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Shaprova ON, Shanshin DV, Kolosova EA, Borisevich SS, Soroka AA, Merkuleva IA, Nikitin AO, Volosnikova EA, Ushkalenko ND, Zaykovskaya AV, Pyankov OV, Elchaninova SA, Shcherbakov DN, Ilyicheva TN. Pre-Pandemic Cross-Reactive Immunity against SARS-CoV-2 among Siberian Populations. Antibodies (Basel) 2023; 12:82. [PMID: 38131804 PMCID: PMC10741209 DOI: 10.3390/antib12040082] [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: 09/28/2023] [Revised: 11/20/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
In December 2019, a new coronavirus, SARS-CoV-2, was found to in Wuhan, China. Cases of infection were subsequently detected in other countries in a short period of time, resulting in the declaration of the COVID-19 pandemic by the World Health Organization (WHO) on 11 March 2020. Questions about the impact of herd immunity of pre-existing immune reactivity to SARS-CoV-2 on COVID-19 severity, associated with the immunity to seasonal manifestation, are still to be resolved and may be useful for understanding some processes that precede the emergence of a pandemic virus. Perhaps this will contribute to understanding some of the processes that precede the emergence of a pandemic virus. We assessed the specificity and virus-neutralizing capacity of antibodies reacting with the nucleocapsid and spike proteins of SARS-CoV-2 in a set of serum samples collected in October and November 2019, before the first COVID-19 cases were documented in this region. Blood serum samples from 799 residents of several regions of Siberia, Russia, (the Altai Territory, Irkutsk, Kemerovo and Novosibirsk regions, the Republic of Altai, Buryatia, and Khakassia) were analyzed. Sera of non-infected donors were collected within a study of seasonal influenza in the Russian Federation. The sample collection sites were located near the flyways and breeding grounds of wild waterfowl. The performance of enzyme-linked immunosorbent assay (ELISA) for the collected sera included the usage of recombinant SARS-CoV-2 protein antigens: full-length nucleocapsid protein (CoVN), receptor binding domain (RBD) of S-protein and infection fragment of the S protein (S5-6). There were 183 (22.9%) sera reactive to the S5-6, 270 (33.8%) sera corresponding to the full-length N protein and 128 (16.2%) sera simultaneously reactive to both these proteins. Only 5 out of 799 sera had IgG antibodies reactive to the RBD. None of the sera exhibited neutralizing activity against the nCoV/Victoria/1/2020 SARS-CoV-2 strain in Vero E6 cell culture. The data obtained in this study suggest that some of the population of the analyzed regions of Russia had cross-reactive humoral immunity against SARS-CoV-2 before the COVID-19 pandemic started. Moreover, among individuals from relatively isolated regions, there were significantly fewer reliably cross-reactive sera. The possible significance of these data and impact of cross-immunity to SARS-CoV-2 on the prevalence and mortality of COVID-19 needs further assessment.
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Affiliation(s)
- Olga N. Shaprova
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
| | - Daniil V. Shanshin
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
- Russian-American Anti-Cancer Center, Altai State University, 656049 Barnaul, Russia
| | - Evgeniia A. Kolosova
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
- Russian-American Anti-Cancer Center, Altai State University, 656049 Barnaul, Russia
| | - Sophia S. Borisevich
- Laboratory of Chemical Physics, Ufa Institute of Chemistry Ufa Federal Research Center, 450078 Ufa, Russia;
- Institute of Intelligent Cybernetic Systems, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 115409 Moscow, Russia;
| | - Artem A. Soroka
- Institute of Intelligent Cybernetic Systems, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 115409 Moscow, Russia;
| | - Iuliia A. Merkuleva
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
| | - Artem O. Nikitin
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
| | - Ekaterina A. Volosnikova
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
| | - Nikita D. Ushkalenko
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
| | - Anna V. Zaykovskaya
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
| | - Oleg V. Pyankov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
| | - Svetlana A. Elchaninova
- Department of Biochemistry and Clinical Laboratory Diagnostics, Altai State Medical University, 656038 Barnaul, Russia;
| | - Dmitry N. Shcherbakov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
- Russian-American Anti-Cancer Center, Altai State University, 656049 Barnaul, Russia
| | - Tatiana N. Ilyicheva
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
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Zhou S, Xia T, Gao X, Lyu T, Wang L, Wang X, Shi L, Dong Y, Zhang H. A high-quality chromosomal-level genome assembly of Greater Scaup (Aythya marila). Sci Data 2023; 10:254. [PMID: 37142629 PMCID: PMC10160052 DOI: 10.1038/s41597-023-02142-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 04/11/2023] [Indexed: 05/06/2023] Open
Abstract
Aythya marila is one of the few species of Anatidae, and the only Aythya to live in the circumpolar. However, there is a relative lack of research on genetics of this species. In this study, we reported and assembled the first high-quality chromosome-level genome assembly of A. marila. This genome was assembled using Nanopore long reads, and errors corrected using Illumina short reads, with a final genome size of 1.14 Gb, scaffold N50 of 85.44 Mb, and contig N50 of 32.46 Mb. 106 contigs were clustered and ordered onto 35 chromosomes based on Hi-C data, covering approximately 98.28% of the genome. BUSCO assessment showed that 97.0% of the highly conserved genes in aves_odb10 were present intact in the genome assembly. In addition, a total of 154.94 Mb of repetitive sequences were identified. 15,953 protein-coding genes were predicted in the genome, and 98.96% of genes were functionally annotated. This genome will be a valuable resource for future genetic diversity and genomics studies of A. marila.
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Affiliation(s)
- Shengyang Zhou
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Tian Xia
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Xiaodong Gao
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Tianshu Lyu
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Lidong Wang
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Xibao Wang
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Lupeng Shi
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Yuehuan Dong
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Honghai Zhang
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China.
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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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Al-Khalaifah H, Alotaibi M, Al-Nasser A. The relation between avian coronaviruses and SARS-CoV-2 coronavirus. Front Microbiol 2022; 13:976462. [PMID: 36312988 PMCID: PMC9608149 DOI: 10.3389/fmicb.2022.976462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/20/2022] [Indexed: 01/04/2023] Open
Abstract
The coronaviruses (CoVs) are a family of ribonucleic acid viruses that are present in both mammals and birds. SARS-CoV and MERS-CoV originated in bats, and there is a possibility that this could be the case for SARS-CoV-2 as well. There is already evidence that a probable intermediary host is responsible for the emergence of viruses in humans as was the case for SARS-CoVs and MERS-CoV. As the SARS-CoV-2 originated from a live animal market, there is always the question if domestic animals are susceptible to these viruses and the possible risk of zoonotic transmission with mammals, including humans. This uncertainty of the transmission of the COVID-19 virus between humans and animals is of great significance worldwide. Hence, this paper focuses on the avian CoVs and their possible relation and interaction with SARS-CoV-2.
