Skip to main content
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Microbiology Resource Announcements
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems
  • Log in
  • My alerts
  • My Cart

Main menu

  • Home
  • Articles
    • Latest Articles
    • Archive
  • Types of Resources
    • Amplicon Sequence Collections
    • Culture Collections/Mutant Libraries
    • Databases and Software
    • Omics Data Sets
    • Other Genetic Resources
    • Genome Sequences
  • For Authors
    • Getting Started
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About MRA
    • Editor in Chief
    • Board of Editors
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Microbiology Resource Announcements
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems

User menu

  • Log in
  • My alerts
  • My Cart

Search

  • Advanced search
Microbiology Resource Announcements
publisher-logosite-logo

Advanced Search

  • Home
  • Articles
    • Latest Articles
    • Archive
  • Types of Resources
    • Amplicon Sequence Collections
    • Culture Collections/Mutant Libraries
    • Databases and Software
    • Omics Data Sets
    • Other Genetic Resources
    • Genome Sequences
  • For Authors
    • Getting Started
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About MRA
    • Editor in Chief
    • Board of Editors
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
Genome Sequences

Genome Sequences of Seven Megrivirus Strains from Chickens in The Netherlands

Kirsty T. T. Kwok, Myrna M. T. de Rooij, Aniek B. Messink, Inge M. Wouters, Marion P. G. Koopmans, My V. T. Phan
Simon Roux, Editor
Kirsty T. T. Kwok
aDepartment of Viroscience, Erasmus MC, Rotterdam, The Netherlands
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Kirsty T. T. Kwok
Myrna M. T. de Rooij
bInstitute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Aniek B. Messink
bInstitute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Inge M. Wouters
bInstitute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Inge M. Wouters
Marion P. G. Koopmans
aDepartment of Viroscience, Erasmus MC, Rotterdam, The Netherlands
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Marion P. G. Koopmans
My V. T. Phan
aDepartment of Viroscience, Erasmus MC, Rotterdam, The Netherlands
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for My V. T. Phan
Simon Roux
DOE Joint Genome Institute
Roles: Editor
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/MRA.01207-20
  • Article
  • Figures & Data
  • Info & Metrics
  • PDF
Loading

ABSTRACT

We report seven chicken megrivirus genome sequences identified in chicken fecal samples from a broiler farm in The Netherlands. The sequences were determined using metagenomic sequencing and would expand our understanding of the genome diversity of megriviruses.

ANNOUNCEMENT

Viruses in the Picornaviridae family possess a positive-sense single-stranded RNA genome and cause a broad range of diseases in humans and animals (1). Among the 63 genera in this family, at least 15 genera, including Megrivirus, have been identified from avian sources (2). Megriviruses have been detected in both healthy and diseased poultry (3, 4) and are suspected to cause transmissible viral proventriculitis in chickens (5) and hepatitis in turkeys (6). Here, we report 7 nearly complete megrivirus genome sequences identified from 7 out of 8 pooled chicken fecal samples that we sequenced as part of a virome profiling study of farm animals. The samples consisted of pooled fresh fecal droppings from 3 to 4 chicks (Gallus gallus domesticus), collected in the same flock during weeks 4 and 5 of the production cycle from a broiler farm in June 2019 in The Netherlands (Table 1). No clinical signs in the examined flock were reported at the time of sampling.

View this table:
  • View inline
  • View popup
  • Download powerpoint
TABLE 1

Sequence data for 7 megrivirus strains

The genome sequences of the virus were generated using metagenomic sequencing. The fecal suspension (30% [wt/vol] in phosphate-buffered saline) was centrifuged for 10 min at 10,000 × g. The supernatant was collected and treated with TURBO DNase (Invitrogen). Virion-protected nucleic acid was extracted using the QIAamp viral RNA minikit (Qiagen). Reverse transcription was performed using nonribosomal random hexamers (7) and SuperScript III reverse transcriptase (Invitrogen), followed by second-strand cDNA synthesis using Klenow fragment 3′–5′ exo- (New England BioLabs). The resulting DNA was subjected to library preparation using a Nextera XT DNA library preparation kit (Illumina) following the manufacturer’s instructions. The library was then purified and size selected using AMPure XP magnetic beads (Beckman Coulter). The final library was sequenced in paired-end format on the Illumina MiSeq platform using reagent kit v3 (600 cycles; Illumina). The total number of reads generated per sample ranged between 2,020,090 and 4,765,832. The raw reads were analyzed using the automated pipeline Genome Detective Virus Tool v1.126 (8), which utilizes Trimmomatic (9) for adapter and quality trimming, DIAMOND (10) for viral read identification, and metaSPAdes (11) for de novo assembly of the sorted viral reads. De novo-assembled genome sequences were inspected and annotated using Geneious v2020.2.3 (12). The lengths of the 7 nearly complete megrivirus genomes range from 8,993 to 9,592 nucleotides (nt). The depths of coverage range from 34× to 576×. According to BLAST searches, these strains shared 83% to 84% identity at the nucleotide level with chicken picornavirus 5 isolate 27C from Hong Kong (2008; GenBank accession number KF979336), chicken megrivirus strain MG9567 from Brazil (2012; MH806866), and Picornaviridae sp. isolates w3chi090pic1 and w3chi091pic1 from China (2018; MT138368 and MT138369, respectively). These reported genome sequences shared 92% to 93% identity at the amino acid (aa) level when comparing viral polyprotein amino acid sequences. The pairwise nucleotide difference of the complete coding region among the 7 strains ranges from 2 to 18 nt; the pairwise amino acid difference ranges from 0 to 4 aa.

