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Ng DYM, Sun W, Sit THC, Brackman CJ, Tse ACN, Bui CHT, Tang AWY, Wong ANC, Tsang ATL, Koo JCT, Cheng SMS, Peiris M, Chin AWH, Poon LLM. Genetic diversity of astroviruses detected in wild aquatic birds in Hong Kong. Virol J 2024; 21:153. [PMID: 38972989 PMCID: PMC11229208 DOI: 10.1186/s12985-024-02423-w] [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] [Received: 05/14/2024] [Accepted: 06/27/2024] [Indexed: 07/09/2024] Open
Abstract
Wild waterfowl serve as a reservoir of some astroviruses. Fecal samples from wild waterfowl collected at Hong Kong's Marshes were tested using pan-astrovirus reverse transcription-PCR. Positive samples underwent subsequent host identification using DNA barcoding. Based on deduced partial sequences, noteworthy samples from three astrovirus groups (mammalian, avian and unclassified astroviruses) were further analyzed by next-generation sequencing. One sample of Avastrovirus 4 clade, MP22-196, had a nearly complete genome identified. The results of ORF2 phylogenetic analysis and genetic distance analysis indicate that Avastrovirus 4 is classified as a distinct subclade within Avastrovirus. MP22-196 has typical astrovirus genome characteristics. The unique characteristics and potential differences of this genome, compared to other avian astrovirus sequences, involve the identification of a modified sgRNA sequence situated near the ORF2 start codon, which precedes the ORF1b stop codon. Additionally, the 3' UTR of MP22-196 is shorter than other avian astroviruses. This study expands our understanding of the Avastrovirus 4 clade.
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Affiliation(s)
- Daisy Y M Ng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Wanying Sun
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Thomas H C Sit
- Agriculture, Fisheries and Conservation Department, Government of the Hong Kong Special Administrative Region, Hong Kong, China
| | - Christopher J Brackman
- Agriculture, Fisheries and Conservation Department, Government of the Hong Kong Special Administrative Region, Hong Kong, China
| | - Anne C N Tse
- Agriculture, Fisheries and Conservation Department, Government of the Hong Kong Special Administrative Region, Hong Kong, China
| | - Christine H T Bui
- Agriculture, Fisheries and Conservation Department, Government of the Hong Kong Special Administrative Region, Hong Kong, China
| | - Amy W Y Tang
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Andrew N C Wong
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Andrew T L Tsang
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Joe C T Koo
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Samuel M S Cheng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Malik Peiris
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Immunology and Infection, Hong Kong Science and Technology Park, Hong Kong, China
| | - Alex W H Chin
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Leo L M Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
- Centre for Immunology and Infection, Hong Kong Science and Technology Park, Hong Kong, China.
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
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Alipour F, Holmes C, Lu YY, Hill KA, Kari L. Leveraging machine learning for taxonomic classification of emerging astroviruses. Front Mol Biosci 2024; 10:1305506. [PMID: 38274100 PMCID: PMC10808839 DOI: 10.3389/fmolb.2023.1305506] [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: 10/01/2023] [Accepted: 12/12/2023] [Indexed: 01/27/2024] Open
Abstract
Astroviruses are a family of genetically diverse viruses associated with disease in humans and birds with significant health effects and economic burdens. Astrovirus taxonomic classification includes two genera, Avastrovirus and Mamastrovirus. However, with next-generation sequencing, broader interspecies transmission has been observed necessitating a reexamination of the current host-based taxonomic classification approach. In this study, a novel taxonomic classification method is presented for emergent and as yet unclassified astroviruses, based on whole genome sequence k-mer composition in addition to host information. An optional component responsible for identifying recombinant sequences was added to the method's pipeline, to counteract the impact of genetic recombination on viral classification. The proposed three-pronged classification method consists of a supervised machine learning method, an unsupervised machine learning method, and the consideration of host species. Using this three-pronged approach, we propose genus labels for 191 as yet unclassified astrovirus genomes. Genus labels are also suggested for an additional eight as yet unclassified astrovirus genomes for which incompatibility was observed with the host species, suggesting cross-species infection. Lastly, our machine learning-based approach augmented by a principal component analysis (PCA) analysis provides evidence supporting the hypothesis of the existence of human astrovirus (HAstV) subgenus of the genus Mamastrovirus, and a goose astrovirus (GoAstV) subgenus of the genus Avastrovirus. Overall, this multipronged machine learning approach provides a fast, reliable, and scalable prediction method of taxonomic labels, able to keep pace with emerging viruses and the exponential increase in the output of modern genome sequencing technologies.
