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Kovacs D, Mambule I, Read JM, Kiran A, Chilombe M, Bvumbwe T, Aston S, Menyere M, Masina M, Kamzati M, Ganiza TN, Iuliano D, McMorrow M, Bar-Zeev N, Everett D, French N, Ho A. Epidemiology of Human Seasonal Coronaviruses Among People With Mild and Severe Acute Respiratory Illness in Blantyre, Malawi, 2011-2017. J Infect Dis 2024; 230:e363-e373. [PMID: 38365443 PMCID: PMC11322416 DOI: 10.1093/infdis/jiad587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 12/18/2023] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND The aim of this study was to characterize the epidemiology of human seasonal coronaviruses (HCoVs) in southern Malawi. METHODS We tested for HCoVs 229E, OC43, NL63, and HKU1 using real-time polymerase chain reaction (PCR) on upper respiratory specimens from asymptomatic controls and individuals of all ages recruited through severe acute respiratory illness (SARI) surveillance at Queen Elizabeth Central Hospital, Blantyre, and a prospective influenza-like illness (ILI) observational study between 2011 and 2017. We modeled the probability of having a positive PCR for each HCoV using negative binomial models, and calculated pathogen-attributable fractions (PAFs). RESULTS Overall, 8.8% (539/6107) of specimens were positive for ≥1 HCoV. OC43 was the most frequently detected HCoV (3.1% [191/6107]). NL63 was more frequently detected in ILI patients (adjusted incidence rate ratio [aIRR], 9.60 [95% confidence interval {CI}, 3.25-28.30]), while 229E (aIRR, 8.99 [95% CI, 1.81-44.70]) was more frequent in SARI patients than asymptomatic controls. In adults, 229E and OC43 were associated with SARI (PAF, 86.5% and 89.4%, respectively), while NL63 was associated with ILI (PAF, 85.1%). The prevalence of HCoVs was similar between children with SARI and controls. All HCoVs had bimodal peaks but distinct seasonality. CONCLUSIONS OC43 was the most prevalent HCoV in acute respiratory illness of all ages. Individual HCoVs had distinct seasonality that differed from temperate settings.
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Affiliation(s)
- Dory Kovacs
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Ivan Mambule
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Research Department, Joint Clinical Research Centre, Kampala, Uganda
| | - Jonathan M. Read
- Centre for Health Information Computation and Statistics, Lancaster Medical School, Lancaster University, Lancaster, United Kingdom
| | - Anmol Kiran
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Moses Chilombe
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Malaria Alert Centre, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Thandiwe Bvumbwe
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Blantyre Malaria Project, Blantyre, Malawi
| | - Stephen Aston
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Mavis Menyere
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Mazuba Masina
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Moses Kamzati
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Thokozani Namale Ganiza
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Danielle Iuliano
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Meredith McMorrow
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Naor Bar-Zeev
- International Vaccine Access Center, Department of international Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States
| | - Dean Everett
- Department of Pathology and Infectious Diseases, College of Medicine and Health Sciences, Abu Dhabi, United Arab Emirates
- Infection Research Unit, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Neil French
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Antonia Ho
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Medical Research Council-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
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2
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Wilson R, Kovacs D, Crosby M, Ho A. Global Epidemiology and Seasonality of Human Seasonal Coronaviruses: A Systematic Review. Open Forum Infect Dis 2024; 11:ofae418. [PMID: 39113828 PMCID: PMC11304597 DOI: 10.1093/ofid/ofae418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 07/16/2024] [Indexed: 08/10/2024] Open
Abstract
Background We characterized the global epidemiology and seasonality of human coronaviruses (HCoVs) OC43, NL63, 229E, and HKU1. Methods In this systematic review, we searched MEDLINE, EMBASE, Web of Science, SCOPUS, CINAHL, and backward citations for studies published until 1 September 2023. We included studies with ≥12 months of consecutive data and tested for ≥1 HCoV species. Case reports, review articles, animal studies, studies focusing on SARS-CoV-1, SARS-CoV-2, and/or Middle East respiratory syndrome, and those including <100 cases were excluded. Study quality and risk of bias were assessed using Joanna Briggs Institute Critical Appraisal Checklist tools. We reported the prevalence of all HCoVs and individual species. Seasonality was reported for studies that included ≥100 HCoVs annually. This study is registered with PROSPERO, CRD42022330902. Results A total of 201 studies (1 819 320 samples) from 68 countries were included. A high proportion were from China (19.4%; n = 39), whereas the Southern Hemisphere was underrepresented. Most were case series (77.1%, n = 155) with samples from secondary care (74.1%, n = 149). Seventeen (8.5%) studies included asymptomatic controls, whereas 76 (37.8%) reported results for all 4 HCoV species. Overall, OC43 was the most prevalent HCoV. Median test positivity of OC43 and NL63 was higher in children, and 229E and HKU1 in adults. Among 18 studies that described seasonality (17 from the Northern Hemisphere), circulation of all HCoVs mostly peaked during cold months. Conclusions In our comprehensive review, few studies reported the prevalence of individual HCoVs or seasonality. Further research on the burden and circulation of HCoVs is needed, particularly from Africa, South Asia, and Central/South America.
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Affiliation(s)
- Rory Wilson
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Dory Kovacs
- College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, UK
| | - Mairi Crosby
- College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, UK
| | - Antonia Ho
- Medical Research Council-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
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3
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Ilboudo AK, Cissé A, Milucky J, Tialla D, Mirza SA, Diallo AO, Bicaba BW, Charlemagne KJ, Diagbouga PS, Owusu D, Waller JL, Talla-Nzussouo N, Charles MD, Whitney CG, Tarnagda Z. Predictors of severity and prolonged hospital stay of viral acute respiratory infections (ARI) among children under five years in Burkina Faso, 2016-2019. BMC Infect Dis 2024; 24:331. [PMID: 38509462 PMCID: PMC10953152 DOI: 10.1186/s12879-024-09219-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 03/13/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Viruses are the leading etiology of acute respiratory infections (ARI) in children. However, there is limited knowledge on drivers of severe acute respiratory infection (SARI) cases involving viruses. We aimed to identify factors associated with severity and prolonged hospitalization of viral SARI among children < 5 years in Burkina Faso. METHODS Data were collected from four SARI sentinel surveillance sites during October 2016 through April 2019. A SARI case was a child < 5 years with an acute respiratory infection with history of fever or measured fever ≥ 38 °C and cough with onset within the last ten days, requiring hospitalization. Very severe ARI cases required intensive care or had at least one danger sign. Oropharyngeal/nasopharyngeal specimens were collected and analyzed by multiplex real-time reverse-transcription polymerase chain reaction (rRT-PCR) using FTD-33 Kit. For this analysis, we included only SARI cases with rRT-PCR positive test results for at least one respiratory virus. We used simple and multilevel logistic regression models to assess factors associated with very severe viral ARI and viral SARI with prolonged hospitalization. RESULTS Overall, 1159 viral SARI cases were included in the analysis after excluding exclusively bacterial SARI cases (n = 273)very severe viral ARI cases were common among children living in urban areas (AdjOR = 1.3; 95% CI: 1.1-1.6), those < 3 months old (AdjOR = 1.5; 95% CI: 1.1-2.3), and those coinfected with Klebsiella pneumoniae (AdjOR = 1.9; 95% CI: 1.2-2.2). Malnutrition (AdjOR = 2.2; 95% CI: 1.1-4.2), hospitalization during the rainy season (AdjOR = 1.71; 95% CI: 1.2-2.5), and infection with human CoronavirusOC43 (AdjOR = 3; 95% CI: 1.2-8) were significantly associated with prolonged length of hospital stay (> 7 days). CONCLUSION Younger age, malnutrition, codetection of Klebsiella pneumoniae, and illness during the rainy season were associated with very severe cases and prolonged hospitalization of SARI involving viruses in children under five years. These findings emphasize the need for preventive actions targeting these factors in young children.