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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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Chu KK, Zhou ZJ, Wang Q, Ye SB, Guo L, Qiu Y, Zhang YZ, Ge XY. Characterization of Deltacoronavirus in Black-Headed Gulls (Chroicocephalus ridibundus) in South China Indicating Frequent Interspecies Transmission of the Virus in Birds. Front Microbiol 2022; 13:895741. [PMID: 35633699 PMCID: PMC9133700 DOI: 10.3389/fmicb.2022.895741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/19/2022] [Indexed: 11/24/2022] Open
Abstract
Deltacoronavirus (DCoV) is a genus of coronavirus (CoV) commonly found in avian and swine, but some DCoVs are capable of infecting humans, which causes the concern about interspecies transmission of DCoVs. Thus, monitoring the existence of DCoVs in animals near communities is of great importance for epidemic prevention. Black-headed gulls (Chroicocephalus ridibundus) are common migratory birds inhabiting in most urban and rural wetlands of Yunnan Province, China, which is a typical habitat for black-headed gulls to overwinter. Whether Yunnan black-headed gulls carry CoV has never been determined. In this study, we identified three strains of DCoVs in fecal samples of Yunnan black-headed gulls by reverse-transcriptional PCR and sequenced their whole genomes. Genomic analysis revealed that these three strains shared genomic identity of more than 99%, thus named DCoV HNU4-1, HNU4-2, and HNU4-3; their NSP12 showed high similarity of amino acid sequence to the homologs of falcon coronavirus UAE-HKU27 (HKU27), houbara coronavirus UAE-HKU28 (HKU28), and pigeon coronavirus UAE-HKU29 (HKU29). Since both HKU28 and HKU29 were found in Dubai, there might be cross-border transmission of these avian DCoVs through specific routes. Further coevolutionary analysis supported this speculation that HNU4 (or its ancestors) in black-headed gulls originated from HKU28 (or its homologous strain) in houbara, which was interspecies transmission between two different avian orders. In addition, interspecies transmission of DCoV, from houbara to falcon, pigeon and white-eye, from sparrow to common-magpie, and quail and mammal including porcine and Asian leopard cat, from munia to magpie-robin, was predicted. This is the first report of black-headed gull DCoV in Asia which was highly homolog to other avian DCoVs, and the very “active” host-switching events in DCoV were predicted, which provides important reference for the study of spread and transmission of DCoVs.
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Affiliation(s)
- Kan-Kan Chu
- College of Biology & Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
- Yunnan Province Key Laboratory of Anti-pathogenic Plant Resources Screening (Cultivation), Yunnan Province Key University Laboratory of Zoonoses Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali, China
| | - Zhi-Jian Zhou
- College of Biology & Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Qiong Wang
- College of Biology & Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Sheng-Bao Ye
- College of Biology & Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Ling Guo
- Yunnan Province Key Laboratory of Anti-pathogenic Plant Resources Screening (Cultivation), Yunnan Province Key University Laboratory of Zoonoses Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali, China
| | - Ye Qiu
- College of Biology & Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
- *Correspondence: Ye Qiu,
| | - Yun-Zhi Zhang
- Yunnan Province Key Laboratory of Anti-pathogenic Plant Resources Screening (Cultivation), Yunnan Province Key University Laboratory of Zoonoses Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali, China
- Yun-Zhi Zhang,
| | - Xing-Yi Ge
- College of Biology & Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
- Xing-Yi Ge,
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Marchenko V, Kolosova N, Danilenko A, Bragina M, Nhai T, Ryzhikov A. Diversity of coronaviruses in wild and domestic birds in Vietnam. ASIAN PAC J TROP MED 2022. [DOI: 10.4103/1995-7645.359785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Patil SS, Shinduja R, Suresh KP, Phukan S, Kumar S, Sengupta PP, G Amachawadi R, Raut A, Roy P, Syed A, Marraiki N, Elgorban AM, Al-Harthi HF, Bahkali AH, Shivamallu C, Shiva Prasad K. A systematic review and meta-analysis on the prevalence of infectious diseases of Duck: A world perspective. Saudi J Biol Sci 2021; 28:5131-5144. [PMID: 34466091 PMCID: PMC8381006 DOI: 10.1016/j.sjbs.2021.05.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 05/14/2021] [Accepted: 05/14/2021] [Indexed: 11/29/2022] Open
Abstract
The Indian poultry industry is one of the fast-growing sectors of which duck farming plays an important role. Duck population in India is 33.51 million that is concentrated towards north-east and southern parts of the country who rears mainly for eggs and meat. Duck diseases are of great concern as they badly affect the financial status of the small, landless farmers. Databases such as Google Scholar, PubMed, J gate were used to search articles between 2000 and 2019 that showed the prevalence of viral, bacterial, and parasitic duck diseases. R open source software was used to derive forest plots by statistical analysis. Pooled prevalence estimates of duck diseases worldwide was found to be 20% (95%-CI:15–26). Also, continent-wise analysis of all duck diseases has revealed highest prevalence in North America, followed by Asia, Africa, Europe,Oceania and South America. This prevalence of data would be helpful to the policymakers to develop appropriate intervention strategies to prevent and control diseases in their respective locations.
