#Coronaviruses Detected in #Bats in Close Contact with Humans in #Rwanda (Ecohealth, abstract)

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

Ecohealth. 2019 Dec 6. doi: 10.1007/s10393-019-01458-8. [Epub ahead of print]

Coronaviruses Detected in Bats in Close Contact with Humans in Rwanda.

Nziza J1, Goldstein T2, Cranfield M3, Webala P4, Nsengimana O5, Nyatanyi T6, Mudakikwa A7, Tremeau-Bravard A2, Byarugaba D8, Tumushime JC3, Mwikarago IE9, Gafarasi I10, Mazet J3,2, Gilardi K3,2.

Author information: 1 Gorilla Doctors, P.O. Box 115, Musanze, Rwanda. nzizavet@gmail.com. 2 Karen C. Drayer Wildlife Health Center, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, CA, USA. 3 Gorilla Doctors, P.O. Box 115, Musanze, Rwanda. 4 Department of Forestry and Wildlife Management, Maasai Mara University, P.O. Box 861, Narok, 20500, Kenya. 5 Rwanda Wildlife Conservation Association, P.O. Box 5427, Kigali, Rwanda. 6 Department of Global Health and Social Medicine, School of Medicine, Harvard University, Boston, USA. 7 Rwanda Development Board, P.O. Box 6932, Kigali, Rwanda. 8 Makerere University Walter Reed Project, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda. 9 National Reference Laboratory, Rwanda Biomedical Center, P.O. Box 83, Kigali, Rwanda. 10 Rwanda Agriculture Board, P.O. Box 5016, Kigali, Rwanda.

 

Abstract

Bats living in close contact with people in Rwanda were tested for evidence of infection with viruses of zoonotic potential. Mucosal swabs from 503 bats representing 17 species were sampled from 2010 to 2014 and screened by consensus PCR for 11 viral families. Samples were negative for all viral families except coronaviruses, which were detected in 27 bats belonging to eight species. Known coronaviruses detected included the betacorona viruses: Kenya bat coronaviruses, Eidolon bat coronavirus, and Bat coronavirus HKU9, as well as an alphacoronavirus, Chaerephon Bat coronavirus. Novel coronaviruses included two betacorona viruses clustering with SARS-CoV, a 2d coronavirus, and an alphacoronavirus.

KEYWORDS: Bats; Coronaviruses; Human–wildlife interfaces; Rwanda

PMID: 31811597 DOI: 10.1007/s10393-019-01458-8

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

——

Identification of a Novel #Betacoronavirus (#Merbecovirus) in Amur #Hedgehogs from #China (Viruses, abstract)

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

Viruses. 2019 Oct 24;11(11). pii: E980. doi: 10.3390/v11110980.

Identification of a Novel Betacoronavirus (Merbecovirus) in Amur Hedgehogs from China.

Lau SKP1,2,3,4, Luk HKH5, Wong ACP6, Fan RYY7, Lam CSF8, Li KSM9, Ahmed SS10, Chow FWN11, Cai JP12, Zhu X13,14, Chan JFW15,16,17,18, Lau TCK19, Cao K20,21, Li M22,23, Woo PCY24,25,26,27, Yuen KY28,29,30,31.

Author information: 1 Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China. skplau@hku.hk. 2 State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong 999077, China. skplau@hku.hk. 3 Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong 999077, China. skplau@hku.hk. 4 Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong 999077, China. skplau@hku.hk. 5 Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China. hkhluk@hku.hk. 6 Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China. antonwcp@connect.hku.hk. 7 Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China. rachelfyy2004@yahoo.com.hk. 8 Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China. carollamsukfun@yahoo.com.hk. 9 Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China. keth105@gmail.com. 10 Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China. shakeel87@gmail.com. 11 Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China. cwn5810@gmail.com. 12 Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China. caijuice@hku.hk. 13 Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China. zhuxun8@mail.sysu.edu.cn. 14 Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China. zhuxun8@mail.sysu.edu.cn. 15 Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China. jfwchan@hku.hk. 16 State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong 999077, China. jfwchan@hku.hk. 17 Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong 999077, China. jfwchan@hku.hk. 18 Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong 999077, China. jfwchan@hku.hk. 19 Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong 999077, China. chiklau@cityu.edu.hk. 20 Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China. caoky@mail.sysu.edu.cn. 21 Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China. caoky@mail.sysu.edu.cn. 22 Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China. limf@mail.sysu.edu.cn. 23 Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China. limf@mail.sysu.edu.cn. 24 Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China. pcywoo@hku.hk. 25 State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong 999077, China. pcywoo@hku.hk. 26 Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong 999077, China. pcywoo@hku.hk. 27 Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong 999077, China. pcywoo@hku.hk. 28 Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China. kyyuen@hku.hk. 29 State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong 999077, China. kyyuen@hku.hk. 30 Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong 999077, China. kyyuen@hku.hk. 31 Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong 999077, China. kyyuen@hku.hk.

