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Lanyon HE, Todd BP, Downard KM. Distinguishing common SARS-CoV2 omicron and recombinant variants with high resolution mass spectrometry. Analyst 2023; 148:6306-6314. [PMID: 37936487 DOI: 10.1039/d3an01376f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
A selected ion monitoring (SIM) approach combined with high resolution mass spectrometry is employed to identify and distinguish common SARS-CoV2 omicron and recombinant variants in clinical specimens. Mutations within the receptor binding domain (RBD) within the surface spike protein of the virus result in a combination of peptide segments of unique sequence and mass that were monitored to detect BA.2.75 (including CH.1.1) and XBB (including 1.5) variants prevalent in the state's population in early 2023. SIM detection of pairs of peptides unique to each variant were confidently detected and differentiated in 57.3% of the specimens, with a further 10 or 17.5% (for a total of 74.8%) detected based on a single peptide biomarker. The BA.2.75 sub-variant was detected in 18.7%, while recombinant variants XBB and XBB.1.5 were detected in 13.3% and 25.3% of the specimens respectively, consistent with circulating levels in the population characterised by RT-PCR. Virus was detected in 75 SARS-CoV2 positive specimens by mass spectrometry down to the low or mid 104 copy level, with a single false positive and no false negative identified. This article is the first paper to characterise recombinant strains of the SARS-CoV2 virus by this, or any other, MS method.
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Affiliation(s)
- Henry E Lanyon
- Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, Australia.
| | - Benjamin P Todd
- Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, Australia.
| | - Kevin M Downard
- Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, Australia.
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2
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Ebrahimi T, Shamshiri AR, Alebouyeh M, Mohebbi SZ. Effectiveness of mouthwashes on reducing SARS-CoV-2 viral load in oral cavity: a systematic review and meta-analysis. BMC Oral Health 2023; 23:443. [PMID: 37400836 PMCID: PMC10318743 DOI: 10.1186/s12903-023-03126-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 06/10/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND The risk of SARS-COV-2 transmission is relatively high during dental procedures. A study was conducted to investigate the effects of mouthwashes on SARS-COV-2 viral load reduction in the oral cavity. METHODS A systematic search was performed in PubMed, EMBASE, Scopus, Web of Science, and Cochrane library for relevant studies up to 20 July, 2022. Randomized and non-randomized clinical trial and quasi-experimental studies evaluating patients with Covid-19 infection (patients) who used mouthwashes (intervention) compared to the same patients before using the mouthwash (comparison) for reducing the SARS-COV-2 load or increasing the cycle threshold (Ct) value (outcome) were searched according to PICO components. Three independent reviewers conducted literature screening and data extraction. The Modified Downs and Black checklist was used for quality assessment. A meta-analysis was performed with a random effects model in the Revman 5.4.1software using the mean difference (MD) of cycle threshold (Ct) values. RESULTS Of 1653 articles, 9 with a high methodological quality were included. A meta-analysis indicated that 1% Povidone-iodine (PVP-I) was an effective mouthwash for reducing the SARS-COV-2 viral load [MD 3.61 (95% confidence interval 1.03, 6.19)]. Cetylpyridinium chloride (CPC) [MD 0.61 (95% confidence interval -1.03, 2.25)] and Chlorhexidine gluconate (CHX) [MD -0.04 95% confidence interval (-1.20, 1.12)] were not effective against SARS-COV-2. CONCLUSION Using mouthwashes containing PVP-I may be recommended for reducing the SARS-COV-2 viral load in the oral cavity of patients before and during dental procedures, while the evidence is not sufficient for such effects for CPC and CHX-containing mouthwashes.
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Affiliation(s)
- Tayebe Ebrahimi
- Research Center for Caries Prevention, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
- Community Oral Health Department, School of Dentistry, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Reza Shamshiri
- Research Center for Caries Prevention, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
- Community Oral Health Department, School of Dentistry, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoud Alebouyeh
- Pediatric Infections Research Centre, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Simin Z Mohebbi
- Research Center for Caries Prevention, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran.
- Community Oral Health Department, School of Dentistry, Tehran University of Medical Sciences, Tehran, Iran.
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Lanyon HE, Hoyle JS, Downard KM. Resolving omicron sub-variants of SARS CoV-2 coronavirus with MALDI mass spectrometry. Analyst 2023; 148:966-972. [PMID: 36757162 DOI: 10.1039/d2an01843h] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Mass mapping using high resolution mass spectrometry has been applied to identify and rapidly distinguish the omicron sub-variants across the BA.1-BA.5 lineages. Lineage-specific protein mutations in the surface spike protein give rise to peptide biomarkers of unique mass that can be confidently and sensitively detected with high resolution mass spectrometry. Those that are most efficiently ionised and detected within the S1 subunit in recombinant forms facilitate their detection in clinical specimens containing other SARS-CoV2 viral proteins and contaminants. A study of five dozen omicron-positive specimens, using a selected ion monitoring approach, detected peptide biomarkers for strains of BA.1, BA.2.75 and BA.4 sub-variants in 23%, 42% and 28% of samples respectively, consistent with their reported levels in the local population. The virus was confidently assigned in over 93% of omicron positive specimens. The ease of detection of the BA.2.75 variant, in particular, is of vital importance given its rapid global spread in late 2022 due to several immune evasive mutations within the receptor-binding domain.
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Affiliation(s)
- Henry E Lanyon
- Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, Australia.
| | - Joshua S Hoyle
- Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, Australia.
| | - Kevin M Downard
- Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, Australia.
