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Szardenings M, Delaroque N, Kern K, Ramirez-Caballero L, Puder M, Ehrentreich-Förster E, Beige J, Zürner S, Popp G, Wolf J, Borte S. Detection of Antibodies against Endemic and SARS-CoV-2 Coronaviruses with Short Peptide Epitopes. Vaccines (Basel) 2023; 11:1403. [PMID: 37766081 PMCID: PMC10535424 DOI: 10.3390/vaccines11091403] [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: 07/14/2023] [Revised: 08/08/2023] [Accepted: 08/17/2023] [Indexed: 09/29/2023] Open
Abstract
(1) Background: Coronavirus proteins are quite conserved amongst endemic strains (eCoV) and SARS-CoV-2. We aimed to evaluate whether peptide epitopes might serve as useful diagnostic biomarkers to stratify previous infections and COVID-19. (2) Methods: Peptide epitopes were identified at an amino acid resolution that applied a novel statistical approach to generate data sets of potential antibody binding peptides. (3) Results: Data sets from more than 120 COVID-19 or eCoV-infected patients, as well as vaccinated persons, have been used to generate data sets that have been used to search in silico for potential epitopes in proteins of SARS-CoV-2 and eCoV. Peptide epitopes were validated with >300 serum samples in synthetic peptide micro arrays and epitopes specific for different viruses, in addition to the identified cross reactive epitopes. (4) Conclusions: Most patients develop antibodies against non-structural proteins, which are useful general markers for recent infections. However, there are differences in the epitope patterns of COVID-19, and eCoV, and the S-protein vaccine, which can only be explained by a high degree of cross-reactivity between the viruses, a pre-existing immune response against some epitopes, and even an alternate processing of the vaccine proteins.
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Affiliation(s)
- Michael Szardenings
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstr. 1, 04103 Leipzig, Germany; (N.D.); (K.K.); (S.Z.); (G.P.)
- epitopic GmbH, Deutscher Platz 5e, 04103 Leipzig, Germany;
| | - Nicolas Delaroque
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstr. 1, 04103 Leipzig, Germany; (N.D.); (K.K.); (S.Z.); (G.P.)
| | - Karolin Kern
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstr. 1, 04103 Leipzig, Germany; (N.D.); (K.K.); (S.Z.); (G.P.)
- epitopic GmbH, Deutscher Platz 5e, 04103 Leipzig, Germany;
| | - Lisbeth Ramirez-Caballero
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstr. 1, 04103 Leipzig, Germany; (N.D.); (K.K.); (S.Z.); (G.P.)
| | - Marcus Puder
- epitopic GmbH, Deutscher Platz 5e, 04103 Leipzig, Germany;
| | - Eva Ehrentreich-Förster
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses IZI-BB, Am Mühlenberg 13, 14476 Potsdam, Germany;
| | - Joachim Beige
- Martin-Luther-University Halle/Wittenberg, Medical Clinic 2, 06112 Halle, Germany;
| | - Sebastian Zürner
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstr. 1, 04103 Leipzig, Germany; (N.D.); (K.K.); (S.Z.); (G.P.)
- WINF/Informationsmanagement, University Leipzig, Grimmaische Straße 12, 04109 Leipzig, Germany
| | - Georg Popp
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstr. 1, 04103 Leipzig, Germany; (N.D.); (K.K.); (S.Z.); (G.P.)
| | - Johannes Wolf
- Department of Laboratory Medicine, Hospital St. Georg, Delitzscher Strasse 141, 04129 Leipzig, Germany; (J.W.); (S.B.)
- ImmunoDeficiencyCenter Leipzig (IDCL), Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiency Diseases, Hospital St. Georg, Delitzscher Strasse 141, 04129 Leipzig, Germany
| | - Stephan Borte
- Department of Laboratory Medicine, Hospital St. Georg, Delitzscher Strasse 141, 04129 Leipzig, Germany; (J.W.); (S.B.)
- ImmunoDeficiencyCenter Leipzig (IDCL), Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiency Diseases, Hospital St. Georg, Delitzscher Strasse 141, 04129 Leipzig, Germany
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Karami H, Sadeghi K, Zadheidar S, Saadatmand F, Mirsalehi N, Ardestani NH, Kalantari S, Farahmand M, Yavarian J, Mokhtari‐Azad T. Surveillance of endemic coronaviruses during the COVID‐19 pandemic in Iran, 2021–2022. Influenza Other Respir Viruses 2023; 17:e13128. [PMID: 36970571 PMCID: PMC10037967 DOI: 10.1111/irv.13128] [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: 01/31/2023] [Accepted: 03/02/2023] [Indexed: 03/26/2023] Open
Abstract
Background Human coronaviruses (HCoVs) 229E, OC43, HKU1, and NL63 are common viruses that continuously circulate in the human population. Previous studies showed the circulation of HCoVs during the cold months in Iran. We studied the circulation of HCoVs during coronavirus disease 2019 (COVID‐19) pandemic to find the impact of pandemic on the circulation of these viruses. Methods As a cross‐sectional survey conducted during 2021 to 2022, of all throat swabs sent to Iran National Influenza Center from patients with severe acute respiratory infection, 590 samples were selected to test for HCoVs using one‐step real‐time RT‐PCR. Results Overall, 28 out of 590 (4.7%) tested samples were found to be positive for at least one HCoVs. HCoV‐OC43 was the most common (14/590 or 2.4%), followed by HCoV‐HKU1 (12/590 or 2%) and HCoV‐229E (4/590 or 0.6%), while HCoV‐NL63 was not detected. HCoVs were detected in patients of all ages and throughout the study period with peaks in the cold months of the year. Conclusions Our multicenter survey provides insight into the low circulation of HCoVs during the COVID‐19 pandemic in Iran in 2021/2022. Hygiene habits and social distancing measures might have important role in decreasing of HCoVs transmission. We believe that surveillance studies are needed to track the pattern of HCoVs distributions and detect changes in the epidemiology of such viruses to set out strategies in order to timely control the future outbreaks of HCoVs throughout the nation.
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Affiliation(s)
- Hassan Karami
- Department of Virology, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Kaveh Sadeghi
- Department of Virology, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Sevrin Zadheidar
- Department of Virology, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Fatemeh Saadatmand
- Department of Virology, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Negar Mirsalehi
- Department of Virology, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Nima Hoveidi Ardestani
- Department of Virology, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Shirin Kalantari
- Department of Virology, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Mohammad Farahmand
- Department of Virology, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Jila Yavarian
- Department of Virology, School of Public HealthTehran University of Medical SciencesTehranIran
- Research Center for Antibiotic Stewardship & Antimicrobial ResistanceTehran University of Medical SciencesTehranIran
| | - Talat Mokhtari‐Azad
- Department of Virology, School of Public HealthTehran University of Medical SciencesTehranIran
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Shah MM, Winn A, Dahl RM, Kniss KL, Silk BJ, Killerby ME. Seasonality of Common Human Coronaviruses, United States, 2014-2021 1. Emerg Infect Dis 2022; 28:1970-1976. [PMID: 36007923 PMCID: PMC9514339 DOI: 10.3201/eid2810.220396] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The 4 common types of human coronaviruses (HCoVs)-2 alpha (HCoV-NL63 and HCoV-229E) and 2 beta (HCoV-HKU1 and HCoV-OC43)-generally cause mild upper respiratory illness. Seasonal patterns and annual variation in predominant types of HCoVs are known, but parameters of expected seasonality have not been defined. We defined seasonality of HCoVs during July 2014-November 2021 in the United States by using a retrospective method applied to National Respiratory and Enteric Virus Surveillance System data. In the 6 HCoV seasons before 2020-21, season onsets occurred October 21-November 12, peaks January 6-February 13, and offsets April 18-June 27; most (>93%) HCoV detection was within the defined seasonal onsets and offsets. The 2020-21 HCoV season onset was 11 weeks later than in prior seasons, probably associated with COVID-19 mitigation efforts. Better definitions of HCoV seasonality can be used for clinical preparedness and for determining expected patterns of emerging coronaviruses.
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Sanghani H, Bansal S, Parmar V, Shah R. Study of Arterial Blood Gas Analysis in Moderate-to-Severe COVID-19 Patients. Cureus 2022; 14:e26715. [PMID: 35967170 PMCID: PMC9362693 DOI: 10.7759/cureus.26715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2022] [Indexed: 01/08/2023] Open
Abstract
Background The high prevalence of pneumonia and renal involvement in coronavirus disease 2019 (COVID-19) leads to frequent acid-base abnormalities in serious patients and affects prognosis. In this study, we aimed to assess the arterial blood gas (ABG) and acid-base patterns in COVID-19 patients admitted to a tertiary care hospital. Methodology A retrospective observational study was conducted in a designated COVID-19 hospital involving 267 reverse transcription-polymerasechain reaction-positive COVID-19 patients. Demographic and laboratory data including ABG data within the first day after admission and in patients with multiple ABG analyses, only the first measurement was collected and analyzed statistically, including its association with comorbidities. Results The most common age group of the patients was 51-60 years (30.8%), with a male predominance (male:female = 2.7:1). The most common comorbidities were hypertension, diabetes mellitus, and chronic obstructive pulmonary disease found in 147 (55%) COVID-19 patients. Alkalosis and acidosis were observed in 145 (54.3%) and 50 (18.7%) patients, respectively. The most common ABG abnormality observed was primary respiratory alkalosis with secondary metabolic acidosis in 67 (25.1%) patients, followed by primary respiratory alkalosis with secondary metabolic alkalosis in 54 (20.2%) patients. Statistically significant negative correlation was found with PaCO2 and pH (r = -0.530, p < 0.0001), statistically significant positive correlation was found between pH and base (r = 0.533, p < 0.0001), pH and TCO2 (r = 0.260, p < 0.0001), and pH and HCO3 (r = 0.354, p < 0.0001). Conclusions Acid-base abnormalities are commonly encountered in COVID-19 patients. Respiratory alkalosis as a part of a single or mixed pattern on ABG was the most common pattern found in critically ill COVID-19 patients. ABG on admission in moderate-to-severe COVID-19 patients can help in the early correction of metabolic abnormalities leading to improved patient outcomes.