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Affiliation(s)
- Fatemeh Alipour
- School of Computer Science, University of Waterloo, Waterloo, ON, Canada
| | - Connor Holmes
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Yang Young Lu
- School of Computer Science, University of Waterloo, Waterloo, ON, Canada
| | - Kathleen A. Hill
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Lila Kari
- School of Computer Science, University of Waterloo, Waterloo, ON, Canada
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Zhigailov AV, Maltseva ER, Perfilyeva YV, Ostapchuk YO, Naizabayeva DA, Berdygulova ZA, Kuatbekova SA, Nizkorodova AS, Mashzhan A, Gavrilov AE, Abayev AZ, Akhmetollayev IA, Mamadaliyev SM, Skiba YA. Prevalence and genetic diversity of coronaviruses, astroviruses and paramyxoviruses in wild birds in southeastern Kazakhstan. Heliyon 2022; 8:e11324. [PMID: 36353173 PMCID: PMC9638769 DOI: 10.1016/j.heliyon.2022.e11324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 06/21/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022] Open
Abstract
Wild birds are natural reservoirs of many emerging viruses, including some zoonoses. Considering that the territory of Kazakhstan is crossed by several bird migration routes, it is important to know pathogenic viruses circulating in migratory birds in this region. Therefore, the aim of this study was to identify the host range, diversity and spatial distribution of avian paramyxoviruses, coronaviruses, and astroviruses in free-ranging wild birds in the southeastern region of Kazakhstan. For this purpose, we collected tracheal and cloacal swabs from 242 wild birds belonging to 51 species and screened them using conventional PCR assays. Overall, 4.1% (10/242) and 2.9% (7/242) of all examined birds tested positive for coronaviruses and astroviruses, respectively. Coronaviruses were found in the orders Pelecaniformes (30%; 3/10), Charadriiformes (30%; 3/10), Columbiformes (20%; 2/10), Anseriformes (10%; 1/10), and Passeriformes (10%; 1/10). All detected strains belonged to the genus Gammacoronavirus. Astroviruses were detected in birds representing the orders Passeriformes (57%; 4/7), Coraciiformes (14%; 1/7), Charadriiformes (14%; 1/7), and Columbiformes (14%; 1/7). Paramyxoviruses were observed in only two birds (0.8%; 2/242). Both strains were closely related to the species APMV-22, which had not been previously detected in Kazakhstan. Phylogenetic analysis of the partial RdRp gene sequences of the virus strains revealed three different clades of astroviruses, two clades of coronaviruses, and one clade of paramyxoviruses. The results of this study provide valuable information on the diversity and spatial distribution of paramyxoviruses, coronaviruses, and astroviruses in wild birds in southeastern Kazakhstan and highlight the importance of further thorough monitoring of wild birds in this region. First study on CoVs and AstroVs in wild birds in Kazakhstan. APMVs, CoVs and AstroVs are confirmed by RT-PCR and partial RdRp gene sequencing. The CoVs prevalence is higher in aquatic birds as compared to terrestrial species. The obtained CoV strains belong to the genus Gammacoronavirus Strains closely related to APMV-22 not previously detected in Kazakhstan are shown.
