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Tian Y, Yu T, Wang J, Zhang H, Jian Y, Li X, Wang G, Wang G, Hu Y, Lu C, Zhou J, Ma L, Liao M. Genetic characterization of the first Deltacoronavirus from wild birds around Qinghai Lake. Front Microbiol 2024; 15:1423367. [PMID: 38933020 PMCID: PMC11199898 DOI: 10.3389/fmicb.2024.1423367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 05/15/2024] [Indexed: 06/28/2024] Open
Abstract
Deltacoronavirus, widely distributed among pigs and wild birds, pose a significant risk of cross-species transmission, including potential human epidemics. Metagenomic analysis of bird samples from Qinghai Lake, China in 2021 reported the presence of Deltacoronavirus. A specific gene fragment of Deltacoronavirus was detected in fecal samples from wild birds at a positive rate of 5.94% (6/101). Next-generation sequencing (NGS) identified a novel Deltacoronavirus strain, which was closely related to isolates from the United Arab Emirates (2018), China (2022), and Poland (2023). Subsequently the strain was named A/black-headed gull/Qinghai/2021(BHG-QH-2021) upon confirmation of the Cytochrome b gene of black-headed gull in the sample. All available genome sequences of avian Deltacoronavirus, including the newly identified BHG-QH-2021 and 5 representative strains of porcine Deltacoronavirus (PDCoV), were classified according to ICTV criteria. In contrast to Coronavirus HKU15, which infects both mammals and birds and shows the possibility of cross-species transmission from bird to mammal host, our analysis revealed that BHG-QH-2021 is classified as Putative species 4. Putative species 4 has been reported to infect 5 species of birds but not mammals, suggesting that cross-species transmission of Putative species 4 is more prevalent among birds. Recombination analysis traced BHG-QH-2021 origin to dut148cor1 and MW01_1o strains, with MW01_1o contributing the S gene. Surprisingly, SwissModle prediction showed that the optimal template for receptor-binding domain (RBD) of BHG-QH-2021 is derived from the human coronavirus 229E, a member of the Alphacoronavirus, rather than the anticipated RBD structure of PDCoV of Deltacoronavirus. Further molecular docking analysis revealed that substituting the loop 1-2 segments of HCoV-229E significantly enhanced the binding capability of BHG-QH-2021 with human Aminopeptidase N (hAPN), surpassing its native receptor-binding domain (RBD). Most importantly, this finding was further confirmed by co-immunoprecipitation experiment that loop 1-2 segments of HCoV-229E enable BHG-QH-2021 RBD binding to hAPN, indicating that the loop 1-2 segment of the RBD in Putative species 4 is a probable key determinant for the virus ability to spill over into humans. Our results summarize the phylogenetic relationships among known Deltacoronavirus, reveal an independent putative avian Deltacoronavirus species with inter-continental and inter-species transmission potential, and underscore the importance of continuous surveillance of wildlife Deltacoronavirus.