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Affiliation(s)
- Hiren Sanghani
- Department of Biochemistry, Shantabaa Medical College and General Hospital, Amreli, IND
| | - Sumit Bansal
- Anesthesiology, Max Super Speciality Hospital, Patparganj, New Delhi, IND
| | - Vijaysinh Parmar
- Department of Biochemistry, Smt. Nathiba Hargovandas Lakhmichand Municipal Medical College, Ahmedabad, IND
| | - Rima Shah
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS) Rajkot, Rajkot, IND
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Gyebi GA, Adegunloye AP, Ibrahim IM, Ogunyemi OM, Afolabi SO, Ogunro OB. Prevention of SARS-CoV-2 cell entry: insight from in silico interaction of drug-like alkaloids with spike glycoprotein, human ACE2, and TMPRSS2. J Biomol Struct Dyn 2022; 40:2121-2145. [PMID: 33089728 PMCID: PMC7594191 DOI: 10.1080/07391102.2020.1835726] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 10/07/2020] [Indexed: 12/28/2022]
Abstract
COVID-19 is a respiratory disease caused by SARS-CoV-2, an enveloped positive sense RNA virus. The SARS-CoV-2 spike glycoprotein, human angiotensin-converting enzyme 2 (ACE2) and human transmembrane protease serine 2 (TMPRSS2) are essential for the host cell-mediated viral entry. Targeting these proteins represent viable options to stop the first stage of infection and transmission. Hence, 97 alkaloids from African medicinal plants with reported antiviral activity were evaluated for this purpose via in silico studies. These alkaloids were docked for their interactions with SARS-CoV-2 spike glycoprotein, ACE2, and TMPRSS2. Top 20 alkaloids with highest binding affinities were further screened for their interactions with spike glycoprotein of SARS-CoV and MERS-CoV, and with ACE2-SARS-CoV-2 receptor-binding domain complex (ACE2-RBD). The energy profiling, molecular dynamics simulation (MDS), binding free energy base on Molecular Mechanics/Generalized Born Surface Area (MMGBSA), clustering of MDS trajectories, and virtual physicochemical and pharmacokinetic screening of the best docked alkaloids were performed. Results revealed that more than 15 alkaloids interacted better than the reference compounds. 10-Hydroxyusambarensine and Cryptospirolepine were docked in a similar binding pattern to the S1-specificy pocket of TMPRSS2 as camostat (reference inhibitor). The strong binding affinities, stability of the alkaloid-protein complexes and amino acid interactions displayed by cryptospirolepine, 10-hydroxyusambarensine, and cryptoquindoline with important binding hotspots of the proteins suggest these alkaloids have the potential of altering the capacity of SARS-CoV-2 membrane mediated host cell entry. Further in vitro and in vivo evaluation of these "drug-like" alkaloids as potential inhibitors of coronavirus cell entry is proposed.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gideon A. Gyebi
- Department of Biological Sciences, Salem University, Lokoja, Nigeria
| | | | - Ibrahim M. Ibrahim
- Faculty of Sciences, Department of Biophysics, Cairo University, Giza, Egypt
| | | | - Saheed O. Afolabi
- Faculty of Basic Medical Sciences, Department of Pharmacology and Therapeutics, University of Ilorin, Ilorin, Nigeria
| | - Olalekan B. Ogunro
- Department of Biological Sciences, KolaDaisi University, Ibadan, Nigeria
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Majumdar A, Dey G, Sinha A. Altered hematological profile: The forerunner of fatalities caused by COVID-19. MEDICAL JOURNAL OF BABYLON 2022. [DOI: 10.4103/mjbl.mjbl_44_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Hidalgo J, Rodríguez-Vega G, Pérez-Fernández J. The sudden appearance of SARS-CoV-2. COVID-19 PANDEMIC 2022. [PMCID: PMC8175630 DOI: 10.1016/b978-0-323-82860-4.00004-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Comparison of 4 Different Threshold Values of Shock Index in Predicting Mortality of COVID-19 Patients. Disaster Med Public Health Prep 2021; 17:e99. [PMID: 34937595 PMCID: PMC8924560 DOI: 10.1017/dmp.2021.374] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVE The object of this study was to examine the accuracy in prehospital shock index (SI) for predicting intensive care unit (ICU) requirement and 30-d mortality among from coronavirus disease 2019 (COVID-19) patients transported to the hospital by ambulance. METHODS All consecutive patients who were the age ≥18 y, transported to the emergency department (ED) by ambulance with a suspected or confirmed COVID-19 in the prehospital frame were included in the study. Four different cutoff points were compared (0.7, 0.8, 0.9, and 1.0) to examine the predictive performance of both the mortality and ICU requirement of the SI. The receiver operating characteristic (ROC) curve and the area under the curve (AUC) was used to evaluate each cut-off value discriminatory for predicting 30-d mortality and ICU admission. RESULTS The total of 364 patients was included in this study. The median age in the study population was 69 y (range, 55-80 y), of which 196 were men and 168 were women. AUC values for 30-d mortality outcome were calculated as 0.672, 0.674, 0.755, and 0.626, respectively, for threshold values of 0.7, 0.8, 0.9 and 1.0. ICU admission was more likely for the patients with prehospital SI > 0.9. Similarly, the mortality rate was higher in patients with prehospital SI > 0.9. CONCLUSIONS Early triage of COVID-19 patients will ensure efficient use of health-care resources. The SI could be a helpful, fast, and powerful tool for predicting mortality status and ICU requirements of adult COVID-19 patients. It was concluded that the most useful threshold value for the shock index in predicting the prognosis of COVID-19 patients is 0.9.
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Dubey DB, Mishra S, Reddy HD, Rizvi A, Ali W. Hematological and serum biochemistry parameters as a prognostic indicator of severally ill versus mild Covid-19 patients: A study from tertiary hospital in North India. CLINICAL EPIDEMIOLOGY AND GLOBAL HEALTH 2021; 12:100806. [PMID: 34179566 PMCID: PMC8214724 DOI: 10.1016/j.cegh.2021.100806] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/30/2021] [Accepted: 06/02/2021] [Indexed: 01/08/2023] Open
Abstract
Background/objectives In, India coronavirus disease (COVID-19) cases are on the rise in terms of the total number of cases. Findings on clinical and hematological parameters alone carry no significance apart from telling patients present status and hence are diminutive. This study aims to assess the hematological and serum biochemistry parameters and correlate them with the presenting symptoms and severity of disease which can help predict the need for intensive care unit (ICU) care, help in triage, assess the severity of the disease which will help clinicians decide their future course of action and further improve patients clinical outcome. Methods A total of 200 COVID-19 positive patients were included. Hematological and serum biochemistry parameters were recorded for the patients at the time of admission and categorized as mild, moderate, and severely ill based on clinical status and then admitted into various wards. Results Total leucocyte count (TLC) was significantly different and higher in severely ill patients (13,200 ± 6,999.2) compared to cases presented with mild and moderate symptoms (12,100 ± 6,488.41& 8,788.20 ± 4,954.32, p = 0.001). The mean difference of TLC, Neutrophil% (N%), Lymphocyte% (L%) and Monocyte (M%) was significantly different between mild and moderate symptoms cases (p = 0.030, p = 0.002, p = 0.004 & p = 0.003). Between groups comparison of moderate vs. severely ill cases showed a significant difference in TLC (p = 0.000), N% (p = 0.000), L% (0.000), and L/N ratio (p = 0.002). The serum ionic calcium (Ca), random blood sugar (RBS), C-reactive protein (CRP), fibrinogen, prothrombin (PT), International Normalized Ratio (INR), ferritin, and Lactate Dehydrogenase (LDH) level also differed significantly between mild, moderate and severely ill cases (p = 0.001, p=<0.001, p = 0.002, p=<00.1, p = 0006, p = 0.005, p=<0.001 and p=<0.001) respectively. Comparison of the mild vs. severely ill cases showed a significant difference in urea, fibrinogen, and procalcitonin (PCT) level (p = 0.005, p = 0.000 & p = 0.048) respectively. Conclusion The preliminary findings of this study suggest hematological and serum biochemistry parameters could be used as a screening tool to identify patients requiring intensive care and thus allowing clinical stratification and triage at the time of presentation.
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Affiliation(s)
- Deval B Dubey
- Department of Medicine, King George Medical University, India
| | - Sridhar Mishra
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, Uttar Pradesh, 226010, India
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Mulabbi EN, Tweyongyere R, Wabwire-Mangen F, Mworozi E, Koehlerb J, Kibuuka H, Millard M, Erima B, Tugume T, Aquino UQ, Byarugaba DK. Seroprevalence of human coronaviruses among patients visiting hospital-based sentinel sites in Uganda. BMC Infect Dis 2021; 21:585. [PMID: 34134656 PMCID: PMC8207497 DOI: 10.1186/s12879-021-06258-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 05/31/2021] [Indexed: 01/12/2023] Open
Abstract
Background Human coronaviruses are causative agents of respiratory infections with several subtypes being prevalent worldwide. They cause respiratory illnesses of varying severity and have been described to be continuously emerging but their prevalence is not well documented in Uganda. This study assessed the seroprevalence of antibodies against the previously known human coronaviruses prior 2019 in Uganda. Methods A total 377 serum samples collected from volunteers that showed influenza like illness in five hospital-based sentinel sites and archived were analyzed using a commercial Qualitative Human Coronavirus Antibody IgG ELISA kit. Although there is no single kit available that can detect the presence of all the circulating coronaviruses, this kit uses a nucleoprotein, aa 340–390 to coat the wells and since there is significant homology among the various human coronavirus strains with regards to the coded for proteins, there is significant cross reactivity beyond HCoV HKU-39849 2003. This gives the kit a qualitative ability to detect the presence of human coronavirus antibodies in a sample. Results The overall seroprevalence for all the sites was 87.53% with no significant difference in the seroprevalence between the Hospital based sentinel sites (p = 0.8). Of the seropositive, the age group 1–5 years had the highest percentage (46.97), followed by 6–10 years (16.67) and then above 20 (16.36). An odds ratio of 1.6 (CI 0.863–2.97, p = 0.136) showed that those volunteers below 5 years of age were more likely to be seropositive compared to those above 5 years. The seropositivity was generally high throughout the year with highest being recorded in March and the lowest in February and December. Conclusions The seroprevalence of Human coronaviruses is alarmingly high which calls for need to identify and characterize the circulating coronavirus strains so as to guide policy on the control strategies.
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Affiliation(s)
- Elijah Nicholas Mulabbi
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.
| | - Robert Tweyongyere
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | | | | | - Jeff Koehlerb
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Hannah Kibuuka
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Monica Millard
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Bernard Erima
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Titus Tugume
- Makerere University Walter Reed Project, Kampala, Uganda
| | | | - Denis K Byarugaba
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.,Makerere University Walter Reed Project, Kampala, Uganda
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Psychosocial status and attitudes of healthcare workers amid the COVID-19 pandemic. JOURNAL OF SURGERY AND MEDICINE 2021. [DOI: 10.28982/josam.860273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Ottogalli ME, Rodríguez PE, Frutos MC, Moreno LB, Ghietto LM, Cuffini CG, Cámara JA, Adamo MP, Valinotto LE, Cámara A. Circulation of human coronaviruses OC43 and 229E in Córdoba, Argentina. Arch Virol 2021; 166:929-933. [PMID: 33492522 PMCID: PMC7829625 DOI: 10.1007/s00705-020-04914-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/25/2020] [Indexed: 01/24/2023]
Abstract
This is the first study of respiratory infections in Córdoba, Argentina, caused by endemic human coronavirus (HCoV)-OC43 and HCOV-229E, which circulated during 2011-2012 at a 3% rate, either as single or multiple infections. They were detected mainly in children, but HCoV-229E was also found in adults. HCoV-229E was detected in five out of 631 samples (0.8%), and HCoV-OC43 was found in 14 out of 631 (2.2%) samples. Clinical manifestations ranged from fever to respiratory distress, and a significant association of HCoV-229E with asthma was observed. Further studies and surveillance are needed to provide better clinical insights, early diagnosis, and medical care of patients, as well as to contribute to epidemiology modeling and prevention.
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Affiliation(s)
- María Emilia Ottogalli
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Pamela Elizabeth Rodríguez
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - María Celia Frutos
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Laura Beatriz Moreno
- Cátedra de Clínica Pediátrica, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Lucía María Ghietto
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Cecilia Gabriela Cuffini
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Jorge Augusto Cámara
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - María Pilar Adamo
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | | | - Alicia Cámara
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina.
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Hu ZW, Wang X, Zhao JP, Ma J, Li HC, Wang GF, Cheng Y, Zhang H. Influenza A virus exposure may cause increased symptom severity and deaths in coronavirus disease 2019. Chin Med J (Engl) 2020; 133:2410-2414. [PMID: 32842015 PMCID: PMC7575176 DOI: 10.1097/cm9.0000000000000966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) outbreak occurred during the flu season around the world. This study aimed to analyze the impact of influenza A virus (IAV) exposure on COVID-19. METHODS Seventy COVID-19 patients admitted to the hospital during January and February 2020 in Wuhan, China were included in this retrospective study. Serum tests including respiratory pathogen immunoglobulin M (IgM) and inflammation biomarkers were performed upon admission. Patients were divided into common, severe, and critical types according to disease severity. Symptoms, inflammation indices, disease severity, and fatality rate were compared between anti-IAV IgM-positive and anti-IAV IgM-negative groups. The effects of the empirical use of oseltamivir were also analyzed in both groups. For comparison between groups, t tests and the Mann-Whitney U test were used according to data distribution. The Chi-squared test was used to compare disease severity and fatality between groups. RESULTS Thirty-two (45.71%) of the 70 patients had positive anti-IAV IgM. Compared with the IAV-negative group, the positive group showed significantly higher proportions of female patients (59.38% vs. 34.21%, χ = 4.43, P = 0.035) and patients with fatigue (59.38% vs. 34.21%, χ = 4.43, P = 0.035). The levels of soluble interleukin 2 receptor (median 791.00 vs. 1075.50 IU/mL, Z = -2.70, P = 0.007) and tumor necrosis factor α (median 10.75 vs. 11.50 pg/mL, Z = -2.18, P = 0.029) were significantly lower in the IAV-positive group. Furthermore, this group tended to have a higher proportion of critical patients (31.25% vs. 15.79%, P = 0.066) and a higher fatality rate (21.88% vs. 7.89%, P = 0.169). Notably, in the IAV-positive group, patients who received oseltamivir had a significantly lower fatality rate (0 vs. 36.84%, P = 0.025) compared with those not receiving oseltamivir. CONCLUSIONS The study suggests that during the flu season, close attention should be paid to the probability of IAV exposure in COVID-19 patients. Prospective studies with larger sample sizes are needed to clarify whether IAV increases the fatality rate of COVID-19 and to elucidate any benefits of empirical usage of oseltamivir.