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Affiliation(s)
- Abdoul Kader Ilboudo
- Laboratoire National de Référence-Grippes (LNR-G), Institut de Recherche en Sciences de la Santé (IRSS), Ouagadougou, Burkina Faso.
| | - Assana Cissé
- Laboratoire National de Référence-Grippes (LNR-G), Institut de Recherche en Sciences de la Santé (IRSS), Ouagadougou, Burkina Faso
| | - Jennifer Milucky
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dieudonné Tialla
- Laboratoire National de Référence-Grippes (LNR-G), Institut de Recherche en Sciences de la Santé (IRSS), Ouagadougou, Burkina Faso
| | - Sara A Mirza
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Alpha Oumar Diallo
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Brice W Bicaba
- Direction de la Protection de la Santé de la Population, Ministère de la Santé, Ouagadougou, Burkina Faso
| | - Kondombo Jean Charlemagne
- Direction de la Protection de la Santé de la Population, Ministère de la Santé, Ouagadougou, Burkina Faso
| | - Potiandi Serge Diagbouga
- Laboratoire National de Référence-Grippes (LNR-G), Institut de Recherche en Sciences de la Santé (IRSS), Ouagadougou, Burkina Faso
| | - Daniel Owusu
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jessica L Waller
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ndahwouh Talla-Nzussouo
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Noguchi Memorial Institute for Medical Research, Legon, Accra, Ghana
- Dexis Professional Services, 1331 Pennsylvania Avenue NW Suite 300, Washington, DC, 20004, USA
| | - Myrna D Charles
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Cynthia G Whitney
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Zekiba Tarnagda
- Laboratoire National de Référence-Grippes (LNR-G), Institut de Recherche en Sciences de la Santé (IRSS), Ouagadougou, Burkina Faso
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Townsend JP, Hassler HB, Lamb AD, Sah P, Alvarez Nishio A, Nguyen C, Tew AD, Galvani AP, Dornburg A. Seasonality of endemic COVID-19. mBio 2023; 14:e0142623. [PMID: 37937979 PMCID: PMC10746271 DOI: 10.1128/mbio.01426-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/04/2023] [Indexed: 11/09/2023] Open
Abstract
IMPORTANCE The seasonality of COVID-19 is important for effective healthcare and public health decision-making. Previous waves of SARS-CoV-2 infections have indicated that the virus will likely persist as an endemic pathogen with distinct surges. However, the timing and patterns of potentially seasonal surges remain uncertain, rendering effective public health policies uninformed and in danger of poorly anticipating opportunities for intervention, such as well-timed booster vaccination drives. Applying an evolutionary approach to long-term data on closely related circulating coronaviruses, our research provides projections of seasonal surges that should be expected at major temperate population centers. These projections enable local public health efforts that are tailored to expected surges at specific locales or regions. This knowledge is crucial for enhancing medical preparedness and facilitating the implementation of targeted public health interventions.
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Affiliation(s)
- Jeffrey P. Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, USA
- Program in Microbiology, Yale University, New Haven, USA
| | - Hayley B. Hassler
- Department of Biostatistics, Yale School of Public Health, New Haven, USA
| | - April D. Lamb
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, USA
| | - Pratha Sah
- Center for Infectious Disease Modeling and Analysis, Yale University, New Haven, USA
| | | | - Cameron Nguyen
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, USA
| | - Alexandra D. Tew
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, USA
| | - Alison P. Galvani
- Center for Infectious Disease Modeling and Analysis, Yale University, New Haven, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, USA
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5
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Tambe LAM, Mathobo P, Munzhedzi M, Bessong PO, Mavhandu-Ramarumo LG. Prevalence and Molecular Epidemiology of Human Coronaviruses in Africa Prior to the SARS-CoV-2 Outbreak: A Systematic Review. Viruses 2023; 15:2146. [PMID: 38005824 PMCID: PMC10675249 DOI: 10.3390/v15112146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Coronaviruses, re-emerging in human populations, cause mild or severe acute respiratory diseases, and occasionally epidemics. This study systematically reviewed human coronavirus (HCoVs) infections in Africa prior to the SARS-CoV-2 outbreak. Forty studies on the prevalence or molecular epidemiology of HCoVs were available from 13/54 African countries (24%). The first published data on HCoV was from South Africa in 2008. Eight studies (20%) reported on HCoV molecular epidemiology. Endemic HCoV prevalence ranged from 0.0% to 18.2%. The prevalence of zoonotic MERS-CoV ranged from 0.0% to 83.5%. Two studies investigated SARS-CoV infection, for which a prevalence of 0.0% was reported. There was heterogeneity in the type of tests used in determining HCoV prevalence. Two studies reported that risk factors for HCoV include exposure to infected animals or humans. The quantity of virologic investigations on HCoV on the African continent was scant, and Africa was not prepared for SARS-CoV-2.
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Affiliation(s)
- Lisa Arrah Mbang Tambe
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Phindulo Mathobo
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Mukhethwa Munzhedzi
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Pascal Obong Bessong
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
- Centre for Global Health Equity, School of Medicine, 1400 University Ave, Charlottesville, VA 22903, USA
| | - Lufuno Grace Mavhandu-Ramarumo
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
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Castillo G, Mora-Díaz JC, Breuer M, Singh P, Nelli RK, Giménez-Lirola LG. Molecular mechanisms of human coronavirus NL63 infection and replication. Virus Res 2023; 327:199078. [PMID: 36813239 PMCID: PMC9944649 DOI: 10.1016/j.virusres.2023.199078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023]
Abstract
Human coronavirus NL63 (HCoV-NL63) is spread globally, causing upper and lower respiratory tract infections mainly in young children. HCoV-NL63 shares a host receptor (ACE2) with severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 but, unlike them, HCoV-NL63 primarily develops into self-limiting mild to moderate respiratory disease. Although with different efficiency, both HCoV-NL63 and SARS-like CoVs infect ciliated respiratory cells using ACE2 as receptor for binding and cell entry. Working with SARS-like CoVs require access to BSL-3 facilities, while HCoV-NL63 research can be performed at BSL-2 laboratories. Thus, HCoV-NL63 could be used as a safer surrogate for comparative studies on receptor dynamics, infectivity and virus replication, disease mechanism, and potential therapeutic interventions against SARS-like CoVs. This prompted us to review the current knowledge on the infection mechanism and replication of HCoV-NL63. Specifically, after a brief overview on the taxonomy, genomic organization and virus structure, this review compiles the current HCoV-NL63-related research in virus entry and replication mechanism, including virus attachment, endocytosis, genome translation, and replication and transcription. Furthermore, we reviewed cumulative knowledge on the susceptibility of different cells to HCoV-NL63 infection in vitro, which is essential for successful virus isolation and propagation, and contribute to address different scientific questions from basic science to the development and assessment of diagnostic tools, and antiviral therapies. Finally, we discussed different antiviral strategies that have been explored to suppress replication of HCoV-NL63, and other related human coronaviruses, by either targeting the virus or enhancing host antiviral mechanisms.
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Affiliation(s)
- Gino Castillo
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Juan Carlos Mora-Díaz
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Mary Breuer
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Pallavi Singh
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA
| | - Rahul K Nelli
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Luis G Giménez-Lirola
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA.
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7
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Ali Dahhas M, M Alkahtani H, Malik A, Almehizia AA, Bakheit AH, Akber Ansar S, AlAbdulkarim AS, S Alrasheed L, Alsenaidy MA. Screening and identification of potential MERS-CoV papain-like protease (PLpro) inhibitors; Steady-state kinetic and Molecular dynamic studies. Saudi Pharm J 2023; 31:228-244. [PMID: 36540698 PMCID: PMC9756750 DOI: 10.1016/j.jsps.2022.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
MERS-CoV belongs to the coronavirus group. Recent years have seen a rash of coronavirus epidemics. In June 2012, MERS-CoV was discovered in the Kingdom of Saudi Arabia, with 2,591 MERSA cases confirmed by lab tests by the end of August 2022 and 894 deaths at a case-fatality ratio (CFR) of 34.5% documented worldwide. Saudi Arabia reported the majority of these cases, with 2,184 cases and 813 deaths (CFR: 37.2%), necessitating a thorough understanding of the molecular machinery of MERS-CoV. To develop antiviral medicines, illustrative investigation of the protein in coronavirus subunits are required to increase our understanding of the subject. In this study, recombinant expression and purification of MERS-CoV (PLpro), a primary goal for the development of 22 new inhibitors, were completed using a high throughput screening methodology that employed fragment-based libraries in conjunction with structure-based virtual screening. Compounds 2, 7, and 20, showed significant biological activity. Moreover, a docking analysis revealed that the three compounds had favorable binding mood and binding free energy. Molecular dynamic simulation demonstrated the stability of compound 2 (2-((Benzimidazol-2-yl) thio)-1-arylethan-1-ones) the strongest inhibitory activity against the PLpro enzyme. In addition, disubstitutions at the meta and para locations are the only substitutions that may boost the inhibitory action against PLpro. Compound 2 was chosen as a MERS-CoV PLpro inhibitor after passing absorption, distribution, metabolism, and excretion studies; however, further investigations are required.