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Affiliation(s)
- Ye Tian
- Key Laboratory of Animal Virology, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
| | - Tianqi Yu
- Key Laboratory of Animal Virology, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
| | - Jun Wang
- Animal Husbandry and Veterinary Workstation of the Third Division, Xinjiang Production and Construction Corps, Tumushuke, China
| | - Haoxiang Zhang
- Key Laboratory of Animal Virology, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
| | - Yingna Jian
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Xiuping Li
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Geping Wang
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Guanghua Wang
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Yong Hu
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Chenhe Lu
- Key Laboratory of Animal Virology, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
| | - Jiyong Zhou
- Key Laboratory of Animal Virology, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
| | - Liqing Ma
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Min Liao
- Key Laboratory of Animal Virology, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
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Bidoudan Y, Mouahid M, Fassi Fihri O, Bollo E, Arbani O, Ducatez M, Banni B, Tligui N, Fellahi S. First Report of Low Pathogenic Avian Influenza Subtype H9N2 in African Houbara Bustards ( Chlamydotis undulata undulata) and Gamebirds in Morocco: Clinico-Pathological Findings, Molecular Characterization, and Associated Coinfections. Viruses 2023; 15:2374. [PMID: 38140613 PMCID: PMC10748250 DOI: 10.3390/v15122374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/26/2023] [Accepted: 08/31/2023] [Indexed: 12/24/2023] Open
Abstract
We report in this paper the first detection of low pathogenic avian influenza (LPAI) subtype H9N2 in houbara bustards and in gamebirds in Morocco. Starting in 2019, an increase in mortality rates related to respiratory distress was recorded in these species. Necropsy of the specimens revealed fibrinous sinusitis and tracheitis with intra-bronchial fibrin casts, which are consistent with H9N2 infection in chickens; therefore, implication of the virus in these outbreaks was strongly suspected. Consequently, between January 2020 and June 2023, birds with respiratory signs were necropsied for pathological lesions, tissue samples were examined by histopathology, and samples of trachea, lungs, and cecal tonsils were analyzed using quantitative real-time PCR for the detection of H9N2 virus. In addition, the sequencing of isolates was performed and lastly differential diagnosis with other respiratory pathogens was carried out. During the study period, 93 samples were collected from suspected H9N2 outbreaks, of which 30 tested positive for H9N2 virus: 23 Houbara bustards, 4 partridges, 2 quails, and 1 pheasant. Moreover, sequencing of the HA gene of the virus showed 97.33% nucleotide identity with strains reported previously in broilers in Morocco in 2017 and in 2022. Phylogenetic analysis grouped the Moroccan partridge isolates in the same cluster as viruses isolated in Morocco between 2016 and 2022, Algeria (2017), Burkina Faso (2017), Nigeria (2019), and Togo (2020). Additionally, 10 house sparrows from the premises of these birds were examined for the presence of H9N2 virus, revealing a 30% positivity rate. In conclusion, LPAIV H9N2 is circulating in houbara bustards and gamebirds in Morocco, and house sparrows might be a possible source of the infection. To our knowledge, this is the first report of LPAI H9N2 in the African species of houbara bustards worldwide and in gamebirds in Morocco.
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Affiliation(s)
- Yassmina Bidoudan
- Mouahid’s Veterinary Clinic, Temara 12010, Morocco; (M.M.); (B.B.)
- Anatomic Pathology Unit, Department of Veterinary Science and Public Health, Agronomy and Veterinary Institute Hassan II, Rabat 10000, Morocco;
| | - Mohamed Mouahid
- Mouahid’s Veterinary Clinic, Temara 12010, Morocco; (M.M.); (B.B.)
| | - Ouafaa Fassi Fihri
- Infectious Diseases Unit, Department of Veterinary Science and Public Health, Agronomy and Veterinary Institute Hassan II, Rabat 10000, Morocco;
| | - Enrico Bollo
- Anatomic Pathology Unit, Department of Veterinary Sciences, University of Turin, 10095 Grugliasco, Italy;
| | - Oumayma Arbani
- Avian Pathology Unit, Department of Veterinary Science and Public Health, Agronomy and Veterinary Institute Hassan II, Rabat 10000, Morocco;
| | - Mariette Ducatez
- Interactions Hôtes-Agents-Pathogènes (IHAP), Toulouse University (ENVT), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, 31300 Toulouse, France;
| | - Brahim Banni
- Mouahid’s Veterinary Clinic, Temara 12010, Morocco; (M.M.); (B.B.)