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Primo JDO, Correa JDS, Horsth DFL, Das A, Zając M, Umek P, Wattiez R, Anaissi FJ, Onderwater RCA, Bittencourt C. Antiviral Properties against SARS-CoV-2 of Nanostructured ZnO Obtained by Green Combustion Synthesis and Coated in Waterborne Acrylic Coatings. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:4345. [PMID: 36500967 PMCID: PMC9740257 DOI: 10.3390/nano12234345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/23/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
The COVID-19 pandemic has increased the need for developing disinfectant surfaces as well as reducing the spread of infections on contaminated surfaces and the contamination risk from the fomite route. The present work reports on the antiviral activity of coatings containing ZnO particles obtained by two simple synthesis routes using Aloe vera (ZnO-aloe) or cassava starch (ZnO-starch) as reaction fuel. After detailed characterization using XRD and NEXAFS, the obtained ZnO particles were dispersed in a proportion of 10% with two different waterborne acrylic coatings (binder and commercial white paint) and brushed on the surface of polycarbonates (PC). The cured ZnO/coatings were characterized by scanning electron microscopes (SEM) and energy-dispersive X-ray spectroscopy (EDS). Wettability tests were performed. The virucidal activity of the ZnO particles dispersed in the waterborne acrylic coating was compared to a reference control sample (PC plates). According to RT-PCR results, the ZnO-aloe/coating displays the highest outcome for antiviral activity against SARS-CoV-2 using the acrylic binder, inactivating >99% of the virus after 24 h of contact relative to reference control.
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Affiliation(s)
- Julia de O. Primo
- Departamento de Química, Universidade Estadual Do Centro-Oeste, Guarapuava 85-040-200, Brazil
- Chimie des Interactions Plasma-Surface (ChIPS), Research Institute for Materials Science and Engineering, University of Mons, 7000 Mons, Belgium
| | - Jamille de S. Correa
- Departamento de Química, Universidade Estadual Do Centro-Oeste, Guarapuava 85-040-200, Brazil
| | - Dienifer F. L. Horsth
- Departamento de Química, Universidade Estadual Do Centro-Oeste, Guarapuava 85-040-200, Brazil
- Chimie des Interactions Plasma-Surface (ChIPS), Research Institute for Materials Science and Engineering, University of Mons, 7000 Mons, Belgium
| | - Arkaprava Das
- Chimie des Interactions Plasma-Surface (ChIPS), Research Institute for Materials Science and Engineering, University of Mons, 7000 Mons, Belgium
| | - Marcin Zając
- National Synchrotron Radiation Centre Solaris, Jagiellonian University, 30-392 Kraków, Poland
| | - Polona Umek
- Solid State Physics Department, Jožef Stefan Institute, 1000 Ljubljana, Slovenia
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, University of Mons, 7000 Mons, Belgium
| | - Fauze J. Anaissi
- Departamento de Química, Universidade Estadual Do Centro-Oeste, Guarapuava 85-040-200, Brazil
| | | | - Carla Bittencourt
- Chimie des Interactions Plasma-Surface (ChIPS), Research Institute for Materials Science and Engineering, University of Mons, 7000 Mons, Belgium
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de Souza AS, de Freitas Amorim VM, Guardia GDA, dos Santos FF, Ulrich H, Galante PAF, de Souza RF, Guzzo CR. Severe Acute Respiratory Syndrome Coronavirus 2 Variants of Concern: A Perspective for Emerging More Transmissible and Vaccine-Resistant Strains. Viruses 2022; 14:827. [PMID: 35458557 PMCID: PMC9029021 DOI: 10.3390/v14040827] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/29/2022] [Accepted: 04/01/2022] [Indexed: 02/06/2023] Open
Abstract
Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) are constantly threatening global public health. With no end date, the pandemic persists with the emergence of novel variants that threaten the effectiveness of diagnostic tests and vaccines. Mutations in the Spike surface protein of the virus are regularly observed in the new variants, potentializing the emergence of novel viruses with different tropism from the current ones, which may change the severity and symptoms of the disease. Growing evidence has shown that mutations are being selected in favor of variants that are more capable of evading the action of neutralizing antibodies. In this context, the most important factor guiding the evolution of SARS-CoV-2 is its interaction with the host's immune system. Thus, as current vaccines cannot block the transmission of the virus, measures complementary to vaccination, such as the use of masks, hand hygiene, and keeping environments ventilated remain essential to delay the emergence of new variants. Importantly, in addition to the involvement of the immune system in the evolution of the virus, we highlight several chemical parameters that influence the molecular interactions between viruses and host cells during invasion and are also critical tools making novel variants more transmissible. In this review, we dissect the impacts of the Spike mutations on biological parameters such as (1) the increase in Spike binding affinity to hACE2; (2) bound time for the receptor to be cleaved by the proteases; (3) how mutations associate with the increase in RBD up-conformation state in the Spike ectodomain; (4) expansion of uncleaved Spike protein in the virion particles; (5) increment in Spike concentration per virion particles; and (6) evasion of the immune system. These factors play key roles in the fast spreading of SARS-CoV-2 variants of concern, including the Omicron.
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Affiliation(s)
- Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| | - Vitor Martins de Freitas Amorim
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| | - Gabriela D. A. Guardia
- Centro de Oncologia Molecular, Hospital Sírio Libanes, São Paulo 01308-060, Brazil; (G.D.A.G.); (F.F.d.S.); (P.A.F.G.)
| | - Filipe F. dos Santos
- Centro de Oncologia Molecular, Hospital Sírio Libanes, São Paulo 01308-060, Brazil; (G.D.A.G.); (F.F.d.S.); (P.A.F.G.)