 

Abstract

While dromedaries are the immediate animal source of Middle East Respiratory Syndrome (MERS) epidemic, viruses related to MERS coronavirus (MERS-CoV) have also been found in bats as well as hedgehogs. To elucidate the evolution of MERS-CoV-related viruses and their interspecies transmission pathway, samples were collected from different mammals in China. A novel coronavirus related to MERS-CoV, Erinaceus amurensis hedgehog coronavirus HKU31 (Ea-HedCoV HKU31), was identified from two Amur hedgehogs. Genome analysis supported that Ea-HedCoV HKU31 represents a novel species under Merbecovirus, being most closely related to Erinaceus CoV from European hedgehogs in Germany, with 79.6% genome sequence identity. Compared to other members of Merbecovirus, Ea-HedCoV HKU31 possessed unique non-structural proteins and putative cleavage sites at ORF1ab. Phylogenetic analysis showed that Ea-HedCoV HKU31 and BetaCoV Erinaceus/VMC/DEU/2012 were closely related to NeoCoV and BatCoV PREDICT from African bats in the spike region, suggesting that the latter bat viruses have arisen from recombination between CoVs from hedgehogs and bats. The predicted HKU31 receptor-binding domain (RBD) possessed only one out of 12 critical amino acid residues for binding to human dipeptidyl peptidase 4 (hDPP4), the MERS-CoV receptor. The structural modeling of the HKU31-RBD-hDPP4 binding interphase compared to that of MERS-CoV and Tylonycteris bat CoV HKU4 (Ty-BatCoV HKU4) suggested that HKU31-RBD is unlikely to bind to hDPP4. Our findings support that hedgehogs are an important reservoir of Merbecovirus, with evidence of recombination with viruses from bats. Further investigations in bats, hedgehogs and related animals are warranted to understand the evolution of MERS-CoV-related viruses.

KEYWORDS: China; Merbecovirus; coronavirus; hedgehog; novel species

PMID: 31653070 DOI: 10.3390/v11110980

Keywords: Betacoronavirus; Coronavirus; MERS-CoV; Merbecovirus; Wildlife; China.

——

#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.

——

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.

——

Identification of Diverse #Bat #Alphacoronaviruses and #Betacoronaviruses in #China Provides New Insights Into the Evolution and Origin of Coronavirus-Related Diseases (Front Microbiol., abstract)

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

Front Microbiol. 2019 Aug 14;10:1900. doi: 10.3389/fmicb.2019.01900. eCollection 2019.

Identification of Diverse Bat Alphacoronaviruses and Betacoronaviruses in China Provides New Insights Into the Evolution and Origin of Coronavirus-Related Diseases.

Han Y1, Du J1, Su H1, Zhang J2, Zhu G3, Zhang S2, Wu Z1, Jin Q1.

Author information: 1 NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. 2 Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China. 3 EcoHealth Alliance, New York, NY, United States.

 

Abstract

Outbreaks of severe acute respiratory syndrome (SARS) in 2002, Middle East respiratory syndrome in 2012 and fatal swine acute diarrhea syndrome in 2017 caused serious infectious diseases in humans and in livestock, resulting in serious public health threats and huge economic losses. All such coronaviruses (CoVs) were confirmed to originate from bats. To continuously monitor the epidemic-related CoVs in bats, virome analysis was used to classify CoVs from 831 bats of 15 species in Yunnan, Guangxi, and Sichuan Provinces between August 2016 and May 2017. We identified 11 CoV strains from 22 individual samples of four bat species. Identification of four alpha-CoVs from Scotophilus kuhlii in Guangxi, which was closely related to a previously reported bat CoV and porcine epidemic diarrhea virus (PEDV), revealed a bat-swine lineage under the genus Alphacoronavirus. A recombinant CoV showed that the PEDV probably originated from the CoV of S. kuhlii. Another alpha-CoV, α-YN2018, from Rhinolophus affinis in Yunnan, suggested that this alpha-CoV lineage had multiple host origins, and α-YN2018 had recombined with CoVs of other bat species over time. We identified five SARS-related CoVs (SARSr-CoVs) in Rhinolophus bats from Sichuan and Yunnan and confirmed that angiotensin-converting enzyme 2 usable SARSr-CoVs were continuously circulating in Rhinolophus spp. in Yunnan. The other beta-CoV, strain β-GX2018, found in Cynopterus sphinx of Guangxi, represented an independently evolved lineage different from known CoVs of Rousettus and Eonycteris bats. The identification of diverse CoVs here provides new genetic data for understanding the distribution and source of pathogenic CoVs in China.

KEYWORDS: bats; coronaviruses; ecological and genetic diversity; porcine epidemic diarrhea virus; severe acute respiratory syndrome coronavirus

PMID: 31474969 PMCID: PMC6702311 DOI: 10.3389/fmicb.2019.01900

Keywords: Alphacoronavirus; Betacoronavirus; Bats; China.

——

#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.

——

#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.

——