#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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#Extension of the known #distribution of a novel clade C #betacoronavirus in a #wildlife host (Epidemiol Infect., abstract)

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

Epidemiol Infect. 2019 Jan;147:e169. doi: 10.1017/S0950268819000207.

Extension of the known distribution of a novel clade C betacoronavirus in a wildlife host.

Saldanha IF1, Lawson B2, Goharriz H3, Rodriguez-Ramos Fernandez J4, John SK2, Fooks AR3, Cunningham AA2, Johnson N3, Horton DL1.

Author information: 1 School of Veterinary Medicine, University of Surrey, Guildford,UK. 2 Institute of Zoology, Zoological Society of London,London,UK. 3 Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency, New Haw, Addlestone,Surrey, KT15 3NB,UK. 4 IDEXX Laboratories Ltd.,Wetherby, West Yorkshire,UK.

 

Abstract

Disease surveillance in wildlife populations presents a logistical challenge, yet is critical in gaining a deeper understanding of the presence and impact of wildlife pathogens. Erinaceus coronavirus (EriCoV), a clade C Betacoronavirus, was first described in Western European hedgehogs (Erinaceus europaeus) in Germany. Here, our objective was to determine whether EriCoV is present, and if it is associated with disease, in Great Britain (GB). An EriCoV-specific BRYT-Green® real-time reverse transcription PCR assay was used to test 351 samples of faeces or distal large intestinal tract contents collected from casualty or dead hedgehogs from a wide area across GB. Viral RNA was detected in 10.8% (38) samples; however, the virus was not detected in any of the 61 samples tested from Scotland. The full genome sequence of the British EriCoV strain was determined using next generation sequencing; it shared 94% identity with a German EriCoV sequence. Multivariate statistical models using hedgehog case history data, faecal specimen descriptions and post-mortem examination findings found no significant associations indicative of disease associated with EriCoV in hedgehogs. These findings indicate that the Western European hedgehog is a reservoir host of EriCoV in the absence of apparent disease.

KEYWORDS: Coronavirus; geographical information systems; virology; wildlife; zoonoses

PMID: 31063092 DOI: 10.1017/S0950268819000207

Keywords: Betacoronavirus; Erinaceus coronavirus; Wildlife; UK.

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#Global #Epidemiology of #Bat #Coronaviruses (Viruses, abstract)

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

Viruses. 2019 Feb 20;11(2). pii: E174. doi: 10.3390/v11020174.

Global Epidemiology of Bat Coronaviruses.

Wong ACP1, Li X2, Lau SKP3,4,5,6,7, Woo PCY8,9,10,11,12.

Author information: 1 Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong. antonwcp@hku.hk. 2 Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong. lixinlyh@connect.hku.hk. 3 Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong. skplau@hku.hk. 4 State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong. skplau@hku.hk. 5 Research Centre of Infection and Immunology, The University of Hong Kong, Pokfulam, Hong Kong. skplau@hku.hk. 6 Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong. skplau@hku.hk. 7 Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong. skplau@hku.hk. 8 Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong. pcywoo@hku.hk. 9 State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong. pcywoo@hku.hk. 10 Research Centre of Infection and Immunology, The University of Hong Kong, Pokfulam, Hong Kong. pcywoo@hku.hk. 11 Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong. pcywoo@hku.hk. 12 Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong. pcywoo@hku.hk.

 

Abstract

Bats are a unique group of mammals of the order Chiroptera. They are highly diversified and are the group of mammals with the second largest number of species. Such highly diversified cell types and receptors facilitate them to be potential hosts of a large variety of viruses. Bats are the only group of mammals capable of sustained flight, which enables them to disseminate the viruses they harbor and enhance the chance of interspecies transmission. This article aims at reviewing the various aspects of the global epidemiology of bat coronaviruses (CoVs). Before the SARS epidemic, bats were not known to be hosts for CoVs. In the last 15 years, bats have been found to be hosts of >30 CoVs with complete genomes sequenced, and many more if those without genome sequences are included. Among the four CoV genera, only alphaCoVs and betaCoVs have been found in bats. As a whole, both alphaCoVs and betaCoVs have been detected from bats in Asia, Europe, Africa, North and South America and Australasia; but alphaCoVs seem to be more widespread than betaCoVs, and their detection rate is also higher. For betaCoVs, only those from subgenera Sarbecovirus, Merbecovirus, Nobecovirus and Hibecovirus have been detected in bats. Most notably, horseshoe bats are the reservoir of SARS-CoV, and several betaCoVs from subgenus Merbecovirus are closely related to MERS-CoV. In addition to the interactions among various bat species themselves, bat⁻animal and bat⁻human interactions, such as the presence of live bats in wildlife wet markets and restaurants in Southern China, are important for interspecies transmission of CoVs and may lead to devastating global outbreaks.