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Key Words
- 3CLpro, 3-Chymotrypsin -like Protease
- ADMET, Absorption, distribution, metabolism, excretion and toxicity
- CFR, Case fatality rate
- DTT, Dithiothreitol
- Drug Design
- Drug Discovery
- E. coli, Escherichia coli
- EDTA, Ethylenediaminetetraacetic acid
- HCoV-, Human Coronavirus
- HIA, Human intestinal absorption
- His-tag, Histidine tag
- IPTG, Isopropyl b-D-1-thiogalactopyranoside
- Inhibitors
- Kan, Kanamicyn
- LB, Luria–Bertani
- MD, Molecular dynamic
- MERS-CoV PLpro Inhibitors
- MOE, Molecular Operating Environment
- MPLpro, MERS papain-like protease
- Molecular Docking
- Molecular dynamic simulation
- Ni-NTA, Nickel-nitrilotri
- Nonstructural proteins
- PLIF, Protein- ligand interaction fingerprint
- Papain-like protease
- Protease
- RMSD, Root Mean Square Deviation
- RMSF, Root Mean Square Fluctuation
- pp1a, Polyprotein 1a
- pp1b, Polyprotein 1b
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Affiliation(s)
- Mohammed Ali Dahhas
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Hamad M Alkahtani
- Department of Pharmaceutical Chemistry, Department Chairman, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Ajamaluddin Malik
- Department of Biochemistry, College of Science, King Saud University. King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | | | - Ahmed H Bakheit
- Department of Pharmaceutical Chemistry, Department Chairman, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Siddique Akber Ansar
- Department of Pharmaceutical Chemistry, Department Chairman, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Abdullah S AlAbdulkarim
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Lamees S Alrasheed
- Department of Pharmaceutical Chemistry, Department Chairman, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Mohammad A Alsenaidy
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
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8
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Li Q, Shah T, Wang B, Qu L, Wang R, Hou Y, Baloch Z, Xia X. Cross-species transmission, evolution and zoonotic potential of coronaviruses. Front Cell Infect Microbiol 2023; 12:1081370. [PMID: 36683695 PMCID: PMC9853062 DOI: 10.3389/fcimb.2022.1081370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/19/2022] [Indexed: 01/09/2023] Open
Abstract
Coronaviruses (CoVs) continuously evolve, crossing species barriers and spreading across host ranges. Over the last two decades, several CoVs (HCoV-229E, HCoV-NL63, HCoV-HKU1, HCoV-OC43, SARS-CoV, MERS-CoV, and SARS-CoV-2) have emerged in animals and mammals, causing significant economic and human life losses. Due to CoV cross-species transmission and the evolution of novel viruses, it is critical to identify their natural reservoiurs and the circumstances under which their transmission occurs. In this review, we use genetic and ecological data to disentangle the evolution of various CoVs in wildlife, humans, and domestic mammals. We thoroughly investigate several host species and outline the epidemiology of CoVs toward specific hosts. We also discuss the cross-species transmission of CoVs at the interface of wildlife, animals, and humans. Clarifying the epidemiology and diversity of species reservoirs will significantly impact our ability to respond to the future emergence of CoVs in humans and domestic animals.
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Affiliation(s)
- Qian Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China,The First Affiliated Hospital & Clinical Medical College, Dali University, Dali, Yunnan, China
| | - Taif Shah
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Binghui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Linyu Qu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Rui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Yutong Hou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Zulqarnain Baloch
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China,*Correspondence: Xueshan Xia,
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9
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Otieno JR, Cherry JL, Spiro DJ, Nelson MI, Trovão NS. Origins and Evolution of Seasonal Human Coronaviruses. Viruses 2022; 14:1551. [PMID: 35891531 PMCID: PMC9320361 DOI: 10.3390/v14071551] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
Four seasonal human coronaviruses (sHCoVs) are endemic globally (229E, NL63, OC43, and HKU1), accounting for 5-30% of human respiratory infections. However, the epidemiology and evolution of these CoVs remain understudied due to their association with mild symptomatology. Using a multigene and complete genome analysis approach, we find the evolutionary histories of sHCoVs to be highly complex, owing to frequent recombination of CoVs including within and between sHCoVs, and uncertain, due to the under sampling of non-human viruses. The recombination rate was highest for 229E and OC43 whereas substitutions per recombination event were highest in NL63 and HKU1. Depending on the gene studied, OC43 may have ungulate, canine, or rabbit CoV ancestors. 229E may have origins in a bat, camel, or an unsampled intermediate host. HKU1 had the earliest common ancestor (1809-1899) but fell into two distinct clades (genotypes A and B), possibly representing two independent transmission events from murine-origin CoVs that appear to be a single introduction due to large gaps in the sampling of CoVs in animals. In fact, genotype B was genetically more diverse than all the other sHCoVs. Finally, we found shared amino acid substitutions in multiple proteins along the non-human to sHCoV host-jump branches. The complex evolution of CoVs and their frequent host switches could benefit from continued surveillance of CoVs across non-human hosts.
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Affiliation(s)
- James R. Otieno
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
| | - Joshua L. Cherry
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - David J. Spiro
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
| | - Martha I. Nelson
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
| | - Nídia S. Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
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10
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Egwang TG, Owalla TJ, Okurut E, Apungia G, Fox A, De Carlo C, Powell RL. Differential pre-pandemic breast milk IgA reactivity against SARS-CoV-2 and circulating human coronaviruses in Ugandan and American mothers. Int J Infect Dis 2021; 112:165-172. [PMID: 34547496 PMCID: PMC8450224 DOI: 10.1016/j.ijid.2021.09.039] [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: 06/28/2021] [Revised: 09/09/2021] [Accepted: 09/15/2021] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE Uganda has registered fewer coronavirus disease 2019 (COVID-19) cases and deaths per capita than Western countries. The lower numbers of cases and deaths might be due to pre-existing cross-immunity induced by circulating common cold human coronaviruses (HCoVs) before the COVID-19 pandemic. To investigate pre-existing mucosal antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, a comparison was performed of IgA reactivity to SARS-CoV-2 and HCoVs in milk from mothers collected in 2018. METHODS Ugandan and United States milk samples were run on an ELISA to measure specific IgA to SARS-CoV-2 and HCoVs NL63, OC43, HKU1, and 229E spike proteins. Pooled plasma from United States SARS-CoV-2-positive and negative cases were positive and negative controls, respectively. RESULTS One Ugandan mother had high milk IgA reactivity against all HCoVs and SARS-CoV-2 spike proteins. Ugandan mothers had significantly higher IgA reactivity against the betacoronavirus HCoV-OC43 than United States mothers (P = 0.018). By contrast, United States mothers had significantly higher IgA reactivity against the alphacoronaviruses HCoV-229E and HCoV-NL63 than Ugandan mothers (P < 0.0001 and P = 0.035, respectively). CONCLUSION Some Ugandan mothers have pre-existing HCoV-induced IgA antibodies against SARS-CoV-2, which may be passed to infants via breastfeeding.
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Affiliation(s)
- Thomas G Egwang
- Human Milk and Lactation Research Center, Med Biotech Laboratories, Kampala, Uganda.
| | - Tonny Jimmy Owalla
- Human Milk and Lactation Research Center, Med Biotech Laboratories, Kampala, Uganda
| | - Emmanuel Okurut
- Human Milk and Lactation Research Center, Med Biotech Laboratories, Kampala, Uganda
| | - Gonzaga Apungia
- Human Milk and Lactation Research Center, Med Biotech Laboratories, Kampala, Uganda
| | - Alisa Fox
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Claire De Carlo
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Rebecca L Powell
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, USA.
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11
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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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12
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Piñana JL, Xhaard A, Tridello G, Passweg J, Kozijn A, Polverelli N, Heras I, Perez A, Sanz J, Berghuis D, Vázquez L, Suárez-Lledó M, Itäla-Remes M, Ozcelik T, Iturrate Basarán I, Karakukcu M, Al Zahrani M, Choi G, Cuesta Casas MA, Batlle Massana M, Viviana A, Blijlevens N, Ganser A, Kuskonmaz B, Labussière-Wallet H, Shaw PJ, Arzu Yegin Z, González-Vicent M, Rocha V, Ferster A, Knelange N, Navarro D, Mikulska M, de la Camara R, Styczynski J. Seasonal Human Coronavirus Respiratory Tract Infection in Recipients of Allogeneic Hematopoietic Stem Cell Transplantation. J Infect Dis 2021; 223:1564-1575. [PMID: 32860509 PMCID: PMC7499673 DOI: 10.1093/infdis/jiaa553] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/27/2020] [Indexed: 11/17/2022] Open
Abstract
Background Little is known about characteristics of seasonal human coronavirus (HCoV) (NL63, 229E, OC43 and HKU1) after allogeneic stem cell transplantation (allo-HCT). Patients and methods this is a collaborative Spanish and European bone marrow transplantation groups retrospective multicentre study, which included allo-HCT recipients (adults and children) with upper and/or lower respiratory tract disease (U/LRTD) caused by seasonal HCoV diagnosed through multiplex PCR assays from January 2012 to January 2019. Results We included 402 allo-HCT recipients who developed 449 HCoV U/LRTD episodes. Median age of recipients was 46 years (range 0.3-73.8 years). HCoV episodes were diagnosed at a median of 222 days after transplantation. The most common HCoV subtype was OC43 (n=170, 38%). LRTD involvement occurred in 121 episodes (27%). HCoV infection frequently required hospitalization (18%), oxygen administration (13%) and intensive care unit (ICU) admission (3%). Three-month overall mortality after HCoV detection was 7% in the whole cohort and 16% in those with LRTD. We identified 3 conditions associated with higher mortality in recipients with LRTD: absolute lymphocyte count <0.1 x10 9/mL [hazard ratio (HR), 10.8], corticosteroid (HR 4.68) and ICU admission (HR 8.22) (p<0.01). Conclusions Seasonal HCoV after allo-HCT may involve the LRTD in many instances, leading to a significant morbidity.