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil;
| | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil;
| | - Pedro A. F. Galante
- Centro de Oncologia Molecular, Hospital Sírio Libanes, São Paulo 01308-060, Brazil; (G.D.A.G.); (F.F.d.S.); (P.A.F.G.)
| | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
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Duran N, Polat MF, Aktas DA, Alagoz MA, Ay E, Cimen F, Tek E, Anil B, Burmaoglu S, Algul O. New chalcone derivatives as effective against SARS-CoV-2 agent. Int J Clin Pract 2021; 75:e14846. [PMID: 34519118 PMCID: PMC8646589 DOI: 10.1111/ijcp.14846] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/28/2021] [Accepted: 09/10/2021] [Indexed: 01/18/2023] Open
Abstract
AIMS Flavonoids and related compounds, such as quercetin-based antiviral drug Gene-Eden-VIR/Novirin, inhibit the protease of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The alkylated chalcones isolated from Angelica keiskei inhibit SARS-CoV proteases. In this study, we aimed to compare the anti-SARS CoV-2 activities of both newly synthesized chalcone derivatives and these two drugs. METHODS Determination of the potent antiviral activity of newly synthesized chalcone derivatives against SARS-CoV-2 by calculating the RT-PCR cycling threshold (Ct ) values. RESULTS Antiviral activities of the compounds varied because of being dose dependent. Compound 6, 7, 9, and 16 were highly effective against SARS-CoV-2 at the concentration of 1.60 µg/mL. Structure-based virtual screening was carried out against the most important druggable SARS-CoV-2 targets, viral RNA-dependent RNA polymerase, to identify putative inhibitors that could facilitate the development of potential anti-coronavirus disease-2019 drug candidates. CONCLUSIONS Computational analyses identified eight compounds inhibiting each target, with binding affinity scores ranging from -4.370 to -2.748 kcal/mol along with their toxicological, ADME, and drug-like properties.
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Affiliation(s)
- Nizami Duran
- Department of Medical MicrobiologyMedical FacultyMustafa Kemal UniversityAntakyaTurkey
| | - M. Fatih Polat
- Department of Pharmaceutical Basic SciencesFaculty of PharmacyErzincan Binali Yildirim UniversityErzincanTurkey
| | - Derya Anil Aktas
- Department of Chemistry and Chemical Process TechnologiesErzurum Vocational High SchoolAtatürk UniversityErzurumTurkey
| | - M. Abdullah Alagoz
- Department of Pharmaceutical ChemistryFaculty of PharmacyInonu UniversityMalatyaTurkey
| | - Emrah Ay
- Department of Medical MicrobiologyMedical FacultyMustafa Kemal UniversityAntakyaTurkey
| | - Funda Cimen
- Department of Medical MicrobiologyMedical FacultyMustafa Kemal UniversityAntakyaTurkey
| | - Erhan Tek
- Department of Medical MicrobiologyMedical FacultyMustafa Kemal UniversityAntakyaTurkey
| | - Baris Anil
- Department of ChemistryFaculty of ScienceAtatürk UniversityErzurumTurkey
| | - Serdar Burmaoglu
- Department of ChemistryFaculty of ScienceAtatürk UniversityErzurumTurkey
| | - Oztekin Algul
- Department of Pharmaceutical ChemistryFaculty of PharmacyMersin UniversityMersinTurkey
- Department of Pharmaceutical ChemistryFaculty of PharmacyErzincan Binali Yildirim UniversityErzincanTurkey
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7
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COVID-19 Infection in Pregnancy: PCR Cycle Thresholds, Placental Pathology, and Perinatal Outcomes. Viruses 2021; 13:v13091884. [PMID: 34578466 PMCID: PMC8473449 DOI: 10.3390/v13091884] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/03/2021] [Accepted: 09/14/2021] [Indexed: 12/13/2022] Open
Abstract
(1) This study aimed to evaluate characteristics, perinatal outcomes, and placental pathology of pregnant women with or without SARS-CoV-2 infection in the context of maternal PCR cycle threshold (CT) values. (2) This was a retrospective case-control study in a third-level health center in Mexico City with universal screening by RT-qPCR. The association of COVID-19 manifestations, preeclampsia, and preterm birth with maternal variables and CT values were assessed by logistic regression models and decision trees. (3) Accordingly, 828 and 298 women had a negative and positive test, respectively. Of those positive, only 2.6% of them presented mild to moderate symptoms. Clinical characteristics between both groups of women were similar. No associations between CT values were found for maternal features, such as pre-gestational BMI, age, and symptomatology. A significantly higher percentage of placental fibrinoid was seen with women with low CTs (<25; p < 0.01). Regarding perinatal outcomes, preeclampsia was found to be significantly associated with symptomatology but not with risk factors or CT values (p < 0.01, aOR = 14.72). Moreover, 88.9% of women diagnosed with COVID-19 at <35 gestational weeks and symptomatic developed preeclampsia. (4) The data support strong guidance for pregnancies with SARS-CoV-2 infection, in particular preeclampsia and placental pathology, which need further investigation.
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Abstract
A pressing concern in the SARS-CoV-2 epidemic and other viral outbreaks, is the extent to which the containment measures are halting the viral spread. A straightforward way to assess this is to tally the active cases and the recovered ones throughout the epidemic. Here, we show how epidemic control can be assessed with molecular information during a well characterized epidemic in Iceland. We demonstrate how the viral concentration decreased in those newly diagnosed as the epidemic transitioned from exponential growth phase to containment phase. The viral concentration in the cases identified in population screening decreased faster than in those symptomatic and considered at high risk and that were targeted by the healthcare system. The viral concentration persists in recovering individuals as we found that half of the cases are still positive after two weeks. We demonstrate that accumulation of mutations in SARS-CoV-2 genome can be exploited to track the rate of new viral generations throughout the different phases of the epidemic, where the accumulation of mutations decreases as the transmission rate decreases in the containment phase. Overall, the molecular signatures of SARS-CoV-2 infections contain valuable epidemiological information that can be used to assess the effectiveness of containment measures. The concentration of SARS-CoV-2 changes during an individual’s infection, and mutations accumulate as viruses are transmitted between people. Here, the authors use data from Iceland to demonstrate how this information can be exploited at the population-level to determine the phase of the epidemic.
