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.

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#Antimicrobial #resistance genotypes and phenotypes of #Campylobacter jejuni isolated in #Italy from #humans, #birds from wild and urban #habitats, and #poultry (PLoS ONE, abstract)

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

OPEN ACCESS /  PEER-REVIEWED / RESEARCH ARTICLE

Antimicrobial resistance genotypes and phenotypes of Campylobacter jejuni isolated in Italy from humans, birds from wild and urban habitats, and poultry

Francesca Marotta  , Giuliano Garofolo , Lisa di Marcantonio , Gabriella Di Serafino , Diana Neri , Romina Romantini , Lorena Sacchini , Alessandra Alessiani , Guido Di Donato , Roberta Nuvoloni , Anna Janowicz , Elisabetta Di Giannatale

Published: October 11, 2019 / DOI: https://doi.org/10.1371/journal.pone.0223804

 

Abstract

Campylobacter jejuni, a common foodborne zoonotic pathogen, causes gastroenteritis worldwide and is increasingly resistant to antibiotics. We aimed to investigate the antimicrobial resistance (AMR) genotypes of C. jejuni isolated from humans, poultry and birds from wild and urban Italian habitats to identify correlations between phenotypic and genotypic AMR in the isolates. Altogether, 644 C. jejuni isolates from humans (51), poultry (526) and wild- and urban-habitat birds (67) were analysed. The resistance phenotypes of the isolates were determined using the microdilution method with EUCAST breakpoints, and AMR-associated genes and single nucleotide polymorphisms were obtained from a publicly available database. Antimicrobial susceptibility testing showed that C. jejuni isolates from poultry and humans were highly resistant to ciprofloxacin (85.55% and 76.47%, respectively), nalidixic acid (75.48% and 74.51%, respectively) and tetracycline (67.87% and 49.02%, respectively). Fewer isolates from the wild- and urban-habitat birds were resistant to tetracycline (19.40%), fluoroquinolones (13.43%), and quinolone and streptomycin (10.45%). We retrieved seven AMR genes (tet (O), cmeA, cmeB, cmeC, cmeR, blaOXA-61 and blaOXA-184) and gyrA-associated point mutations. Two major B-lactam genes called blaOXA-61 and blaOXA-184 were prevalent at 62.93% and 82.08% in the poultry and the other bird groups, respectively. Strong correlations between genotypic and phenotypic resistance were found for fluoroquinolones and tetracycline. Compared with the farmed chickens, the incidence of AMR in the C. jejuni isolates from the other bird groups was low, confirming that the food-production birds are much more exposed to antimicrobials. The improper and overuse of antibiotics in the human population and in animal husbandry has resulted in an increase in antibiotic-resistant infections, particularly fluoroquinolone resistant ones. Better understanding of the AMR mechanisms in C. jejuni is necessary to develop new strategies for improving AMR programs and provide the most appropriate therapies to human and veterinary populations.

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Citation: Marotta F, Garofolo G, di Marcantonio L, Di Serafino G, Neri D, Romantini R, et al. (2019) Antimicrobial resistance genotypes and phenotypes of Campylobacter jejuni isolated in Italy from humans, birds from wild and urban habitats, and poultry. PLoS ONE 14(10): e0223804. https://doi.org/10.1371/journal.pone.0223804

Editor: Grzegorz Woźniakowski, Panstwowy Instytut Weterynaryjny – Panstwowy Instytut Badawczy w Pulawach, POLAND

Received: July 12, 2019; Accepted: September 27, 2019; Published: October 11, 2019

Copyright: © 2019 Marotta 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: We have uploaded our study’s minimal underlying data set as Supporting Information file S1 Table.

Funding: This work was supported by the Italian Ministry of Health, grant number: MSRCTE0717. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Keywords: Antibiotics; Drugs Resistance; Campylobacter jejuni; Human; Poultry; Wildlife; Italy.

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#Quantification of visits of #wild #fauna to a commercial free-range layer #farm in the #Netherlands located in an #avian #influenza hot-spot area assessed by video-camera monitoring (Transbound Emerg Dis., abstract)

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

Transbound Emerg Dis. 2019 Oct 6. doi: 10.1111/tbed.13382. [Epub ahead of print]

Quantification of visits of wild fauna to a commercial free-range layer farm in the Netherlands located in an avian influenza hot-spot area assessed by video-camera monitoring.

Elbers ARW1, Gonzales JL1.

Author information: 1 Dept. of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Houtribweg 39, 3848 BW, Lelystad, Netherlands.

