Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses

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Abstract

Background

Wild birds may harbor and transmit viruses that are potentially pathogenic to humans, domestic animals, and other wildlife.

Results

Using the viral metagenomic approach, we investigated the virome of cloacal swab specimens collected from 3182 birds (the majority of them wild species) consisting of > 87 different species in 10 different orders within the Aves classes. The virus diversity in wild birds was higher than that in breeding birds. We acquired 707 viral genomes from 18 defined families and 4 unclassified virus groups, with 265 virus genomes sharing < 60% protein sequence identities with their best matches in GenBank comprising new virus families, genera, or species. RNA viruses containing the conserved RdRp domain with no phylogenetic affinity to currently defined virus families existed in different bird species. Genomes of the astrovirus, picornavirus, coronavirus, calicivirus, parvovirus, circovirus, retrovirus, and adenovirus families which include known avian pathogens were fully characterized. Putative cross-species transmissions were observed with viruses in wild birds showing > 95% amino acid sequence identity to previously reported viruses in domestic poultry. Genomic recombination was observed for some genomes showing discordant phylogenies based on structural and non-structural regions. Mapping the next-generation sequencing (NGS) data respectively against the 707 genomes revealed that these viruses showed distribution pattern differences among birds with different habitats (breeding or wild), orders, and sampling sites but no significant differences between birds with different behavioral features (migratory and resident).

Conclusions

The existence of a highly diverse virome highlights the challenges in elucidating the evolution, etiology, and ecology of viruses in wild birds.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40168-022-01246-7.

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Most cited references 86

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A pneumonia outbreak associated with a new coronavirus of probable bat origin

Peng Zhou, Xing-Lou Yang, Xian-Guang Wang … (2020)

Since the outbreak of severe acute respiratory syndrome (SARS) 18 years ago, a large number of SARS-related coronaviruses (SARSr-CoVs) have been discovered in their natural reservoir host, bats 1–4 . Previous studies have shown that some bat SARSr-CoVs have the potential to infect humans 5–7 . Here we report the identification and characterization of a new coronavirus (2019-nCoV), which caused an epidemic of acute respiratory syndrome in humans in Wuhan, China. The epidemic, which started on 12 December 2019, had caused 2,794 laboratory-confirmed infections including 80 deaths by 26 January 2020. Full-length genome sequences were obtained from five patients at an early stage of the outbreak. The sequences are almost identical and share 79.6% sequence identity to SARS-CoV. Furthermore, we show that 2019-nCoV is 96% identical at the whole-genome level to a bat coronavirus. Pairwise protein sequence analysis of seven conserved non-structural proteins domains show that this virus belongs to the species of SARSr-CoV. In addition, 2019-nCoV virus isolated from the bronchoalveolar lavage fluid of a critically ill patient could be neutralized by sera from several patients. Notably, we confirmed that 2019-nCoV uses the same cell entry receptor—angiotensin converting enzyme II (ACE2)—as SARS-CoV.

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MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

Sudhir Kumar, Glen Stecher, Koichiro Tamura (2016)

We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.

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MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

Fredrik Ronquist, Maxim Teslenko, Paul van der Mark … (2012)

Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.

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Author and article information

Contributors

Guangzhi Tong: gztong@shvri.ac.cn

Wen Zhang:

ORCID: http://orcid.org/0000-0002-9352-6153

zhangwen@ujs.edu.cn

Journal

Journal ID (nlm-ta): Microbiome

Journal ID (iso-abbrev): Microbiome

Title: Microbiome

Publisher: BioMed Central (London )

ISSN (Electronic): 2049-2618

Publication date (Electronic): 12 April 2022

Publication date PMC-release: 12 April 2022

Publication date Collection: 2022

Volume: 10

Electronic Location Identifier: 60

Affiliations

[1 ]GRID grid.464410.3, ISNI 0000 0004 1758 7573, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, ; Shanghai, 200241 China

[2 ]GRID grid.440785.a, ISNI 0000 0001 0743 511X, School of Medicine, , Jiangsu University, ; Zhenjiang, 212003 Jiangsu China

[3 ]GRID grid.443403.4, ISNI 0000 0004 0605 1466, School of Geography and Tourism, , Harbin University, ; Harbin, 150886 Heilongjiang China

[4 ]Key Laboratory of Wildlife diseases and Biosecurity Management of Heilongjiang Province, Harbin, 150886 Heilongjiang China

[5 ]GRID grid.417303.2, ISNI 0000 0000 9927 0537, Department of Clinical Laboratory, , The Affiliated Huai’an Hospital of Xuzhou Medical University, ; Huai’an, 223002 Jiangsu China

[6 ]GRID grid.440680.e, ISNI 0000 0004 1808 3254, Animal Science College, , Tibet Agriculture and Animal Husbandry University, ; Nyingchi, 860000 Tibet China

[7 ]GRID grid.412246.7, ISNI 0000 0004 1789 9091, Wildlife and Protected Area College/Center of Conservation Medicine and Ecological Safety Northeast Forestry University, ; Harbin, 150006 Heilongjiang China

[8 ]GRID grid.418404.d, ISNI 0000 0004 0395 5996, Vitalant Research Institute, ; San Francisco, CA 94118 USA

[9 ]GRID grid.20561.30, ISNI 0000 0000 9546 5767, College of Veterinary Medicine, , South China Agricultural University, ; Guangzhou, 510642 Guangdong China

[10 ]GRID grid.266102.1, ISNI 0000 0001 2297 6811, Department of Laboratory Medicine, , University of California San Francisco, ; San Francisco, CA 94118 USA

[11 ]GRID grid.268415.c, Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, , Yangzhou University, ; Yangzhou, 225009 Jiangsu China

[12 ]GRID grid.440785.a, ISNI 0000 0001 0743 511X, International Center for Genomics Research, , Jiangsu University, ; Zhenjiang, 212013 Jiangsu China

Author information

Wen Zhang http://orcid.org/0000-0002-9352-6153

Article

Publisher ID: 1246

DOI: 10.1186/s40168-022-01246-7

PMC ID: 9001828

PubMed ID: 35413940

SO-VID: 394eeeca-a320-4119-91a0-a98aa3dabc46

License:

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

History

Date received : 4 September 2021

Date accepted : 16 February 2022

Funding

Funded by: National Key Research and Development Programs of China for Virome in Important Wildlife

Award ID: 2017YFC1200201

Award Recipient : Wen Zhang

Funded by: Jiangsu Provincial Key Research and Development Projects

Award ID: BE2017693

Award Recipient : Wen Zhang

Custom metadata

Keywords: wild bird,virome,recombinant,complete genome,phylogenetic analysis,cross-species infection

Data availability:

Keywords: wild bird, virome, recombinant, complete genome, phylogenetic analysis, cross-species infection

Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses

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Abstract

Background

Results

Conclusions

Supplementary Information

Related collections

Tick microbiome

Most cited references 86

A pneumonia outbreak associated with a new coronavirus of probable bat origin

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

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