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Asante IA, Adusei-Poku M, Bonney HK, Bonney EY, Odoom JK, Obodai E, Aboagye J, Kotey EN, Nyarko S, Boatemaa L, Magnusen V, Lamptey H, Kyei GB, Ampofo WK. Molecular diagnosis for the novel coronavirus SARS-CoV-2: lessons learnt from the Ghana experience. Ghana Med J 2021; 54:77-85. [PMID: 33976445 PMCID: PMC8087367 DOI: 10.4314/gmj.v54i4s.12] [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] [Indexed: 12/24/2022] Open
Abstract
Background A novel coronavirus, SARS-CoV-2 is currently causing a worldwide pandemic. The first cases of SARS-CoV-2 infection were recorded in Ghana on March 12, 2020. Since then, the country has been combatting countrywide community spread. This report describes how the Virology Department, Noguchi Memorial Institute for Medical Research (NMIMR) is supporting the Ghana Health Service (GHS) to diagnose infections with this virus in Ghana. Methods The National Influenza Centre (NIC) in the Virology Department of the NMIMR, adopted real-time Polymerase Chain Reaction (rRT-PCR) assays for the diagnosis of the SARS-CoV-2 in January 2020. Samples from suspected cases and contact tracing across Ghana were received and processed for SARS-CoV-2. Samples were ‘pooled’ to enable simultaneous batch testing of samples without reduced sensitivity. Outcomes From February 3 to August 21, the NMIMR processed 283 946 (10%) samples. Highest number of cases were reported in June when the GHS embarked on targeted contact tracing which led to an increase in number of samples processed daily, peaking at over 7,000 samples daily. There were several issues to overcome including rapid consumption of reagents and consumables. Testing however continued successfully due to revised procedures, additional equipment and improved pipeline of laboratory supplies. Test results are now provided within 24 to 48 hours of sample submission enabling more effective response and containment. Conclusion Following the identification of the first cases of SARS-CoV-2infection by the NMIMR, the Institute has trained other centres and supported the ramping up of molecular testing capacity in Ghana. This provides a blueprint to enable Ghana to mitigate further epidemics and pandemics. Funding The laboratory work was supported with materials from the Ghana Health Service Ministry of Health, the US Naval Medical Research Unit #3, the World Health Organization, the Jack Ma Foundation and the University of Ghana Noguchi Memorial Institute for Medical Research. Other research projects hosted by the Noguchi Memorial Institute for Medical Research contributed reagents and laboratory consumables. The funders had no role in the preparation of this manuscript.
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Affiliation(s)
- Ivy A Asante
- Department of Virology, University of Ghana, Noguchi Memorial Institute for Medical Research, Legon, Ghana
| | - Mildred Adusei-Poku
- Department of Virology, University of Ghana, Noguchi Memorial Institute for Medical Research, Legon, Ghana.,Department of Medical Microbiology, University of Ghana Medical School, Accra, Ghana
| | - Humphrey K Bonney
- Department of Virology, University of Ghana, Noguchi Memorial Institute for Medical Research, Legon, Ghana
| | - Evelyn Y Bonney
- Department of Virology, University of Ghana, Noguchi Memorial Institute for Medical Research, Legon, Ghana
| | - John K Odoom
- Department of Virology, University of Ghana, Noguchi Memorial Institute for Medical Research, Legon, Ghana
| | - Evangeline Obodai
- Department of Virology, University of Ghana, Noguchi Memorial Institute for Medical Research, Legon, Ghana
| | - James Aboagye
- Department of Virology, University of Ghana, Noguchi Memorial Institute for Medical Research, Legon, Ghana
| | - Erasmus N Kotey
- Department of Virology, University of Ghana, Noguchi Memorial Institute for Medical Research, Legon, Ghana
| | - Stephen Nyarko
- Department of Virology, University of Ghana, Noguchi Memorial Institute for Medical Research, Legon, Ghana
| | - Linda Boatemaa
- Department of Virology, University of Ghana, Noguchi Memorial Institute for Medical Research, Legon, Ghana
| | - Vanessa Magnusen
- Department of Virology, University of Ghana, Noguchi Memorial Institute for Medical Research, Legon, Ghana
| | - Helena Lamptey
- Department of Immunology, University of Ghana, Noguchi Memorial Institute for Medical Research, Legon, Ghana
| | - George B Kyei
- Department of Virology, University of Ghana, Noguchi Memorial Institute for Medical Research, Legon, Ghana
| | - William K Ampofo
- Department of Virology, University of Ghana, Noguchi Memorial Institute for Medical Research, Legon, Ghana
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Chen L, Zhang G, Liu L, Li Z. Emerging biosensing technologies for improved diagnostics of COVID-19 and future pandemics. Talanta 2021; 225:121986. [PMID: 33592734 PMCID: PMC7733602 DOI: 10.1016/j.talanta.2020.121986] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/25/2020] [Accepted: 12/05/2020] [Indexed: 02/07/2023]
Abstract
Diagnostic tools play significant roles in the fight against COVID-19 and other pandemics. Existing tests, such as RT-qPCR, have limitations including long assay time, low throughput, inadequate sensitivity, and suboptimal portability. Emerging biosensing technologies hold the promise to develop tests that are rapid, highly sensitive, and suitable for point-of-care testing, which could significantly facilitate the testing of COVID-19. Despite that, practical applications of such biosensors in pandemics have yet to be achieved. In this review, we consolidate the newly developed diagnostic tools for COVID-19 using emerging biosensing technologies and discuss their application promise. In particular, we present nucleic acid tests and antibody tests of COVID-19 based on both conventional and emerging biosensing methods. We then provide perspectives on the existing challenges and potential solutions.