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Affiliation(s)
- Jose Luis Piñana
- Hematology Division, Hospital Universitario y Politécnico La Fe, Valencia, Spain.,CIBERONC, Instituto Carlos III, Madrid, Spain
| | - Aliénor Xhaard
- Service d'Hématologie-Greffe, Hôpital Saint-Louis, Université Paris-Diderot, Paris, France
| | - Gloria Tridello
- Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | | | - Anne Kozijn
- European Society for Blood and Marrow Transplantation Data Office Leiden, Leiden, The Netherlands
| | - Nicola Polverelli
- Unit of Blood Diseases and Stem Cell Transplantation, University of Brescia Azienda Socio Sanitaria Territoriale Spedali Civili di Brescia, Brescia, Italy
| | | | - Ariadna Perez
- Hematology Division, Hospital Clínico de Valencia, Valencia, Spain
| | - Jaime Sanz
- Hematology Division, Hospital Universitario y Politécnico La Fe, Valencia, Spain.,CIBERONC, Instituto Carlos III, Madrid, Spain
| | - Dagmar Berghuis
- Willem Alexander Children's Hospital/Leiden University Medical Center, Leiden, The Netherlands
| | - Lourdes Vázquez
- Hematology Division, Hospital Universitario de Salamanca, Salamanca, Spain
| | | | | | | | | | - Musa Karakukcu
- Erciyes University, Faculty of Medicine, Erciyes Pediatric Bone Marrow Transplant Center, Kayseri, Turkey
| | | | - Goda Choi
- University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Montserrat Batlle Massana
- Hematology Division, Instituto Catalan de Oncologia-Hospital Germans Trias i Pujol, Barcelona, Spain
| | | | | | - Arnold Ganser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation. Hannover Medical School, Hannover, Germany
| | | | | | - Peter J Shaw
- Children's Hospital at Westmead, Sydney, Australia
| | | | | | | | - Alina Ferster
- Children's University Hospital Queen Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Nina Knelange
- Service d'Hématologie-Greffe, Hôpital Saint-Louis, Université Paris-Diderot, Paris, France
| | - David Navarro
- Hematology Division, Hospital Morales Meseguer, Murcia, Spain
| | - Malgorzata Mikulska
- University of Genoa (Dipartimento di Scienze della Salute) and Istituto Nazionale per la Ricerca sul Cancro Ospedale Policlinico San Martino, Genova, Italy
| | | | - Jan Styczynski
- Department of Pediatric Hematology and Oncology, Collegium Medicum, Nicolaus Copernicus University Torun Uniwersytet Mikołaja Kopernika, University Hospital, Bydgoszcz, Poland
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13
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Georgakopoulou VE, Petsinis G, Mantzouranis K, Damaskos C, Melemeni D, Gkoufa A, Chlapoutakis S, Garmpis N, Sklapani P, Trakas N, Tsiafaki X. First Detection of Human Coronavirus HKU1 in Greece, in an Immunocompromised Patient With Severe Lower Respiratory Tract Infection. Acta Med Litu 2021; 28:121-126. [PMID: 34393634 PMCID: PMC8311844 DOI: 10.15388/amed.2021.28.1.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/30/2021] [Accepted: 05/06/2021] [Indexed: 11/22/2022] Open
Abstract
Human coronavirus HKU1 (HCoV-HKU1) is a RNA virus which gets in the human cells by binding to the receptor of N-acetyl-9-O-acetylneuraminic acid. Human Coronaviruses (HCoVs), including HCoV-HKU1, are globally found. HCoV-HKU1 is responsible for upper and lower respiratory tract infections, usually with mild symptoms. In severe cases, HCoV-HKU1 can cause life-threatening respiratory illness especially in vulnerable hosts such as elderly, children and immunocompromised patients. In Greece, Respiratory Syncytial Virus (RSV) and influenza are the most common viruses causing respiratory tract infections. Traditionally, HCoVs are responsible for less than 3% of respiratory infections in Greek population. HCoVs 229E and OC43 have been shown to circulate in Greece. We report the first case of lung infection in an immunocompromised woman due to HCoV-HKU1, that has never been before detected in Greece. HCoV-HKU1 is related to severe disease even in healthy individuals and must be considered in the differential diagnosis of severe respiratory infections.
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Affiliation(s)
| | | | | | - Christos Damaskos
- Second Department of Propedeutic Surgery, Laiko General Hospital, Medical School, National and Kapodistrian University of Athens, Athens
| | | | - Aikaterini Gkoufa
- First Department of Internal Medicine, Laiko General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Nikolaos Garmpis
- Second Department of Propedeutic Surgery, Laiko General Hospital, Medical School, National and Kapodistrian University of Athens, Athens Greece
| | | | - Nikolaos Trakas
- Department of Biochemistry, Sismanogleio Hospital, Athens, Greece
| | - Xanthi Tsiafaki
- 1 Pulmonology Department Sismanogleio Hospital, Athens, Greece
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14
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Zhang Y, Su L, Chen Y, Yu S, Zhang D, Mao H, Fang L. Etiology and clinical characteristics of SARS-CoV-2 and other human coronaviruses among children in Zhejiang Province, China 2017-2019. Virol J 2021; 18:89. [PMID: 33931105 PMCID: PMC8085659 DOI: 10.1186/s12985-021-01562-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 04/21/2021] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND A novel coronavirus (SARS-CoV-2) emerging has put global public health institutes on high alert. Little is known about the epidemiology and clinical characteristics of human coronaviruses infections in relation to infections with other respiratory viruses. METHODS From February 2017 to December 2019, 3660 respiratory samples submitted to Zhejiang Children Hospital with acute respiratory symptoms were tested for four human coronaviruses RNA by a novel two-tube multiplex reverse transcription polymerase chain reaction assays. Samples were also screened for the occurrence of SARS-CoV-2 by reverse transcription-PCR analysis. RESULTS Coronavirus RNAs were detected in 144 (3.93%) specimens: HCoV-HKU1 in 38 specimens, HCoV-NL63 in 62 specimens, HCoV-OC43 in 38 specimens and HCoV-229E in 8 specimens. Genomes for SARS-CoV-2 were absent in all specimens by RT-PCR analysis during the study period. The majority of HCoV infections occurred during fall months. No significant differences in gender, sample type, year were seen across species. 37.5 to 52.6% of coronaviruses detected were in specimens testing positive for other respiratory viruses. Phylogenic analysis identified that Zhejiang coronaviruses belong to multiple lineages of the coronaviruses circulating in other countries and areas. CONCLUSION Common HCoVs may have annual peaks of circulation in fall months in the Zhejiang province, China. Genetic relatedness to the coronaviruses in other regions suggests further surveillance on human coronaviruses in clinical samples are clearly needed to understand their patterns of activity and role in the emergence of novel coronaviruses.
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Affiliation(s)
- Yanjun Zhang
- Department of Laboratory, School of Medical Technology, Zhejiang Chinese Medical University, Hangzhou, 310053, China.,Zhejiang Provincial Center of Disease Control and Prevention, 3399 Bincheng Road, Hangzhou, 310051, China
| | - Lingxuan Su
- Department of Laboratory, School of Medical Technology, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yin Chen
- Zhejiang Provincial Center of Disease Control and Prevention, 3399 Bincheng Road, Hangzhou, 310051, China
| | - Sicong Yu
- Department of Laboratory, School of Medical Technology, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Dan Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, China
| | - Haiyan Mao
- Zhejiang Provincial Center of Disease Control and Prevention, 3399 Bincheng Road, Hangzhou, 310051, China
| | - Lei Fang
- Zhejiang Provincial Center of Disease Control and Prevention, 3399 Bincheng Road, Hangzhou, 310051, China.
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15
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Mulabbi EN, Tweyongyere R, Byarugaba DK. The history of the emergence and transmission of human coronaviruses. Onderstepoort J Vet Res 2021; 88:e1-e8. [PMID: 33567843 PMCID: PMC7876959 DOI: 10.4102/ojvr.v88i1.1872] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 09/25/2020] [Indexed: 12/15/2022] Open
Abstract
Human coronaviruses are known respiratory pathogens associated with a range of respiratory illnesses, and there are considerable morbidity and hospitalisation amongst immune-compromised individuals of all age groups. The emergence of a highly pathogenic human coronavirus in China in 2019 has confirmed the long-held opinion that these viruses are important emerging and re-emerging pathogens. In this review article, we trace the discovery and emergence of coronaviruses (CoVs) over time since they were first reported. The review article will enrich our understanding on the host range, diversity and evolution, transmission of human CoVs and the threat posed by these viruses circulating in animal populations but overtime have spilled over to humans because of the increased proximity between humans and animals.
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Affiliation(s)
- Elijah N Mulabbi
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala.