To conclude, we report 7 megrivirus genome sequences identified in The Netherlands. The prevalence of these viruses might have been overlooked in the poultry population thus far. Future studies should investigate the prevalence and diversity of megriviruses and their potential clinical implications.

Data availability.The genome sequences described in this study have been deposited in GenBank under the accession numbers MW054505 to MW054511. The raw reads are available in the SRA under the BioProject accession number PRJNA670873.

ACKNOWLEDGMENTS

We thank the Human Genomics Facility of the Genetic Laboratory of the Department of Internal Medicine at Erasmus Medical Center for providing sequencing services and Pelle van der Wal and Gaby van Dijk for providing sequencing support. We thank the participating poultry farmers for their cooperation.

This study was supported by ZonMW TOP project 91217040 (K.T.T.K., M.M.T.D.R., and M.P.G.K.) and a Marie Sklodowska-Curie Individual Fellowship, funded by the European Union’s Horizon 2020 research and innovation program (grant agreement number 799417; M.V.T.P.). Sample collection was funded with intramural funds from the University of Utrecht (M.M.T.D.R., A.B.M., and I.M.W.).

FOOTNOTES

    • Received 27 October 2020.
    • Accepted 2 November 2020.
    • Published 19 November 2020.
  • Copyright © 2020 Kwok et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

