B Mahony
- Regional Virology Laboratory, St. Joseph's Hospital, 50 Charlton Ave. East, Hamilton, ON L8N 4A6, Canada.
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Inoue M, Barkham T, Keong LK, Gee LS, Wanjin H. Performance of single-step gel-based reverse transcription-PCR (RT-PCR) assays equivalent to that of real-time RT-PCR assays for detection of the severe acute respiratory syndrome-associated coronavirus. J Clin Microbiol 2005; 43:4262-5. [PMID: 16081995 PMCID: PMC1233944 DOI: 10.1128/jcm.43.8.4262-4265.2005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Simple gel-based one-step reverse transcription-PCR (RT-PCR) assays, used to investigate patients during the 2003 severe acute respiratory syndrome (SARS) outbreak in Singapore, were found to be as sensitive as commercial and in-house real-time RT-PCR assays. The detection limit was approximately 1 genome equivalent (GE) per 5 microl PCR mixture. One PFU of SARS coronavirus was estimated to be 258 +/- 46 GE.
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Affiliation(s)
- Masafumi Inoue
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673.
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He Q, Du Q, Lau S, Manopo I, Lu L, Chan SW, Fenner BJ, Kwang J. Characterization of monoclonal antibody against SARS coronavirus nucleocapsid antigen and development of an antigen capture ELISA. J Virol Methods 2005; 127:46-53. [PMID: 15893565 PMCID: PMC7112885 DOI: 10.1016/j.jviromet.2005.03.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2004] [Revised: 03/04/2005] [Accepted: 03/08/2005] [Indexed: 12/14/2022]
Abstract
This report describes the production of several MAbs against N195 protein, a major immunodomain of SARS CoV nucleocapsid protein [He, Q., Chong, K.H., Chang, H.H., Leung, B., Ling, A.E., Wei, T., Chan, S.W., Ooi, E.E., Kwang, J., 2004. Development of a Western blot assay for detection of antibodies against coronavirus causing severe acute respiratory syndrome. Clin. Diagn. Lab. Immunol. 11 (2) 417–422.]. One representative IgG1 monoclonal antibody (MAb), S-A5D5, was selected and characterized. S-A5D5 reacted specifically react with both recombinant and native nucleocapsid protein of SARS CoV. The reactivity of S-A5D5 with purified N195 protein and utilization of the MAb as a detector antibody to develop an antigen capture ELISA was assessed. As little as 37.5 pg of purified N protein and 50 TCID50 of SARS CoV could be detected by the antigen capture ELISA. Specific binding of the MAb S-A5D5 to both purified N195 and SARS CoV nucleocapsid antigen was effectively inhibited by human SARS positive serum and guinea pig anti-N195 serum. The N protein in N195-spike recombinant baculovirus-infected Sf-9 cells could also be identified. N protein was detected in 18 IFA IgM-positive serum samples collected from SARS confirmed patients, but not in nine samples collected from SARS recovery patient. No false positive results were given when 60 samples from healthy individuals were tested, and no cross-reaction occurred when infectious bronchitis virus (IBV), chicken coronavirus, was tested. This monoclonal antibody-based antigen capture ELISA is thus a powerful tool for early diagnosis of SARS CoV infection.
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Affiliation(s)
| | | | | | | | | | | | | | - Jimmy Kwang
- Corresponding author. Tel.: +65 68727473; fax: +65 68727007.
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