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16
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Nyaguthii DM, Otieno GP, Kombe IK, Koech D, Mutunga M, Medley GF, Nokes DJ, Munywoki PK. Infection patterns of endemic human coronaviruses in rural households in coastal Kenya. Wellcome Open Res 2021; 6:27. [PMID: 34957334 PMCID: PMC8669777 DOI: 10.12688/wellcomeopenres.16508.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2021] [Indexed: 12/20/2022] Open
Abstract
Background: The natural history and transmission patterns of endemic human coronaviruses are of increased interest following the emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Methods: In rural Kenya 483 individuals from 47 households were followed for six months (2009-10) with nasopharyngeal swabs collected twice weekly regardless of symptoms. A total of 16,918 swabs were tested for human coronavirus (hCoV) OC43, NL63 and 229E and other respiratory viruses using polymerase chain reaction. Results: From 346 (71.6%) household members, 629 hCoV infection episodes were defined, with 36.3% being symptomatic: varying by hCoV type and decreasing with age. Symptomatic episodes (aHR=0.6 (95% CI:0.5-0.8) or those with elevated peak viral load (medium aHR=0.4 (0.3-0.6); high aHR=0.31 (0.2-0.4)) had longer viral shedding compared to their respective counterparts. Homologous reinfections were observed in 99 (19.9%) of 497 first infections. School-age children (55%) were the most common index cases with those having medium (aOR=5.3 (2.3 - 12.0)) or high (8.1 (2.9 - 22.5)) peak viral load most often generating secondary cases. Conclusion: Household coronavirus infection was common, frequently asymptomatic and mostly introduced by school-age children. Secondary transmission was influenced by viral load of index cases. Homologous-type reinfection was common. These data may be insightful for SARS-CoV-2.
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Affiliation(s)
- Dickson Machira Nyaguthii
- Epidemiology and Demography department, KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
- Department of Veterinary Public Health, Pharmacology and Toxicology, Egerton University, Egerton, Kenya
| | - Grieven P. Otieno
- Epidemiology and Demography department, KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | - Ivy K. Kombe
- Epidemiology and Demography department, KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | - Dorothy Koech
- Epidemiology and Demography department, KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | - Martin Mutunga
- Epidemiology and Demography department, KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | - Graham F. Medley
- Centre for Mathematical Modelling of Infectious Disease, London School of Hygiene and Tropical Medicine, London, UK
| | - D. James Nokes
- Epidemiology and Demography department, KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Patrick K. Munywoki
- Epidemiology and Demography department, KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
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17
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Rabaan AA, Al-Ahmed SH, Sah R, Alqumber MA, Haque S, Patel SK, Pathak M, Tiwari R, Yatoo MI, Haq AU, Bilal M, Dhama K, Rodriguez-Morales AJ. MERS-CoV: epidemiology, molecular dynamics, therapeutics, and future challenges. Ann Clin Microbiol Antimicrob 2021; 20:8. [PMID: 33461573 PMCID: PMC7812981 DOI: 10.1186/s12941-020-00414-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 12/22/2020] [Indexed: 02/07/2023] Open
Abstract
The Severe Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has gained research attention worldwide, given the current pandemic. Nevertheless, a previous zoonotic and highly pathogenic coronavirus, the Middle East Respiratory Syndrome coronavirus (MERS-CoV), is still causing concern, especially in Saudi Arabia and neighbour countries. The MERS-CoV has been reported from respiratory samples in more than 27 countries, and around 2500 cases have been reported with an approximate fatality rate of 35%. After its emergence in 2012 intermittent, sporadic cases, nosocomial infections and many community clusters of MERS continued to occur in many countries. Human-to-human transmission resulted in the large outbreaks in Saudi Arabia. The inherent genetic variability among various clads of the MERS-CoV might have probably paved the events of cross-species transmission along with changes in the inter-species and intra-species tropism. The current review is drafted using an extensive review of literature on various databases, selecting of publications irrespective of favouring or opposing, assessing the merit of study, the abstraction of data and analysing data. The genome of MERS-CoV contains around thirty thousand nucleotides having seven predicted open reading frames. Spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins are the four main structural proteins. The surface located spike protein (S) of betacoronaviruses has been established to be one of the significant factors in their zoonotic transmission through virus-receptor recognition mediation and subsequent initiation of viral infection. Three regions in Saudi Arabia (KSA), Eastern Province, Riyadh and Makkah were affected severely. The epidemic progression had been the highest in 2014 in Makkah and Riyadh and Eastern Province in 2013. With a lurking epidemic scare, there is a crucial need for effective therapeutic and immunological remedies constructed on sound molecular investigations.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
| | - Shamsah H Al-Ahmed
- Specialty Paediatric Medicine, Qatif Central Hospital, Qatif, Saudi Arabia
| | - Ranjit Sah
- Tribhuvan University Institute of Medicine, Kathmandu, Nepal
| | - Mohammed A Alqumber
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Albaha University, Albaha, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Shailesh Kumar Patel
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243 122, India
| | - Mamta Pathak
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243 122, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura, 281001, India
| | - Mohd Iqbal Yatoo
- Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shuhama, Alusteng Srinagar, Shalimar, Srinagar, Jammu and Kashmir, 190006, India
| | - Abrar Ul Haq
- Division of Clinical Veterinary Medicine Ethics & Jurisprudence, Faculty of Veterinary Sciences and Animal Husbandry, Sher E Kashmir University of Agricultural Sciences and Technology, Kashmir, Shuhama, Srinagar, 190006, India
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243 122, India.
| | - Alfonso J Rodriguez-Morales
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia. .,Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Americas, Pereira, Risaralda, Colombia. .,School of Medicine, Universidad Privada Franz Tamayo (UNIFRANZ), Cochabamba, Bolivia.
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18
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Mulabbi EN, Tweyongyere R, Byarugaba DK. The history of the emergence and transmission of human coronaviruses. Onderstepoort J Vet Res 2020. [DOI: 10.4102/ojvr.v87i1.1872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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19
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Motayo BO, Oluwasemowo OO, Akinduti PA. Evolutionary dynamics and geographic dispersal of beta coronaviruses in African bats. PeerJ 2020; 8:e10434. [PMID: 33304657 PMCID: PMC7700737 DOI: 10.7717/peerj.10434] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/06/2020] [Indexed: 11/20/2022] Open
Abstract
Bats have been shown to serve as reservoir host of various viral agents including coronaviruses. They have also been associated with the novel coronavirus SARS-CoV-2. This has made them an all important agent for CoV evolution and transmission. Our objective in this study was to investigate the dispersal, phylogenomics and evolution of betacoronavirus (βCoV) among African bats. We retrieved sequence data from established databases such as GenBank and Virus Pathogen Resource, covering the partial RNA dependent RNA polymerase (RdRP) gene of bat coronaviruses from eight African, three Asian, five European, two South American countries and Australia. We analyzed for phylogeographic information relating to genetic diversity and evolutionary dynamics. Our study revealed that majority of the African strains fell within Norbecovirus subgenera, with an evolutionary rate of 1.301 × 10-3, HPD (1.064 × 10-3-1.434 × 10-3) subs/site/year. The African strains diversified into three main subgenera, Norbecovirus, Hibecovirus and Merbecovirus. The time to most common recent ancestor for Norbecovirus strains was 1973, and 2007, for the African Merbecovirus strains. There was evidence of inter species transmission of Norbecovirus among bats in Cameroun and DRC. Phlylogeography showed that there were inter-continental spread of Bt-CoV from Europe, China and Hong Kong into Central and Southern Africa, highlighting the possibility of long distance transmission. Our study has elucidated the possible evolutionary origins of βCoV among African bats; we therefore advocate for broader studies of whole genome sequences of BtCoV to further understand the drivers for their emergence and zoonotic spillovers into human population.
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Affiliation(s)
- Babatunde O Motayo
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria.,Department of Medical Microbiology and Parasitology, Federal Medical Center, Abeokuta, Nigeria, Abeokuta, Ogun, Nigeria
| | | | - Paul A Akinduti
- Department of Biological Science, Covenant University, Otta, Ogun, Nigeria
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20
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Otieno GP, Murunga N, Agoti CN, Gallagher KE, Awori JO, Nokes DJ. Surveillance of endemic human coronaviruses (HCoV-NL63, OC43 and 229E) associated with childhood pneumonia in Kilifi, Kenya. Wellcome Open Res 2020; 5:150. [PMID: 32995556 PMCID: PMC7512035 DOI: 10.12688/wellcomeopenres.16037.2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2020] [Indexed: 12/31/2022] Open
Abstract
Introduction: Human coronaviruses (HCoVs) circulate endemically in human populations, often with seasonal variation. We describe the long-term patterns of paediatric disease associated with three of these viruses, HCoV-NL63, OC43 and 229E, in coastal Kenya. Methods: Continuous surveillance of pneumonia admissions was conducted at the Kilifi county hospital (KCH) located in the northern coastal region of Kenya. Children aged <5 years admitted to KCH with clinically defined syndromic severe or very severe pneumonia were recruited. Respiratory samples were taken and tested for 15 virus targets, using real-time polymerase chain reaction. Unadjusted odds ratios were used to estimate the association between demographic and clinical characteristics and HCoV positivity. Results: From 2007 to 2019, we observed 11,445 pneumonia admissions, of which 314 (3.9%) tested positive for at least one of the HCoV types surveyed in the study. There were 129 (41.1%) OC43, 99 (31.5%) 229E, 74 (23.6%) NL63 positive cases and 12 (3.8%) cases of HCoV to HCoV coinfection. Among HCoV positive cases, 47% (n=147) were coinfected with other respiratory virus pathogens. The majority of HCoV cases were among children aged <1 year (66%, n=208), though there was was no change in the proportion infected by age. HCoV-OC43 was predominant of the three HCoV types throughout the surveillance period. Evidence for seasonality was not identified. Conclusions: Overall, 4% of paediatric pneumonia admissions were associated with three endemic HCoVs, with a high proportion of cases co-occurring with another respiratory virus, no clear seasonal pattern, and with the age-distribution of cases following that of pneumonia admissions (i.e. highest in infants). These observations suggest, at most, a small severe disease contribution of endemic HCoVs in this tropical setting and offer insight into their potential future burden and epidemiological characteristics.