KEYWORDS: Alphacoronavirus; Betacoronavirus; bat; coronavirus; epidemiology; global; host; interspecies transmission

PMID: 30791586 DOI: 10.3390/v11020174

Keywords: Alphacoronavirus; Betacoronavirus; SARS; MERS-CoV; Bats.

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#Human #coronaviruses #OC43 and #HKU1 bind to 9-O-acetylated #sialic acids via a conserved receptor-binding site in spike protein domain A (Proc Natl Acad Sci USA, abstract)

[Source: Proceedings of the National Academy of Sciences of the United States of America, full page: (LINK). Abstract, edited.]

Human coronaviruses OC43 and HKU1 bind to 9-O-acetylated sialic acids via a conserved receptor-binding site in spike protein domain A

Ruben J. G. Hulswit, Yifei Lang, Mark J. G. Bakkers, Wentao Li, Zeshi Li, Arie Schouten, Bram Ophorst, Frank J. M. van Kuppeveld, Geert-Jan Boons, Berend-Jan Bosch, Eric G. Huizinga, and Raoul J. de Groot

PNAS published ahead of print January 24, 2019 / DOI: https://doi.org/10.1073/pnas.1809667116

Edited by Mary K. Estes, Baylor College of Medicine, Houston, TX, and approved December 19, 2018 (received for review June 6, 2018)

 

Significance

Human coronaviruses OC43 and HKU1 are related, yet distinct respiratory pathogens, associated with common colds, but also with severe disease in the frail. Both viruses employ sialoglycan-based receptors with 9-O-acetylated sialic acid (9-O-Ac-Sia) as key component. Here, we identify the 9-O-Ac-Sia–specific receptor-binding site of OC43 S and demonstrate it to be conserved and functional in HKU1. The considerable difference in receptor-binding affinity between OC43 and HKU1 S, attributable to differences in local architecture and receptor-binding site accessibility, is suggestive of differences between OC43 and HKU1 in their adaptation to the human sialome. The data will enable studies into the evolution and pathobiology of OC43 and HKU1 and open new avenues toward prophylactic and therapeutic intervention.

 

Abstract

Human betacoronaviruses OC43 and HKU1 are endemic respiratory pathogens and, while related, originated from independent zoonotic introductions. OC43 is in fact a host-range variant of the species Betacoronavirus-1, and more closely related to bovine coronavirus (BCoV)—its presumptive ancestor—and porcine hemagglutinating encephalomyelitis virus (PHEV). The β1-coronaviruses (β1CoVs) and HKU1 employ glycan-based receptors carrying 9-O-acetylated sialic acid (9-O-Ac-Sia). Receptor binding is mediated by spike protein S, the main determinant of coronavirus host specificity. For BCoV, a crystal structure for the receptor-binding domain S1A is available and for HKU1 a cryoelectron microscopy structure of the complete S ectodomain. However, the location of the receptor-binding site (RBS), arguably the single-most important piece of information, is unknown. Here we solved the 3.0-Å crystal structure of PHEV S1A. We then took a comparative structural analysis approach to map the β1CoV S RBS, using the general design of 9-O-Ac-Sia-binding sites as blueprint, backed-up by automated ligand docking, structure-guided mutagenesis of OC43, BCoV, and PHEV S1A, and infectivity assays with BCoV-S–pseudotyped vesicular stomatitis viruses. The RBS is not exclusive to OC43 and related animal viruses, but is apparently conserved and functional also in HKU1 S1A. The binding affinity of the HKU1 S RBS toward short sialoglycans is significantly lower than that of OC43, which we attribute to differences in local architecture and accessibility, and which may be indicative for differences between the two viruses in receptor fine-specificity. Our findings challenge reports that would map the OC43 RBS elsewhere in S1A and that of HKU1 in domain S1B.

coronavirus – spike – 9-O-acetylated sialic acid – OC43 – HKU1

 