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Affiliation(s)
- Sharanagouda S Patil
- ICAR-National Institute of Veterinary Epidem iology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, India
| | - Rajamani Shinduja
- ICAR-National Institute of Veterinary Epidem iology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, India
| | | | - Sulekha Phukan
- Department of Parasitology, College of Veterinary Science, Khanapara, Guwahati, Assam, India
| | - Sachin Kumar
- Department of Biosciences and Bioengineering, IIT, Guwahati, Assam, India
| | - Pinaki Prasad Sengupta
- ICAR-National Institute of Veterinary Epidem iology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, India
| | - Raghavendra G Amachawadi
- Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Ashwin Raut
- ICAR-National Institute of High Security Animal Diseases (NIHSAD), Bhopal, Madhya Pradesh, India
| | - Parimal Roy
- ICAR-National Institute of Veterinary Epidem iology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, India
| | - Asad Syed
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Najat Marraiki
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdallah M Elgorban
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Helal F Al-Harthi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ali H Bahkali
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Chandan Shivamallu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research (JSS AHER), Mysuru, Karnataka 570 015, India
| | - Kollur Shiva Prasad
- Department of Sciences, Amrita School of Arts and Sciences, Amrita Vishwa Vidyapeetham, Mysuru Campus, Mysuru, Karnataka 570 026, India
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Hubálek Z. Pathogenic microorganisms associated with gulls and terns (Laridae). JOURNAL OF VERTEBRATE BIOLOGY 2021. [DOI: 10.25225/jvb.21009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Zdeněk Hubálek
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic; e-mail:
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Domańska-Blicharz K, Miłek-Krupa J, Pikuła A. Diversity of Coronaviruses in Wild Representatives of the Aves Class in Poland. Viruses 2021; 13:v13081497. [PMID: 34452362 PMCID: PMC8402903 DOI: 10.3390/v13081497] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/15/2021] [Accepted: 07/23/2021] [Indexed: 02/06/2023] Open
Abstract
The revealed prevalence of coronaviruses in wild bird populations in Poland was 4.15% and the main reservoirs were birds from orders Anseriformes and Charadriiformes, with a prevalence of 3.51% and 5.59%, respectively. Gammacoronaviruses were detected more often than deltacoronaviruses, with detection rates of 3.5% and 0.7%, respectively. Gammacoronaviruses were detected in birds belonging to six orders, including Anseriformes, Charadriiformes, Columbiformes, Galliformes, Gruiformes, and Passeriformes, indicating a relatively wide host range. Interestingly, this was the only coronavirus detected in Anseriformes (3.51%), while in Charadriiformes, the prevalence was 3.1%. The identified gammacoronaviruses belonged to the Igacovirus and Brangacovirus subgeneras. Most of these were igacoviruses and formed a common phylogenetic group with a Duck Coronavirus 2714 and two with an Avian Coronavirus/Avian Coronavirus9203, while the viruses from the pigeons formed a distinct “pigeon-like” group, not yet officially represented. The presence of deltacoronaviruses was detected in birds belonging to three orders, Charadriiformes, Galliformes, and Suliformes indicating a narrower host range. Most identified deltacoronaviruses belonged to the Buldecovirus subgenus, while only one belonged to Herdecovirus. Interestingly, the majority of buldecoviruses were identified in gulls, and they formed a distinct phylogenetic lineage not represented by any officially ratified virus species. Another separate group of buldecoviruses, also not represented by the official species, was formed by a virus identified in a common snipe. Only one identified buldecovirus (from common pheasant) formed a group with the ratified species Coronavirus HKU15. The results obtained indicate the high diversity of detected coronaviruses, and thus also the need to update their taxonomy (establishing new representative virus species). The serological studies performed revealed antibodies against an infectious bronchitis virus in the sera of white storks and mallards.
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12
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Rahman MM, Talukder A, Chowdhury MMH, Talukder R, Akter R. Coronaviruses in wild birds - A potential and suitable vector for global distribution. Vet Med Sci 2020; 7:264-272. [PMID: 32970935 PMCID: PMC7537155 DOI: 10.1002/vms3.360] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/18/2020] [Accepted: 09/09/2020] [Indexed: 01/08/2023] Open
Abstract
The recurrent appearance of novel coronaviruses (CoVs) and the mortality and morbidity caused by their outbreaks aroused a widespread response among the global science community. Wild birds' high biodiversity, perching and migratory activity, ability to travel long distances and possession of a special adaptive immune system may make them alarming sources of zoonotic CoV‐spreading vectors. This review gathers the available evidence on the global spread of CoVs in wild birds to date. The major wild birds associated with different types of CoVs are Anseriformes, Charadriiformes, Columbiformes, Pelecaniformes, Galliformes, Passeriformes, Psittaciformes, Accipitriformes, Ciconiiformes, Gruiformes and so on. However, the main type of CoVs found in wild birds is gammacoronavirus, followed by deltacoronavirus. Consequently, it is imperative to enable thorough research and continuous monitoring to fill the study gap in terms of understanding their role as zoonotic vectors and the frequent appearance of novel CoVs.
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Affiliation(s)
- Md Mijanur Rahman
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Asma Talukder
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | | | - Reshma Talukder
- Department of Architecture, State University of Bangladesh, Dhaka, Bangladesh
| | - Rekha Akter
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram, Bangladesh
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13
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Wille M, Holmes EC. Wild birds as reservoirs for diverse and abundant gamma- and deltacoronaviruses. FEMS Microbiol Rev 2020; 44:631-644. [PMID: 32672814 PMCID: PMC7454673 DOI: 10.1093/femsre/fuaa026] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/30/2020] [Indexed: 12/17/2022] Open
Abstract
Wild birds interconnect all parts of the globe through annual cycles of migration with little respect for country or continental borders. Although wild birds are reservoir hosts for a high diversity of gamma- and deltacoronaviruses, we have little understanding of the ecology or evolution of any of these viruses. In this review, we use genome sequence and ecological data to disentangle the evolution of coronaviruses in wild birds. Specifically, we explore host range at the levels of viral genus and species, and reveal the multi-host nature of many viral species, albeit with biases to certain types of avian host. We conclude that it is currently challenging to infer viral ecology due to major sampling and technical limitations, and suggest that improved assay performance across the breadth of gamma- and deltacoronaviruses, assay standardization, as well as better sequencing approaches, will improve both the repeatability and interpretation of results. Finally, we discuss cross-species virus transmission across both the wild bird - poultry interface as well as from birds to mammals. Clarifying the ecology and diversity in the wild bird reservoir has important ramifications for our ability to respond to the likely future emergence of coronaviruses in socioeconomically important animal species or human populations.
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Affiliation(s)
- Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
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14
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Domańska-Blicharz K, Woźniakowski G, Konopka B, Niemczuk K, Welz M, Rola J, Socha W, Orłowska A, Antas M, Śmietanka K, Cuvelier-Mizak B. Animal Coronaviruses in the Light of COVID-19. J Vet Res 2020; 64:333-345. [PMID: 32984621 PMCID: PMC7497757 DOI: 10.2478/jvetres-2020-0050] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 07/20/2020] [Indexed: 12/24/2022] Open
Abstract
Coronaviruses are extremely susceptible to genetic changes due to the characteristic features of the genome structure, life cycle and environmental pressure. Their remarkable variability means that they can infect many different species of animals and cause different disease symptoms. Moreover, in some situations, coronaviruses might be transmitted across species. Although they are commonly found in farm, companion and wild animals, causing clinical and sometimes serious signs resulting in significant economic losses, not all of them have been classified by the World Organization for Animal Health (OIE) as hazardous and included on the list of notifiable diseases. Currently, only three diseases caused by coronaviruses are on the OIE list of notifiable terrestrial and aquatic animal diseases. However, none of these three entails any administrative measures. The emergence of the SARS-CoV-2 infections that have caused the COVID-19 pandemic in humans has proved that the occurrence and variability of coronaviruses is highly underestimated in the animal reservoir and reminded us of the critical importance of the One Health approach. Therefore, domestic and wild animals should be intensively monitored, both to broaden our knowledge of the viruses circulating among them and to understand the mechanisms of the emergence of viruses of relevance to animal and human health.