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Affiliation(s)
- Zhan-Wei Hu
- Department of Respiratory and Critical Care Medicine, Peking University First Hospital, Beijing 100034, China
| | - Xi Wang
- Department of Respiratory and Critical Care Medicine, Peking University First Hospital, Beijing 100034, China
| | - Jian-Ping Zhao
- Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Jing Ma
- Department of Respiratory and Critical Care Medicine, Peking University First Hospital, Beijing 100034, China
| | - Hai-Chao Li
- Department of Respiratory and Critical Care Medicine, Peking University First Hospital, Beijing 100034, China
| | - Guang-Fa Wang
- Department of Respiratory and Critical Care Medicine, Peking University First Hospital, Beijing 100034, China
| | - Yuan Cheng
- Department of Respiratory and Critical Care Medicine, Peking University First Hospital, Beijing 100034, China
| | - Hong Zhang
- Department of Respiratory and Critical Care Medicine, Peking University First Hospital, Beijing 100034, China
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14
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Usul E, Şan İ, Bekgöz B, Şahin A. Role of hematological parameters in COVID-19 patients in the emergency room. Biomark Med 2020; 14:1207-1215. [PMID: 32692248 PMCID: PMC7372996 DOI: 10.2217/bmm-2020-0317] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/06/2020] [Indexed: 01/08/2023] Open
Abstract
Aim: In this study, the roles of biomarkers from a peripheral blood sample in the diagnosis of COVID-19 patients who have visited the emergency room have been evaluated. Materials & methods: Peripheral blood parameters, systemic inflammatory index (SII), neutrophil lymphocyte ratio (NLR) and platelet lymphocyte ratio were compared in patients with and without confirmed COVID-19 infection. Results: Comparisons made according to real-time PCR test results revealed that while no statistically significant difference was observed between test groups (negative-positive) regarding lymphocyte and platelet lymphocyte ratio values (p > 0.05), a statistically significant difference (p < 0.05) was found between the test groups regarding platelet, hemoglobin, leukocyte, neutrophil, NLR and SII values. Conclusion: Leukocyte, neutrophil, platelet count, NLR and SII values can be used in the diagnosis of COVID-19.
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Affiliation(s)
- Eren Usul
- Sincan Dr Nafiz Körez State Hospital, Emergency Service, Ankara, Turkey
| | - İshak Şan
- Department of Emergency Medicine, University of Health Sciences, Ankara City Hospital, Ankara, Turkey
| | - Burak Bekgöz
- Department of Emergency Medicine, University of Health Sciences, Ankara City Hospital, Ankara, Turkey
| | - Ali Şahin
- Etimesgut State Hospital, Emergency Service, Ankara, Turkey
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15
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Wang Y, Li X, Liu W, Gan M, Zhang L, Wang J, Zhang Z, Zhu A, Li F, Sun J, Zhang G, Zhuang Z, Luo J, Chen D, Qiu S, Zhang L, Xu D, Mok CKP, Zhang F, Zhao J, Zhou R, Zhao J. Discovery of a subgenotype of human coronavirus NL63 associated with severe lower respiratory tract infection in China, 2018. Emerg Microbes Infect 2020; 9:246-255. [PMID: 31996093 PMCID: PMC7034077 DOI: 10.1080/22221751.2020.1717999] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Human coronavirus NL63 (HCoV-NL63) is primarily associated with common cold in children, elderly and immunocompromised individuals. Outbreaks caused by HCoV-NL63 are rare. Here we report a cluster of HCoV-NL63 cases with severe lower respiratory tract infection that arose in Guangzhou, China, in 2018. Twenty-three hospitalized children were confirmed to be HCoV-NL63 positive, and most of whom were hospitalized with severe pneumonia or acute bronchitis. Whole genomes of HCoV-NL63 were obtained using next-generation sequencing. Phylogenetic and single amino acid polymorphism analyses showed that this outbreak was associated with two subgenotypes (C3 and B) of HCoV-NL63. Half of patients were identified to be related to a new subgenotype C3. One unique amino acid mutation at I507 L in spike protein receptor binding domain (RBD) was detected, which segregated this subgenotype C3 from other known subgenotypes. Pseudotyped virus bearing the I507 L mutation in RBD showed enhanced entry into host cells as compared to the prototype virus. This study proved that HCoV-NL63 was undergoing continuous mutation and has the potential to cause severe lower respiratory disease in humans.
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Affiliation(s)
- Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Xin Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Wenkuan Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Mian Gan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Lu Zhang
- Institute of Infectious disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Jin Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Airu Zhu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Fang Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Jing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Guoxian Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Zhen Zhuang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Jiaying Luo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Dehui Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Shuyan Qiu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Li Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Duo Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Chris Ka Pun Mok
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China.,The HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Fuchun Zhang
- Institute of Infectious disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Rong Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China.,Institute of Infectious disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
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16
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Zhao Y, Lu R, Shen J, Xie Z, Liu G, Tan W. Comparison of viral and epidemiological profiles of hospitalized children with severe acute respiratory infection in Beijing and Shanghai, China. BMC Infect Dis 2019; 19:729. [PMID: 31429710 PMCID: PMC6701130 DOI: 10.1186/s12879-019-4385-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 08/15/2019] [Indexed: 12/16/2022] Open
Abstract
Background No comparison data have been reported on viral and epidemiological profiles of hospitalized children with severe acute respiratory infection (SARI) in Beijing or Shanghai, China. Methods We collected 700 nasopharyngeal aspirates (NPA) from hospitalized children with SARI in Beijing (northern China) and Shanghai (southern China). Multiple respiratory viruses (including 15 common viruses) were screened by validated polymerase chain reaction (PCR) or real-time reverse transcription-PCR assays and confirmed by sequencing. Demographic data and the distribution of viral infections were also examined. Results Of 700 samples, 547 (78.1%) tested positive for viral infections. The picornaviruses (PIC), which included rhinovirus (RV) and enterovirus (EV), were the most common (34.0%), followed by respiratory syncytial virus (RSV) (28.3%), human bocavirus (HBoV) (19.1%), adenovirus (ADV) (13.7%), human coronaviruses (HCoV) (10.7%), influenza A and B (8.9%), parainfluenza virus (PIV 1–3) (7.9%), and human metapneumovirus (HMPV) (5.0%). PIC (RV/EV) and RSV were the most prevalent etiological agents of SARI in both cities. The total and age-matched prevalence of RSV, HCoV, and hMPV among SARI children under 5 years old were significantly higher in Beijing than in Shanghai. Different age and seasonal distribution patterns of the viral infections were found between Beijing and Shanghai. Conclusions Viral infection was tested and shown to be the most prevalent etiological agent among children with SARI in either the Beijing or the Shanghai area, while showing different patterns of viral and epidemiological profiles. Our findings provide a better understanding of the roles of geographic location and climate in respiratory viral infections in hospitalized children with SARI.
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Affiliation(s)
- Yanjie Zhao
- Key Laboratory of Laboratory Medicine, Ministry of Education, and Institute of Medical Virology, Wenzhou Medical University, Zhejiang, China.,National Institute for Viral Disease Control and Prevention, China CDC, 155Changbai Road, Beijing, 102206, Changping District, China
| | - Roujian Lu
- National Institute for Viral Disease Control and Prevention, China CDC, 155Changbai Road, Beijing, 102206, Changping District, China
| | - Jun Shen
- Children's Hospital of Fudan University, Shanghai, China
| | - Zhengde Xie
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, 100045, China
| | - Gaoshan Liu
- Key Laboratory of Laboratory Medicine, Ministry of Education, and Institute of Medical Virology, Wenzhou Medical University, Zhejiang, China
| | - Wenjie Tan
- Key Laboratory of Laboratory Medicine, Ministry of Education, and Institute of Medical Virology, Wenzhou Medical University, Zhejiang, China. .,National Institute for Viral Disease Control and Prevention, China CDC, 155Changbai Road, Beijing, 102206, Changping District, China.
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17
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High-Throughput Screening and Identification of Potent Broad-Spectrum Inhibitors of Coronaviruses. J Virol 2019; 93:JVI.00023-19. [PMID: 30918074 PMCID: PMC6613765 DOI: 10.1128/jvi.00023-19] [Citation(s) in RCA: 205] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/17/2019] [Indexed: 12/28/2022] Open
Abstract
Currently, there is no approved therapy to treat coronavirus infection; therefore, broad-spectrum inhibitors of emerging and endemic CoVs are needed. Based on our high-throughput screening assay using a compound library, we identified seven compounds with broad-spectrum efficacy against the replication of four CoVs in vitro. Additionally, one compound (lycorine) was found to protect BALB/c mice against HCoV-OC43-induced lethality by decreasing viral load in the central nervous system. This inhibitor might offer promising therapeutic possibilities for combatting novel CoV infections in the future. Coronaviruses (CoVs) act as cross-species viruses and have the potential to spread rapidly into new host species and cause epidemic diseases. Despite the severe public health threat of severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome CoV (MERS-CoV), there are currently no drugs available for their treatment; therefore, broad-spectrum inhibitors of emerging and endemic CoVs are urgently needed. To search for effective inhibitory agents, we performed high-throughput screening (HTS) of a 2,000-compound library of approved drugs and pharmacologically active compounds using the established genetically engineered human CoV OC43 (HCoV-OC43) strain expressing Renilla luciferase (rOC43-ns2Del-Rluc) and validated the inhibitors using multiple genetically distinct CoVs in vitro. We screened 56 hits from the HTS data and validated 36 compounds in vitro using wild-type HCoV-OC43. Furthermore, we identified seven compounds (lycorine, emetine, monensin sodium, mycophenolate mofetil, mycophenolic acid, phenazopyridine, and pyrvinium pamoate) as broad-spectrum inhibitors according to their strong inhibition of replication by four CoVs in vitro at low-micromolar concentrations. Additionally, we found that emetine blocked MERS-CoV entry according to pseudovirus entry assays and that lycorine protected BALB/c mice against HCoV-OC43-induced lethality by decreasing viral load in the central nervous system. This represents the first demonstration of in vivo real-time bioluminescence imaging to monitor the effect of lycorine on the spread and distribution of HCoV-OC43 in a mouse model. These results offer critical information supporting the development of an effective therapeutic strategy against CoV infection. IMPORTANCE Currently, there is no approved therapy to treat coronavirus infection; therefore, broad-spectrum inhibitors of emerging and endemic CoVs are needed. Based on our high-throughput screening assay using a compound library, we identified seven compounds with broad-spectrum efficacy against the replication of four CoVs in vitro. Additionally, one compound (lycorine) was found to protect BALB/c mice against HCoV-OC43-induced lethality by decreasing viral load in the central nervous system. This inhibitor might offer promising therapeutic possibilities for combatting novel CoV infections in the future.
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18
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Zhao Y, Shen J, Wu B, Liu G, Lu R, Tan W. Genotypic Diversity and Epidemiology of Human Rhinovirus Among Children With Severe Acute Respiratory Tract Infection in Shanghai, 2013-2015. Front Microbiol 2018; 9:1836. [PMID: 30131797 PMCID: PMC6090050 DOI: 10.3389/fmicb.2018.01836] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/23/2018] [Indexed: 12/12/2022] Open
Abstract
Human rhinovirus (HRV), and particularly HRV-C, is increasingly recognized as a cause of severe acute respiratory infections (SARIs). However, little is known about the genotypic diversity and epidemiology of HRV among children with SARI. Thus, we investigated the genotypic diversity and epidemiology of HRV in children with SARI in China over a 2-year period. In total 1,003, nasopharyngeal aspirates were collected from children hospitalized with SARI in Shanghai from 2013 to 2015. HRV was screened for by a PCR method targeting the viral 5' UTR and was genotyped by sequencing of the VP4-VP2 region of the HRV genome. We also screened for 15 other common respiratory viruses to assess the prevalence of co-infection with HRV. The patient demographic and clinical data were reviewed. HRV was detected in 280 (27.9%) of the 1,003 specimens: HRV-A in 140 (14.0%), HRV-B in 21 (2.1%), HRV-C in 56 (5.6%), and HRV-untyped in 63 (6.3%). A phylogenetic analysis identified 77 genotypes (43 HRV-A, 10 HRV-B, and 24 HRV-C), among which A78, A12, A89, B70, C2, C6, and C24 predominated. HRV-A was detected mainly in winter 2013 and autumn 2014, while HRV-C detection peaked in autumn 2013 and 2014. The detection frequency of HRV-A was highest in patients <5 years old. Most HRV co-infections involved adenovirus, human bocavirus, and/or human respiratory syncytial virus. In conclusion, HRV-A and -C predominate in children with SARI in Shanghai. Among the 77 genotypes detected, A78, A12, A89, B70, C2, C6, and C24 were the most frequent. The HRV species responsible for SARIs differs according to season and age.