- Anatomic Pathology Unit, Department of Veterinary Science and Public Health, Agronomy and Veterinary Institute Hassan II, Rabat 10000, Morocco;
| | - Noursaid Tligui
- Anatomic Pathology Unit, Department of Veterinary Science and Public Health, Agronomy and Veterinary Institute Hassan II, Rabat 10000, Morocco;
| | - Siham Fellahi
- Avian Pathology Unit, Department of Veterinary Science and Public Health, Agronomy and Veterinary Institute Hassan II, Rabat 10000, Morocco;
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Williams RAJ, Sánchez-Llatas CJ, Doménech A, Madrid R, Fandiño S, Cea-Callejo P, Gomez-Lucia E, Benítez L. Emerging and Novel Viruses in Passerine Birds. Microorganisms 2023; 11:2355. [PMID: 37764199 PMCID: PMC10536639 DOI: 10.3390/microorganisms11092355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
There is growing interest in emerging viruses that can cause serious or lethal disease in humans and animals. The proliferation of cloacal virome studies, mainly focused on poultry and other domestic birds, reveals a wide variety of viruses, although their pathogenic significance is currently uncertain. Analysis of viruses detected in wild birds is complex and often biased towards waterfowl because of the obvious interest in avian influenza or other zoonotic viruses. Less is known about the viruses present in the order Passeriformes, which comprises approximately 60% of extant bird species. This review aims to compile the most significant contributions on the DNA/RNA viruses affecting passerines, from traditional and metagenomic studies. It highlights that most passerine species have never been sampled. Especially the RNA viruses from Flaviviridae, Orthomyxoviridae and Togaviridae are considered emerging because of increased incidence or avian mortality/morbidity, spread to new geographical areas or hosts and their zoonotic risk. Arguably poxvirus, and perhaps other virus groups, could also be considered "emerging viruses". However, many of these viruses have only recently been described in passerines using metagenomics and their role in the ecosystem is unknown. Finally, it is noteworthy that only one third of the viruses affecting passerines have been officially recognized.
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Affiliation(s)
- Richard A. J. Williams
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
| | - Christian J. Sánchez-Llatas
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
| | - Ana Doménech
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
- Deparment of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro, s/n, 28040 Madrid, Spain
| | - Ricardo Madrid
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
| | - Sergio Fandiño
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
- Deparment of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro, s/n, 28040 Madrid, Spain
| | - Pablo Cea-Callejo
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
| | - Esperanza Gomez-Lucia
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
- Deparment of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro, s/n, 28040 Madrid, Spain
| | - Laura Benítez
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
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Domańska-Blicharz K, Miłek-Krupa J, Pikuła A. Gulls as a host for both gamma and deltacoronaviruses. Sci Rep 2023; 13:15104. [PMID: 37704675 PMCID: PMC10499781 DOI: 10.1038/s41598-023-42241-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023] Open
Abstract
The coronaviruses (CoV) are ubiquitous pathogens found in wide variety of hosts that constantly pose a threat to human and animal health as a result of their enormous capacity to generate genetic changes. Constant monitoring of virus reservoirs can constitute an early-warning tool and control the spread and evolution of the virus. Coronaviruses are common in wild birds, globally, and birds of the Charadriiformes in particular have been demonstrated to be carriers of delta- (dCoV) and gammacoronaviruses (gCoV). In this paper, we present the genetic characterisation of five CoV strains from black-headed (Chroicocephalus ridibundus) and common (Larus canus) gulls. Whole genome sequence analysis showed high similarity of detected dCoV in gulls to previously identified strains from falcon, houbara, pigeon and gulls from Asia (UAE, China). However, phylogenetic analysis revealed bifurcation within a common branch. Furthermore, the accumulation of numerous amino acid changes within the S-protein was demonstrated, indicating further evolution of dCoV within a single gull host. In turn, phylogenetic analysis for the most of the structural and non-structural genes of identified gCoV confirmed that the strain belongs to the duck coronavirus 2714 (DuCoV2714) species within Igacovirus subgenera, while for the spike protein it forms a separate branch not closely related to any gCoV species known to date. The current study provides new and significant insights into the evolution and diversification of circulating coronaviruses in members of Laridae family.
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Affiliation(s)
- Katarzyna Domańska-Blicharz
- Department of Poultry Diseases, National Veterinary Research Institute, al. Partyzantow 57, 24-100, Pulawy, Poland.