Footnotes

1 R.J.G.H., Y.L., and M.J.G.B. contributed equally to this work.

2 Present address: Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115.

3 To whom correspondence should be addressed. Email: r.j.degroot@uu.nl.

Author contributions: R.J.G.H. and M.J.G.B conceived the study; R.J.d.G. coordinated and supervised the study; R.J.G.H., Y.L., M.J.G.B., W.L., E.G.H., and R.J.d.G. designed research; R.J.G.H., Y.L., M.J.G.B., A.S., B.O., and E.G.H. performed research; W.L., Z.L., G.-J.B., and B.-J.B. contributed new reagents/analytic tools; R.J.G.H. and A.S. performed crystallization experiments; M.J.G.B., Y.L., and E.G.H. refined the PHEV S1A structure and performed automated ligand docking; Y.L. established assays to detect HKU1 S receptor binding and performed infection experiments with pseudotyped vesicular stomatitis virus; E.G.H. supervised crystal structure analysis; R.J.G.H., Y.L., M.J.G.B., W.L., Z.L., A.S., F.J.M.v.K., G.-J.B., B.-J.B., E.G.H., and R.J.d.G. analyzed data; M.J.G.B. performed in silico structural analysis to identify the RBS; and R.J.G.H., Y.L., M.J.G.B., E.G.H., and R.J.d.G. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

Data deposition: The atomic coordinates and structure factors have been deposited in the Protein Data Bank, www.wwpdb.org (PDB ID code 6QFY). The amino acid sequences of the S1A–Fc fusion proteins were deposited in the GenBank database (accession no. MG999832-35).

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1809667116/-/DCSupplemental.

Published under the PNAS license.

Keywords: Coronavirus; Betacoronavirus; HCoV-OC43; HCoV-HKU1; Viral pathogenesis.

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Identification and characterization of #Coronaviridae #genomes from #Vietnamese #bats and rats based on conserved protein domains (Virus Evol., abstract)

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

Virus Evol. 2018 Dec 15;4(2):vey035. doi: 10.1093/ve/vey035. eCollection 2018 Jul.

Identification and characterization of Coronaviridae genomes from Vietnamese bats and rats based on conserved protein domains.

Phan MVT1,2, Ngo Tri T3, Hong Anh P3, Baker S3, Kellam P4,5, Cotten M1,2.

Author information: 1 Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK. 2 Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands. 3 Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. 4 Department of Infection and Immunity, Imperial College London, London, UK. 5 Kymab Ltd, Babraham Research Campus, Cambridge, UK.

 

Abstract

The Coronaviridae family of viruses encompasses a group of pathogens with a zoonotic potential as observed from previous outbreaks of the severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus. Accordingly, it seems important to identify and document the coronaviruses in animal reservoirs, many of which are uncharacterized and potentially missed by more standard diagnostic assays. A combination of sensitive deep sequencing technology and computational algorithms is essential for virus surveillance, especially for characterizing novel- or distantly related virus strains. Here, we explore the use of profile Hidden Markov Model-defined Pfam protein domains (Pfam domains) encoded by new sequences as a Coronaviridae sequence classification tool. The encoded domains are used first in a triage to identify potential Coronaviridae sequences and then processed using a Random Forest method to classify the sequences to the Coronaviridae genus level. The application of this algorithm on Coronaviridae genomes assembled from agnostic deep sequencing data from surveillance of bats and rats in Dong Thap province (Vietnam) identified thirty-four Alphacoronavirus and eleven Betacoronavirus genomes. This collection of bat and rat coronaviruses genomes provided essential information on the local diversity of coronaviruses and substantially expanded the number of coronavirus full genomes available from bat and rats and may facilitate further molecular studies on this group of viruses.

KEYWORDS: Pfam; machine learning; profile Hidden Markov model; protein domains; random forest; virus classification

PMID: 30568804 PMCID: PMC6295324 DOI: 10.1093/ve/vey035

Keywords: Coronavirus; Alphacoronavirus; Betacoronavirus; Bats; Vietnam.

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Middle East respiratory syndrome #coronavirus (#MERS-CoV): #Impact on #Saudi Arabia, 2015 (Saudi J Biol Sci., abstract)

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

Saudi J Biol Sci. 2018 Nov;25(7):1402-1405. doi: 10.1016/j.sjbs.2016.09.020. Epub 2016 Oct 1.