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Affiliation(s)
- Grieven P. Otieno
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Nickson Murunga
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Charles N. Agoti
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Katherine E. Gallagher
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- London School of Hygiene and Tropical Medicine,, London, UK
| | - Juliet O. Awori
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - D. James Nokes
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
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21
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Saha RP, Sharma AR, Singh MK, Samanta S, Bhakta S, Mandal S, Bhattacharya M, Lee SS, Chakraborty C. Repurposing Drugs, Ongoing Vaccine, and New Therapeutic Development Initiatives Against COVID-19. Front Pharmacol 2020; 11:1258. [PMID: 32973505 PMCID: PMC7466451 DOI: 10.3389/fphar.2020.01258] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/30/2020] [Indexed: 12/15/2022] Open
Abstract
As the COVID-19 is still growing throughout the globe, a thorough investigation into the specific immunopathology of SARS-CoV-2, its interaction with the host immune system and pathogen evasion mechanism may provide a clear picture of how the pathogen can breach the host immune defenses in elderly patients and patients with comorbid conditions. Such studies will also reveal the underlying mechanism of how children and young patients can withstand the disease better. The study of the immune defense mechanisms and the prolonged immune memory from patients population with convalescent plasma may help in designing a suitable vaccine candidate not only for the current outbreak but also for similar outbreaks in the future. The vital drug candidates, which are being tested as potential vaccines or therapeutics against COVID-19, include live attenuated vaccine, inactivated or killed vaccine, subunit vaccine, antibodies, interferon treatment, repurposing existing drugs, and nucleic acid-based vaccines. Several organizations around the world have fast-tracked the development of a COVID-19 vaccine, and some drugs already went to phase III of clinical trials. Hence, here, we have tried to take a quick glimpse of the development stages of vaccines or therapeutic approaches to treat this deadly disease.
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Affiliation(s)
- Rudra P. Saha
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, South Korea
| | - Manoj K. Singh
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, India
| | - Saikat Samanta
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, India
| | - Swarnav Bhakta
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, India
| | - Snehasish Mandal
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, India
| | - Manojit Bhattacharya
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, South Korea
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, South Korea
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, India
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, South Korea
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22
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Gupta A, Kumar S, Kumar R, Choudhary AK, Kumari K, Singh P, Kumar V. COVID-19: Emergence of Infectious Diseases, Nanotechnology Aspects, Challenges, and Future Perspectives. ChemistrySelect 2020; 5:7521-7533. [PMID: 32835089 PMCID: PMC7361534 DOI: 10.1002/slct.202001709] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/22/2020] [Indexed: 01/08/2023]
Abstract
Wuhan, a city of China, is the epicenter for the pandemic outbreak of coronavirus disease-2019 (COVID-19). It has become a severe public health challenge to the world and established a public health emergency of international worry. This infectious disease has pulled down the economy of almost all top developed nations. The coronaviruses (CoVs) known for various epidemics caused time to time. Infectious diseases such as severe acute respiratory syndrome (SARS) and middle east respiratory syndrome (MERS), followed by COVID-19, are all coronaviruses led outbreaks that scourged the history of mankind. CoVs evolved themselves to more infectious, transmissible, and more pandemic with time. To prevent the spread of the SARS-CoV-2, many countries have ordered the complete lockdown to combat the outbreak. This paper briefly discussed the historical background of CoVs and the evolution of human coronaviruses (HCoVs), the case studies and the development of their antiviral medications. The viral infection encountered with present-day challenges and futuristic approaches with the help of nanotechnology to minimize the spread of infectious viruses. The antiviral drugs and their clinical advances, along with herbal medicines for viral inhibition and immunity boosters, are described. Elaboration of tables related to CoVs for the compilation of the literature has been adopted for the better understanding.
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Affiliation(s)
- Akanksha Gupta
- Department of ChemistrySri Venkateswara CollegeUniversity of DelhiIndia.
| | - Sanjay Kumar
- Department of ChemistryDeshbandhu CollegeUniversity of DelhiIndia.
| | - Ravinder Kumar
- Department of Chemistry, Gurukula Kangri VishwavidyalayaHaridwarIndia.
| | | | - Kamlesh Kumari
- Department of ZoologyDeen Dayal Upadhyaya CollegeDelhiIndia.
| | - Prashant Singh
- Department of ChemistryAtma Ram Sanatan Dharma CollegeDelhi UniversityNew DelhiIndia.
| | - Vinod Kumar
- Department of ChemistryKirori Mal CollegeUniversity of DelhiIndia
- Special Centre for Nano SciencesJawaharlal Nehru UniversityDelhiIndia
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23
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Otieno GP, Murunga N, Agoti CN, Gallagher KE, Awori JO, Nokes DJ. Surveillance of endemic human coronaviruses (HCoV-NL63, OC43 and 229E) associated with pneumonia in Kilifi, Kenya. Wellcome Open Res 2020; 5:150. [PMID: 32995556 PMCID: PMC7512035 DOI: 10.12688/wellcomeopenres.16037.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2020] [Indexed: 03/30/2024] Open
Abstract
Introduction: Human coronaviruses (HCoVs) circulate endemically in human populations, often with seasonal variation. We describe the long-term patterns of paediatric disease associated with three of these viruses, HCoV-NL63, OC43 and 229E, in coastal Kenya. Methods: Continuous surveillance of pneumonia admissions was conducted at the Kilifi county hospital (KCH) located in the northern coastal region of Kenya. Children aged <5 years admitted to KCH with clinically defined syndromic severe or very severe pneumonia were recruited. Respiratory samples were taken and tested for 15 virus targets, using real-time polymerase chain reaction. Unadjusted odds ratios were used to estimate the association between demographic and clinical characteristics and HCoV positivity. Results: From 2007 to 2019, we observed 11,445 pneumonia admissions, of which 314 (3.9%) tested positive for at least one HCoV type. There were 129 (41.1%) OC43, 99 (31.5%) 229E, 74 (23.6%) NL63 positive cases and 12 (3.8%) cases of HCoV to HCoV coinfection. Among HCoV positive cases, 47% (n=147) were coinfected with other respiratory virus pathogens. The majority of HCoV cases were among children aged <1 year (66%, n=208), though there was no age-dependence in the proportion testing positive. HCoV-OC43 was predominant of the three HCoV types throughout the surveillance period. Evidence for seasonality was not identified. Conclusions: Overall, 4% of paediatric pneumonia admissions were associated with three endemic HCoVs, with a high proportion of cases co-occurring with another respiratory virus, with no clear seasonal pattern, and with the age-distribution of cases following that of pneumonia admissions (i.e. highest in infants). These observations suggest, at most, a small severe disease contribution of endemic HCoVs in this tropical setting and offer insight into the potential future burden and epidemiological characteristics of SARS-CoV-2.
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Affiliation(s)
- Grieven P. Otieno
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Nickson Murunga
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Charles N. Agoti
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Katherine E. Gallagher
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- London School of Hygiene and Tropical Medicine,, London, UK
| | - Juliet O. Awori
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - D. James Nokes
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
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24
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Abidha CA, Nyiro J, Kamau E, Abdullahi O, Nokes DJ, Agoti CN. Transmission and evolutionary dynamics of human coronavirus OC43 strains in coastal Kenya investigated by partial spike sequence analysis, 2015-16. Virus Evol 2020; 6:veaa031. [PMID: 32523779 PMCID: PMC7266483 DOI: 10.1093/ve/veaa031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Human coronavirus OC43 (HCoV-OC43) is a major contributor to seasonal outbreaks of acute respiratory illness (ARI). The origins of locally circulating HCoV-OC43 strains and characteristics of their genetic diversity are unknown for most settings despite significance to effective HCoV control strategies. Between December 2015 and June 2016, we undertook ARI surveillance in coastal Kenya in nine outpatients and one inpatient health facility (HF). Ninety-two patient samples tested HCoV-OC43 positive and forty (43.5%) were successfully sequenced in spike (S) gene region (2,864 long, ∼70%). Phylogenetic analysis confirmed co-circulation of two distinct HCoV-OC43 clades that closely clustered with genotype G (n = 34, 85%) and genotype H (n = 6, 15%) reference strains. Local viruses within the same clade displayed low genetic diversity yielding identical sequences in multiple HF. Furthermore, the newly sequenced Kenyan viruses showed close phylogenetic relationship to other contemporaneous sampled strains (2015-16) including those originating from distant places (e.g. USA and China). Using a genetic similarity threshold of 99.1 per cent at nucleotide level, the HCoV-OC43 strains sampled globally between 1967 and 2019 fell into nine sequence clusters. Notably, some of these clusters appeared to have become extinct, or occurred only sporadically in a few geographical areas while others persisted globally for multiple years. In conclusion, we found that HCoV-OC43 strains spread rapidly both locally and across the globe with limited genetic evolution in the spike gene. Full-genome sequences that are spatio-temporally representative are required to advance understanding of the transmission pathways of this important human respiratory pathogen.