| | - Justyna Miłek-Krupa
- Department of Poultry Diseases, National Veterinary Research Institute, al. Partyzantow 57, 24-100, Pulawy, Poland
- Holy Cross Cancer Center, Stefana Artwińskiego 3, 25-734, Kielce, Poland
| | - Anna Pikuła
- Department of Poultry Diseases, National Veterinary Research Institute, al. Partyzantow 57, 24-100, Pulawy, Poland
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François S, Nazki S, Vickers SH, Fournié G, Perrins CM, Broadbent AJ, Pybus OG, Hill SC. Genetic diversity, recombination and cross-species transmission of a waterbird gammacoronavirus in the wild. J Gen Virol 2023; 104. [PMID: 37589541 DOI: 10.1099/jgv.0.001883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023] Open
Abstract
Viruses emerging from wildlife can cause outbreaks in humans and domesticated animals. Predicting the emergence of future pathogens and mitigating their impacts requires an understanding of what shapes virus diversity and dynamics in wildlife reservoirs. In order to better understand coronavirus ecology in wild species, we sampled birds within a coastal freshwater lagoon habitat across 5 years, focussing on a large population of mute swans (Cygnus olor) and the diverse species that they interact with. We discovered and characterised the full genome of a divergent gammacoronavirus belonging to the Goose coronavirus CB17 species. We investigated the genetic diversity and dynamics of this gammacoronavirus using untargeted metagenomic sequencing of 223 faecal samples from swans of known age and sex, and RT-PCR screening of 1632 additional bird samples. The virus circulated persistently within the bird community; virus prevalence in mute swans exhibited seasonal variations, but did not change with swan age-class or epidemiological year. One whole genome was fully characterised, and revealed that the virus originated from a recombination event involving an undescribed gammacoronavirus species. Multiple lineages of this gammacoronavirus co-circulated within our study population. Viruses from this species have recently been detected in aquatic birds from both the Anatidae and Rallidae families, implying that host species habitat sharing may be important in shaping virus host range. As the host range of the Goose coronavirus CB17 species is not limited to geese, we propose that this species name should be updated to 'Waterbird gammacoronavirus 1'. Non-invasive sampling of bird coronaviruses may provide a tractable model system for understanding the evolutionary and cross-species dynamics of coronaviruses.
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Affiliation(s)
- Sarah François
- Department of Biology, University of Oxford, South Park Road, Oxford, OX1 3SY, UK
| | - Salik Nazki
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7FZ, UK
- The Pirbright Institute, Ash Rd, Pirbright, Woking GU24 0NF, UK
| | - Stephen H Vickers
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
| | - Guillaume Fournié
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, Marcy l'Etoile, France
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint-Gènes-Champanelle, France
| | | | - Andrew J Broadbent
- The Pirbright Institute, Ash Rd, Pirbright, Woking GU24 0NF, UK
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD20742, USA
| | - Oliver G Pybus
- Department of Biology, University of Oxford, South Park Road, Oxford, OX1 3SY, UK
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
| | - Sarah C Hill
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
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Hemnani M, Silva PGD, Thompson G, Poeta P, Rebelo H, Mesquita JR. First Report of Alphacoronavirus Circulating in Cavernicolous Bats from Portugal. Viruses 2023; 15:1521. [PMID: 37515207 PMCID: PMC10384150 DOI: 10.3390/v15071521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/03/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
The emergence of novel coronaviruses (CoVs) has emphasized the need to understand their diversity and distribution in animal populations. Bats have been identified as crucial reservoirs for CoVs, and they are found in various bat species worldwide. In this study, we investigated the presence of CoVs of four cavernicolous bats in six locations in the centre and south of Portugal. We collected faeces, anal, and buccal swab samples, as well as air samples from the locations using a Coriolis air sampler. Our results indicate that CoVs were more readily detected in faecal samples compared to anal and buccal swab samples. No CoVs were detected in the air samples. Phylogenetic analysis showed that the detected viruses belong to the Alphacoronavirus genus. This study represents the first report of Alphacoronaviruses circulating in bats in Portugal and highlights the importance of continuous surveillance for novel CoVs in bat populations globally. Ongoing surveillance for CoVs in bat populations is essential as they are a vital source of these viruses. It is crucial to understand the ecological relationships between animals, humans, and the environment to prevent and control the emergence and transmission of infectious diseases. Further ecological studies are needed to investigate the factors contributing to the emergence and transmission of zoonotic viruses.