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Affiliation(s)
| | - Grzegorz Woźniakowski
- Department of Swine Diseases, National Veterinary Research Institute, 24-100Puławy, Poland
| | | | - Krzysztof Niemczuk
- Director General, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Mirosław Welz
- General Veterinary Inspectorate, 00-930Warsaw, Poland
| | - Jerzy Rola
- Department of Virology, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Wojciech Socha
- Department of Virology, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Anna Orłowska
- Department of Virology, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Marta Antas
- Department of Swine Diseases, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Krzysztof Śmietanka
- Department of Poultry Diseases, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Beata Cuvelier-Mizak
- Department of Veterinary Pharmacy, National Veterinary Research Institute, 24-100Puławy, Poland
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15
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On the Coronaviruses and Their Associations with the Aquatic Environment and Wastewater. WATER 2020. [DOI: 10.3390/w12061598] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The outbreak of Coronavirus Disease 2019 (COVID-19), a severe respiratory disease caused by betacoronavirus SARS-CoV-2, in 2019 that further developed into a pandemic has received an unprecedented response from the scientific community and sparked a general research interest into the biology and ecology of Coronaviridae, a family of positive-sense single-stranded RNA viruses. Aquatic environments, lakes, rivers and ponds, are important habitats for bats and birds, which are hosts for various coronavirus species and strains and which shed viral particles in their feces. It is therefore of high interest to fully explore the role that aquatic environments may play in coronavirus spread, including cross-species transmissions. Besides the respiratory tract, coronaviruses pathogenic to humans can also infect the digestive system and be subsequently defecated. Considering this, it is pivotal to understand whether wastewater can play a role in their dissemination, particularly in areas with poor sanitation. This review provides an overview of the taxonomy, molecular biology, natural reservoirs and pathogenicity of coronaviruses; outlines their potential to survive in aquatic environments and wastewater; and demonstrates their association with aquatic biota, mainly waterfowl. It also calls for further, interdisciplinary research in the field of aquatic virology to explore the potential hotspots of coronaviruses in the aquatic environment and the routes through which they may enter it.
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16
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Decaro N, Lorusso A. Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses. Vet Microbiol 2020; 244:108693. [PMID: 32402329 PMCID: PMC7195271 DOI: 10.1016/j.vetmic.2020.108693] [Citation(s) in RCA: 229] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/10/2020] [Accepted: 04/10/2020] [Indexed: 12/16/2022]
Abstract
The recent pandemic caused by the novel human coronavirus, referrred to as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), not only is having a great impact on the health care systems and economies in all continents but it is also causing radical changes of common habits and life styles. The novel coronavirus (CoV) recognises, with high probability, a zoonotic origin but the role of animals in the SARS-CoV-2 epidemiology is still largely unknown. However, CoVs have been known in animals since several decades, so that veterinary coronavirologists have a great expertise on how to face CoV infections in animals, which could represent a model for SARS-CoV-2 infection in humans. In the present paper, we provide an up-to-date review of the literature currently available on animal CoVs, focusing on the molecular mechanisms that are responsible for the emergence of novel CoV strains with different antigenic, biologic and/or pathogenetic features. A full comprehension of the mechanisms driving the evolution of animal CoVs will help better understand the emergence, spreading, and evolution of SARS-CoV-2.
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Affiliation(s)
- Nicola Decaro
- Department of Veterinary Medicine, University of Bari, Valenzano, Bari, Italy.
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise 'G. Caporale', Teramo, Italy
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17
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Suryaman GK, Soejoedono RD, Setiyono A, Poetri ON, Handharyani E. Isolation and characterization of avian coronavirus from healthy Eclectus parrots ( Eclectus roratus) from Indonesia. Vet World 2019; 12:1797-1805. [PMID: 32009759 PMCID: PMC6925039 DOI: 10.14202/vetworld.2019.1797-1805] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/09/2019] [Indexed: 12/16/2022] Open
Abstract
Background and Aim: Avian coronavirus has a wide range of hosts, from chickens and turkeys to wild birds. This virus causes an economically and, possibly, environmentally, important loss in the poultry industry. Therefore, research into the avian coronavirus in various species of birds is required. The Eclectus parrot (Eclectus roratus) is an endemic bird to Indonesia and Northern Australia and often kept as pets. At present, there has been limited information about avian coronavirus infection among birds. This study aimed to determine the presence of and to characterize avian coronavirus isolated from Eclectus parrots in Indonesia. Materials and Methods: Cloacal swab samples were taken from 10 healthy Eclectus parrots (E. roratus). Each isolate was propagated into specific pathogen-free embryonated chicken eggs. The presence of avian coronavirus was determined using three sets of primers targeting the 3’ untranslated region (3’-UTR) of avian coronavirus (UTR41+/11−), the N gene of the infectious bronchitis virus (IBVN+/−), and the S1 gene of the IBV (XCE2+/XCE2−). The infectious bronchitis vaccine strain H120 was used as a positive control. Resulting positive bands were sequenced for the S1 gene. Results: None of the isolates was positive for the 3’-UTR, four isolates were positive for the N gene of infectious bronchitis, and two isolates were positive for the S1 gene of the IBV. However, only one isolate (parrot/Indonesia/BX9/16) was sequenced for the partial S1 gene with primers XCE2+/XCE2−. The partial nucleotide sequence of this isolate showed 100% homology with the IBV GI-13 lineage, specifically with a field isolate of the 4/91 variant 1 Israel and the 4/91 vaccine on the hypervariable region 3 site of the S1 gene. Conclusion: An IB-like avian coronavirus was isolated from healthy Eclectus parrots. Our results indicate that IBV has a wide range of hosts, which prompt the need to understand the interspecies connection of this virus better.