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Affiliation(s)
- Carol A Abidha
- Department of Public Health, School of Health and Human Sciences, Pwani University, P.O. Box 195, Kilifi-80108, Kenya.,Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, P.O. Box 230, Kilifi-80108, Kenya.,Faculty of Medicine, Heidelberg Institute of Global Health (HIGH), University of Heidelberg, Germany, Im Neuenheimer Feld 324 - 69120 Heidelberg, Germany
| | - Joyce Nyiro
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, P.O. Box 230, Kilifi-80108, Kenya
| | - Everlyn Kamau
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, P.O. Box 230, Kilifi-80108, Kenya
| | - Osman Abdullahi
- Department of Public Health, School of Health and Human Sciences, Pwani University, P.O. Box 195, Kilifi-80108, Kenya.,Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, P.O. Box 230, Kilifi-80108, Kenya
| | - David James Nokes
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, P.O. Box 230, Kilifi-80108, Kenya.,School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, CV4, 7AL UK
| | - Charles N Agoti
- Department of Public Health, School of Health and Human Sciences, Pwani University, P.O. Box 195, Kilifi-80108, Kenya.,Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, P.O. Box 230, Kilifi-80108, Kenya
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25
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Roussel Y, Giraud-Gatineau A, Jimeno MT, Rolain JM, Zandotti C, Colson P, Raoult D. SARS-CoV-2: fear versus data. Int J Antimicrob Agents 2020; 55:105947. [PMID: 32201354 PMCID: PMC7102597 DOI: 10.1016/j.ijantimicag.2020.105947] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 03/14/2020] [Indexed: 12/31/2022]
Abstract
SARS-CoV-2, the novel coronavirus from China, is spreading around the world, causing a huge reaction despite its current low incidence outside China and the Far East. Four common coronaviruses are in current circulation and cause millions of cases worldwide. This article compares the incidence and mortality rates of these four common coronaviruses with those of SARS-CoV-2 in Organisation for Economic Co-operation and Development countries. It is concluded that the problem of SARS-CoV-2 is probably being overestimated, as 2.6 million people die of respiratory infections each year compared with less than 4000 deaths for SARS-CoV-2 at the time of writing.
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Affiliation(s)
- Yanis Roussel
- Institut Hospitalo-universitaire Méditerranée Infection, Marseille, France; Aix Marseille Université, Institut de Recherche pour le Développement, Assistance Publique-Hôpitaux de Marseille, Microbes Evolution Phylogénie et Infections, Marseille, France
| | - Audrey Giraud-Gatineau
- Institut Hospitalo-universitaire Méditerranée Infection, Marseille, France; Aix Marseille Université, Institut de Recherche pour le Développement, Assistance Publique-Hôpitaux de Marseille, Service de Santé des Armées, Vecteurs - Infections Tropicales et Méditerranéennes, Marseille, France; Centre d'Epidémiologie et de Santé Publique des Armées, Marseille, France; Assistance Publique - Hôpitaux de Marseille, Marseille, France
| | | | - Jean-Marc Rolain
- Institut Hospitalo-universitaire Méditerranée Infection, Marseille, France; Aix Marseille Université, Institut de Recherche pour le Développement, Assistance Publique-Hôpitaux de Marseille, Microbes Evolution Phylogénie et Infections, Marseille, France
| | - Christine Zandotti
- Institut Hospitalo-universitaire Méditerranée Infection, Marseille, France; Aix Marseille Université, Institut de Recherche pour le Développement, Assistance Publique-Hôpitaux de Marseille, Microbes Evolution Phylogénie et Infections, Marseille, France
| | - Philippe Colson
- Institut Hospitalo-universitaire Méditerranée Infection, Marseille, France; Aix Marseille Université, Institut de Recherche pour le Développement, Assistance Publique-Hôpitaux de Marseille, Microbes Evolution Phylogénie et Infections, Marseille, France
| | - Didier Raoult
- Institut Hospitalo-universitaire Méditerranée Infection, Marseille, France; Aix Marseille Université, Institut de Recherche pour le Développement, Assistance Publique-Hôpitaux de Marseille, Microbes Evolution Phylogénie et Infections, Marseille, France.
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26
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Raoult D, Zumla A, Locatelli F, Ippolito G, Kroemer G. Coronavirus infections: Epidemiological, clinical and immunological features and hypotheses. Cell Stress 2020; 4:66-75. [PMID: 32292881 PMCID: PMC7064018 DOI: 10.15698/cst2020.04.216] [Citation(s) in RCA: 198] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Coronaviruses (CoVs) are a large family of enveloped, positive-strand RNA viruses. Four human CoVs (HCoVs), the non-severe acute respiratory syndrome (SARS)-like HCoVs (namely HCoV 229E, NL63, OC43, and HKU1), are globally endemic and account for a substantial fraction of upper respiratory tract infections. Non-SARS-like CoV can occasionally produce severe diseases in frail subjects but do not cause any major (fatal) epidemics. In contrast, SARS like CoVs (namely SARS-CoV and Middle-East respiratory syndrome coronavirus, MERS-CoV) can cause intense short-lived fatal outbreaks. The current epidemic caused by the highly contagious SARS-CoV-2 and its rapid spread globally is of major concern. There is scanty knowledge on the actual pandemic potential of this new SARS-like virus. It might be speculated that SARS-CoV-2 epidemic is grossly underdiagnosed and that the infection is silently spreading across the globe with two consequences: (i) clusters of severe infections among frail subjects could haphazardly occur linked to unrecognized index cases; (ii) the current epidemic could naturally fall into a low-level endemic phase when a significant number of subjects will have developed immunity. Understanding the role of paucisymptomatic subjects and stratifying patients according to the risk of developing severe clinical presentations is pivotal for implementing reasonable measures to contain the infection and to reduce its mortality. Whilst the future evolution of this epidemic remains unpredictable, classic public health strategies must follow rational patterns. The emergence of yet another global epidemic underscores the permanent challenges that infectious diseases pose and underscores the need for global cooperation and preparedness, even during inter-epidemic periods.
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Affiliation(s)
- Didier Raoult
- Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - Alimuddin Zumla
- Division of Infection and Immunity, Center for Clinical Microbiology, University College London, London, UK.,The National Institute of Health Research Biomedical Research Centre at UCL Hospitals, London, UK
| | - Franco Locatelli
- Department of Pediatric Hematology and Oncology IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Giuseppe Ippolito
- National Institute for Infectious Diseases, Lazzaro Spallanzani, IRCCS, Rome, Italy
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, INSERM U1138, Institut Universitaire de France, Paris, France.,Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France.,Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France.,Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China.,Karolinska Institute, Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden
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27
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Incidence, significance, and persistence of human coronavirus infection in hematopoietic stem cell transplant recipients. Bone Marrow Transplant 2018; 54:1058-1066. [PMID: 30385869 PMCID: PMC7091595 DOI: 10.1038/s41409-018-0386-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/30/2018] [Accepted: 10/12/2018] [Indexed: 11/08/2022]
Abstract
Hematopoietic stem cell transplant (HSCT) recipients are at increased risk of respiratory viral infections and their associated complications. Unlike other respiratory viruses, little is known about the clinical significance of human coronavirus infection (HCoV) in this population. We retrospectively identified all HSCT recipients who were transplanted between May 2013 and June 2017 at our institution and characterized the cumulative incidence of post-transplant HCoV infection. Of 678 patients who underwent HSCT during the study period, 112 (17%) developed HCoV infection, making HCoV the fourth most common respiratory viral infection. Thirty-four (30%) HCoV-infected patients progressed to proven or probable lower respiratory tract infection (LRTI). Age ≥50, graft-versus-host disease, corticosteroids, hypoalbuminemia, and inpatient status at the time of infection were independently associated with progression to LRTI. Twenty-seven (59%) patients who underwent repeat NP swab had persistent viral shedding for ≥21 days, with a median duration of 4 weeks of viral shedding. We conclude that HCoV is common and clinically significant in HSCT recipients, with nearly one-third of patients progressing to proven or probable LRTI. Evaluating for LRTI risk factors found in this study may identify patients who require closer surveillance and aggressive supportive care when infected with HCoV.