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Affiliation(s)
- Mahima Hemnani
- School of Medicine and Biomedical Sciences, Porto University, 4050-313 Porto, Portugal
| | - Priscilla Gomes da Silva
- School of Medicine and Biomedical Sciences, Porto University, 4050-313 Porto, Portugal
- Epidemiology Research Unit (EPIunit), Institute of Public Health, University of Porto, 4099-002 Porto, Portugal
- Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), 4050-313 Porto, Portugal
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnotlogy and Energy, Faculty of Engineering, University of Porto, 4099-002 Porto, Portugal
- ALiCE-Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, 4099-002 Porto, Portugal
| | - Gertrude Thompson
- School of Medicine and Biomedical Sciences, Porto University, 4050-313 Porto, Portugal
- Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Patricia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os Montes e Alto Douro, 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisbon, 1099-085 Caparica, Portugal
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal
- Veterinary and Animal Research Centre, Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), 5000-801 Vila Real, Portugal
| | - Hugo Rebelo
- Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal
- ESS, Instituto Politécnico de Setúbal, 2910-761 Setúbal, Portugal
| | - João R Mesquita
- School of Medicine and Biomedical Sciences, Porto University, 4050-313 Porto, Portugal
- Epidemiology Research Unit (EPIunit), Institute of Public Health, University of Porto, 4099-002 Porto, Portugal
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Sharshov K, Dubovitskiy N, Derko A, Loginova A, Kolotygin I, Zhirov D, Sobolev I, Kurskaya O, Alekseev A, Druzyaka A, Ktitorov P, Kulikova O, He G, Wang Z, Bi Y, Shestopalov A. Does Avian Coronavirus Co-Circulate with Avian Paramyxovirus and Avian Influenza Virus in Wild Ducks in Siberia? Viruses 2023; 15:v15051121. [PMID: 37243207 DOI: 10.3390/v15051121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Avian coronaviruses (ACoV) have been shown to be highly prevalent in wild bird populations. More work on avian coronavirus detection and diversity estimation is needed for the breeding territories of migrating birds, where the high diversity and high prevalence of Orthomyxoviridae and Paramyxoviridae have already been shown in wild birds. In order to detect ACoV RNA, we conducted PCR diagnostics of cloacal swab samples from birds, which we monitored during avian influenza A virus surveillance activities. Samples from two distant Asian regions of Russia (Sakhalin region and Novosibirsk region) were tested. Amplified fragments of the RNA-dependent RNA-polymerase (RdRp) of positive samples were partially sequenced to determine the species of Coronaviridae represented. The study revealed a high presence of ACoV among wild birds in Russia. Moreover, there was a high presence of birds co-infected with avian coronavirus, avian influenza virus, and avian paramyxovirus. We found one case of triple co-infection in a Northern Pintail (Anas acuta). Phylogenetic analysis revealed the circulation of a Gammacoronavirus species. A Deltacoronavirus species was not detected, which supports the data regarding the low prevalence of deltacoronaviruses among surveyed bird species.
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Affiliation(s)
- Kirill Sharshov
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk 630117, Russia
| | - Nikita Dubovitskiy
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk 630117, Russia
| | - Anastasiya Derko
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk 630117, Russia
| | - Arina Loginova
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk 630117, Russia
| | - Ilya Kolotygin
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk 630117, Russia
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630073, Russia
| | - Dmitry Zhirov
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk 630117, Russia
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630073, Russia
| | - Ivan Sobolev
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk 630117, Russia
| | - Olga Kurskaya
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk 630117, Russia