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Affiliation(s)
- Yanjie Zhao
- Key Laboratory of Laboratory Medicine, Ministry of Education, Institute of Medical Virology, Wenzhou Medical University, Wenzhou, China.,National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jun Shen
- Infectious Disease Department, Children's Hospital of Fudan University, Shanghai, China
| | - Bingjie Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Institute of Medical Virology, Wenzhou Medical University, Wenzhou, China
| | - Gaoshan Liu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Institute of Medical Virology, Wenzhou Medical University, Wenzhou, China
| | - Roujian Lu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Institute of Medical Virology, Wenzhou Medical University, Wenzhou, China.,National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wenjie Tan
- Key Laboratory of Laboratory Medicine, Ministry of Education, Institute of Medical Virology, Wenzhou Medical University, Wenzhou, China.,National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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19
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Kiyuka PK, Agoti CN, Munywoki PK, Njeru R, Bett A, Otieno JR, Otieno GP, Kamau E, Clark TG, van der Hoek L, Kellam P, Nokes DJ, Cotten M. Human Coronavirus NL63 Molecular Epidemiology and Evolutionary Patterns in Rural Coastal Kenya. J Infect Dis 2018; 217:1728-1739. [PMID: 29741740 PMCID: PMC6037089 DOI: 10.1093/infdis/jiy098] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 02/27/2018] [Indexed: 11/13/2022] Open
Abstract
Background Human coronavirus NL63 (HCoV-NL63) is a globally endemic pathogen causing mild and severe respiratory tract infections with reinfections occurring repeatedly throughout a lifetime. Methods Nasal samples were collected in coastal Kenya through community-based and hospital-based surveillance. HCoV-NL63 was detected with multiplex real-time reverse transcription PCR, and positive samples were targeted for nucleotide sequencing of the spike (S) protein. Additionally, paired samples from 25 individuals with evidence of repeat HCoV-NL63 infection were selected for whole-genome virus sequencing. Results HCoV-NL63 was detected in 1.3% (75/5573) of child pneumonia admissions. Two HCoV-NL63 genotypes circulated in Kilifi between 2008 and 2014. Full genome sequences formed a monophyletic clade closely related to contemporary HCoV-NL63 from other global locations. An unexpected pattern of repeat infections was observed with some individuals showing higher viral titers during their second infection. Similar patterns for 2 other endemic coronaviruses, HCoV-229E and HCoV-OC43, were observed. Repeat infections by HCoV-NL63 were not accompanied by detectable genotype switching. Conclusions In this coastal Kenya setting, HCoV-NL63 exhibited low prevalence in hospital pediatric pneumonia admissions. Clade persistence with low genetic diversity suggest limited immune selection, and absence of detectable clade switching in reinfections indicates initial exposure was insufficient to elicit a protective immune response.
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Affiliation(s)
- Patience K Kiyuka
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
| | - Charles N Agoti
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
- School of Health and Human Sciences, Pwani University, Kilifi, Kenya
| | - Patrick K Munywoki
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
| | - Regina Njeru
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
| | - Anne Bett
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
| | - James R Otieno
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
| | - Grieven P Otieno
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
| | - Everlyn Kamau
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Academic Medical Center of the University of Amsterdam, the Netherlands
| | - Paul Kellam
- Department of Medicine, Division of Infectious Diseases, Imperial College London
- Kymab Ltd., Babraham Research Campus, Cambridge
| | - D James Nokes
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
- School of Life Sciences and Zeeman Institute, University of Warwick, Coventry
| | - Matthew Cotten
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
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20
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Zhang SF, Tuo JL, Huang XB, Zhu X, Zhang DM, Zhou K, Yuan L, Luo HJ, Zheng BJ, Yuen KY, Li MF, Cao KY, Xu L. Epidemiology characteristics of human coronaviruses in patients with respiratory infection symptoms and phylogenetic analysis of HCoV-OC43 during 2010-2015 in Guangzhou. PLoS One 2018; 13:e0191789. [PMID: 29377913 PMCID: PMC5788356 DOI: 10.1371/journal.pone.0191789] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/11/2018] [Indexed: 12/24/2022] Open
Abstract
Human coronavirus (HCoV) is one of the most common causes of respiratory tract infection throughout the world. To investigate the epidemiological and genetic variation of HCoV in Guangzhou, south China, we collected totally 13048 throat and nasal swab specimens from adults and children with fever and acute upper respiratory infection symptoms in Gunazhou, south China between July 2010 and June 2015, and the epidemiological features of HCoV and its species were studied. Specimens were screened for HCoV by real-time RT-PCR, and 7 other common respiratory viruses were tested simultaneously by PCR or real-time PCR. HCoV was detected in 294 cases (2.25%) of the 13048 samples, with most of them inpatients (251 cases, 85.4% of HCoV positive cases) and young children not in nursery (53.06%, 156 out of 294 HCoV positive cases). Four HCoVs, as OC43, 229E, NL63 and HKU1 were detected prevalent during 2010–2015 in Guangzhou, and among the HCoV positive cases, 60.20% were OC43, 16.67% were 229E, 14.97% were NL63 and 7.82% were HKU1. The month distribution showed that totally HCoV was prevalent in winter, but differences existed in different species. The 5 year distribution of HCoV showed a peak-valley distribution trend, with the detection rate higher in 2011 and 2013 whereas lower in 2010, 2012 and 2014. The age distribution revealed that children (especially those <3 years old) and old people (>50 years) were both high risk groups to be infected by HCoV. Of the 294 HCoV positive patients, 34.69% (101 cases) were co-infected by other common respiratory viruses, and influenza virus was the most common co-infecting virus (30/101, 29.70%). Fifteen HCoV-OC43 positive samples of 2013–2014 were selected for S gene sequencing and phylogenetic analysis, and the results showed that the 15 strains could be divided into 2 clusters in the phylogenetic tree, 12 strains of which formed a separate cluster that was closer to genotype G found in Malaysia. It was revealed for the first time that genotype B and genotype G of HCoV-OC43 co-circulated and the newly defined genotype G was epidemic as a dominant genotype during 2013–2014 in Guanzhou, south China.
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Affiliation(s)
- Su-Fen Zhang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong Province, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Clinical Laboratory and Institute of Medical Genetics, Women and Children's Healthcare Hospital of Zhuhai City, Zhuhai, Guangdong Province, China
| | - Jiu-Ling Tuo
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong Province, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Sun Yat-sen University-University of Hong Kong Joint Laboratory of Infectious Disease Surveillance, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Xu-Bin Huang
- Medical ICU, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Xun Zhu
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong Province, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Sun Yat-sen University-University of Hong Kong Joint Laboratory of Infectious Disease Surveillance, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Ding-Mei Zhang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong Province, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Sun Yat-sen University-University of Hong Kong Joint Laboratory of Infectious Disease Surveillance, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Kai Zhou
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong Province, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Sun Yat-sen University-University of Hong Kong Joint Laboratory of Infectious Disease Surveillance, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Lei Yuan
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong Province, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Sun Yat-sen University-University of Hong Kong Joint Laboratory of Infectious Disease Surveillance, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Hong-Jiao Luo
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong Province, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Sun Yat-sen University-University of Hong Kong Joint Laboratory of Infectious Disease Surveillance, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Bo-Jian Zheng
- Sun Yat-sen University-University of Hong Kong Joint Laboratory of Infectious Disease Surveillance, Sun Yat-sen University, Guangzhou, Guangdong Province, China.,Department of Microbiology, University of Hong Kong, Hong Kong SAR, China
| | - Kwok-Yung Yuen
- Sun Yat-sen University-University of Hong Kong Joint Laboratory of Infectious Disease Surveillance, Sun Yat-sen University, Guangzhou, Guangdong Province, China.,Department of Microbiology, University of Hong Kong, Hong Kong SAR, China
| | - Meng-Feng Li
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong Province, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Sun Yat-sen University-University of Hong Kong Joint Laboratory of Infectious Disease Surveillance, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Kai-Yuan Cao
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong Province, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Sun Yat-sen University-University of Hong Kong Joint Laboratory of Infectious Disease Surveillance, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Lin Xu
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong Province, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Sun Yat-sen University-University of Hong Kong Joint Laboratory of Infectious Disease Surveillance, Sun Yat-sen University, Guangzhou, Guangdong Province, China
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21
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Zeng ZQ, Chen DH, Tan WP, Qiu SY, Xu D, Liang HX, Chen MX, Li X, Lin ZS, Liu WK, Zhou R. Epidemiology and clinical characteristics of human coronaviruses OC43, 229E, NL63, and HKU1: a study of hospitalized children with acute respiratory tract infection in Guangzhou, China. Eur J Clin Microbiol Infect Dis 2017; 37:363-369. [PMID: 29214503 PMCID: PMC5780525 DOI: 10.1007/s10096-017-3144-z] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 11/14/2017] [Indexed: 01/06/2023]
Abstract
Human coronaviruses (HCoV) OC43, 229E, NL63, and HKU1 are common respiratory viruses which cause various respiratory diseases, including pneumonia. There is a paucity of evidence on the epidemiology and clinical manifestations of these four HCoV strains worldwide. We collected 11,399 throat swabs from hospitalized children with acute respiratory tract infection from July 2009 to June 2016 in Guangzhou, China. These were tested for four strains of HCoV infection using real-time polymerase chain reaction (PCR). HCoV-positive patients were then tested for 11 other respiratory pathogens. 4.3% (489/11399) of patients were positive for HCoV, of which 3.0% were positive for OC43 (346/11399), 0.6% for 229E (65/11399), 0.5% for NL63 (60/11399), and 0.3% for HKU1 (38/11399). Patients aged 7–12 months had the highest prevalence of HCoV and OC43 when compared with other age groups (p < 0.001). The peak seasons of infection varied depending on the HCoV strain. Patients infected with a single strain of HCoV infection were less likely to present fever (≥ 38 °C) (p = 0.014) and more likely to present pulmonary rales (p = 0.043) than those co-infected with more than one HCoV strain or other respiratory pathogens. There were also significant differences in the prevalence of certain symptoms, including coughing (p = 0.032), pneumonia (p = 0.026), and abnormal pulmonary rales (p = 0.002) according to the strain of HCoV detected. This retrospective study of the prevalence of four HCoV strains and clinical signs among a large population of pediatric patients in a subtropical region of China provides further insight into the epidemiology and clinical features of HCoV.
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Affiliation(s)
- Zhi-Qi Zeng
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - De-Hui Chen
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, 510120, China
| | - Wei-Ping Tan
- Department of Pediatrics, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510120, China
| | - Shu-Yan Qiu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Duo Xu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Huan-Xi Liang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Mei-Xin Chen
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Xiao Li
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Zheng-Shi Lin
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Wen-Kuan Liu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, 510182, China.
| | - Rong Zhou
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, 510182, China.
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22
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Han X, Zhang DK, Zhang F, Lin JZ, Jiang H, Lan Y, Xiong X, Han L, Yang M, Fu CM. A Novel Strategy for Bitter Taste Masking of Gankeshuangqing Dispersible Tablets Based on Particle Coating Technology. Pharmacogn Mag 2017; 13:400-406. [PMID: 28839363 PMCID: PMC5551356 DOI: 10.4103/pm.pm_240_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 06/27/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Currently, acute upper respiratory tract infections (AURTIs) are increasingly becoming a significant health burden. Gankeshuangqing dispersible tablets (GKSQDT) which have a good effect on treating AURTIs. GKSQDT is composed of baicalin and andrographolide. However, its severe bitterness limits application of patients. Due to the addition of plentiful accessories, common masking methods are unsuitable for GKSQDT. It is thus necessary to develop a new masking method. MATERIALS AND METHODS The Previous study showed that baicalin was less bitter than andrographolide. Thus, particle coating technology was adapted to prepare composite particles that baicalin coated on the surface of andrographolide to decrease bitterness. Initially, particle size of baicalin and coating time of composite was investigated to prepare composite. Then, scanning electron microscopy, wettability, and infrared (IR) spectrogram were used to characterize the microstructure of composite. Furthermore, electronic tongue test, animal preference experiment, and human sensory test were applied to evaluate the masking effect. RESULTS To produce composite, baicalin should be ground in vibromill for 6 min. Then, andrographolide fine powder was added to grind together for 6 min. Contact angle of composite was smaller than mixture, and more similar to baicalin. Other physical characterization including microstructure, wettability, and IR also suggested that andrographolide was successfully coated by baicalin superfine. Furthermore, taste-masking test indicated taste-masked tablets was less bitter than original tablets. CONCLUSION The study indicated that particle coating technology can be used for taste masking of GKSQDT without adding other substance. Moreover, it provides a new strategy of taste masking for national medicine. SUMMARY A new strategy to mask bitterness without adding any other substance based on coating technology was providedThe masking effect was confirmed by electronic tongue test, animal preference experiment and human sensory test. Abbreviations used: AURTIs: Acute Upper Respiratory Tract Infections; GSQDT: Gankeshuangqing Dispersible Tablets; IR: Infrared Spectrogram; LHPC: Low-substituted Hydroxypropyl Cellulose; CAs: Contact Angles; FTIR: Fourier Transform Infrared Spectra.