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Affiliation(s)
- G K Suryaman
- Department of Clinic Reproduction and Pathology, Faculty of Veterinary Medicine, Bogor Agricultural University, Jl. Agatis, Kampus IPB, Dramaga, Bogor 16680, Indonesia
| | - R D Soejoedono
- Department of Animal Disease and Veterinary Public Health, Faculty of Veterinary Medicine, Bogor Agricultural University, Jl. Agatis, Kampus IPB, Dramaga, Bogor 16680, Indonesia
| | - A Setiyono
- Department of Clinic Reproduction and Pathology, Faculty of Veterinary Medicine, Bogor Agricultural University, Jl. Agatis, Kampus IPB, Dramaga, Bogor 16680, Indonesia
| | - O N Poetri
- Department of Animal Disease and Veterinary Public Health, Faculty of Veterinary Medicine, Bogor Agricultural University, Jl. Agatis, Kampus IPB, Dramaga, Bogor 16680, Indonesia
| | - E Handharyani
- Department of Clinic Reproduction and Pathology, Faculty of Veterinary Medicine, Bogor Agricultural University, Jl. Agatis, Kampus IPB, Dramaga, Bogor 16680, Indonesia
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18
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Wille M, Shi M, Klaassen M, Hurt AC, Holmes EC. Virome heterogeneity and connectivity in waterfowl and shorebird communities. THE ISME JOURNAL 2019; 13:2603-2616. [PMID: 31239538 PMCID: PMC6775988 DOI: 10.1038/s41396-019-0458-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/02/2019] [Accepted: 05/27/2019] [Indexed: 11/09/2022]
Abstract
Models of host-microbe dynamics typically assume a single-host population infected by a single pathogen. In reality, many hosts form multi-species aggregations and may be infected with an assemblage of pathogens. We used a meta-transcriptomic approach to characterize the viromes of nine avian species in the Anseriformes (ducks) and Charadriiformes (shorebirds). This revealed the presence of 27 viral species, of which 24 were novel, including double-stranded RNA viruses (Picobirnaviridae and Reoviridae), single-stranded RNA viruses (Astroviridae, Caliciviridae, Picornaviridae), a retro-transcribing DNA virus (Hepadnaviridae), and a single-stranded DNA virus (Parvoviridae). These viruses comprise multi-host generalist viruses and those that are host-specific, indicative of both virome connectivity (host sharing) and heterogeneity (host specificity). Virome connectivity was apparent in two well described multi-host virus species -avian coronavirus and influenza A virus- and a novel Rotavirus species that were shared among some Anseriform species, while virome heterogeneity was reflected in the absence of viruses shared between Anseriformes and Charadriiformes, as well as differences in viral abundance and alpha diversity among species. Overall, we demonstrate complex virome structures across host species that co-exist in multi-species aggregations.
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Affiliation(s)
- Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
| | - Mang Shi
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Marcel Klaassen
- Centre for Integrative Ecology, Deakin University, Geelong, Australia
| | - Aeron C Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia.
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19
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Canuti M, Kroyer ANK, Ojkic D, Whitney HG, Robertson GJ, Lang AS. Discovery and Characterization of Novel RNA Viruses in Aquatic North American Wild Birds. Viruses 2019; 11:E768. [PMID: 31438486 PMCID: PMC6784231 DOI: 10.3390/v11090768] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/16/2019] [Accepted: 08/18/2019] [Indexed: 12/25/2022] Open
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.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John's, NL A1B 3X9, Canada.
| | - Ashley N K Kroyer
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John's, NL A1B 3X9, Canada
| | - Davor Ojkic
- Animal Health Laboratory, Laboratory Services Division, University of Guelph, 419 Gordon St., Guelph, ON N1H 6R8, Canada
| | - Hugh G Whitney
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John's, NL A1B 3X9, Canada
| | - Gregory J Robertson
- Wildlife Research Division, Environment and Climate Change Canada, 6 Bruce Street, Mount Pearl, NL A1N 4T3, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John's, NL A1B 3X9, Canada.
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20
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Pauly M, Snoeck CJ, Phoutana V, Keosengthong A, Sausy A, Khenkha L, Nouanthong P, Samountry B, Jutavijittum P, Vilivong K, Hübschen JM, Black AP, Pommasichan S, Muller CP. Cross-species transmission of poultry pathogens in backyard farms: ducks as carriers of chicken viruses. Avian Pathol 2019; 48:503-511. [PMID: 31199168 DOI: 10.1080/03079457.2019.1628919] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In backyard farms of Lao People's Democratic Republic, mixed-species rearing of poultry is a breeding-ground for cross-species transmission. Here, the epidemiology of viruses circulating among backyard poultry in Vientiane Province was assessed to guide future control strategies. Oral/tracheal and cloacal swabs, collected from 605 poultry (308 ducks, 297 chickens) between 2011 and 2015, were screened by PCR for Newcastle disease virus (NDV), coronavirus (CoV) and chicken anaemia virus (CAV). Chicken sera were screened for anti-NDV antibodies by ELISA. Statistical and phylogenetic analyses revealed transmission patterns and relationships. Closely related strains co-circulated in chickens and ducks. While CoV RNA was detected in oral/tracheal swabs of 9.3% of the chickens and 2.4% of the ducks, rates were higher in faecal swabs of both species (27.3% and 48.2%). RNA of infectious bronchitis virus (IBV) and duck CoV was found in faecal swabs of chickens (19.7% and 7.1%) and ducks (4.1% and 44.1%). Moreover, DNA of the generally chicken-specific CAV was detected in oral/tracheal swabs of chickens (18.1%) and, sporadically, of ducks (2.4%). Despite serological evidence of NDV circulation or vaccination (86.9%), NDV RNA was not detected. We found a high prevalence and indication for cross-species transmission of different CoV strains in backyard poultry. Interestingly, ducks served as biological, or at least mechanical, carriers of viral strains closely related not only to IBV, but also to CAV. Bird containment and poultry species separation could be first steps to avoid cross-species transmission and emergence of novel strains with broad host range and enhanced pathogenicity. RESEARCH HIGHLIGHTS High rates of avian viruses were detected by PCR in backyard poultry from Lao PDR. Diverse coronavirus and chicken anemia virus strains co-circulated. Phylogenetic analyses suggested virus transmission between chickens and ducks. Serological evidence of Newcastle disease was found, but viral RNA was not detected.