 

Abstract

Free-range poultry farms have a high risk of introduction of avian influenza viruses (AIV), and it is presumed that wild (water)birds are the source of introduction. There is very scarce quantitative data on wild fauna visiting free-range poultry farms. We quantified visits of wild fauna to a free-range area of a layer farm, situated in an AIV hot-spot area, assessed by video-camera monitoring. A total of 5,016 hours (209 days) of video recordings, covering all 12 months of a year, were analyzed. A total of 16 families of wild birds and five families of mammals visited the free-range area of the layer farm. Wild birds, except for the dabbling ducks, visited the free-range area almost exclusively in the period between sunrise and the moment the chickens entered the free-range area. Known carriers of AIV visited the outdoor facility regularly: species of gulls almost daily in the period January – August; dabbling ducks only in the night in the period November – May, with a distinct peak in the period December – February. Only a small fraction of visits of wild fauna had overlap with presence of chickens at the same time in the free-range area. No direct contact between chickens and wild birds was observed. It is hypothesized that AIV transmission to poultry on free-range poultry farms will predominantly take place via indirect contact: taking up AIV by chickens via wild-bird-faeces-contaminated water or soil in the free-range area. The free-range poultry farmer has several possibilities to potentially lower the attractiveness of the free-range area for wild (bird)fauna: daily inspection of the free-range area and removal of carcasses and eggs; prevention of forming of water pools in the free range facility. Furthermore, there are ways to scare-off wild birds e.g. use of laser equipment or trained dogs.

© 2019 Blackwell Verlag GmbH.

KEYWORDS: avian influenza; ducks; free-range poultry; gulls; water pools; wild fauna

PMID: 31587498 DOI: 10.1111/tbed.13382

Keywords: Avian Influenza; Wild Birds; Poultry; Wildlife; Netherlands.

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Lek-associated movement of a putative #Ebolavirus #reservoir, the hammer-headed fruit #bat (Hypsignathus monstrosus), in northern Republic of #Congo (PLoS One, abstract)

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

PLoS One. 2019 Oct 1;14(10):e0223139. doi: 10.1371/journal.pone.0223139. eCollection 2019.

Lek-associated movement of a putative Ebolavirus reservoir, the hammer-headed fruit bat (Hypsignathus monstrosus), in northern Republic of Congo.

Olson SH1, Bounga G2, Ondzie A2, Bushmaker T3, Seifert SN3, Kuisma E2, Taylor DW1, Munster VJ3, Walzer C1,4.

Author information: 1 Wildlife Conservation Society, Health Program, Bronx, New York, United States of America. 2 Wildlife Conservation Society, Brazzaville, Republic of Congo. 3 Virus Ecology Section, Laboratory of Virology, Division of Intramural Research, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America. 4 Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria.

 

Abstract

The biology and ecology of Africa’s largest fruit bat remains largely understudied and enigmatic despite at least two highly unusual attributes. The acoustic lek mating behavior of the hammer-headed bat (Hypsignathus monstrosus) in the Congo basin was first described in the 1970s. More recently molecular testing implicated this species and other African bats as potential reservoir hosts for Ebola virus and it was one of only two fruit bat species epidemiologically linked to the 2008 Luebo, Democratic Republic of Congo, Ebola outbreak. Here we share findings from the first pilot study of hammer-headed bat movement using GPS tracking and accelerometry units and a small preceding radio-tracking trial at an apparent lekking site. The radio-tracking revealed adult males had high rates of nightly visitation to the site compared to females (only one visit) and that two of six females day-roosted ~100 m west of Libonga, the nearest village that is ~1.6 km southwest. Four months later, in mid-April 2018, five individual bats, comprised of four males and one female, were tracked from two to 306 days, collecting from 67 to 1022 GPS locations. As measured by mean distance to the site and proportion of nightly GPS locations within 1 km of the site (percent visitation), the males were much more closely associated with the site (mean distance 1.4 km; 51% visitation), than the female (mean 5.5 km; 2.2% visitation). Despite the small sample size, our tracking evidence supports our original characterization of the site as a lek, and the lek itself is much more central to male than female movement. Moreover, our pilot demonstrates the technical feasibility of executing future studies on hammer-headed bats that will help fill problematic knowledge gaps about zoonotic spillover risks and the conservation needs of fruit bats across the continent.

PMID: 31574111 DOI: 10.1371/journal.pone.0223139

Keywords: Ebolavirus; Wildlife; Bats; Rep. of Congo.

