#Diversity of dromedary #camel #coronavirus #HKU23 in #African camels revealed multiple #recombination events among closely related #Betacoronaviruses of the subgenus #Embecovirus (J Virol., abstract)

[Source: Journal of Virology, full page: (LINK). Abstract, edited.]

Diversity of dromedary camel coronavirus HKU23 in African camels revealed multiple recombination events among closely related Betacoronaviruses of the subgenus Embecovirus.

Ray T. Y. So, Daniel K. W. Chu, Eve Miguel, Ranawaka A. P. M. Perera, Jamiu O. Oladipo, Ouafaa Fassi-Fihri, Gelagay Aylet, Ronald L. W. Ko, Ziqi Zhou, Mo-Sheung Cheng, Sulyman A. Kuranga, François L. Roger, Veronique Chevalier, Richard J. Webby, Patrick C. Y. Woo, Leo L. M. Poon, Malik Peiris

DOI: 10.1128/JVI.01236-19

 

ABSTRACT

Genetic recombination has frequently been observed in coronaviruses. Here, we sequenced multiple complete genomes of dromedary camel coronavirus HKU23 (DcCoV-HKU23) from Nigeria, Morocco and Ethiopia and identified several genomic positions indicative of cross species virus recombination events among other Betacoronaviruses of the subgenus Embecovirus (clade A β-CoVs). Recombinant fragments of a rabbit coronavirus (RbCoV-HKU14) were identified at the hemagglutinin esterase gene position. Homolog fragments of a rodent CoV were also observed at the 8.9 kDa open reading frame 4a at the 3′ end of the spike gene. The patterns of recombination varied geographically across the African region, highlighting a mosaic structure of DcCoV-HKU23 genomes circulating in dromedaries. Our results highlighted active recombination of coronaviruses circulating in dromedaries and is also relevant to the emergence and evolution of other Betacoronaviruses including MERS-coronavirus (MERS-CoV).

 

IMPORTANCE

Genetic recombination is often demonstrated in coronaviruses and can result in host range expansion or alteration in tissue tropism. Here, we showed interspecies recombination events of an endemic dromedary camel coronavirus HKU23 with other clade A Betacoronaviruses. Our results supported the possibility that the zoonotic pathogen, MERS-CoV, which also co-circulates in the same camel species, may have undergone similar recombination events facilitating its emergence or may do so in its future evolution.

Copyright © 2019 American Society for Microbiology. All Rights Reserved.

Keywords: Coronavirus; Betacoronavirus; Embecovirus; MERS-CoV; Camels; Africa Region; Recombination.

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First #Report of #Coronaviruses in Northern #European #Bats (Vector Borne Zoo Dis., abstract)

[Source: Vector Borne and Zoonotic Diseases, full page: (LINK). Abstract, edited.]

First Report of Coronaviruses in Northern European Bats

Ilkka Kivistö, Eeva-Maria Tidenberg, Thomas Lilley, Kati Suominen, Kristian M. Forbes, Olli Vapalahti, Anita Huovilainen, and Tarja Sironen

Published Online: 10 Sep 2019 / DOI: https://doi.org/10.1089/vbz.2018.2367

 

Abstract

Coronaviruses (CoVs) represent a global public health threat, exemplified by the severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) outbreaks. Using fecal samples collected from five bat species between 2014 and 2016 in Finland and RT-PCR, RT-qPCR, and NGS, we identified CoVs in 10 of 79 (13%) samples, including two novel bat species–CoV relationships. Phylogenetic analysis revealed Alphacoronavirus and Betacoronavirus species clustered among previously identified bat and human viruses. These results expand the known northern distribution and host species range of bat-borne CoVs.

Keywords: Coronavirus; Betacoronavirus; Alphacoronavirus; Bats; Wildlife; Finland.

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#Discovery and Characterization of Novel #RNA #Viruses in Aquatic North #American #WildBirds (Viruses, abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Viruses. 2019 Aug 21;11(9). pii: E768. doi: 10.3390/v11090768.

Discovery and Characterization of Novel RNA Viruses in Aquatic North American Wild Birds.

Canuti M1, Kroyer ANK2, Ojkic D3, Whitney HG2, Robertson GJ4, Lang AS5.

Author information: 1 Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada. marta.canuti@gmail.com. 2 Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada. 3 Animal Health Laboratory, Laboratory Services Division, University of Guelph, 419 Gordon St., Guelph, ON N1H 6R8, Canada. 4 Wildlife Research Division, Environment and Climate Change Canada, 6 Bruce Street, Mount Pearl, NL A1N 4T3, Canada. 5 Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada. aslang@mun.ca.