| | - Alexander Alekseev
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk 630117, Russia
| | - Alexey Druzyaka
- Institute of Animal Systematics and Ecology, Novosibirsk 630091, Russia
| | - Pavel Ktitorov
- Institute of Biological Problems of the North, Magadan 685000, Russia
| | - Olga Kulikova
- Institute of Biological Problems of the North, Magadan 685000, Russia
| | - Guimei He
- School of Life Sciences, East China Normal University, Shanghai 200062, China
| | - Zhenghuan Wang
- School of Life Sciences, East China Normal University, Shanghai 200062, China
| | - Yuhai Bi
- Center for Influenza Research and Early-warning (CASCIRE), CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Alexander Shestopalov
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk 630117, Russia
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Molecular Detection and Characterization of Coronaviruses in Migratory Ducks from Portugal Show the Circulation of Gammacoronavirus and Deltacoronavirus. Animals (Basel) 2022; 12:ani12233283. [PMID: 36496804 PMCID: PMC9736399 DOI: 10.3390/ani12233283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/11/2022] [Accepted: 11/23/2022] [Indexed: 11/26/2022] Open
Abstract
Coronaviruses (CoVs) are part of the Coronaviridae family, and the genera Gamma (γ) and Delta (δ) are found mostly in birds. Migratory birds have an enormous potential for dispersing pathogenic microorganisms. Ducks (order Anseriformes) can host CoVs from birds, with pathogenic expression and high economic impact. This study aimed to identify and characterize the diversity of CoVs in migratory ducks from Portugal. Duck stool samples were collected using cloacal swabs from 72 individuals (Anas platyrhynchos, Anas acuta, and Anas crecca). Among the 72 samples tested, 24 showed amplicons of the expected size. Twenty-three were characterized as Gammacoronavirus and one as Deltacoronavirus (accession numbers ON368935-ON368954; ON721380-ON721383). The Gammacoronaviruses sequences showed greater similarities to those obtained in ducks (Anas platyrhynchos) from Finland and Poland, Anas crecca duck from the USA, and mute swans from Poland. Birds can occupy many habitats and therefore play diverse ecological roles in various ecosystems, especially given their ability to migrate exceptional distances, facilitating the dispersal of microorganisms with animal and/or human impact. There are a considerable number of studies that have detected CoVs in ducks, but none in Portugal. The present study assessed the circulation of CoVs in wild ducks from Portugal, being the first description of CoVs for these animals in Portugal.
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Marchenko V, Danilenko A, Kolosova N, Bragina M, Molchanova M, Bulanovich Y, Gorodov V, Leonov S, Gudymo A, Onkhonova G, Svyatchenko S, Ryzhikov A. Diversity of gammacoronaviruses and deltacoronaviruses in wild birds and poultry in Russia. Sci Rep 2022; 12:19412. [PMID: 36371465 PMCID: PMC9653423 DOI: 10.1038/s41598-022-23925-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/07/2022] [Indexed: 11/14/2022] Open
Abstract
Coronaviruses of the genera Gammacoronavirus and Deltacoronavirus are globally widespread and circulate primarily in wild and domestic birds. Prior studies have established frequently occurring crossover events from avian to mammalian reservoirs. However, there is limited understanding of the diversity and geographical distribution of coronaviruses among birds. In this study, the surveillance of coronaviruses in birds in Russia during 2020 revealed the presence of coronaviruses in 12% of samples from birds. Targeted NGS approach was used for the evaluation of genetic diversity based on RdRp gene. While gammacoronviruses were found in both wild birds and poultry, deltacoronaviruses were found in wild birds only and represent the first detections for Russia. A number of cases with the simultaneous detection of gamma- and deltacoronaviruses in one bird was reported. The results of this study highlight the importance of further research concerning the spread and diversity of coronaviruses among birds within and migrating throughout the territory of Russia across the globe.