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Affiliation(s)
- Maude Pauly
- Department of Infection and Immunity, Luxembourg Institute of Health , Esch-sur-Alzette , Luxembourg
| | - Chantal J Snoeck
- Department of Infection and Immunity, Luxembourg Institute of Health , Esch-sur-Alzette , Luxembourg
| | - Vannaphone Phoutana
- The Faculty of Agriculture, National University of Laos - Nabong Campus , Vientiane , Lao People's Democratic Republic
| | - Amphone Keosengthong
- The Faculty of Agriculture, National University of Laos - Nabong Campus , Vientiane , Lao People's Democratic Republic
| | - Aurélie Sausy
- Department of Infection and Immunity, Luxembourg Institute of Health , Esch-sur-Alzette , Luxembourg
| | - Latdavone Khenkha
- Lao-Lux-Laboratory, Institute Pasteur du Laos , Vientiane , Lao People's Democratic Republic
| | | | - Bounthome Samountry
- Department of Pathology, Faculty of Basic Sciences, Ministry of Public Health, University of Health Sciences , Vientiane , Lao People's Democratic Republic
| | - Prapan Jutavijittum
- Department of Pathology, Faculty of Medicine, Chiang Mai University , Chiang Mai , Thailand
| | - Keooudomphone Vilivong
- National Centre for Laboratory and Epidemiology, Lao Ministry of Health , Vientiane , Lao People's Democratic Republic
| | - Judith M Hübschen
- Department of Infection and Immunity, Luxembourg Institute of Health , Esch-sur-Alzette , Luxembourg
| | - Antony P Black
- Lao-Lux-Laboratory, Institute Pasteur du Laos , Vientiane , Lao People's Democratic Republic
| | - Sisavath Pommasichan
- The Faculty of Agriculture, National University of Laos - Nabong Campus , Vientiane , Lao People's Democratic Republic
| | - Claude P Muller
- Department of Infection and Immunity, Luxembourg Institute of Health , Esch-sur-Alzette , Luxembourg.,Lao-Lux-Laboratory, Institute Pasteur du Laos , Vientiane , Lao People's Democratic Republic.,Laboratoire National de Santé , Dudelange , Luxembourg
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21
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Barbosa CM, Durigon EL, Thomazelli LM, Ometto T, Marcatti R, Nardi MS, de Aguiar DM, Pinho JB, Petry MV, Neto IS, Serafini P, Rodrigues RC, de Azevedo Junior SM, Góes LGB, de Araujo J. Divergent coronaviruses detected in wild birds in Brazil, including a central park in São Paulo. Braz J Microbiol 2019; 50:547-556. [PMID: 30877663 PMCID: PMC6863219 DOI: 10.1007/s42770-019-00065-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 12/07/2018] [Indexed: 12/17/2022] Open
Abstract
Coronaviruses are single-stranded positive-sense RNA viruses associated with important avian diseases. Their relatively high rates of mutation and recombination frequencies allow them to adapt to new hosts and ecological niches. Although Brazil has 18% of global avian species diversity, studies regarding the presence of avian viral diseases in wild birds in South America are scarce. In this study, we performed a retrospective analysis of the presence of CoVs in 746 wild birds. Oropharyngeal and cloacal swabs were obtained and placed together in vials containing VTM transport medium collected in different regions of Brazil between 2006 and 2013. Screening for viral nucleic acid was performed using conventional RT-PCR and pancoronavirus nested PCR. Positive samples were characterized by partial sequencing of the RNA-dependent RNA polymerase (RdRp) gene, and ensuing phylogenetic analysis was performed to investigate the association between virus epidemiology and bird migration routes. Coronavirus RNA were detected and sequenced from six samples, in which three were related to gammacoronaviruses group and the other three to deltacoronavirus group. Our study documents the presence of CoVs related to avian gamma- and deltacoronaviruses circulating in both urban- and poultry-farm regions of Brazil, implicating wild birds as potential carriers of CoVs which may represent a risk to poultry farms and public health in Brazil.
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Affiliation(s)
- Carla M Barbosa
- Institute of Biomedical Sciences, University of Sao Paulo, 1374 Prof. Lineu Prestes avenue, São Paulo, 05508-900, Brazil
| | - Edison L Durigon
- Institute of Biomedical Sciences, University of Sao Paulo, 1374 Prof. Lineu Prestes avenue, São Paulo, 05508-900, Brazil
| | - Luciano M Thomazelli
- Institute of Biomedical Sciences, University of Sao Paulo, 1374 Prof. Lineu Prestes avenue, São Paulo, 05508-900, Brazil
| | - Tatiana Ometto
- Institute of Biomedical Sciences, University of Sao Paulo, 1374 Prof. Lineu Prestes avenue, São Paulo, 05508-900, Brazil
| | - Roberta Marcatti
- Wildlife and Green Areas Department, São Paulo Municipality, São Paulo, Brazil
| | | | - Daniel M de Aguiar
- Laboratório de Virologia e Rickettsioses, Hospital Veterinário, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - João Batista Pinho
- Laboratório de Ecologia de Aves, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Maria Virginia Petry
- Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Rio Grande do Sul, Brazil
| | - Isaac Simão Neto
- Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio), Brasília, Brazil
| | - Patrícia Serafini
- Centro Nacional de Pesquisa e Conservação de Aves Silvestres (CEMAVE), Cabedelo, Paraíba, Brazil
| | | | | | - Luiz Gustavo B Góes
- Institute of Biomedical Sciences, University of Sao Paulo, 1374 Prof. Lineu Prestes avenue, São Paulo, 05508-900, Brazil
| | - Jansen de Araujo
- Institute of Biomedical Sciences, University of Sao Paulo, 1374 Prof. Lineu Prestes avenue, São Paulo, 05508-900, Brazil.
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22
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Wille M, Eden JS, Shi M, Klaassen M, Hurt AC, Holmes EC. Virus-virus interactions and host ecology are associated with RNA virome structure in wild birds. Mol Ecol 2018; 27:5263-5278. [PMID: 30375075 PMCID: PMC6312746 DOI: 10.1111/mec.14918] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/11/2018] [Accepted: 10/18/2018] [Indexed: 12/13/2022]
Abstract
Little is known about the factors that shape the ecology of RNA viruses in nature. Wild birds are an important case in point, as other than influenza A virus, avian samples are rarely tested for viruses, especially in the absence of overt disease. Using bulk RNA-sequencing ("meta-transcriptomics"), we revealed the viral diversity present in Australian wild birds through the lens of the ecological factors that may determine virome structure and abundance. A meta-transcriptomic analysis of four Anseriformes (waterfowl) and Charadriiformes (shorebird) species sampled in temperate and arid Australia revealed the presence of 27 RNA virus genomes, 18 of which represent newly described species. The viruses identified included a previously described gammacoronavirus and influenza A viruses. Additionally, we identified novel virus species from the families Astroviridae, Caliciviridae, Reoviridae, Rhabdoviridae, Picobirnaviridae and Picornaviridae. We noted differences in virome structure that reflected underlying differences in location and influenza A infection status. Red-necked Avocets (Recurvirostra novaehollandiae) from Australia's arid interior possessed the greatest viral diversity and abundance, markedly higher than individuals sampled in temperate Australia. In Ruddy Turnstones (Arenaria interpres) and dabbling ducks (Anas spp.), viral abundance and diversity were higher and more similar in hosts that were positive for influenza A infection compared to those that were negative for this virus, despite samples being collected on the same day and from the same location. This study highlights the extent and diversity of RNA viruses in wild birds and lays the foundation for understanding the factors that determine virome structure in wild populations.