 

Abstract

Wild birds are recognized viral reservoirs but our understanding about avian viral diversity is limited. We describe here three novel RNA viruses that we identified in oropharyngeal/cloacal swabs collected from wild birds. The complete genome of a novel gull metapneumovirus (GuMPV B29) was determined. Phylogenetic analyses indicated that this virus could represent a novel avian metapneumovirus (AMPV) sub-group, intermediate between AMPV-C and the subgroup of the other AMPVs. This virus was detected in an American herring (1/24, 4.2%) and great black-backed (4/26, 15.4%) gulls. A novel gull coronavirus (GuCoV B29) was detected in great black-backed (3/26, 11.5%) and American herring (2/24, 8.3%) gulls. Phylogenetic analyses of GuCoV B29 suggested that this virus could represent a novel species within the genus Gammacoronavirus, close to other recently identified potential novel avian coronaviral species. One GuMPV-GuCoV co-infection was detected. A novel duck calicivirus (DuCV-2 B6) was identified in mallards (2/5, 40%) and American black ducks (7/26, 26.9%). This virus, of which we identified two different types, was fully sequenced and was genetically closest to other caliciviruses identified in Anatidae, but more distant to other caliciviruses from birds in the genus Anas. These discoveries increase our knowledge about avian virus diversity and host distributions.

KEYWORDS: avian viruses; calicivirus; coronavirus; metapneumovirus; novel viruses; viral epidemiology; virus discovery

PMID: 31438486 DOI: 10.3390/v11090768

Keywords: Coronavirus; Metapneumovirus; Calicivirus; Wild Birds; North American Region.

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#Paramyxo- and #Coronaviruses in #Rwandan #Bats (Trop Med Infect Dis., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Trop Med Infect Dis. 2019 Jul 2;4(3). pii: E99. doi: 10.3390/tropicalmed4030099.

Paramyxo- and Coronaviruses in Rwandan Bats.

Markotter W1, Geldenhuys M2, Jansen van Vuren P2,3, Kemp A3, Mortlock M2, Mudakikwa A4, Nel L5, Nziza J6, Paweska J2,3, Weyer J2,3.

Author information: 1 Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, Gauteng 0001, South Africa. wanda.markotter@up.ac.za. 2 Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, Gauteng 0001, South Africa. 3 Centre for Emerging Zoonotic and Parasitic diseases, National Institute for Communicable Diseases, National Health laboratory Services, Sandringham, Johannesburg 2131, South Africa. 4 Rwanda Development Board, Department of tourism and Conservation, P.O Box 6239, Kigali, Rwanda. 5 Centre for Viral Zoonoses, Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, Gauteng 0001, South Africa. 6 Mountain Gorilla Veterinary Project, P.O Box 115, Musanze, Rwanda.

 

Abstract

A high diversity of corona- and paramyxoviruses have been detected in different bat species at study sites worldwide, including Africa, however no biosurveillance studies from Rwanda have been reported. In this study, samples from bats collected from caves in Ruhengeri, Rwanda, were tested for the presence of corona- and paramyxoviral RNA using reverse transcription PCR assays. Positive results were further characterized by DNA sequencing and phylogenetic analysis. In addition to morphological identification of bat species, we also did molecular confirmation of species identities, contributing to the known genetic database available for African bat species. We detected a novel Betacoronavirus in two Geoffroy’s horseshoe bats (Rhinolophus clivosus) bats. We also detected several different paramyxoviral species from various insectivorous bats. One of these viral species was found to be homologous to the genomes of viruses belonging to the Jeilongvirus genus. Additionally, a Henipavirus-related sequence was detected in an Egyptian rousette fruit bat (Rousettus aegyptiacus). These results expand on the known diversity of corona- and paramyxoviruses and their geographical distribution in Africa.

KEYWORDS: Rwanda; barcoding; bat; caves; coronavirus; henipavirus; jeilongvirus; paramyxovirus; surveillance

PMID: 31269631 DOI: 10.3390/tropicalmed4030099

Keywords: Coronavirus; Betacoronavirus; Paramyxovirus; Henipavirus; Bats; Rwanda.

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#Human #coronavirus alone or in co-infection with #rhinovirus C is a #risk factor for #SARI and admission to the #PICU: A one-year study in Southeast #Brazil (PLoS One, abstract)

[Source: PLoS One, full page: (LINK). Abstract, edited.]

OPEN ACCESS /  PEER-REVIEWED / RESEARCH ARTICLE

Human coronavirus alone or in co-infection with rhinovirus C is a risk factor for severe respiratory disease and admission to the pediatric intensive care unit: A one-year study in Southeast Brazil

Alessandra K. Matsuno  , Talita B. Gagliardi , Flavia E. Paula, Luciano K. S. Luna, Bruna L. S. Jesus, Renato T. Stein, Davi C. Aragon, Ana P. C. P. Carlotti , Eurico Arruda

Published: June 3, 2019 / DOI: https://doi.org/10.1371/journal.pone.0217744

 

Abstract

Objective

We aimed to assess the profile of respiratory viruses in young children hospitalized for acute lower respiratory tract infection (ALRI) and its association with disease severity, defined as need for pediatric intensive care unit (PICU) admission.