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Affiliation(s)
- Linzhe Chen
- Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen, 518060, China,Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Guoliang Zhang
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Shenzhen, 518112, China
| | - Longqi Liu
- BGI-Shenzhen, Shenzhen, 518083, China,Corresponding author
| | - Zida Li
- Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen, 518060, China,Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen, 518060, China,Corresponding author. Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen, 518060, China
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11
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Dollman NL, Griffin JH, Downard KM. Detection, Mapping, and Proteotyping of SARS-CoV-2 Coronavirus with High Resolution Mass Spectrometry. ACS Infect Dis 2020; 6:3269-3276. [PMID: 33205948 PMCID: PMC7688050 DOI: 10.1021/acsinfecdis.0c00664] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Indexed: 12/17/2022]
Abstract
A high resolution mass spectrometry approach has been applied for the first time to detect and characterize SARS-CoV-2 coronavirus in cell cultured and nasopharyngeal swab specimens. Peptide ions for three of the most abundant structural viral proteins (membrane, nucleocapid, and spike) are detected and assigned directly, by virtue of the high resolution and mass accuracy within the mass maps of whole virus digests, without the need for tandem mass spectrometry (MS/MS). MALDI-MS based approaches offer high sample throughput and speed, compared with those of LC-MS strategies, and detection limits at some 105 copies, or orders of magnitude less with selected ion monitoring, that compete favorably with conventional reverse transcription polymerase chain reaction (RT-PCR) strategies. The detection of signature peptides unique to SARS-CoV-2 coronavirus over those from the influenza virus allows for its unambiguous detection.
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Affiliation(s)
- Nicholas L. Dollman
- Infectious Disease Responses Laboratory,
Prince of Wales Clinical Sciences Research, Sydney, NSW 2031,
Australia
| | - Justin H. Griffin
- Infectious Disease Responses Laboratory,
Prince of Wales Clinical Sciences Research, Sydney, NSW 2031,
Australia
| | - Kevin M. Downard
- Infectious Disease Responses Laboratory,
Prince of Wales Clinical Sciences Research, Sydney, NSW 2031,
Australia
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12
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Malagón-Rojas J, Parra E, Mercado M. Letter to the editor on "Asymptomatic infection by SARS 2 coronavirus: Invisible but invincible" by Nikolai et al. 2020. Int J Infect Dis 2020; 101:391-392. [PMID: 33075536 PMCID: PMC7566696 DOI: 10.1016/j.ijid.2020.10.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/10/2020] [Indexed: 01/04/2023] Open
Affiliation(s)
- Jeadran Malagón-Rojas
- Doctorado en Salud Pública, Faculty of Medicine, El Bosque University, Colombia; Instituto Nacional de Salud, Colombia.
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Manabe T, Akatsu H, Kotani K, Kudo K. Trends in clinical features of novel coronavirus disease (COVID-19): A systematic review and meta-analysis of studies published from December 2019 to February 2020. Respir Investig 2020; 58:409-418. [PMID: 32653383 PMCID: PMC7321050 DOI: 10.1016/j.resinv.2020.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/26/2020] [Accepted: 05/30/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND Since novel coronavirus disease (COVID-19) emerged, various clinical features of COVID-19 have been reported. METHODS We conducted a systematic review of published studies reporting the clinical features of COVID-19. Two investigators independently searched PubMed (December 2019-February 2020) for eligible articles. A meta-analysis was performed to measure the frequencies of clinical outcomes and symptoms of COVID-19. A stratified analysis was conducted according to the timeline of outbreak and exposure histories: Group I, most patients were exposed to the Hunan seafood wholesale market and lived in Wuhan, Hubei province; Group II, patients lived in Hubei province but were not directly exposed to the market; and Group III, patients lived outside Hubei. RESULTS Thirteen studies, all from China, were eligible. The estimated mortality rate among all studies was 2.12%, but that in Group I was 8.66%. The incidence of acute respiratory distress syndrome in Group I was 20.00%. Both fever and cough were major symptoms, and their frequencies were higher in Group I than in Groups II and III, while the frequency of diarrhea in Group I was lower than that in Group III. The estimated frequency of dyspnea in Group I was 37.18%, while those in Groups II and III were 16.95% and 7.03%, respectively. CONCLUSIONS The trends in the clinical features of COVID-19 changed from December 2019 to February 2020. During this observation period, as the infection continued to spread, the clinical conditions for majority of patients became less severe with the changes in the route of transmission.