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Affiliation(s)
- Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia.,The Westmead Institute for Medical Research, Centre for Virus Research, Sydney, New South Wales, Australia
| | - Mang Shi
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Marcel Klaassen
- Centre for Integrative Ecology, Deakin University, Geelong, Victoria, Australia
| | - Aeron C Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
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23
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Miłek J, Blicharz-Domańska K. Coronaviruses in Avian Species - Review with Focus on Epidemiology and Diagnosis in Wild Birds. J Vet Res 2018; 62:249-255. [PMID: 30584600 PMCID: PMC6296008 DOI: 10.2478/jvetres-2018-0035] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/19/2018] [Indexed: 12/12/2022] Open
Abstract
Coronaviruses (CoVs) are a large group of enveloped viruses with a single-strand RNA genome, which continuously circulate in mammals and birds and pose a threat to livestock, companion animals, and humans. CoVs harboured by avian species are classified to the genera gamma- and deltacoronaviruses. Within the gamma-CoVs the main representative is avian coronavirus, a taxonomic name which includes the highly contagious infectious bronchitis viruses (IBVs) in chickens and similar viruses infecting other domestic birds such as turkeys, guinea fowls, or quails. Additionally, IBVs have been detected in healthy wild birds, demonstrating that they may act as the vector between domestic and free-living birds. Moreover, CoVs other than IBVs, are identified in wild birds, which suggests that wild birds play a key role in the epidemiology of other gammaCoVs and deltaCoVs. Development of molecular techniques has significantly improved knowledge of the prevalence of CoVs in avian species. The methods adopted in monitoring studies of CoVs in different avian species are mainly based on detection of conservative regions within the viral replicase, nucleocapsid genes, and 3'UTR or 5'UTR. The purpose of this review is to summarise recent discoveries in the areas of epidemiology and diagnosis of CoVs in avian species and to understand the role of wild birds in the virus distribution.
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Affiliation(s)
- Justyna Miłek
- Department of Poultry Diseases, National Veterinary Research Institute, 24-100Puławy, Poland
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24
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Detection and characterisation of coronaviruses in migratory and non-migratory Australian wild birds. Sci Rep 2018; 8:5980. [PMID: 29654248 PMCID: PMC5899083 DOI: 10.1038/s41598-018-24407-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/26/2018] [Indexed: 12/18/2022] Open
Abstract
We evaluated the presence of coronaviruses by PCR in 918 Australian wild bird samples collected during 2016–17. Coronaviruses were detected in 141 samples (15.3%) from species of ducks, shorebirds and herons and from multiple sampling locations. Sequencing of selected positive samples found mainly gammacoronaviruses, but also some deltacoronaviruses. The detection rate of coronaviruses was improved by using multiple PCR assays, as no single assay could detect all coronavirus positive samples. Sequencing of the relatively conserved Orf1 PCR amplicons found that Australian duck gammacoronaviruses were similar to duck gammacoronaviruses around the world. Some sequenced shorebird gammacoronaviruses belonged to Charadriiformes lineages, but others were more closely related to duck gammacoronaviruses. Australian duck and heron deltacoronaviruses belonged to lineages with other duck and heron deltacoronaviruses, but were almost 20% different in nucleotide sequence to other deltacoronavirus sequences available. Deltacoronavirus sequences from shorebirds formed a lineage with a deltacoronavirus from a ruddy turnstone detected in the United States. Given that Australian duck gammacoronaviruses are highly similar to those found in other regions, and Australian ducks rarely come into contact with migratory Palearctic duck species, we hypothesise that migratory shorebirds are the important vector for moving wild bird coronaviruses into and out of Australia.
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25
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Martini MC, Caserta LC, Dos Santos MMAB, Barnabé ACS, Durães-Carvalho R, Padilla MA, Simão RM, Rizotto LS, Simas PVM, Bastos JCS, Cardoso TC, Felippe PAN, Ferreira HL, Arns CW. Avian coronavirus isolated from a pigeon sample induced clinical disease, tracheal ciliostasis, and a high humoral response in day-old chicks. Avian Pathol 2018. [PMID: 29517348 DOI: 10.1080/03079457.2018.1442557] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The detection of avian coronaviruses (AvCoV) in wild birds and the emergence of new AvCoV have increased in the past few years. In the present study, the pathogenicity of three AvCoV isolates was investigated in day-old chicks. One AvCoV isolated from a pigeon, which clustered with the Massachusetts vaccine serotype, and two AvCoV isolated from chickens, which grouped with a Brazilian genotype lineage, were used. Clinical signs, gross lesions, histopathological changes, ciliary activity, viral RNA detection, and serology were evaluated during 42 days post infection. All AvCoV isolates induced clinical signs, gross lesions in the trachea, moderate histopathological changes in the respiratory tract, and mild changes in other tissues. AvCoV isolated from the pigeon sample caused complete tracheal ciliostasis over a longer time span. Specific viral RNA was detected in all tissues, but the highest RNA loads were detected in the digestive tract (cloacal swabs and ileum). The highest antibody levels were also detected in the group infected with an isolate from the pigeon. These results confirm the pathogenicity of Brazilian variants, which can cause disease and induce gross lesions and histopathological changes in chickens. Our results suggest that non-Galliformes birds can also play a role in the ecology of AvCoV.