Design

Prospective observational cohort study.

Setting

A tertiary-care university hospital in Brazil.

Patients

Children younger than three years attending the pediatric emergency room with ALRI who were admitted to the hospital.

Interventions

None.

Measurements and main results

Nasopharyngeal aspirates were collected from patients from June 1st, 2008 to May 31st, 2009within the first 48 hours of hospitalization. Nasopharyngeal aspirates were tested for 17 human respiratory viruses by molecular and immunofluorescence based assays. Simple and multiple log-binomial regression models were constructed to assess associations of virus type with a need for PICU admission. Age, prematurity, the presence of an underlying disease and congenital heart disease were covariates. Nasopharyngeal aspirates were positive for at least one virus in 236 patients. Rhinoviruses were detected in 85.6% of samples, with a preponderance of rhinovirus C (RV-C) (61.9%). Respiratory syncytial virus was detected in 59.8% and human coronavirus (HCoV) in 11% of the samples. Co-detections of two to five viruses were found in 78% of the patients. The detection of HCoV alone (adjusted relative risk (RR) 2.18; 95% CI 1.15–4.15) or in co-infection with RV-C (adjusted RR 2.37; 95% CI 1.23–4.58) was independently associated with PICU admission.

Conclusions

The detection of HCoV alone or in co-infection with RV-C was independently associated with PICU admission in young children hospitalized for ALRI.

___

Citation: Matsuno AK, Gagliardi TB, Paula FE, Luna LKS, Jesus BLS, Stein RT, et al. (2019) Human coronavirus alone or in co-infection with rhinovirus C is a risk factor for severe respiratory disease and admission to the pediatric intensive care unit: A one-year study in Southeast Brazil. PLoS ONE 14(6): e0217744. https://doi.org/10.1371/journal.pone.0217744

Editor: Raymond J. Pickles, University of North Carolina at Chapel Hill, UNITED STATES

Received: October 2, 2018; Accepted: May 19, 2019; Published: June 3, 2019

Copyright: © 2019 Matsuno et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All relevant data are within the manuscript and its Supporting Information files.

Funding: AKM and EAN supported mainly by an academic grant from Abbott Laboratórios do Brasil Ltda based on an unrestricted investigator-generated proposal. EAN Additional funding was provided by a grant from the Sao Paulo State Research Foundation (FAPESP) and by FAEPA – “Fundação de Apoio ao Ensino Pesquisa e Assistência” (in English would be “Foundation of Support to Teaching Research and Assistance) of the University of Sao Paulo Hospital of Ribeirão Preto. EA has long standing scholarship support from the Brazilian Research Council (CNPq). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: AKM and EAN were supported by an academic grant from Abbott Laboratórios do Brasil Ltda, based on an unrestricted investigator-generated proposal. This does not alter our adherence to PLOS ONE policies on sharing data and materials, as detailed online in the guide for authors: https://journals.plos.org/plosone/s/competing-interests).

Keywords: Coronavirus; Rhinovirus; SARI; Intensive Care; Pediatrics; Brazil.

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High-Throughput #Screening and Identification of Potent Broad-Spectrum #Inhibitors of #Coronaviruses (J Virol., abstract)

[Source: Journal of Virology, full page: (LINK). Abstract, edited.]

High-Throughput Screening and Identification of Potent Broad-Spectrum Inhibitors of Coronaviruses

Liang Shen, Junwei Niu, Chunhua Wang, Baoying Huang, Wenling Wang, Na Zhu, Yao Deng, Huijuan Wang, Fei Ye, Shan Cen, Wenjie Tan

Tom Gallagher, Editor

DOI: 10.1128/JVI.00023-19

 