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Affiliation(s)
- Andrey V. Zhigailov
- Almaty Branch of the National Center for Biotechnology, Almaty, Kazakhstan
- M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
| | - Elina R. Maltseva
- Almaty Branch of the National Center for Biotechnology, Almaty, Kazakhstan
- M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
- Tethys Scientific Society, Almaty, Kazakhstan
| | - Yuliya V. Perfilyeva
- Almaty Branch of the National Center for Biotechnology, Almaty, Kazakhstan
- M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
- Corresponding author.
| | - Yekaterina O. Ostapchuk
- Almaty Branch of the National Center for Biotechnology, Almaty, Kazakhstan
- M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
| | - Dinara A. Naizabayeva
- Almaty Branch of the National Center for Biotechnology, Almaty, Kazakhstan
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | | | | | - Anna S. Nizkorodova
- Almaty Branch of the National Center for Biotechnology, Almaty, Kazakhstan
- M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
| | - Akzhigit Mashzhan
- Almaty Branch of the National Center for Biotechnology, Almaty, Kazakhstan
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | | | | | | | | | - Yuriy A. Skiba
- Almaty Branch of the National Center for Biotechnology, Almaty, Kazakhstan
- M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
- Tethys Scientific Society, Almaty, Kazakhstan
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Fernández-Correa I, Truchado DA, Gomez-Lucia E, Doménech A, Pérez-Tris J, Schmidt-Chanasit J, Cadar D, Benítez L. A novel group of avian astroviruses from Neotropical passerine birds broaden the diversity and host range of Astroviridae. Sci Rep 2019; 9:9513. [PMID: 31266971 PMCID: PMC6606752 DOI: 10.1038/s41598-019-45889-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/10/2019] [Indexed: 01/04/2023] Open
Abstract
Metagenomics is helping to expand the known diversity of viruses, especially of those with poorly studied hosts in remote areas. The Neotropical region harbors a considerable diversity of avian species that may play a role as both host and short-distance vectors of unknown viruses. Viral metagenomics of cloacal swabs from 50 Neotropical birds collected in French Guiana revealed the presence of four complete astrovirus genomes. They constitute an early diverging novel monophyletic clade within the Avastrovirus phylogeny, representing a putative new astrovirus species (provisionally designated as Avastrovirus 5) according to the International Committee on Taxonomy of Viruses (ICTV) classification criteria. Their genomic organization shares some characteristics with Avastrovirus but also with Mamastrovirus. The pan-astrovirus RT-PCR analysis of the cloacal samples of 406 wild Neotropical birds showed a community-level prevalence of 4.9% (5.1% in passerines, the highest described so far in this order of birds). By screening birds of a remote region, we expanded the known host range of astroviruses to the avian families Cardinalidae, Conopophagidae, Furnariidae, Thamnophilidae, Turdidae and Tyrannidae. Our results provide important first insights into the unexplored viral communities, the ecology, epidemiology and features of host-pathogen interactions that shape the evolution of avastroviruses in a remote Neotropical rainforest.
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Affiliation(s)
- Izaskun Fernández-Correa
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, José Antonio Novais, 12, 28040, Madrid, Spain
| | - Daniel A Truchado
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, José Antonio Novais, 12, 28040, Madrid, Spain.,Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Complutense University of Madrid, José Antonio Novais, 12, 28040, Madrid, Spain
| | - Esperanza Gomez-Lucia
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, Avda. Puerta de Hierro s/n, 28040, Madrid, Spain
| | - Ana Doménech
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, Avda. Puerta de Hierro s/n, 28040, Madrid, Spain
| | - Javier Pérez-Tris
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Complutense University of Madrid, José Antonio Novais, 12, 28040, Madrid, Spain
| | - Jonas Schmidt-Chanasit
- Bernhard-Nocht-Institut fur Tropenmedizin, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, National Reference Centre for Tropical Infectious Diseases, Bernhard-Nocht-Strasse 74, 20359, Hamburg, Germany.,University of Hamburg, Faculty of Mathematics, Informatics and Natural Sciences, Hamburg, Germany
| | - Daniel Cadar
- Bernhard-Nocht-Institut fur Tropenmedizin, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, National Reference Centre for Tropical Infectious Diseases, Bernhard-Nocht-Strasse 74, 20359, Hamburg, Germany
| | - Laura Benítez
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, José Antonio Novais, 12, 28040, Madrid, Spain.
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