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.

——

#Serological evidence of #MERS-CoV and #HKU8-related #Coronavirus #coinfection in #Kenyan #camels (Emerg Microbes Infect., abstract)

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

Emerg Microbes Infect. 2019;8(1):1528-1534. doi: 10.1080/22221751.2019.1679610.

Serological evidence of MERS-CoV and HKU8-related CoV co-infection in Kenyan camels.

Zhang W1, Zheng XS1,2, Agwanda B3, Ommeh S4, Zhao K1,2, Lichoti J5, Wang N1, Chen J1,2, Li B1, Yang XL1, Mani S6, Ngeiywa KJ5,7, Zhu Y1, Hu B1, Onyuok SO1, Yan B1, Anderson DE6, Wang LF6, Zhou P1, Shi ZL1.

Author information: 1 CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People’s Republic of China. 2 University of Chinese Academy of Sciences , Beijing , People’s Republic of China. 3 Department of Zoology, National Museums of Kenya , Nairobi , Kenya. 4 Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology , Nairobi , Kenya. 5 Directorate of Veterinary Services, State Department of Livestock, Ministry of Agriculture , Livestock and Fisheries , Kenya. 6 Programme in Emerging Infectious Diseases Duke-NUS Medical School , Singapore , Singapore. 7 Kenya Camel Association , Nairobi , Kenya.

 

Abstract

Dromedary camels are important reservoir hosts of various coronaviruses, including Middle East respiratory syndrome coronavirus (MERS-CoV) that cause human infections. CoV genomes regularly undergo recombination during infection as observed in bat SARS-related CoVs. Here we report for the first time that only a small proportion of MERS-CoV receptor-binding domain positive (RBD) of spike protein positive camel sera in Kenya were also seropositive to MERS-CoV nucleocapsid (NP). In contrast, many of them contain antibodies against bat HKU8-related (HKU8r)-CoVs. Among 584 camel samples that were positive against MERS-CoV RBD, we found only 0.48 (8.22%) samples were also positive for NP. Furthermore, we found bat HKU8r-CoV NP antibody in 73 (12.5%) of the MERS-CoV RBD positive and NP negative samples, yet found only 3 (0.43%) of the HKU8r-CoV S1 antibody in the same samples. These findings may indicate co-infection with MERS-CoV and a HKU8r-CoV in camels. It may also raise the possibility of the circulation of a recombinant coronavirus virus with the spike of MERS-CoV and the NP of a HKU8r-CoV in Kenya. We failed to find molecular evidence of an HKU8r-CoV or a putative recombinant virus. Our findings should alert other investigators to look for molecular evidence of HKU8r-CoV or recombinants.

KEYWORDS: HKU8; MERS; bat; camel; coronavirus

PMID: 31645223 DOI: 10.1080/22221751.2019.1679610

Keywords: MERS-CoV; Coronavirus; Bats; Camels; Recombination; Kenya.

——

#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.

——

#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.

—–

#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.

——

#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.

——