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Affiliation(s)
- Xue Han
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, PR China
| | - Ding-Kun Zhang
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, PR China
| | - Fang Zhang
- Pharmacy, Maternal and Child Health Care Hospital of Changzhi, Changzhi 046011, PR China
| | - Jun-Zhi Lin
- Central Laboratory, The Affiliated Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Chengdu 610072, PR China
| | - Hong Jiang
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, PR China
| | - Yang Lan
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, PR China
| | - Xi Xiong
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, PR China
| | - Li Han
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, PR China
| | - Ming Yang
- Key Laboratory of Modern Preparation of Traditional Chinese Medicine, Ministry of Education, Jiangxi University of Traditional Chinese Medicine, Nanchang 330004, PR China
| | - Chao-Mei Fu
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, PR China
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23
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Kanwar A, Selvaraju S, Esper F. Human Coronavirus-HKU1 Infection Among Adults in Cleveland, Ohio. Open Forum Infect Dis 2017; 4:ofx052. [PMID: 28616442 PMCID: PMC5466428 DOI: 10.1093/ofid/ofx052] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 03/20/2017] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Human coronaviruses (CoV) have been long recognized as a common cause of respiratory tract disease including severe respiratory tract illness. Coronavirus-HKU1 has been described predominantly among children less than 5 years of age in the United States with few studies characterizing the disease spectrum among adults. METHODS Nasopharyngeal specimens of patients with respiratory symptoms were analyzed for CoV-HKU1 by NxTAG Respiratory Pathogen Panel multiplex assay from February 7, 2016 to April 30, 2016. Epidemiologic, clinical, and laboratory data were collected on adults (patients >18 years) whose samples screened positive. RESULTS Of 832 adult respiratory specimens screened, 13 (1.6%) cases of CoV-HKU1 were identified. Adults age ranged between 23 and 75 years and 6 (46%) were males. All of whom had 1 or more respiratory symptoms, and 5 (38%) also reported 1 or more gastrointestinal symptoms. Eleven (85%) reported history of smoking and 5 (38%) used inhaled steroids. Seven (54%) required hospitalization, 5 (71%) of these needed supplemental oxygen, and 2 (29%) were admitted to intensive care. Median length of hospitalization was 5 days. Eight (62%) received antibiotics despite identification of CoV-HKU1. Infectious work-up in 1 patient who died did not reveal any other pathogen. In 2 (15%) CoV-HKU1-positive adults, the only viral coinfection detected was influenza A. CONCLUSIONS Coronavirus-HKU1 accounted for 1.6% of adult respiratory infections and should be considered in differential diagnosis of severe respiratory illnesses among adults.
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Affiliation(s)
- Anubhav Kanwar
- Department of Internal Medicine, Division of Infectious Diseases and HIV Medicine and
| | - Suresh Selvaraju
- Department of Pathology, MetroHealth Medical Center, Cleveland, Ohio
| | - Frank Esper
- Department of Pediatrics, Division of Infectious Diseases, University Hospitals, Cleveland Medical Center, Ohio
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24
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Hu J, Ma L, Wang H, Yan H, Zhang D, Li Z, Jiang J, Li Y. A novel benzo-heterocyclic amine derivative N30 inhibits influenza virus replication by depression of Inosine-5'-Monophospate Dehydrogenase activity. Virol J 2017; 14:55. [PMID: 28298229 PMCID: PMC5353780 DOI: 10.1186/s12985-017-0724-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 03/07/2017] [Indexed: 01/02/2023] Open
Abstract
BACKGROUD Influenza virus is still a huge threat to the world-wide public health. Host inosine-5'- monophosphate dehydrogenase (IMPDH) involved in the synthesis of guanine nucleotides, is known to be a potential target to inhibit the replication of viruses. Herein, we evaluated antiviral activity of a benzo-heterocyclic amine derivative N30, which was designed to inhibit IMPDH. RESULTS The results demonstrated that N30 inhibited the replication of H1N1, H3N2, influenza B viruses, including oseltamivir and amantadine resistant strains in vitro. Mechanistically, neuraminidase inhibition assay and hemagglutination inhibition assay suggested that N30 did not directly target the two envelope glycoproteins required for viral adsorption or release. Instead, the compound could depress the activity of IMPDH type II. Based on these findings, we further confirmed that N30 provided a strong inhibition on the replication of respiratory syncytial virus, coronavirus, enterovirus 71 and a diverse strains of coxsackie B virus. CONCLUSIONS We identified the small molecule N30, as an inhibitor of IMPDH, might be a potential candidate to inhibit the replication of various viruses.
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Affiliation(s)
- Jin Hu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Linlin Ma
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huiqiang Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haiyan Yan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dajun Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhuorong Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiandong Jiang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuhuan Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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25
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Madhi A, Ghalyanchilangeroudi A, Soleimani M. Evidence of human coroanvirus (229E), in patients with respiratory infection, Iran, 2015: the first report. IRANIAN JOURNAL OF MICROBIOLOGY 2016; 8:316-320. [PMID: 28149491 PMCID: PMC5277600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
BACKGROUND AND OBJECTIVES Human coronaviruses (HCoVs) are one of the main causes of upper respiratory tract infections in humans. While more often responsible for mild illness, they have been associated with illnesses that require hospitalization. MATERIALS AND METHODS 270 Samples from patients hospitalized with the respiratory infection during the autumn season of 2015 were evaluated for the presence of four HCoVs (OC43, 229E, HUK1, and NL63) using an optimized SYBR green RT-PCR assay. RESULTS Fifteen HCoV-229E positive samples were identified (5.5 % positive). 85% of positive samples were male with the range of age between 12- 75 years old. CONCLUSION It is the first comprehensive study on determination of the role of human coronaviruses in respiratory infections in Iran. Our data provide a novel insight into the epidemiology of HCoVs in Iran. Further studies are needed and should include the isolation and molecular characterization of HCoVs in Iran.
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Affiliation(s)
- Ali Madhi
- Department of Microbiology, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Arash Ghalyanchilangeroudi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran,Corresponding author: Arash Ghalyanchi Langeroudi, Department of Microbiology, Faculty of Veterinary Medicine, University of Tehran, Azadi Ave, Tehran, Iran. PO.Cod:1419963111., Tel: 021-61117154, Fax: 021-66933222,
| | - Mohammad Soleimani
- Department of Microbiology, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran
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26
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Soonnarong R, Thongpan I, Payungporn S, Vuthitanachot C, Vuthitanachot V, Vichiwattana P, Vongpunsawad S, Poovorawan Y. Molecular epidemiology and characterization of human coronavirus in Thailand, 2012-2013. SPRINGERPLUS 2016; 5:1420. [PMID: 27625974 PMCID: PMC4999384 DOI: 10.1186/s40064-016-3101-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 08/18/2016] [Indexed: 02/02/2023]
Abstract
BACKGROUND Coronavirus causes respiratory infections in humans. To determine the prevalence of human coronavirus (HCoV) infection among patients with influenza-like illness, 5833 clinical samples from nasopharyngeal swabs and aspirates collected between January 2012 and December 2013 were examined. RESULTS HCoV was found in 46 (0.79 %) samples. There were 19 (0.32 %) HCoV-HKU1, 19 (0.32 %) HCoV-NL63, 5 (0.09 %) HCoV-229E, and 3 (0.05 %) HCoV-OC43. None of the sample tested positive for MERS-CoV. The majority (54 %) of the HCoV-positive patients were between the ages of 0 and 5 years. HCoV was detected throughout the 2-year period and generally peaked from May to October, which coincided with the rainy season. Phylogenetic trees based on the alignment of the spike (S) gene sequences suggest an emergence of a new clade for HCoV-229E. CONCLUSIONS The data in this study provide an insight into the prevalence of the recent circulating HCoVs in the region.
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Affiliation(s)
- Rapeepun Soonnarong
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Ilada Thongpan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sunchai Payungporn
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | | | - Preeyaporn Vichiwattana
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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27
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Al-Khannaq MN, Ng KT, Oong XY, Pang YK, Takebe Y, Chook JB, Hanafi NS, Kamarulzaman A, Tee KK. Molecular epidemiology and evolutionary histories of human coronavirus OC43 and HKU1 among patients with upper respiratory tract infections in Kuala Lumpur, Malaysia. Virol J 2016; 13:33. [PMID: 26916286 PMCID: PMC4766700 DOI: 10.1186/s12985-016-0488-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/11/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Despite the worldwide circulation of human coronavirus OC43 (HCoV-OC43) and HKU1 (HCoV-HKU1), data on their molecular epidemiology and evolutionary dynamics in the tropical Southeast Asia region is lacking. METHODS The study aimed to investigate the genetic diversity, temporal distribution, population history and clinical symptoms of betacoronavirus infections in Kuala Lumpur, Malaysia between 2012 and 2013. A total of 2,060 adults presented with acute respiratory symptoms were screened for the presence of betacoronaviruses using multiplex PCR. The spike glycoprotein, nucleocapsid and 1a genes were sequenced for phylogenetic reconstruction and Bayesian coalescent inference. RESULTS A total of 48/2060 (2.4 %) specimens were tested positive for HCoV-OC43 (1.3 %) and HCoV-HKU1 (1.1 %). Both HCoV-OC43 and HCoV-HKU1 were co-circulating throughout the year, with the lowest detection rates reported in the October-January period. Phylogenetic analysis of the spike gene showed that the majority of HCoV-OC43 isolates were grouped into two previously undefined genotypes, provisionally assigned as novel lineage 1 and novel lineage 2. Sign of natural recombination was observed in these potentially novel lineages. Location mapping showed that the novel lineage 1 is currently circulating in Malaysia, Thailand, Japan and China, while novel lineage 2 can be found in Malaysia and China. Molecular dating showed the origin of HCoV-OC43 around late 1950s, before it diverged into genotypes A (1960s), B (1990s), and other genotypes (2000s). Phylogenetic analysis revealed that 27.3 % of the HCoV-HKU1 strains belong to genotype A while 72.7 % belongs to genotype B. The tree root of HCoV-HKU1 was similar to that of HCoV-OC43, with the tMRCA of genotypes A and B estimated around the 1990s and 2000s, respectively. Correlation of HCoV-OC43 and HCoV-HKU1 with the severity of respiratory symptoms was not observed. CONCLUSIONS The present study reported the molecular complexity and evolutionary dynamics of human betacoronaviruses among adults with acute respiratory symptoms in a tropical country. Two novel HCoV-OC43 genetic lineages were identified, warranting further investigation on their genotypic and phenotypic characteristics.
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Affiliation(s)
| | - Kim Tien Ng
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Xiang Yong Oong
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Yong Kek Pang
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Yutaka Takebe
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
- AIDS Research Center, National Institute of Infectious Diseases, Toyama, Shinjuku-ku, Tokyo, Japan.