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28
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Killerby ME, Biggs HM, Haynes A, Dahl RM, Mustaquim D, Gerber SI, Watson JT. Human coronavirus circulation in the United States 2014-2017. J Clin Virol 2018; 101:52-56. [PMID: 29427907 PMCID: PMC7106380 DOI: 10.1016/j.jcv.2018.01.019] [Citation(s) in RCA: 205] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/29/2018] [Indexed: 11/28/2022]
Abstract
BACKGROUND Human coronaviruses (HCoVs) -OC43, -229E, -NL63 and -HKU1 cause upper and lower respiratory tract infections. HCoVs are globally distributed and the predominant species may vary by region or year. Prior studies have shown seasonal patterns of HCoV species and annual variation in species prevalence but national circulation patterns in the US have not yet been described. OBJECTIVES To describe circulation patterns of HCoVs -OC43, -229E, -NL63 and -HKU1 in the US. STUDY DESIGN We reviewed real-time reverse transcription polymerase chain reaction (rRT-PCR) test results for HCoV-OC43, -229E, -NL63 and -HKU1 reported to The National Respiratory and Enteric Virus Surveillance System (NREVSS) by U.S. laboratories from July 2014-June 2017. We calculated the total number of tests and percent positive by week. For a subset of HCoV positive submissions with age and sex of the patient available, we tested for differences in age and sex across the four HCoV species using Chi Square and Kruskal Wallace tests. RESULTS 117 laboratories reported 854,575 HCoV tests; 2.2% were positive for HCoV-OC43, 1.0% for HCoV-NL63, 0.8% for HCoV-229E, and 0.6% for HCoV-HKU1. The percentage of positive tests peaked during December - March each year. No significant differences in sex were seen across species, although a significant difference in age distribution was noted. CONCLUSIONS Common HCoVs may have annual peaks of circulation in winter months in the US, and individual HCoVs may show variable circulation from year to year. Different HCoV species may be detected more frequently in different age groups. Further years of data are needed to better understand patterns of activity for HCoVs.
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Affiliation(s)
- Marie E Killerby
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA; Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA.
| | - Holly M Biggs
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Amber Haynes
- IHRC, Incorporated, Contracting agency to National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Rebecca M Dahl
- MAXIMUS Federal, Contracting agency to National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Desiree Mustaquim
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Susan I Gerber
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - John T Watson
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
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Liu P, Shi L, Zhang W, He J, Liu C, Zhao C, Kong SK, Loo JFC, Gu D, Hu L. Prevalence and genetic diversity analysis of human coronaviruses among cross-border children. Virol J 2017; 14:230. [PMID: 29166910 PMCID: PMC5700739 DOI: 10.1186/s12985-017-0896-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 11/15/2017] [Indexed: 12/16/2022] Open
Abstract
Background More than a decade after the outbreak of human coronaviruses (HCoVs) SARS in Guangdong province and Hong Kong SAR of China in 2002, there is still no reoccurrence, but the evolution and recombination of the coronaviruses in this region are still unknown. Therefore, surveillance on the prevalence and the virus variation of HCoVs circulation in this region is conducted. Methods A total of 3298 nasopharyngeal swabs samples were collected from cross-border children (<6 years, crossing border between Southern China and Hong Kong SAR) showing symptoms of respiratory tract infection, such as fever (body temperature > 37.5 °C), from 2014 May to 2015 Dec. Viral nucleic acids were analyzed and sequenced to study the prevalence and genetic diversity of the four human coronaviruses. The statistical significance of the data was evaluated with Fisher chi-square test. Results 78 (2.37%; 95%CI 1.8-2.8%) out of 3298 nasopharyngeal swabs specimens were found to be positive for OC43 (36;1.09%), HKU1 (34; 1.03%), NL63 (6; 0.18%) and 229E (2;0.01%). None of SARS or MERS was detected. The HCoVs predominant circulating season was in transition of winter to spring, especially January and February and NL63 detected only in summer and fall. Complex population with an abundant genetic diversity of coronaviruses was circulating and they shared homology with the published strains (99-100%). Besides, phylogenetic evolutionary analysis indicated that OC43 coronaviruses were clustered into three clades (B,D,E), HKU1 clustered into two clades(A,B) and NL63 clustered into two clades(A,B). Moreover, several novel mutations including nucleotides substitution and the insertion of spike of the glycoprotein on the viral surface were discovered. Conclusions The detection rate and epidemic trend of coronaviruses were stable and no obvious fluctuations were found. The detected coronaviruses shared a conserved gene sequences in S and RdRp. However, mutants of the epidemic strains were detected, suggesting continuous monitoring of the human coronaviruses is in need among cross-border children, who are more likely to get infected and transmit the viruses across the border easily, in addition to the general public.
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Affiliation(s)
- Peilin Liu
- Department of Health Inspection and Quarantine, School of Public Health, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China.,Central Laboratory of Health quarantine, Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518033, People's Republic of China
| | - Lei Shi
- Central Laboratory of Health quarantine, Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518033, People's Republic of China
| | - Wei Zhang
- Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, 430071, People's Republic of China
| | - Jianan He
- Central Laboratory of Health quarantine, Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518033, People's Republic of China
| | - Chunxiao Liu
- Central Laboratory of Health quarantine, Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518033, People's Republic of China
| | - Chunzhong Zhao
- Central Laboratory of Health quarantine, Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518033, People's Republic of China
| | - Siu Kai Kong
- Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Jacky Fong Chuen Loo
- Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China. .,Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China.
| | - Dayong Gu
- Central Laboratory of Health quarantine, Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518033, People's Republic of China. .,Shenzhen Academy of Inspection and Quarantine, Shenzhen, 518010, People's Republic of China.
| | - Longfei Hu
- Central Laboratory of Health quarantine, Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518033, People's Republic of China. .,Shenzhen Academy of Inspection and Quarantine, Shenzhen, 518010, People's Republic of China.
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Piñana JL, Madrid S, Pérez A, Hernández-Boluda JC, Giménez E, Terol MJ, Calabuig M, Navarro D, Solano C. Epidemiologic and Clinical Characteristics of Coronavirus and Bocavirus Respiratory Infections after Allogeneic Stem Cell Transplantation: A Prospective Single-Center Study. Biol Blood Marrow Transplant 2017; 24:563-570. [PMID: 29155041 PMCID: PMC7110838 DOI: 10.1016/j.bbmt.2017.11.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/01/2017] [Indexed: 11/23/2022]
Abstract
Human coronavirus are common after allogeneic stem cell transplantation and can progress to LRTDs, and in some cases this leads to hospitalization and requires supportive care. Human bocavirus are quite rare after allogeneic stem cell transplantation and are commonly detected in conjunction with other viral co-pathogens.
Epidemiologic data about coronaviruses (CoVs) and human bocavirus (HBoV) in the setting of allogeneic hematopoietic stem cell transplantation (allo-HSCT) are scarce. We conducted a prospective longitudinal study on respiratory viral infections (RVIs) in allo-HSCT recipients with respiratory symptoms from December 2013 until June 2016. Respiratory virus in upper and/or lower respiratory tract (URT and LRT) specimens were tested using Luminex xTAG RVP Fast v1 assay. Seventy-nine consecutive allo-HSCT recipients developed a total of 192 virologically documented RVI episodes over 30 months. The median follow-up after RVI was 388 days (range, 5 to 923). CoV or HBoV was detected in 27 of 192 episodes (14%); 18 of 79 recipients (23%) developed a total of 21 CoV RVI episodes, whereas 6 recipients (8%) had 1 HBoV RVI episode each. Fourteen CoV RVI episodes were limited to the URT, whereas 7 affected the LRT. Co-pathogens were detected in 8 (38%) CoV cases. Type OC43 CoV was the dominant type (48%) followed by NL63 (24%), KHU1 (19%), and 229E (9%); the CoV hospitalization rate was 19%, whereas mortality was 5% (1 patient without any other microbiologic documentation). Among the 6 recipients with HBoV (3%), only 1 had LRT involvement and no one died from respiratory failure. In 5 cases (83%) HBoV was detected along with other viral co-pathogens. CoV RVIs are common after allo-HSCT, and in a significant proportion of cases CoV progressed to LRT and showed moderate to severe clinical features. In contrast, HBoV RVIs were rare and mostly presented in the context of co-infections.
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Affiliation(s)
- José Luis Piñana
- Department of Hematology, Hospital Clínico Universitario, Fundación INCLIVA, Valencia, Spain; Department of Hematology, Hospital Universitari i Politècnic la Fe, Valencia, Spain; CIBERONC, Instituto Carlos III, Madrid, Spain.
| | - Silvia Madrid
- Microbiology Service, Hospital Clínico Universitario, Valencia, Spain
| | - Ariadna Pérez
- Department of Hematology, Hospital Clínico Universitario, Fundación INCLIVA, Valencia, Spain
| | | | - Estela Giménez
- Microbiology Service, Hospital Clínico Universitario, Valencia, Spain
| | - María José Terol
- Department of Hematology, Hospital Clínico Universitario, Fundación INCLIVA, Valencia, Spain
| | - Marisa Calabuig
- Department of Hematology, Hospital Clínico Universitario, Fundación INCLIVA, Valencia, Spain
| | - David Navarro
- Microbiology Service, Hospital Clínico Universitario, Valencia, Spain; Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain
| | - Carlos Solano
- Department of Hematology, Hospital Clínico Universitario, Fundación INCLIVA, Valencia, Spain; Department of Medicine, School of Medicine, University of Valencia, Valencia, Spain
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