ABSTRACT

Coronaviruses (CoVs) act as cross-species viruses and have the potential to spread rapidly into new host species and cause epidemic diseases. Despite the severe public health threat of severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome CoV (MERS-CoV), there are currently no drugs available for their treatment; therefore, broad-spectrum inhibitors of emerging and endemic CoVs are urgently needed. To search for effective inhibitory agents, we performed high-throughput screening (HTS) of a 2,000-compound library of approved drugs and pharmacologically active compounds using the established genetically engineered human CoV OC43 (HCoV-OC43) strain expressing Renilla luciferase (rOC43-ns2Del-Rluc) and validated the inhibitors using multiple genetically distinct CoVs in vitro. We screened 56 hits from the HTS data and validated 36 compounds in vitro using wild-type HCoV-OC43. Furthermore, we identified seven compounds (lycorine, emetine, monensin sodium, mycophenolate mofetil, mycophenolic acid, phenazopyridine, and pyrvinium pamoate) as broad-spectrum inhibitors according to their strong inhibition of replication by four CoVs in vitroat low-micromolar concentrations. Additionally, we found that emetine blocked MERS-CoV entry according to pseudovirus entry assays and that lycorine protected BALB/c mice against HCoV-OC43-induced lethality by decreasing viral load in the central nervous system. This represents the first demonstration of in vivo real-time bioluminescence imaging to monitor the effect of lycorine on the spread and distribution of HCoV-OC43 in a mouse model. These results offer critical information supporting the development of an effective therapeutic strategy against CoV infection.

 

IMPORTANCE

Currently, there is no approved therapy to treat coronavirus infection; therefore, broad-spectrum inhibitors of emerging and endemic CoVs are needed. Based on our high-throughput screening assay using a compound library, we identified seven compounds with broad-spectrum efficacy against the replication of four CoVs in vitro. Additionally, one compound (lycorine) was found to protect BALB/c mice against HCoV-OC43-induced lethality by decreasing viral load in the central nervous system. This inhibitor might offer promising therapeutic possibilities for combatting novel CoV infections in the future.

 

FOOTNOTES

Received 7 January 2019. Accepted 17 March 2019. Accepted manuscript posted online 27 March 2019.

Supplemental material for this article may be found at https://doi.org/10.1128/JVI.00023-19.

Copyright © 2019 American Society for Microbiology. All Rights Reserved.

Keywords: Antivirals; Coronavirus.

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Analysis of #Coronavirus Temperature-Sensitive Mutants Reveals an Interplay between the Macrodomain and Papain-Like Protease Impacting #Replication and #Pathogenesis (J Virol., abstract)

[Source: Journal of Virology, full page: (LINK). Abstract, edited.]

Analysis of Coronavirus Temperature-Sensitive Mutants Reveals an Interplay between the Macrodomain and Papain-Like Protease Impacting Replication and Pathogenesis

Xufang Deng, Robert C. Mettelman, Amornrat O’Brien, John A. Thompson, Timothy E. O’Brien, Susan C. Baker

Julie K. Pfeiffer, Editor

DOI: 10.1128/JVI.02140-18

 

ABSTRACT

Analysis of temperature-sensitive (ts) mutant viruses is a classic method allowing researchers to identify genetic loci involved in viral replication and pathogenesis. Here, we report genetic analysis of a ts strain of mouse hepatitis virus (MHV), tsNC11, focusing on the role of mutations in the macrodomain (MAC) and the papain-like protease 2 (PLP2) domain of nonstructural protein 3 (nsp3), a component of the viral replication complex. Using MHV reverse genetics, we generated a series of mutant viruses to define the contributions of macrodomain- and PLP2-specific mutations to the ts phenotype. Viral replication kinetics and efficiency-of-plating analysis performed at permissive and nonpermissive temperatures revealed that changes in the macrodomain alone were both necessary and sufficient for the ts phenotype. Interestingly, mutations in the PLP2 domain were not responsible for the temperature sensitivity but did reduce the frequency of reversion of macrodomain mutants. Coimmunoprecipitation studies are consistent with an interaction between the macrodomain and PLP2. Expression studies of the macrodomain-PLP2 portion of nsp3 indicate that the ts mutations enhance proteasome-mediated degradation of the protein. Furthermore, we found that during virus infection, the replicase proteins containing the MAC and PLP2 mutations were more rapidly degraded at the nonpermissive temperature than were the wild-type proteins. Importantly, we show that the macrodomain and PLP2 mutant viruses trigger production of type I interferon in vitro and are attenuated in mice, further highlighting the importance of the macrodomain-PLP2 interplay in viral pathogenesis.

 

IMPORTANCE

Coronaviruses (CoVs) are emerging human and veterinary pathogens with pandemic potential. Despite the established and predicted threat these viruses pose to human health, there are currently no approved countermeasures to control infections with these viruses in humans. Viral macrodomains, enzymes that remove posttranslational ADP-ribosylation of proteins, and viral multifunctional papain-like proteases, enzymes that cleave polyproteins and remove polyubiquitin chains via deubiquitinating activity, are two important virulence factors. Here, we reveal an unanticipated interplay between the macrodomain and the PLP2 domain that is important for replication and antagonizing the host innate immune response. Targeting the interaction of these enzymes may provide new therapeutic opportunities to treat CoV disease.

Copyright © 2019 American Society for Microbiology. All Rights Reserved.

Keywords: Coronavirus; Viral pathogenesis.

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