- School of Medicine, Yokohama City University, Yokohama, Kanagawa, Japan.
| | - Jack Bee Chook
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Nik Sherina Hanafi
- Department of Primary Care Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Adeeba Kamarulzaman
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Kok Keng Tee
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
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28
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Sipulwa LA, Ongus JR, Coldren RL, Bulimo WD. Molecular characterization of human coronaviruses and their circulation dynamics in Kenya, 2009-2012. Virol J 2016; 13:18. [PMID: 26833249 PMCID: PMC4736488 DOI: 10.1186/s12985-016-0474-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 01/20/2016] [Indexed: 12/02/2022] Open
Abstract
Background Human Coronaviruses (HCoV) are a common cause of respiratory illnesses and are responsible for considerable morbidity and hospitalization across all age groups especially in individuals with compromised immunity. There are six known species of HCoV: HCoV-229E, HCoV-NL63, HCoV-HKU1, HCoV-OC43, MERS-CoV and SARS-HCoV. Although studies have shown evidence of global distribution of HCoVs, there is limited information on their presence and distribution in Kenya. Methods HCoV strains that circulated in Kenya were retrospectively diagnosed and molecularly characterized. A total of 417 nasopharyngeal specimens obtained between January 2009 and December 2012 from around Kenya were analyzed by a real time RT-PCR using HCoV-specific primers. HCoV-positive specimens were subsequently inoculated onto monolayers of LL-CMK2 cells. The isolated viruses were characterized by RT-PCR amplification and sequencing of the partial polymerase (pol) gene. Results The prevalence of HCoV infection was as follows: out of the 417 specimens, 35 (8.4 %) were positive for HCoV, comprising 10 (2.4 %) HCoV-NL63, 12 (2.9 %) HCoV-OC43, 9 (2.1 %) HCoV-HKU1, and 4 (1 %) HCoV-229E. The Kenyan HCoV strains displayed high sequence homology to the prototypes and contemporaneous strains. Evolution analysis showed that the Kenyan HCoV-OC43 and HCoV-NL63 isolates were under purifying selection. Phylogenetic evolutionary analyses confirmed the identities of three HCoV-HKU1, five HCoV-NL63, eight HCoV-OC43 and three HCoV-229E. Conclusions There were yearly variations in the prevalence and circulation patterns of individual HCoVs in Kenya. This paper reports on the first molecular characterization of human Coronaviruses in Kenya, which play an important role in causing acute respiratory infections among children.
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Affiliation(s)
- Lenata A Sipulwa
- College of Health Sciences (COHES), Jomo Kenyatta University of Agriculture and Technology, (JKUAT), Nairobi, Kenya.
| | - Juliette R Ongus
- College of Health Sciences (COHES), Jomo Kenyatta University of Agriculture and Technology, (JKUAT), Nairobi, Kenya.
| | - Rodney L Coldren
- Department of Emerging Infectious Diseases, US Army Medical Research Unit-Kenya, P.O. Box 606 00621, Village Market, Nairobi, Kenya. .,Special Foreign Activity of the Walter Reed Army Institute of Research, Silver Spring, MD, USA.
| | - Wallace D Bulimo
- Department of Emerging Infectious Diseases, US Army Medical Research Unit-Kenya, P.O. Box 606 00621, Village Market, Nairobi, Kenya. .,Special Foreign Activity of the Walter Reed Army Institute of Research, Silver Spring, MD, USA. .,Department of Biochemistry, School of Medicine, University of Nairobi, Nairobi, Kenya.
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29
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Niu P, Shen J, Zhu N, Lu R, Tan W. Two-tube multiplex real-time reverse transcription PCR to detect six human coronaviruses. Virol Sin 2016; 31:85-8. [PMID: 26826078 PMCID: PMC7091384 DOI: 10.1007/s12250-015-3653-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Peihua Niu
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jun Shen
- Children's Hospital of Fudan University, Shanghai, 200032, China
| | - Na Zhu
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Roujian Lu
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Wenjie Tan
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
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30
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Wang Y, Zhu N, Li Y, Lu R, Wang H, Liu G, Zou X, Xie Z, Tan W. Metagenomic analysis of viral genetic diversity in respiratory samples from children with severe acute respiratory infection in China. Clin Microbiol Infect 2016; 22:458.e1-9. [PMID: 26802214 PMCID: PMC7172101 DOI: 10.1016/j.cmi.2016.01.006] [Citation(s) in RCA: 52] [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: 10/09/2015] [Revised: 12/21/2015] [Accepted: 01/11/2016] [Indexed: 12/11/2022]
Abstract
Severe acute respiratory infection (SARI) in children is thought to be mainly caused by infection with various viruses, some of which have been well characterized; however, analyses of respiratory tract viromes among children with SARI versus those without are limited. In this study, nasopharyngeal swabs from children with and without SARI (135 versus 15) were collected in China between 2008 and 2010 and subjected to multiplex metagenomic analyses using a next-generation sequencing platform. The results show that members of the Paramyxoviridae, Coronaviridae, Parvoviridae, Orthomyxoviridae, Picornaviridae, Anelloviridae and Adenoviridae families represented the most abundant species identified (>50% genome coverage) in the respiratory tracts of children with SARI. The viral population found in the respiratory tracts of children without SARI was less diverse and mainly dominated by the Anelloviridae family with only a small proportion of common epidemic respiratory viruses. Several almost complete viral genomes were assembled, and the genetic diversity was determined among several samples based on next-generation sequencing. This research provides comprehensive mapping of the viromes of children with SARI and indicates high heterogeneity of known viruses present in the childhood respiratory tract, which may benefit the detection and prevention of respiratory disease.
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Affiliation(s)
- Y Wang
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China
| | - N Zhu
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China
| | - Y Li
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China
| | - R Lu
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China
| | - H Wang
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China
| | - G Liu
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China
| | - X Zou
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China
| | - Z Xie
- Key Laboratory of Major Diseases in Children and National Key Discipline of Paediatrics Capital Medical University, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - W Tan
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, China.
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Berry M, Fielding BC, Gamieldien J. Potential Broad Spectrum Inhibitors of the Coronavirus 3CLpro: A Virtual Screening and Structure-Based Drug Design Study. Viruses 2015; 7:6642-60. [PMID: 26694449 PMCID: PMC4690886 DOI: 10.3390/v7122963] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 11/16/2015] [Accepted: 11/30/2015] [Indexed: 01/29/2023] Open
Abstract
Human coronaviruses represent a significant disease burden; however, there is currently no antiviral strategy to combat infection. The outbreak of severe acute respiratory syndrome (SARS) in 2003 and Middle East respiratory syndrome (MERS) less than 10 years later demonstrates the potential of coronaviruses to cross species boundaries and further highlights the importance of identifying novel lead compounds with broad spectrum activity. The coronavirus 3CL(pro) provides a highly validated drug target and as there is a high degree of sequence homology and conservation in main chain architecture the design of broad spectrum inhibitors is viable. The ZINC drugs-now library was screened in a consensus high-throughput pharmacophore modeling and molecular docking approach by Vina, Glide, GOLD and MM-GBSA. Molecular dynamics further confirmed results obtained from structure-based techniques. A highly defined hit-list of 19 compounds was identified by the structure-based drug design methodologies. As these compounds were extensively validated by a consensus approach and by molecular dynamics, the likelihood that at least one of these compounds is bioactive is excellent. Additionally, the compounds segregate into 15 significantly dissimilar (p < 0.05) clusters based on shape and features, which represent valuable scaffolds that can be used as a basis for future anti-coronaviral inhibitor discovery experiments. Importantly though, the enriched subset of 19 compounds identified from the larger library has to be validated experimentally.
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Affiliation(s)
- Michael Berry
- South African Medical Research Council Bioinformatics Capacity Development Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa.
- Molecular Biology and Virology Laboratory, Department of Medical BioSciences, Faculty of Natural Sciences, University of the Western Cape, Western Cape, Bellville 7535, South Africa.
| | - Burtram C Fielding
- Molecular Biology and Virology Laboratory, Department of Medical BioSciences, Faculty of Natural Sciences, University of the Western Cape, Western Cape, Bellville 7535, South Africa.
| | - Junaid Gamieldien
- South African Medical Research Council Bioinformatics Capacity Development Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa.
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Recent insights into the development of therapeutics against coronavirus diseases by targeting N protein. Drug Discov Today 2015; 21:562-72. [PMID: 26691874 PMCID: PMC7108309 DOI: 10.1016/j.drudis.2015.11.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/11/2015] [Accepted: 11/30/2015] [Indexed: 12/18/2022]
Abstract
Coronavirus nucleocapsid proteins are appealing drug targets against coronavirus-induced diseases. A variety of compounds targeting the coronavirus nucleocapsid protein have been developed. Many of these compounds show potential antiviral activity.
The advent of severe acute respiratory syndrome (SARS) in the 21st century and the recent outbreak of Middle-East respiratory syndrome (MERS) highlight the importance of coronaviruses (CoVs) as human pathogens, emphasizing the need for development of novel antiviral strategies to combat acute respiratory infections caused by CoVs. Recent studies suggest that nucleocapsid (N) proteins from coronaviruses and other viruses can be useful antiviral drug targets against viral infections. This review aims to provide readers with a concise survey of the structural features of coronavirus N proteins and how these features provide insights into structure-based development of therapeutics against coronaviruses. We will also present our latest results on MERS-CoV N protein and its potential as an antiviral drug target.
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Han HJ, Yu H, Yu XJ. Evidence for zoonotic origins of Middle East respiratory syndrome coronavirus. J Gen Virol 2015; 97:274-280. [PMID: 26572912 PMCID: PMC7087374 DOI: 10.1099/jgv.0.000342] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Middle East respiratory syndrome (MERS) is an emerging infectious disease, caused by Middle East respiratory syndrome coronavirus (MERS-CoV) and is considered to be a zoonosis. However, the natural reservoirs of MERS-CoV remain obscure, with bats and camels as the most suspected sources. In this article, we review the evidence supporting a bat/camel origin of human MERS-CoV infection and current knowledge on the modes of camel-to-human transmission of MERS-CoV.
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Affiliation(s)
- Hui-Ju Han
- School of Public Health, Shandong University, Jinan 250012, Shandong Province, PR China
| | - Hao Yu
- School of Medicine, Fudan University, Shanghai 200433, PR China.,Departments of Pathology and Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555-0609, USA
| | - Xue-Jie Yu
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, USA.,Departments of Pathology and Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555-0609, USA.,School of Public Health, Shandong University, Jinan 250012, Shandong Province, PR China
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34
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Gorse GJ, Donovan MM, Patel GB, Balasubramanian S, Lusk RH. Coronavirus and Other Respiratory Illnesses Comparing Older with Young Adults. Am J Med 2015; 128:1251.e11-20. [PMID: 26087047 PMCID: PMC7093847 DOI: 10.1016/j.amjmed.2015.05.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 05/13/2015] [Accepted: 05/19/2015] [Indexed: 11/01/2022]
Abstract
BACKGROUND Study of human coronavirus and other virus-associated respiratory illnesses is needed to describe their clinical effects on chronically ill, older adults. METHODS A prospective study during 2009 to 2013 clinically assessed acute respiratory illnesses soon after onset and 3 to 4 weeks later in patients aged ≥60 years with chronic lung and heart diseases (group 1, 100 subjects) and healthy adults aged 18 to 40 years (group 2, 101 subjects). Respiratory secretions were tested for nucleic acids of a panel of respiratory viruses. An increase in antibody titer was assessed for 4 coronavirus strains. RESULTS Virus-associated illnesses (29 [39.1%] of 74 illnesses in group 1 and 59 [48.7%] of 121 illnesses in group 2) occurred in all calendar quarters, most commonly in the first and fourth quarters. Coronaviruses (group 1: 14 [18.9%] illnesses; group 2: 26 [21.5%] illnesses) and enteroviruses/rhinoviruses (group 1: 14 [18.9%] illnesses; group 2: 37 [30.6%] illnesses) were most common. Virus co-infections occurred in 10 illnesses. Illnesses with 9 to 11 symptoms were more common in group 1 (17 [23.0%]) than in group 2 (15 [12.4%]) (P < .05). Compared with group 2, more group 1 subjects reported dyspnea, more severe disease of longer duration, and treatment for acute illness with prednisone and antibiotics. Coronavirus-associated illnesses (percent of illnesses, group 1 vs group 2) were characterized by myalgias (21% vs 68%, P < .01), chills (50% vs 52%), dyspnea (71% vs 24%, P < .01), headache (64% vs 72%), malaise (64% vs 84%), cough (86% vs 68%), sputum production (86% vs 60%), sore throat (64% vs 80%), and nasal congestion (93% vs 96%). CONCLUSIONS Respiratory illnesses were commonly associated with coronaviruses and enteroviruses/rhinoviruses affecting chronically ill, older patients more than healthy, young adults.