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Affiliation(s)
- Matheus C Martini
- a Laboratory of Animal Virology , Institute of Biology, University of Campinas-UNICAMP , Campinas , SP , Brazil
| | - Leonardo C Caserta
- a Laboratory of Animal Virology , Institute of Biology, University of Campinas-UNICAMP , Campinas , SP , Brazil
| | | | - Ana C S Barnabé
- a Laboratory of Animal Virology , Institute of Biology, University of Campinas-UNICAMP , Campinas , SP , Brazil
| | - Ricardo Durães-Carvalho
- a Laboratory of Animal Virology , Institute of Biology, University of Campinas-UNICAMP , Campinas , SP , Brazil
| | - Marina A Padilla
- a Laboratory of Animal Virology , Institute of Biology, University of Campinas-UNICAMP , Campinas , SP , Brazil
| | - Raphael M Simão
- c Postgraduate Program in Experimental Epidemiology of Zoonoses, Faculty of Veterinary Medicine and Animal Science , University of Sao Paulo (FMVZ-USP) , Sao Paulo , SP , Brazil
| | - Laís S Rizotto
- c Postgraduate Program in Experimental Epidemiology of Zoonoses, Faculty of Veterinary Medicine and Animal Science , University of Sao Paulo (FMVZ-USP) , Sao Paulo , SP , Brazil
| | - Paulo V M Simas
- a Laboratory of Animal Virology , Institute of Biology, University of Campinas-UNICAMP , Campinas , SP , Brazil
| | - Juliana C S Bastos
- a Laboratory of Animal Virology , Institute of Biology, University of Campinas-UNICAMP , Campinas , SP , Brazil
| | - Tereza C Cardoso
- e DAPSA Department, Laboratory of Animal Virology and Cell Culture , College of Veterinary Medicine, Universidade Estadual Paulista , Araçatuba , SP , Brazil
| | - Paulo A N Felippe
- a Laboratory of Animal Virology , Institute of Biology, University of Campinas-UNICAMP , Campinas , SP , Brazil
| | - Helena L Ferreira
- b Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering , University of Sao Paulo (FZEA-USP) , Pirassununga , SP , Brazil.,c Postgraduate Program in Experimental Epidemiology of Zoonoses, Faculty of Veterinary Medicine and Animal Science , University of Sao Paulo (FMVZ-USP) , Sao Paulo , SP , Brazil
| | - Clarice W Arns
- a Laboratory of Animal Virology , Institute of Biology, University of Campinas-UNICAMP , Campinas , SP , Brazil
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26
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Hepojoki S, Lindh E, Vapalahti O, Huovilainen A. Prevalence and genetic diversity of coronaviruses in wild birds, Finland. Infect Ecol Epidemiol 2017; 7:1408360. [PMID: 30788065 PMCID: PMC6369310 DOI: 10.1080/20008686.2017.1408360] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/17/2017] [Indexed: 12/25/2022] Open
Abstract
Introduction: Migratory birds act as hosts for a number of zoonotic viruses, and have the ability to disperse these viruses to distant geographic locations. Coronaviruses (CoVs) represent a family of zoonotic viruses with wide variety of animal hosts, including birds and humans. The infections caused by coronaviruses vary from mild to severe, depending on the viral species and the host. Since the coronaviruses exhibit extraordinary large RNA genome, also the rate of homologous recombination is high, which in turn contributes to the genetic diversity and interspecies host-switches of CoVs. The emergence of novel CoVs has been rich during the last decades, and wild birds seem to serve as reservoirs for a variety of CoV strains. We examined the CoVs circulating among wild birds in Finland. Materials and methods: Samples (cloacal swab, tracheal swab, oropharyngeal swab, or tissue) representing 61 bird species were collected during 2010-2013, and examined by RT-PCR targeting the RdRp gene for the presence of CoV RNA. Results: Altogether 51/939 (5.4%) of the examined birds were found positive by RT-PCR. Diverse gamma- and deltacoronavirus sequences were detected. Discussion: Gamma- and deltacoronaviruses circulate among wild birds in Finland. The number of CoV-positive birds detected each year varies greatly.
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Affiliation(s)
| | - Erika Lindh
- Virology, University of Helsinki, Helsinki, Finland.,Helsinki University Hospital, Helsinki, Finland
| | - Olli Vapalahti
- Virology, University of Helsinki, Helsinki, Finland.,Helsinki University Hospital, Helsinki, Finland.,Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Anita Huovilainen
- Research and Laboratory Department, Veterinary Virology, Finnish Food Safety Authority, Evira, Helsinki, Finland
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27
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Wille M, Lindqvist K, Muradrasoli S, Olsen B, Järhult JD. Urbanization and the dynamics of RNA viruses in Mallards (Anas platyrhynchos). INFECTION GENETICS AND EVOLUTION 2017; 51:89-97. [PMID: 28323070 PMCID: PMC7106234 DOI: 10.1016/j.meegid.2017.03.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 03/08/2017] [Accepted: 03/16/2017] [Indexed: 11/26/2022]
Abstract
Urbanization is intensifying worldwide, and affects the epidemiology of infectious diseases. However, the effect of urbanization on natural host-pathogen systems remains poorly understood. Urban ducks occupy an interesting niche in that they directly interact with both humans and wild migratory birds, and either directly or indirectly with food production birds. Here we have collected samples from Mallards (Anas platyrhynchos) residing in a pond in central Uppsala, Sweden, from January 2013 to January 2014. This artificial pond is kept ice-free during the winter months, and is a popular location where the ducks are fed, resulting in a resident population of ducks year-round. Nine hundred and seventy seven (977) fecal samples were screened for RNA viruses including: influenza A virus (IAV), avian paramyxovirus 1, avian coronavirus (CoV), and avian astrovirus (AstroV). This intra-annual dataset illustrates that these RNA viruses exhibit similar annual patterns to IAV, suggesting similar ecological factors are at play. Furthermore, in comparison to wild ducks, autumnal prevalence of IAV and CoV are lower in this urban population. We also demonstrate that AstroV might be a larger burden to urban ducks than IAV, and should be better assessed to demonstrate the degree to which wild birds contribute to the epidemiology of these viruses. The presence of economically relevant viruses in urban Mallards highlights the importance of elucidating the ecology of wildlife pathogens in urban environments, which will become increasingly important for managing disease risks to wildlife, food production animals, and humans. Influenza virus, coronavirus, paramyxovirus, astrovirus detected in urban Mallards Viruses share intra-annual dynamics, with autumnal prevalence peak Avian astrovirus had the highest prevalence in urban Mallards. Prevalence of influenza and coronavirus lower in urban versus to migrating Mallard
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Affiliation(s)
- Michelle Wille
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
| | - Kristine Lindqvist
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Shaman Muradrasoli
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institute, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Björn Olsen
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Section for Infectious Diseases, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Josef D Järhult
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Section for Infectious Diseases, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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