REFERENCES

  1. 1.↵
    1. Cathcart AL,
    2. Baggs EL,
    3. Semler BL
    . 2015. Picornaviruses: pathogenesis and molecular biology. In Reference module in biomedical sciences. Elsevier, Irvine, CA.
  2. 2.↵
    1. Lefkowitz EJ,
    2. Dempsey DM,
    3. Hendrickson RC,
    4. Orton RJ,
    5. Siddell SG,
    6. Smith DB
    . 2018. Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV). Nucleic Acids Res 46:D708–D717. doi:10.1093/nar/gkx932.
    OpenUrlCrossRef
  3. 3.↵
    1. Boros Á,
    2. Pankovics P,
    3. Adonyi Á,
    4. Fenyvesi H,
    5. Day JM,
    6. Phan TG,
    7. Delwart E,
    8. Reuter G
    . 2016. A diarrheic chicken simultaneously co-infected with multiple picornaviruses: complete genome analysis of avian picornaviruses representing up to six genera. Virology 489:63–74. doi:10.1016/j.virol.2015.12.002.
    OpenUrlCrossRef
  4. 4.↵
    1. Kwok KTT,
    2. Nieuwenhuijse DF,
    3. Phan MVT,
    4. Koopmans MPG
    . 2020. Virus metagenomics in farm animals: a systematic review. Viruses 12:107. doi:10.3390/v12010107.
    OpenUrlCrossRef
  5. 5.↵
    1. Kim H-R,
    2. Yoon S-J,
    3. Lee H-S,
    4. Kwon Y-K
    . 2015. Identification of a picornavirus from chickens with transmissible viral proventriculitis using metagenomic analysis. Arch Virol 160:701–709. doi:10.1007/s00705-014-2325-7.
    OpenUrlCrossRef
  6. 6.↵
    1. Honkavuori KS,
    2. Shivaprasad HL,
    3. Briese T,
    4. Street C,
    5. Hirschberg DL,
    6. Hutchison SK,
    7. Lipkin WI
    . 2011. Novel picornavirus in turkey poults with hepatitis, California, USA. Emerg Infect Dis 17:480–487. doi:10.3201/eid1703.101410.
    OpenUrlCrossRefPubMed
  7. 7.↵
    1. Endoh D,
    2. Mizutani T,
    3. Kirisawa R,
    4. Maki Y,
    5. Saito H,
    6. Kon Y,
    7. Morikawa S,
    8. Hayashi M
    . 2005. Species-independent detection of RNA virus by representational difference analysis using non-ribosomal hexanucleotides for reverse transcription. Nucleic Acids Res 33:e65. doi:10.1093/nar/gni064.
    OpenUrlCrossRefPubMed
  8. 8.↵
    1. Vilsker M,
    2. Moosa Y,
    3. Nooij S,
    4. Fonseca V,
    5. Ghysens Y,
    6. Dumon K,
    7. Pauwels R,
    8. Alcantara LC,
    9. Vanden Eynden E,
    10. Vandamme A-M,
    11. Deforche K,
    12. de Oliveira T
    . 2019. Genome Detective: an automated system for virus identification from high-throughput sequencing data. Bioinformatics 35:871–873. doi:10.1093/bioinformatics/bty695.
    OpenUrlCrossRef
  9. 9.↵
    1. Bolger AM,
    2. Lohse M,
    3. Usadel B
    . 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. doi:10.1093/bioinformatics/btu170.
    OpenUrlCrossRefPubMedWeb of Science
  10. 10.↵
    1. Buchfink B,
    2. Xie C,
    3. Huson DH
    . 2015. Fast and sensitive protein alignment using DIAMOND. Nat Methods 12:59–60. doi:10.1038/nmeth.3176.
    OpenUrlCrossRefPubMed
  11. 11.↵
    1. Nurk S,
    2. Meleshko D,
    3. Korobeynikov A,
    4. Pevzner PA
    . 2017. MetaSPAdes: a new versatile metagenomic assembler. Genome Res 27:824–834. doi:10.1101/gr.213959.116.
    OpenUrlAbstract/FREE Full Text
  12. 12.↵
    1. Kearse M,
    2. Moir R,
    3. Wilson A,
    4. Stones-Havas S,
    5. Cheung M,
    6. Sturrock S,
    7. Buxton S,
    8. Cooper A,
    9. Markowitz S,
    10. Duran C,
    11. Thierer T,
    12. Ashton B,
    13. Meintjes P,
    14. Drummond A
    . 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649. doi:10.1093/bioinformatics/bts199.
    OpenUrlCrossRefPubMedWeb of Science
View Abstract
PreviousNext
Back to top
Download PDF
Citation Tools
Genome Sequences of Seven Megrivirus Strains from Chickens in The Netherlands
Kirsty T. T. Kwok, Myrna M. T. de Rooij, Aniek B. Messink, Inge M. Wouters, Marion P. G. Koopmans, My V. T. Phan
Microbiology Resource Announcements Nov 2020, 9 (47) e01207-20; DOI: 10.1128/MRA.01207-20

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Print
Alerts
Sign In to Email Alerts with your Email Address
Email

Thank you for sharing this Microbiology Resource Announcements article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
Genome Sequences of Seven Megrivirus Strains from Chickens in The Netherlands
(Your Name) has forwarded a page to you from Microbiology Resource Announcements
(Your Name) thought you would be interested in this article in Microbiology Resource Announcements.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Genome Sequences of Seven Megrivirus Strains from Chickens in The Netherlands
Kirsty T. T. Kwok, Myrna M. T. de Rooij, Aniek B. Messink, Inge M. Wouters, Marion P. G. Koopmans, My V. T. Phan
Microbiology Resource Announcements Nov 2020, 9 (47) e01207-20; DOI: 10.1128/MRA.01207-20
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • ANNOUNCEMENT
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
  • Figures & Data
  • Info & Metrics
  • PDF

Related Articles

Cited By...

About

  • About MRA
  • Editor in Chief
  • Board of Editors
  • Policies
  • For Reviewers
  • For the Media
  • For Librarians
  • For Advertisers
  • Alerts
  • RSS
  • FAQ
  • Permissions
  • Journal Announcements

Authors

  • Getting Started
  • Submit a Manuscript
  • Author Warranty
  • Ethics
  • Contact Us
  • ASM Author Center

Follow #MRAJournal

@ASMicrobiology

       

ASM Journals

ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.

About ASM | Contact Us | Press Room

 

ASM is a member of

Scientific Society Publisher Alliance

 

American Society for Microbiology
1752 N St. NW
Washington, DC 20036
Phone: (202) 737-3600

Copyright © 2021 American Society for Microbiology | Privacy Policy | Website feedback

Online ISSN: 2576-098X