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Affiliation(s)
- Vasily Marchenko
- grid.419755.bState Research Center of Virology and Biotechnology Vector Rospotrebnadzor, Koltsovo, 630559 Russia
| | - Alexey Danilenko
- grid.419755.bState Research Center of Virology and Biotechnology Vector Rospotrebnadzor, Koltsovo, 630559 Russia
| | - Natalia Kolosova
- grid.419755.bState Research Center of Virology and Biotechnology Vector Rospotrebnadzor, Koltsovo, 630559 Russia
| | - Maria Bragina
- grid.419755.bState Research Center of Virology and Biotechnology Vector Rospotrebnadzor, Koltsovo, 630559 Russia
| | - Marina Molchanova
- grid.419755.bState Research Center of Virology and Biotechnology Vector Rospotrebnadzor, Koltsovo, 630559 Russia
| | - Yuliya Bulanovich
- grid.419755.bState Research Center of Virology and Biotechnology Vector Rospotrebnadzor, Koltsovo, 630559 Russia
| | - Vladimir Gorodov
- Siberian Federal Scientific Centre of Agro-BioTechnologies, RAS, Novosibirsk, Russia
| | - Sergey Leonov
- Siberian Federal Scientific Centre of Agro-BioTechnologies, RAS, Novosibirsk, Russia
| | - Andrey Gudymo
- grid.419755.bState Research Center of Virology and Biotechnology Vector Rospotrebnadzor, Koltsovo, 630559 Russia
| | - Galina Onkhonova
- grid.419755.bState Research Center of Virology and Biotechnology Vector Rospotrebnadzor, Koltsovo, 630559 Russia
| | - Svetlana Svyatchenko
- grid.419755.bState Research Center of Virology and Biotechnology Vector Rospotrebnadzor, Koltsovo, 630559 Russia
| | - Alexander Ryzhikov
- grid.419755.bState Research Center of Virology and Biotechnology Vector Rospotrebnadzor, Koltsovo, 630559 Russia
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Occurrence and Phylogenetic Analysis of Avian Coronaviruses in Domestic Pigeons (Columba livia domestica) in Poland between 2016 and 2020. Pathogens 2022; 11:pathogens11060646. [PMID: 35745500 PMCID: PMC9230530 DOI: 10.3390/pathogens11060646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 05/27/2022] [Accepted: 06/01/2022] [Indexed: 12/04/2022] Open
Abstract
While disease control in racing pigeons and the potential role of pigeons as vectors transmitting viruses to poultry are of importance, there is still a paucity of data concerning the occurrence of coronaviruses in pigeons. In this study, 215 domestic pigeons were tested for the presence of coronaviral genetic material using the nested PCR method, which revealed 57 positive samples (26.51%). The difference in coronavirus prevalence between young and adult pigeons (34.34% and 19.83%, respectively) has been found statistically significant. In contrast, no statistically significant difference has been demonstrated between the prevalence in symptomatic and asymptomatic birds, leaving the influence of coronavirus presence on pigeon health uncertain. Phylogenetic analysis of the RdRp gene fragment allowed us to assign all the obtained strains to the Gammacoronavirus genus and Igacovirus subgenus. The phylogenetic tree plotted using the ML method revealed that those sequences formed a group most similar to pigeon coronavirus strains from China, Finland, and Poland, and to a single strain from a common starling from Poland, which suggests wide geographical distribution of the virus and its possible transmission between various species.
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Domańska-Blicharz K, Lisowska A, Opolska J, Pikuła A, Sajewicz-Krukowska J. Molecular Epidemiology of Turkey Coronaviruses in Poland. Viruses 2022; 14:v14051023. [PMID: 35632765 PMCID: PMC9148103 DOI: 10.3390/v14051023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/05/2022] [Accepted: 05/09/2022] [Indexed: 02/04/2023] Open
Abstract
The only knowledge of the molecular structure of European turkey coronaviruses (TCoVs) comes from France. These viruses have a quite distinct S gene from North American isolates. The aim of the study was to estimate the prevalence of TCoV strains in a Polish turkey farm during a twelve-year period, between 2008 and 2019, and to characterize their full-length S gene. Out of the 648 flocks tested, 65 (10.0%, 95% CI: 7.9–12.6) were positive for TCoV and 16 of them were molecularly characterized. Phylogenetic analysis showed that these strains belonged to two clusters, one formed by the early isolates identified at the beginning of the TCoV monitoring (from 2009 to 2010), and the other, which was formed by more recent strains from 2014 to 2019. Our analysis of the changes observed in the deduced amino acids of the S1 protein suggests the existence of three variable regions. Moreover, although the selection pressure analysis showed that the TCoV strains were evolving under negative selection, some sites of the S1 subunit were positively selected, and most of them were located within the proposed variable regions. Our sequence analysis also showed one TCoV strain had recombined with another one in the S1 gene. The presented investigation on the molecular feature of the S gene of TCoVs circulating in the turkey population in Poland contributes interesting data to the current state of knowledge.