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Affiliation(s)
- Toshie Manabe
- Jichi Medical University, Center of Community Medicine, Tochigi, Japan.
| | - Hiroyasu Akatsu
- Nagoya City University Graduate School of Medicine, Department of Community-based Medical Education, Aichi, Japan
| | - Kazuhiko Kotani
- Jichi Medical University, Center of Community Medicine, Tochigi, Japan
| | - Koichiro Kudo
- Yurin Hospital, Tokyo, Japan; Waseda University, Regional and Inter-Regional Studies, Tokyo, Japan
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14
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Rapid and efficient detection methods of pathogenic swine enteric coronaviruses. Appl Microbiol Biotechnol 2020; 104:6091-6100. [PMID: 32430534 PMCID: PMC7235545 DOI: 10.1007/s00253-020-10645-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/18/2020] [Accepted: 04/26/2020] [Indexed: 02/06/2023]
Abstract
Abstract Porcine enteric coronaviruses (CoVs) cause highly contagious enteric diarrhea in suckling piglets. These COV infections are characterized by clinical signs of vomiting, watery diarrhea, dehydration, and high morbidity and mortality, resulting in significant economic losses and tremendous threats to the pig farming industry worldwide. Because the clinical manifestations of pigs infected by different CoVs are similar, it is difficult to differentiate between the specific pathogens. Effective high-throughput detection methods are powerful tools used in the prevention and control of diseases. The immune system of piglets is not well developed, so serological methods to detect antibodies against these viruses are not suitable for rapid and early detection. This paper reviews various PCR-based methods used for the rapid and efficient detection of these pathogenic CoVs in swine intestines. Key points Swine enteric coronaviruses (CoVs) emerged and reemerged in past years. Enteric CoVs infect pigs at all ages with high mortality rate in suckling pigs. Rapid and efficient detection methods are needed and critical for diagnosis.
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15
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Iwata-Yoshikawa N, Uda A, Suzuki T, Tsunetsugu-Yokota Y, Sato Y, Morikawa S, Tashiro M, Sata T, Hasegawa H, Nagata N. Effects of Toll-like receptor stimulation on eosinophilic infiltration in lungs of BALB/c mice immunized with UV-inactivated severe acute respiratory syndrome-related coronavirus vaccine. J Virol 2014; 88:8597-614. [PMID: 24850731 PMCID: PMC4135953 DOI: 10.1128/jvi.00983-14] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 05/13/2014] [Indexed: 12/12/2022] Open
Abstract
UNLABELLED Severe acute respiratory syndrome-related coronavirus (SARS-CoV) is an emerging pathogen that causes severe respiratory illness. Whole UV-inactivated SARS-CoV (UV-V), bearing multiple epitopes and proteins, is a candidate vaccine against this virus. However, whole inactivated SARS vaccine that includes nucleocapsid protein is reported to induce eosinophilic infiltration in mouse lungs after challenge with live SARS-CoV. In this study, an ability of Toll-like receptor (TLR) agonists to reduce the side effects of UV-V vaccination in a 6-month-old adult BALB/c mouse model was investigated, using the mouse-passaged Frankfurt 1 isolate of SARS-CoV. Immunization of adult mice with UV-V, with or without alum, resulted in partial protection from lethal doses of SARS-CoV challenge, but extensive eosinophil infiltration in the lungs was observed. In contrast, TLR agonists added to UV-V vaccine, including lipopolysaccharide, poly(U), and poly(I·C) (UV-V+TLR), strikingly reduced excess eosinophilic infiltration in the lungs and induced lower levels of interleukin-4 and -13 and eotaxin in the lungs than UV-V-immunization alone. Additionally, microarray analysis showed that genes associated with chemotaxis, eosinophil migration, eosinophilia, and cell movement and the polarization of Th2 cells were upregulated in UV-V-immunized but not in UV-V+TLR-immunized mice. In particular, CD11b(+) cells in the lungs of UV-V-immunized mice showed the upregulation of genes associated with the induction of eosinophils after challenge. These findings suggest that vaccine-induced eosinophil immunopathology in the lungs upon SARS-CoV infection could be avoided by the TLR agonist adjuvants. IMPORTANCE Inactivated whole severe acute respiratory syndrome-related coronavirus (SARS-CoV) vaccines induce neutralizing antibodies in mouse models; however, they also cause increased eosinophilic immunopathology in the lungs upon SARS-CoV challenge. In this study, the ability of adjuvant Toll-like receptor (TLR) agonists to reduce the side effects of UV-inactivated SARS-CoV vaccination in a BALB/c mouse model was tested, using the mouse-passaged Frankfurt 1 isolate of SARS-CoV. We found that TLR stimulation reduced the high level of eosinophilic infiltration that occurred in the lungs of mice immunized with UV-inactivated SARS-CoV. Microarray analysis revealed that genes associated with chemotaxis, eosinophil migration, eosinophilia, and cell movement and the polarization of Th2 cells were upregulated in UV-inactivated SARS-CoV-immunized mice. This study may be helpful for elucidating the pathogenesis underlying eosinophilic infiltration resulting from immunization with inactivated vaccine.
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Affiliation(s)
| | - Akihiko Uda
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Yuko Sato
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shigeru Morikawa
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masato Tashiro
- Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsutaro Sata
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hideki Hasegawa
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Noriyo Nagata
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
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Lee GI, Yoen JP, Kang JS, Hwang SY, Hong YM, Yang JH, Yoon HK. A comparison of oligonucleotide-based microarray and real-time PCR for the detection of sexually transmitted infections. BIOCHIP JOURNAL 2013; 7:68-74. [PMID: 32226590 PMCID: PMC7096812 DOI: 10.1007/s13206-013-7111-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 11/15/2012] [Indexed: 11/25/2022]
Abstract
Many diagnostic methods for sexually transmitted infections (STIs) have been developed. Because various infection agents are associated with STIs, and because infected persons sometimes show no symptoms, the diagnosis of STIs using nucleic acid amplification tests(NAATs) has required not only simultaneous multi-targeting, but also sensitive detection. Here, we compare microarray and real-time PCR for the detection of three common STIs agents, Ureaplasma urealyticum, Mycoplasma genitalium, and Chlamydia trachomatis, using human urine samples. The detection results showed that microarray and real-time PCR technology are both effective tools for the detection of STI agents. In conclusion, real-time PCR detection offers more sensitivity and specificity than microarray, because of the quantitative method employed. But, microarray offers better performance, in terms of high-throughput and simultaneous multi-targeting.