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Affiliation(s)
- Geoffrey J Gorse
- Section of Infectious Diseases, VA St Louis Health Care System, and Division of Infectious Diseases, Allergy & Immunology, Saint Louis University School of Medicine, St Louis, Mo.
| | - Mary M Donovan
- Research Service, VA St Louis Health Care System, and Division of Infectious Diseases, Allergy & Immunology, Saint Louis University School of Medicine, St Louis, Mo
| | - Gira B Patel
- Research Service, VA St Louis Health Care System, and Division of Infectious Diseases, Allergy & Immunology, Saint Louis University School of Medicine, St Louis, Mo
| | - Sumitra Balasubramanian
- Research Service, VA St Louis Health Care System, and Washington University in St Louis, St Louis, Mo
| | - Rodney H Lusk
- Section of Infectious Diseases, VA St Louis Health Care System, and Division of Infectious Diseases, Allergy & Immunology, Saint Louis University School of Medicine, St Louis, Mo
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Obuchi M, Yagi SI, Oguri A, Takizawa T, Kimura H, Sata T. Outbreak of human bocavirus 1 infection in young children in Toyama, Japan. Jpn J Infect Dis 2015; 68:259-61. [PMID: 25993976 DOI: 10.7883/yoken.jjid.2015.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Hara M, Takao S. Coronavirus Infections in Pediatric Outpatients with Febrile Respiratory Tract Infections in Hiroshima, Japan, over a 3-Year Period. Jpn J Infect Dis 2015; 68:523-5. [PMID: 25971327 DOI: 10.7883/yoken.jjid.2014.591] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Previously, we conducted a 3-year prospective study to determine the viral causes of acute respiratory tract infections among 495 febrile pediatric outpatients. We collected 495 nasopharyngeal aspirate specimens, and used both real-time PCR assays and viral culture to test each for respiratory viruses other than coronavirus. Here, we used real-time PCR to test the 495 archival specimens for four human coronavirus strains. We identified 15 coronavirus-positive specimens: eight with OC43, 5 with NL63, 2 with HKU1, and none with 229E. Of the 15 children (5 boys) infected with human coronavirus, the mean age was 3.5 years, and the age range was 1.1 to 5.8 years; one child was diagnosed with lower respiratory infection; the other 14 were diagnosed with upper respiratory infection. Of these 15 patients, none were hospitalized, 5 were infected with coronavirus alone, 8 were co-infected with another virus, and 2 were co-infected with 2 other viruses. The multi-virus infections involved 6 adenoviruses, 3 respiratory syncytial viruses, 2 parainfluenza viruses, and 1 rhinovirus. In conclusion, the burden of human coronaviruses was relatively light among this cohort of 495 pediatric outpatients, and the incidence of these infections was low.
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Liu J, Ai H, Xiong Y, Li F, Wen Z, Liu W, Li T, Qin K, Wu J, Liu Y. Prevalence and correlation of infectious agents in hospitalized children with acute respiratory tract infections in Central China. PLoS One 2015; 10:e0119170. [PMID: 25751402 PMCID: PMC4353725 DOI: 10.1371/journal.pone.0119170] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 01/10/2015] [Indexed: 11/20/2022] Open
Abstract
Acute respiratory tract infections (ARTIs) are associated with significant morbidity and mortality worldwide, especially in children under the age of 5 years. Almost 2 million children die from ARTIs each year, and most of them are from developing countries. The prevalence and correlation of pathogens in ARTIs are poorly understood, but are critical for improving case prevention, treatment, and management. In this study, we investigated the prevalence and correlation of infectious agents in children with ARTIs. A total of 39,756 children with one or more symptoms, including fever, cough, sore throat, tonsillitis, pharyngitis, herpangina, pneumonia, and bronchiolitis, were enrolled in the study. All patients were hospitalized in Wuhan Children’s Hospital between October 1, 2010 and September 30, 2012, and were evaluated for infectious agents. Pathogens, including Mycoplasma pneumoniae, influenza A virus, influenza B virus, adenoviruses, respiratory syncytial virus, parainfluenza virus, Legionella pneumophila, Chlamydophila pneumoniae, and Coxiella burnetii, were screened simultaneously in patient blood samples using anti-pathogen IgM tests. Regression analysis was used to reveal correlations among the pathogens. Our results showed that one or more pathogens were identified in 10,206 patients, and that Mycoplasma pneumoniae, adenoviruses, and influenza B virus were the leading infectious agents. Mixed-infections of pathogens were detected in 2,391 cases, with Mycoplasma pneumoniae as the most frequent pathogen. The most common agents in the co-infections were Mycoplasma pneumoniae and influenza B virus. Regression analysis revealed a linear correlation between the proportion of mixed infections and the incidence of multi-pathogen infections. The prevalence of infectious agents in children with ARTIs was determined. Equations were established to estimate multiple infections by single-pathogen detection. This revealed a linear correlation for pathogens in children with ARTIs. This study provides useful information for improving case prevention and management.
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Affiliation(s)
- Jia Liu
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, China
| | - Hongwu Ai
- Department of Clinical Laboratory, Wuhan Children’s Hospital, Wuhan, China
| | - Ying Xiong
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, China
| | - Fu Li
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhou Wen
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, China
| | - Weiyong Liu
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, China
| | - Tongya Li
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, China
| | - Kai Qin
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, China
| | - Jianguo Wu
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail: (JW); (YL)
| | - Yingle Liu
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail: (JW); (YL)
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Identification of new respiratory viruses in the new millennium. Viruses 2015; 7:996-1019. [PMID: 25757061 PMCID: PMC4379558 DOI: 10.3390/v7030996] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/23/2015] [Accepted: 02/26/2015] [Indexed: 12/13/2022] Open
Abstract
The rapid advancement of molecular tools in the past 15 years has allowed for the retrospective discovery of several new respiratory viruses as well as the characterization of novel emergent strains. The inability to characterize the etiological origins of respiratory conditions, particularly in children, led several researchers to pursue the discovery of the underlying etiology of disease. In 2001, this led to the discovery of human metapneumovirus (hMPV) and soon following that the outbreak of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) promoted an increased interest in coronavirology and the latter discovery of human coronavirus (HCoV) NL63 and HCoV-HKU1. Human bocavirus, with its four separate lineages, discovered in 2005, has been linked to acute respiratory tract infections and gastrointestinal complications. Middle East Respiratory Syndrome coronavirus (MERS-CoV) represents the most recent outbreak of a completely novel respiratory virus, which occurred in Saudi Arabia in 2012 and presents a significant threat to human health. This review will detail the most current clinical and epidemiological findings to all respiratory viruses discovered since 2001.
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Oany AR, Ahmad SAI, Hossain MU, Jyoti TP. Identification of highly conserved regions in L-segment of Crimean-Congo hemorrhagic fever virus and immunoinformatic prediction about potential novel vaccine. Adv Appl Bioinform Chem 2015; 8:1-10. [PMID: 25609983 PMCID: PMC4293217 DOI: 10.2147/aabc.s75250] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne zoonotic viral disease with a disease fatality rate between 15% and 70%. Despite the wide range of distribution, the virus (CCHFV) is basically endemic in Africa, Asia, eastern Europe, and the Middle East. Acute febrile illness associated with petechiae, disseminated intravascular coagulation, and multiple-organ failure are the main symptoms of the disease. With all these fatal effects, CCHFV is considered a huge threat as no successful therapeutic approach is currently available for the treatment of this disease. In the present study, we have used the immunoinformatics approach to design a potential epitope-based vaccine against the RNA-dependent RNA polymerase-L of CCHFV. Both the T-cell and B-cell epitopes were assessed, and the epitope "DCSSTPPDR" was found to be the most potential one, with 100% conservancy among all the strains of CCHFV. The epitope was also found to interact with both type I and II major histocompatibility complex molecules and is considered nonallergenic as well. In vivo study of our proposed peptide is advised for novel universal vaccine production, which might be an effective path to prevent CCHF disease.
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Affiliation(s)
- Arafat Rahman Oany
- Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Santosh, Tangail, Bangladesh
| | - Shah Adil Ishtiyaq Ahmad
- Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Santosh, Tangail, Bangladesh
| | - Mohammad Uzzal Hossain
- Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Santosh, Tangail, Bangladesh
| | - Tahmina Pervin Jyoti
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
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Matoba Y, Abiko C, Ikeda T, Aoki Y, Suzuki Y, Yahagi K, Matsuzaki Y, Itagaki T, Katsushima F, Katsushima Y, Mizuta K. Detection of the human coronavirus 229E, HKU1, NL63, and OC43 between 2010 and 2013 in Yamagata, Japan. Jpn J Infect Dis 2014; 68:138-41. [PMID: 25420656 DOI: 10.7883/yoken.jjid.2014.266] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The available literature on human coronaviruses (HCoVs) in Japan is limited to epidemiological studies conducted over a maximum of 1 year. We conducted a 4-year study of HCoVs by analyzing 4,342 respiratory specimens obtained in Yamagata, Japan, between January 2010 and December 2013. A pan-coronavirus reverse transcription-PCR screening assay was performed, and all HCoV-positive specimens were subsequently confirmed by sequencing of the PCR products. We detected in 332 (7.6%) HCoV strains during the study period, comprising 133 (3.1%) HCoV-NL63, 83 (1.9%) HCoV-HKU1, 78 (1.8%) HCoV-OC43, and 38 (0.9%) HCoV-229E strains. HCoV detection per year ranged from 3.5% to 9.7%. HCoVs were detected mainly in winter, with January (28.5%) and February (25.3%) 2011 and December 2012 (14.6%) being the only months in which HCoV-NL63 detection per month exceeded 10.0%. HCoV-HKU1 displayed clear biennial peaks in January (18.3%) and February (10.7%) 2010 and in February (18.8%) and March (14.7%) 2012. The peak detection of HCoV-OC43 was 13.6% in November 2010, while that of HCoV-229E was 10.8% in March 2013. Our results indicated that there may be annual variations in the circulation of individual HCoV strains. Further long-term surveillance is necessary to clarify HCoV prevalence and circulation patterns in Japan.
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Affiliation(s)
- Yohei Matoba
- Department of Microbiology, Yamagata Prefectural Institute of Public Health
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Prevalence and genetic diversity analysis of human coronavirus OC43 among adult patients with acute respiratory infections in Beijing, 2012. PLoS One 2014; 9:e100781. [PMID: 24987849 PMCID: PMC4079595 DOI: 10.1371/journal.pone.0100781] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 05/27/2014] [Indexed: 02/08/2023] Open
Abstract
To determine the prevalence, epidemiology and genetic diversity of human coronavirus OC43 (HCoV-OC43) among adult patients with acute respiratory infections (ARI) in Beijing,five hundred and fifty-nine nasopharyngeal swab samples were collected from adult patients with ARI in Beijing. The prevalence of HCoV-OC43 infection among these patients was assessed using two different OneStep reverse transcription polymerase chain reaction (RT-PCR) assays. The epidemiological profiles of the patients with HCoV-OC43 infection were described. Partial S and N genes of HCoV-OC43 circulating strains were sequenced followed by phylogenetic analysis and amino acid alignment. Our results showed that the prevalence of HCoV-OC43 infection was 12.52% (95% CI: 9.78–15.26%), and the epidemic peak occurred in autumn. Fifty partial S and 40 partial N fragments were obtained from these patients. Phylogenetic analysis based on neighbour-joining method showed that at least three distinct clusters (A, B, C/D) of HCoV-OC43 strains were circulating among adult patients with ARI in Beijing. In addition, some novel unique clusters (UNT) of HCoV-OC43 were found in the S- and N-based phylogenetic trees. Furthermore, consensus amino acids substitutes for each cluster were also found after alignment of partial S or N sequence coding region in this study. In conclusion, we herein describe the prevalence of HCoV-OC43 among adult patients and provide substantial evidence for the genetic diversity of HCoV-OC43 circulating in Beijing.
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Zhang D, He Z, Xu L, Zhu X, Wu J, Wen W, Zheng Y, Deng Y, Chen J, Hu Y, Li M, Cao K. Epidemiology characteristics of respiratory viruses found in children and adults with respiratory tract infections in southern China. Int J Infect Dis 2014; 25:159-64. [PMID: 24927663 PMCID: PMC7110535 DOI: 10.1016/j.ijid.2014.02.019] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 02/18/2014] [Accepted: 02/21/2014] [Indexed: 11/22/2022] Open
Abstract
Background The World Health Organization (WHO) ranks respiratory tract infection (RTI) as the second leading cause of death worldwide for children under 5 years of age. The aim of this work was to evaluate the epidemiology characteristics of respiratory viruses found in children and adults with RTI from July 2009 to June 2012 in southern China. Methods In this work, a total of 14 237 nasopharyngeal swabs (14 237 patients from 25 hospitals) were analyzed, and seven respiratory viruses (influenza virus, respiratory syncytial virus, parainfluenza virus, adenovirus, human metapneumovirus, human coronavirus, human bocavirus) were detected using PCR/RT-PCR from nasopharyngeal swabs. Results The demographic characteristics, viral prevalence, age distribution, seasonal distribution, and pathogen spectrum of the patients with RTIs were analyzed. Co-infection was observed in 483 specimens, but it was more common in male patients, inpatients, children, and young adults. It varied by season, being more prevalent in the spring and summer and less so in the winter. Human coronavirus and human bocavirus were the most common pathogens, tending to occur in co-infection with other respiratory viruses. Conclusions This work adds to our knowledge of the epidemiology characteristics of these seven common respiratory viruses among patients with RTI in southern China. The detection of the specific viral causes of infection provides a useful starting point for an understanding of illness attributable to respiratory infection, and might also provide data relevant to the development of prevention strategies.