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Abstract
Hedgehogs are common in the majority of European countries and are known to host various pathogens, including viruses. The recent discovery of MERS-related coronaviruses (CoVs) in hedgehogs from Germany, France, the UK, China, and Italy suggests that hedgehogs may represent a wild reservoir of betacoronaviruses. This study reports the first detection and characterization of novel betacoronovirus, subgenus Merbecovirus in wild hedgehogs in Poland. The CoV RNA was detected in 10 out of 40 hedgehogs' rectal swabs and in 1 out of 18 samples of the lung. No viral RNA was identified in the duodenum and kidney. There was no significant relationship between clinical status, gender, hedgehogs' age, and coronaviral RNA detection. Phylogenetic analysis showed that CoVs detected in our study grouped together with other representatives of Hedgehog coronavirus 1 species identified in Western Europe. Our findings provide further evidence that hedgehogs are a natural reservoir of Merbecovirus. Considering the high mutation rate of CoVs and their potential for crossing interspecies barriers, the proper management of hedgehogs admitted to wildlife rehabilitation centres is needed. It cannot be excluded that merbecovirus strains detected in hedgehogs may recombine with other CoVs leading to new viruses with potential for interspecies transmission.
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Tarasiuk K, Kycko A, Knitter M, Świętoń E, Wyrostek K, Domańska-Blicharz K, Bocian Ł, Meissner W, Śmietanka K. Pathogenicity of highly pathogenic avian influenza H5N8 subtype for herring gulls (Larus argentatus): impact of homo- and heterosubtypic immunity on the outcome of infection. Vet Res 2022; 53:108. [PMID: 36517883 PMCID: PMC9749649 DOI: 10.1186/s13567-022-01125-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/01/2022] [Indexed: 12/23/2022] Open
Abstract
To improve understanding of the pathobiology of highly pathogenic avian influenza virus (HPAIV) infections in wild birds, pathogenicity and transmissibility of HPAIV H5N8 subtype clade 2.3.4.4b was evaluated in ~ 8-week-old herring gulls (Larus argentatus) divided into 3 groups: naïve birds (group A), birds previously exposed to low pathogenic avian influenza virus (LPAIV) H5N1 (group B) and LPAIV H13N6 (group C). The HPAIV H5N8 virus was highly virulent for naïve gulls, that showed early morbidity, high mortality, a broad spectrum of clinical signs, including violent neurological disorders, systemic distribution of the virus in organs accompanied by high level of shedding and transmission to contact birds. Pre-exposure to homologous and heterologous LPAIV subtypes conferred only partial protection: we observed increased survival rate (statistically significant only in group B), nervous signs, pantropic distribution of virus in organs, shedding (significantly reduced in gulls of group C in the early phase of disease and asymptomatic shedding in the late phase), transmission to contact gulls (more pronounced in group B) and near-complete seroconversion in survivors. Histopathological and immunohistochemical results indicate virus tropism for the neural, respiratory and myocardial tissues. In conclusion, we demonstrate that HPAIV H5N8 clade 2.3.4.4b is highly virulent and lethal for fully susceptible herring gulls and that pre-exposure to homo- and heterosubtypic LPAIV only partially modulates the disease outcome.
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Affiliation(s)
- Karolina Tarasiuk
- grid.419811.4Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100 Puławy, Poland
| | - Anna Kycko
- grid.419811.4Department of Pathology, National Veterinary Research Institute, Al. Partyzantów 57, 24-100 Puławy, Poland
| | - Małgorzata Knitter
- grid.8585.00000 0001 2370 4076Ornithology Unit, Department of Vertebrate Ecology & Zoology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Edyta Świętoń
- grid.419811.4Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100 Puławy, Poland
| | - Krzysztof Wyrostek
- grid.419811.4Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100 Puławy, Poland
| | - Katarzyna Domańska-Blicharz
- grid.419811.4Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100 Puławy, Poland
| | - Łukasz Bocian
- grid.419811.4Department of Epidemiology and Risk Assessment, National Veterinary Research Institute, Al. Partyzantów 57, 24-100 Puławy, Poland
| | - Włodzimierz Meissner
- grid.8585.00000 0001 2370 4076Ornithology Unit, Department of Vertebrate Ecology & Zoology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Krzysztof Śmietanka
- grid.419811.4Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100 Puławy, Poland
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