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Affiliation(s)
- Gyeong-In Lee
- Department of Laboratory Medicine, National Police Hospital, Seoul, Korea
| | - Jong Pil Yoen
- GenoCheck Co., LTD., Sa-Dong, Sangnok-Gu, Ansan, Gyeonggi-Do, Korea
| | - Jin Seok Kang
- Department of Biochemistry, Hanyang University, Sa-Dong, Sangnok-Gu, Ansan, Gyeonggi-Do, Korea
| | - Seung Yong Hwang
- GenoCheck Co., LTD., Sa-Dong, Sangnok-Gu, Ansan, Gyeonggi-Do, Korea
- Department of Biochemistry, Hanyang University, Sa-Dong, Sangnok-Gu, Ansan, Gyeonggi-Do, Korea
| | - Yu-Min Hong
- Molecular Diagnostic Research Institute, Bioneer Corporation, Daejeon, Korea
| | - Jeong-Ha Yang
- Molecular Diagnostic Research Institute, Bioneer Corporation, Daejeon, Korea
| | - Hyun Kyu Yoon
- Molecular Diagnostic Research Institute, Bioneer Corporation, Daejeon, Korea
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17
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Kim SH, Kim IJ, Pyo HM, Tark DS, Song JY, Hyun BH. Multiplex real-time RT-PCR for the simultaneous detection and quantification of transmissible gastroenteritis virus and porcine epidemic diarrhea virus. J Virol Methods 2007; 146:172-7. [PMID: 17697717 PMCID: PMC7119650 DOI: 10.1016/j.jviromet.2007.06.021] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Revised: 05/07/2007] [Accepted: 06/27/2007] [Indexed: 11/24/2022]
Abstract
Transmissible gastroenteritis virus (TGEV) and porcine epidemic diarrhea virus (PEDV) are major etiological agents of diarrhea and death in piglets. Multiplex real-time reverse transcriptase (RT)-PCR was developed for simultaneous differential quantification of each virus in a single reaction tube, using Cy5- and FAM-labeled TaqMan-probes based on sequences from the TGEV and PEDV nucleocapsid genes. The copy numbers for transcripts of TGEV and PEDV were quantified using this assay over a range from 9 × 107 to 9 × 101 copies and 7 × 107 to 7 × 101 copies, respectively. The variability of the intra-assay and inter-assay were evaluated using standard solutions of each transcript, with coefficients of variation (CV) less than 3.43 and 3.33%, respectively. Piglets were experimentally infected with virulent TGEV and PEDV, and the amounts of virus from the onset of diarrhea were measured. Samples obtained from farms experiencing PED or TGE were quantified between 102 and 105 RNA copies. In conclusion, this assay provides an effective etiological diagnostic tool for detecting and quantifying viral loads. The assay may also prove useful for detecting infections, ultimately leading to better disease control on farms.
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Affiliation(s)
| | | | | | | | | | - Bang-Hun Hyun
- Corresponding author at: (430-824) 480, Anyang 6-dong, Manan-gu, Anyang-City, Gyeonggi-do, Republic of Korea. Tel.: +82 31 467 1783; fax: +82 31 467 1797.
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18
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Keyaerts E, Vijgen L, Pannecouque C, Van Damme E, Peumans W, Egberink H, Balzarini J, Van Ranst M. Plant lectins are potent inhibitors of coronaviruses by interfering with two targets in the viral replication cycle. Antiviral Res 2007; 75:179-87. [PMID: 17428553 PMCID: PMC7114093 DOI: 10.1016/j.antiviral.2007.03.003] [Citation(s) in RCA: 189] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Revised: 03/05/2007] [Accepted: 03/05/2007] [Indexed: 11/26/2022]
Abstract
We describe the antiviral activity of plant lectins with specificity for different glycan structures against the severe acute respiratory syndrome coronavirus (SARS-CoV) and the feline infectious peritonitis virus (FIPV) in vitro. The SARS-CoV emerged in 2002 as an important cause of severe lower respiratory tract infection in humans, and FIPV infection causes a chronic and often fatal peritonitis in cats. A unique collection of 33 plant lectins with different specificities were evaluated. The plant lectins possessed marked antiviral properties against both coronaviruses with EC50 values in the lower microgram/ml range (middle nanomolar range), being non-toxic (CC50) at 50–100 μg/ml. The strongest anti-coronavirus activity was found predominantly among the mannose-binding lectins. In addition, a number of galactose-, N-acetylgalactosamine-, glucose-, and N-acetylglucosamine-specific plant agglutinines exhibited anti-coronaviral activity. A significant correlation (with an r-value of 0.70) between the EC50 values of the 10 mannose-specific plant lectins effective against the two coronaviruses was found. In contrast, little correlation was seen between the activity of other types of lectins. Two targets of possible antiviral intervention were identified in the replication cycle of SARS-CoV. The first target is located early in the replication cycle, most probably viral attachment, and the second target is located at the end of the infectious virus cycle.