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Affiliation(s)
- Dingmei Zhang
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China; Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, Guangdong 510080, China
| | - Zhenjian He
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China; Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, Guangdong 510080, China
| | - Lin Xu
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, Guangdong 510080, China
| | - Xun Zhu
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, Guangdong 510080, China
| | - Jueheng Wu
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, Guangdong 510080, China
| | - Weitao Wen
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, Guangdong 510080, China
| | - Yun Zheng
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, Guangdong 510080, China
| | - Yu Deng
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, Guangdong 510080, China
| | - Jieling Chen
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, Guangdong 510080, China
| | - Yiwen Hu
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, Guangdong 510080, China
| | - Mengfeng Li
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, Guangdong 510080, China.
| | - Kaiyuan Cao
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, Guangdong 510080, China.
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Sharmin R, Islam ABMMK. A highly conserved WDYPKCDRA epitope in the RNA directed RNA polymerase of human coronaviruses can be used as epitope-based universal vaccine design. BMC Bioinformatics 2014; 15:161. [PMID: 24884408 PMCID: PMC4041900 DOI: 10.1186/1471-2105-15-161] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 05/19/2014] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Coronaviruses are the diverse group of RNA virus. From 1960, six strains of human coronaviruses have emerged that includes SARS-CoV and the recent infection by deadly MERS-CoV which is now going to cause another outbreak. Prevention of these viruses is urgent and a universal vaccine for all strain could be a promising solution in this circumstance. In this study we aimed to design an epitope based vaccine against all strain of human coronavirus. RESULTS Multiple sequence alignment (MSA) approach was employed among spike (S), membrane (M), enveloped (E) and nucleocapsid (N) protein and replicase polyprotein 1ab to identify which one is highly conserve in all coronaviruses strains. Next, we use various in silico tools to predict consensus immunogenic and conserved peptide. We found that conserved region is present only in the RNA directed RNA polymerase protein. In this protein we identified one epitope WDYPKCDRA is highly immunogenic and 100% conserved among all available human coronavirus strains. CONCLUSIONS Here we suggest in vivo study of our identified novel peptide antigen in RNA directed RNA polymerase protein for universal vaccine--which may be the way to prevent all human coronavirus disease.
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Affiliation(s)
- Refat Sharmin
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Science Complex Building, Dhaka 1000, Bangladesh
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Dominguez SR, Shrivastava S, Berglund A, Qian Z, Góes LGB, Halpin RA, Fedorova N, Ransier A, Weston PA, Durigon EL, Jerez JA, Robinson CC, Town CD, Holmes KV. Isolation, propagation, genome analysis and epidemiology of HKU1 betacoronaviruses. J Gen Virol 2014; 95:836-848. [PMID: 24394697 DOI: 10.1099/vir.0.059832-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
From 1 January 2009 to 31 May 2013, 15 287 respiratory specimens submitted to the Clinical Virology Laboratory at the Children's Hospital Colorado were tested for human coronavirus RNA by reverse transcription-PCR. Human coronaviruses HKU1, OC43, 229E and NL63 co-circulated during each of the respiratory seasons but with significant year-to-year variability, and cumulatively accounted for 7.4-15.6 % of all samples tested during the months of peak activity. A total of 79 (0.5 % prevalence) specimens were positive for human betacoronavirus HKU1 RNA. Genotypes HKU1 A and B were both isolated from clinical specimens and propagated on primary human tracheal-bronchial epithelial cells cultured at the air-liquid interface and were neutralized in vitro by human intravenous immunoglobulin and by polyclonal rabbit antibodies to the spike glycoprotein of HKU1. Phylogenetic analysis of the deduced amino acid sequences of seven full-length genomes of Colorado HKU1 viruses and the spike glycoproteins from four additional HKU1 viruses from Colorado and three from Brazil demonstrated remarkable conservation of these sequences with genotypes circulating in Hong Kong and France. Within genotype A, all but one of the Colorado HKU1 sequences formed a unique subclade defined by three amino acid substitutions (W197F, F613Y and S752F) in the spike glycoprotein and exhibited a unique signature in the acidic tandem repeat in the N-terminal region of the nsp3 subdomain. Elucidating the function of and mechanisms responsible for the formation of these varying tandem repeats will increase our understanding of the replication process and pathogenicity of HKU1 and potentially of other coronaviruses.
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Affiliation(s)
- Samuel R Dominguez
- Departments of Microbiology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 E 19th Ave, Room P18-9403B, Aurora, CO 80045, USA.,Departments of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 E 19th Ave, Room P18-9403B, Aurora, CO 80045, USA
| | - Susmita Shrivastava
- Department of Pathology and Clinical Medicine, Children's Hospital Colorado, 13123 E 16th Ave, Aurora, CO 80045, USA
| | - Andrew Berglund
- Departments of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 E 19th Ave, Room P18-9403B, Aurora, CO 80045, USA
| | - Zhaohui Qian
- Departments of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 E 19th Ave, Room P18-9403B, Aurora, CO 80045, USA
| | - Luiz Gustavo Bentim Góes
- Interdisciplinary Graduate Program in Biotechnology, University of São Paulo, Av Prof. Lineu Prestes, 2415, ICB-III, Cidade Universitária, CEP: 05508-900, São Paulo, SP - Brazil.,J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
| | - Rebecca A Halpin
- Department of Pathology and Clinical Medicine, Children's Hospital Colorado, 13123 E 16th Ave, Aurora, CO 80045, USA
| | - Nadia Fedorova
- Department of Pathology and Clinical Medicine, Children's Hospital Colorado, 13123 E 16th Ave, Aurora, CO 80045, USA
| | - Amy Ransier
- Department of Pathology and Clinical Medicine, Children's Hospital Colorado, 13123 E 16th Ave, Aurora, CO 80045, USA
| | - Philip A Weston
- Departments of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 E 19th Ave, Room P18-9403B, Aurora, CO 80045, USA
| | - Edison Luiz Durigon
- Interdisciplinary Graduate Program in Biotechnology, University of São Paulo, Av Prof. Lineu Prestes, 2415, ICB-III, Cidade Universitária, CEP: 05508-900, São Paulo, SP - Brazil.,J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
| | - José Antonio Jerez
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av Prof. Lineu Prestes 1374, ICB-II, Cidade Universitária, CEP: 05580-900, São Paulo, SP - Brazil.,J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
| | - Christine C Robinson
- Department of Preventive Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, Cidade Universitária, CEP: 05508-270, Sao Paulo, SP - Brazil
| | - Christopher D Town
- Department of Pathology and Clinical Medicine, Children's Hospital Colorado, 13123 E 16th Ave, Aurora, CO 80045, USA
| | - Kathryn V Holmes
- Departments of Microbiology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 E 19th Ave, Room P18-9403B, Aurora, CO 80045, USA
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Zhou W, Lin F, Teng L, Li H, Hou J, Tong R, Zheng C, Lou Y, Tan W. Prevalence of herpes and respiratory viruses in induced sputum among hospitalized children with non typical bacterial community-acquired pneumonia. PLoS One 2013; 8:e79477. [PMID: 24260230 PMCID: PMC3832587 DOI: 10.1371/journal.pone.0079477] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 09/23/2013] [Indexed: 12/25/2022] Open
Abstract
Objective Few comprehensive studies have searched for viruses in infants and young children with community-acquired pneumonia (CAP) in China. The aim of this study was to investigate the roles of human herpes viruses (HHVs) and other respiratory viruses in CAP not caused by typical bacterial infection and to determine their prevalence and clinical significance. Methods Induced sputum (IS) samples were collected from 354 hospitalised patients (infants, n = 205; children, n = 149) with respiratory illness (CAP or non-CAP) admitted to Wenling Hospital of China. We tested for HHVs and respiratory viruses using PCR-based assays. The epidemiological profiles were also analysed. Results High rate of virus detection (more than 98%) and co-infection (more than 80%) were found among IS samples from 354 hospitalised infants and children with respiratory illness in this study. Of 273 CAP samples tested, CMV (91.6%), HHV-6 (50.9%), RSV (37.4%), EBV (35.5%), HBoV (28.2%), HHV-7 (18.3%) and rhinovirus (17.2%) were the most commonly detected viruses. Of 81 non- CAP samples tested, CMV (63%), RSV (49.4%), HHV-6 (42%), EBV (24.7%), HHV-7 (13.6%) and HBoV (8.6%) were the dominant viruses detected. The prevalence of several viral agents (rhinovirus, bocavirus, adenovirus and CMV) among IS samples of CAP were significantly higher than that of non-CAP control group. We also found the prevalence of RSV coinfection with HHVs was also higher among CAP group than that of non-CAP control. Conclusions With sensitive molecular detection techniques and IS samples, high rates of viral identification were achieved in infants and young children with respiratory illness in a rural area of China. The clinical significance of rhinovirus, bocavirus, adenovirus and HHV (especially CMV) infections should receive greater attention in future treatment and prevention studies of CAP in infants and children.
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Affiliation(s)
- Weimin Zhou
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Feng Lin
- Wenling Affiliated Hospital, Wenzhou Medical College, Wenling, Zhejiang, China
| | - Lingfang Teng
- Wenling Affiliated Hospital, Wenzhou Medical College, Wenling, Zhejiang, China
| | - Hua Li
- Wenling Affiliated Hospital, Wenzhou Medical College, Wenling, Zhejiang, China
| | - Jianyi Hou
- Wenling Affiliated Hospital, Wenzhou Medical College, Wenling, Zhejiang, China
| | - Rui Tong
- Institute of Medical Virology, Wenzhou Medical College, Wenzhou, Zhejiang, China
| | - Changhua Zheng
- Wenling Affiliated Hospital, Wenzhou Medical College, Wenling, Zhejiang, China
| | - Yongliang Lou
- Institute of Medical Virology, Wenzhou Medical College, Wenzhou, Zhejiang, China
| | - Wenjie Tan
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
- Institute of Medical Virology, Wenzhou Medical College, Wenzhou, Zhejiang, China
- * E-mail:
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Al-Tawfiq JA. Middle East Respiratory Syndrome-coronavirus infection: an overview. J Infect Public Health 2013; 6:319-22. [PMID: 23999347 PMCID: PMC7102700 DOI: 10.1016/j.jiph.2013.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 06/05/2013] [Indexed: 11/25/2022] Open
Abstract
Middle East Respiratory Syndrome-coronavirus (MERS-CoV) was reported from a number of countries in the Middle East and Europe with a reported high mortality rate. MERS-CoV was initially isolated from a patient from Bisha, Saudi Arabia. A recent outbreak of MERS-CoV infection was described in a healthcare facility. Although, the recent publications on this topic had shed light on the epidemiology of the disease, many questions remain to be answered.
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Affiliation(s)
- Jaffar A Al-Tawfiq
- Specialty Internal Medicine Unit, Dhahran Health Center, Saudi Aramco Medical Services Organization, Saudi Aramco, Dhahran, Saudi Arabia.
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47
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Measles virus infection of epithelial cells in the macaque upper respiratory tract is mediated by subepithelial immune cells. J Virol 2013; 87:4033-42. [PMID: 23365435 DOI: 10.1128/jvi.03258-12] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Measles virus (MV), one of the most contagious viruses infecting humans, causes a systemic infection leading to fever, immune suppression, and a characteristic maculopapular rash. However, the specific mechanism or mechanisms responsible for the spread of MV into the respiratory epithelium in the late stages of the disease are unknown. Here we show the crucial role of PVRL4 in mediating the spread of MV from immune to epithelial cells by generating a PVRL4 "blind" recombinant wild-type MV and developing a novel in vitro coculture model of B cells with primary differentiated normal human bronchial epithelial cells. We utilized the macaque model of measles to analyze virus distribution in the respiratory tract prior to and at the peak of MV replication. Expression of PVRL4 was widespread in both the lower and upper respiratory tract (URT) of macaques, indicating MV transmission can be facilitated by more than only epithelial cells of the trachea. Analysis of tissues collected at early time points after experimental MV infection demonstrated the presence of MV-infected lymphoid and myeloid cells contacting respiratory tract epithelium in the absence of infected epithelial cells, suggesting that these immune cells seed the infection in vivo. Thereafter, lateral cell-to-cell spread of MV led to the formation of large foci of infected cells in the trachea and high levels of MV infection in the URT, particularly in the nasal cavity. These novel findings have important implications for our understanding of the high transmissibility of measles.
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