Middle East respiratory syndrome coronavirus (MERS-CoV): Impact on Saudi Arabia, 2015.

Faridi U1.

Author information: 1 Department of Biochemistry, Tabuk University, Tabuk, Saudi Arabia.

 

Abstract

Middle East respiratory syndrome is the acute respiratory syndrome caused by betacoronavirus MERS-CoV. The first case of this disease was reported from Saudi Arabia in 2012. This virus is lethal and is a close relative of a severe acute respiratory syndrome (SARS), which is responsible for more than 3000 deaths in 2002-2003. According to Ministry of Health, Saudi Arabia. The number of new cases is 457 in 2015. Riyadh has the highest number of reports in comparison to the other cities. According to this report, males are more susceptible than female, especially after the age of 40. Because of the awareness and early diagnosis the incidence is falling gradually. The pre-existence of another disease like cancer or diabetic etc. boosts the infection. MERS is a zoonotic disease and human to human transmission is low. The MERS-CoV is a RNA virus with protein envelope. On the outer surface, virus has spike like glycoprotein which is responsible for the attachment and entrance inside host cells. There is no specific treatment for the MERS-CoV till now, but drugs are in pipeline which bind with the spike glycoprotein and inhibit its entrance host cells. MERS-CoV and SAR-CoV are from the same genus, so it was thought that the drugs which inhibit the growth of SARS-CoV can also inhibit the growth of MERS-CoV but those drugs are not completely inhibiting virus activity. Until we don’t have proper structure and the treatment of MERS-CoV, We should take precautions, especially the health care workers, Camel owners and Pilgrims during Hajj and Umrah, because they are at a higher risk of getting infected.

KEYWORDS: Betacoronavirus; MERS-CoV; SARS; Saudi Arabia

PMID: 30505188 PMCID: PMC6252006  DOI: 10.1016/j.sjbs.2016.09.020

Keywords: Coronavirus; Betacoronavirus; MERS-CoV; SARS; Saudi Arabia; Human; Camels.

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Molecular #identification of #Betacoronavirus in #bats from #Sardinia (#Italy): first detection and phylogeny (Virus Genes., abstract)

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

Virus Genes. 2018 Nov 13. doi: 10.1007/s11262-018-1614-8. [Epub ahead of print]

Molecular identification of Betacoronavirus in bats from Sardinia (Italy): first detection and phylogeny.

Lecis R1,2, Mucedda M3, Pidinchedda E3, Pittau M4,5, Alberti A4,5.

Author information: 1 Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy. rlecis@uniss.it. 2 Mediterranean Centre for Disease Control, University of Sassari, Via Vienna 2, 07100, Sassari, Italy. rlecis@uniss.it. 3 Centro Pipistrelli Sardegna, Via G. Leopardi 1, 07100, Sassari, Italy. 4 Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy. 5 Mediterranean Centre for Disease Control, University of Sassari, Via Vienna 2, 07100, Sassari, Italy.

 

Abstract

Bats may be natural reservoirs for a large variety of emerging viruses, including mammalian coronaviruses (CoV). The recent emergence of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) in humans, with evidence that these viruses may have their ancestry in bats, highlights the importance of virus surveillance in bat populations. Here, we report the identification and molecular characterization of a bat β-Coronavirus, detected during a viral survey carried out on different bat species in the island of Sardinia (Italy). Cutaneous, oral swabs, and faecal samples were collected from 46 bats, belonging to 15 different species, and tested for viral presence. Coronavirus RNA was detected in faecal samples from three different species: the greater horseshoe bat (Rhinolophus ferrumequinum), the brown long-eared bat (Plecotus auritus), and the European free-tailed bat (Tadarida teniotis). Phylogenetic analyses based on RNA-dependent RNA polymerase (RdRp) sequences assigned the detected CoV to clade 2b within betacoronaviruses, clustering with SARS-like bat CoVs previously reported. These findings point to the need for continued surveillance of bat CoV circulating in Sardinian bats, and extend the current knowledge on CoV ecology with novel sequences detected in bat species not previously described as β-Coronavirus hosts.

KEYWORDS: Bats; Coronavirus; RNA-dependent RNA polymerase; Rhinolophus ferrumequinum; Sardinia

PMID: 30426315 DOI: 10.1007/s11262-018-1614-8

Keywords: Coronavirus; Betacoronavirus; SARS; Bats; Italy.

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