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Affiliation(s)
- Els Keyaerts
- Laboratory of Clinical & Epidemiological Virology, Department of Microbiology & Immunology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Leen Vijgen
- Laboratory of Clinical & Epidemiological Virology, Department of Microbiology & Immunology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Christophe Pannecouque
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, University of Leuven, Belgium
| | - Els Van Damme
- Department of Molecular Biotechnology, University of Gent, Belgium
| | - Willy Peumans
- Department of Molecular Biotechnology, University of Gent, Belgium
| | - Herman Egberink
- Department of Infectious Diseases & Immunology, Veterinary Faculty, Utrecht, The Netherlands
| | - Jan Balzarini
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, University of Leuven, Belgium
- Corresponding author. Tel.: +32 16 337352; fax: +32 16 337340.
| | - Marc Van Ranst
- Laboratory of Clinical & Epidemiological Virology, Department of Microbiology & Immunology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
- Corresponding author at: Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium. Tel.: +32 16 347908; fax: +32 16 347900.
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Hashimoto Y, Valles SM, Strong CA. Detection and quantitation of Solenopsis invicta virus in fire ants by real-time PCR. J Virol Methods 2006; 140:132-9. [PMID: 17174411 DOI: 10.1016/j.jviromet.2006.11.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Revised: 11/03/2006] [Accepted: 11/08/2006] [Indexed: 10/23/2022]
Abstract
A quantitative real-time PCR (QPCR) method was developed to detect and quantify the amount of Solenopsis invicta virus (SINV) infecting individual ants of S. invicta. The two-step method utilized a gene-specific oligonucleotide primer targeting the SINV RNA-dependent RNA polymerase (RdRp) for cDNA synthesis. Dithiothreitol used in the cDNA synthesis step was found to significantly decrease the detection sensitivity for SINV RdRp and was therefore omitted. SINV RdRp cDNA was then quantified by QPCR using SYBR Green dye and a standard curve generated from SINV RdRp plasmid clones. A standard curve was successfully constructed from clones of the SINV RdRp region. A strong linear relationship [r2=0.998; y=(-3.63+/-0.37)x+(39.19+/-1.33)] between C(T) and starting SINV RdRp copy number was observed within a dynamic range of 5-5 x 10(6) copies. SINV RdRp copy number was determined with the optimized QPCR method in individual S. invicta ants taken from an infected field colony. Worker ants exhibited the highest RdRp copy number (2.1 x 10(9) copies/worker ant) and pupae exhibited the lowest (4.2 x 10(2) copies/pupa). Mean RdRp copy number was lowest in early larvae and pupae. Overall, SINV RdRp copy number increased through larval development, sharply declined during pupation, then sharply increased in adults.
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Affiliation(s)
- Yoshifumi Hashimoto
- Center for Medical, Agricultural and Veterinary Entomology, USDA-ARS, 1600 SW 23rd Drive, Gainesville, FL 32608, USA
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20
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Escutenaire S, Mohamed N, Isaksson M, Thorén P, Klingeborn B, Belák S, Berg M, Blomberg J. SYBR Green real-time reverse transcription-polymerase chain reaction assay for the generic detection of coronaviruses. Arch Virol 2006; 152:41-58. [PMID: 16941059 PMCID: PMC7087200 DOI: 10.1007/s00705-006-0840-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Accepted: 07/12/2006] [Indexed: 12/02/2022]
Abstract
Coronaviruses are etiologic agents of respiratory and enteric diseases in humans and in animals. In this study, a one-step real-time reverse transcription-polymerase chain reaction (RT-PCR) assay based on SYBR Green chemistry and degenerate primers was developed for the generic detection of coronaviruses. The primers, designed in the open reading frame 1b, enabled the detection of 32 animal coronaviruses including strains of canine coronavirus, feline coronavirus, transmissible gastroenteritis virus (TGEV), bovine coronavirus (BCoV), murine hepatitis virus (MHV) and infectious bronchitis virus (IBV). A specific amplification was also observed with the human coronaviruses (HCoV) HCoV-NL63, HCoV-OC43, HCoV-229E and severe acute respiratory syndrome coronavirus (SARS-CoV). The real-time RT-PCR detected down to 10 cRNA copies from TGEV, BCoV, SARS-CoV and IBV. In addition, the assay exhibited a high sensitivity and specificity on clinical samples from different animal species. The developed assay represents a potential tool for laboratory diagnostics and for detecting still uncharacterized coronaviruses.
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Affiliation(s)
- S Escutenaire
- Department of Virology, National Veterinary Institute, Uppsala, Sweden
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Keyaerts E, Vijgen L, Maes P, Neyts J, Van Ranst M. Growth kinetics of SARS-coronavirus in Vero E6 cells. Biochem Biophys Res Commun 2005; 329:1147-51. [PMID: 15752773 PMCID: PMC7092881 DOI: 10.1016/j.bbrc.2005.02.085] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2005] [Indexed: 01/19/2023]
Abstract
Vero E6 cells are commonly used for in vitro studies of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) and for antiviral evaluation purposes. A better understanding of the SARS-CoV growth kinetics in Vero E6 cells is crucial to help elucidate the mechanism of antiviral activity of selective antiviral agents. In this study, the growth kinetics of SARS-CoV in Vero E6 cells were studied by quantitation of intra- and extracellular viral RNA load as well as extracellular virus yield at different time points post-infection. At 12 h post-infection, the intracellular viral RNA load was 3 × 102-fold higher than at the time of infection, and the extracellular viral RNA load was increased with a factor of 2 × 103. Intracellular viral RNA levels started to rise at 6 h post-infection. One hour later (at 7 h post-infection), the levels of extracellular SARS-CoV RNA also began to rise. This was corroborated by the fact that infectious progeny SARS-CoV also first appeared in the supernatant between 6 and 7 h post-infection. At 12 h post-infection, SARS-CoV reached titers in the supernatant of 5.2 × 103 CCID50/ml.
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Affiliation(s)
- Els Keyaerts
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Belgium
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