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Infection of Western Gray #Kangaroos (Macropus fuliginosus) with #Australian #Arboviruses Associated with #Human #Infection (Vector Borne Zoo Dis., abstract)

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

Infection of Western Gray Kangaroos (Macropus fuliginosus) with Australian Arboviruses Associated with Human Infection

Narayan Gyawali, Andrew W. Taylor-Robinson, Richard S. Bradbury, Abbey Potter, and John G. Aaskov

Published Online: 26 Sep 2019

 

Abstract

More than 75 arboviruses (arthropod-borne viruses) have been identified in Australia. While Alfuy virus (ALFV), Barmah Forest virus (BFV), Edge Hill virus (EHV), Kokobera virus (KOKV), Murray Valley encephalitis virus (MVEV), Sindbis virus (SINV), Ross River virus (RRV), Stratford virus (STRV), and West Nile virus strain Kunjin (KUNV) have been associated with human infection, there remains a paucity of data regarding their respective transmission cycles and any potential nonhuman vertebrate hosts. It is likely that these viruses are maintained in zoonotic cycles involving native animals rather than solely by human-to-human transmission. A serosurvey (n = 100) was undertaken to determine the prevalence of neutralizing antibodies against a panel of Australian arboviruses in western gray kangaroos (Macropus fuliginosus) obtained from 11 locations in the midwest to southwest of Western Australia. Neutralizing antibodies against RRV were detected in 25%, against BFV in 14%, and antibodies to both viruses in 34% of serum samples. The prevalence of antibodies against these two viruses was the same in males and females, but higher in adult than in subadult kangaroos (p < 0.05). Twenty-one percent of samples had neutralizing antibodies against any one or more of the flaviviruses ALFV, EHV, KOKV, MVEV, and STRV. No neutralizing antibodies against SINV and KUNV were detected. If this sample of kangaroo sera was representative of the broader Australian population of macropods, it suggests that they are common hosts for RRV and BFV. The absence or low seroprevalence of antibodies against the remaining arboviruses suggests that they are not prevalent in the region or that kangaroos are not commonly infected with them. The detection of neutralizing antibodies to MVEV requires further investigation as this virus has not been identified previously so far south in Western Australia.

Keywords: Arbovirus; Flavivirus; Kangaroos; Wildlife; Human; Australia.

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#Density-dependence and #persistence of #Morogoro #arenavirus #transmission in a fluctuating population of its reservoir host (J Anim Ecol., abstract)

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

J Anim Ecol. 2019 Sep 23. doi: 10.1111/1365-2656.13107. [Epub ahead of print]

Density-dependence and persistence of Morogoro arenavirus transmission in a fluctuating population of its reservoir host.

Mariën J1, Borremans B1,2,3, Verhaeren C1, Kirkpatrick L1, Gryseels S1,4,5, Goüy de Bellocq J6, Günther S7, Sabuni CA8, Massawe AW8, Reijniers J1,9, Leirs H1.

Author information: 1 Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium. 2 Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA. 3 Interuniversity Institute for Biostatistics and statistical Bioinformatics (I-BIOSTAT), Hasselt University, Hasselt, Belgium. 4 Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, USA. 5 Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium. 6 Institute of Vertebrate Biology, Research Facility Studenec, The Czech Academy of Sciences, Brno, Czech Republic. 7 Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany. 8 PestManagement Centre, Sokoine University of Agriculture, Morogoro, Tanzania. 9 Department of Engineering Management, University of Antwerp, Antwerp, Belgium.

 

Abstract

1.A key aim in wildlife disease ecology is to understand how host and parasite characteristics influence parasite transmission and persistence. Variation in host population density can have strong impacts on transmission and outbreaks, and theory predicts particular transmission-density patterns depending on how parasites are transmitted between individuals. Here, we present the results of a study on the dynamics of Morogoro arenavirus in a population of multimammate mice (Mastomys natalensis). This widespread African rodent, which is also the reservoir host of Lassa arenavirus in West Africa, is known for its strong seasonal density fluctuations driven by food availability.

2.We investigated to what degree virus transmission changes with host population density and how the virus might be able to persist during periods of low host density.

3.A seven-year capture-mark-recapture study was conducted in Tanzania where rodents were trapped monthly and screened for the presence of antibodies against Morogoro virus. Observed seasonal seroprevalence patterns were compared with those generated by mathematical transmission models to test different hypotheses regarding the degree of density-dependence and the role of chronically infected individuals.

4.We observed that Morogoro virus seroprevalence correlates positively with host density with a lag of one to four months. Model results suggest that the observed seasonal seroprevalence dynamics can be best explained by a combination of vertical and horizontal transmission, and that a small number of animals needs to be infected chronically to ensure viral persistence.

5.Transmission dynamics and viral persistence were best explained by the existence of both acutely and chronically infected individuals, and by seasonally changing transmission rates. Due to the presence of chronically infected rodents, rodent control is unlikely to be a feasible approach for eliminating arenaviruses such as Lassa virus from Mastomys populations.

© 2019 The Authors. Journal of Animal Ecology © 2019 British Ecological Society.

PMID: 31545505 DOI: 10.1111/1365-2656.13107

Keywords: Arenavirus; Wildlife; Rodents; Morogoro virus; Seroprevalence; Tanzania.

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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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