Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing

Robert Dyrdak, Monika Mastafa, Emma B. Hodcroft, View ORCID ProfileRichard A. Neher, View ORCID ProfileJan Albert
doi: https://doi.org/10.1101/420836
Robert Dyrdak
1Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
2Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Monika Mastafa
1Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
2Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Emma B. Hodcroft
3Biozentrum, University of Basel, Basel, Switzerland
4Swiss Institute of Bioinformatics, Basel, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Richard A. Neher
3Biozentrum, University of Basel, Basel, Switzerland
4Swiss Institute of Bioinformatics, Basel, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Richard A. Neher
Jan Albert
1Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
2Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jan Albert
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

Worldwide outbreaks of enterovirus D68 (EV-D68) in 2014 and 2016 have caused serious respiratory and neurological disease. To investigate diversity, spread, and evolution of EV-D68 we performed near full-length deep sequencing in 54 samples obtained in Sweden during the 2014 and 2016 outbreaks. In most samples, intrapatient variability was low and dominated by rare synonymous variants, but three patients showed evidence of dual infections with distinct EV-D68 variants from the same subclade. Interpatient evolution showed a very strong temporal signal, with an evolutionary rate of 0.0039 ± 0.0001 substitutions per site and year. Phylogenetic trees reconstructed from the sequences suggest that EV-D68 was introduced into Stockholm several times during the 2016 outbreak. Putative neutralization targets in the BC and DE loops of the VP1 protein were slightly more diverse within-host and tended to undergo more frequent substitution than other genomic regions. However, evolution in these loops did not appear to have been driven the emergence of the 2016 B3-subclade directly from the 2014 B1-subclade. Instead, the most recent ancestor of both clades was dated to 2009. The study provides a comprehensive description of the intra- and interpatient evolution of EV-D68, including the first report of intrapatient diversity and dual infections. The new data along with publicly available EV-D68 sequences are included in an interactive phylodynamic analysis on nextstrain.org/enterovirus/d68 to facilitate timely EV-D68 tracking in the future.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Back to top
PreviousNext
Posted March 04, 2019.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing
Robert Dyrdak, Monika Mastafa, Emma B. Hodcroft, Richard A. Neher, Jan Albert
bioRxiv 420836; doi: https://doi.org/10.1101/420836
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing
Robert Dyrdak, Monika Mastafa, Emma B. Hodcroft, Richard A. Neher, Jan Albert
bioRxiv 420836; doi: https://doi.org/10.1101/420836

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Microbiology
Subject Areas
All Articles
  • Animal Behavior and Cognition (4383)
  • Biochemistry (9599)
  • Bioengineering (7095)
  • Bioinformatics (24866)
  • Biophysics (12619)
  • Cancer Biology (9958)
  • Cell Biology (14357)
  • Clinical Trials (138)
  • Developmental Biology (7953)
  • Ecology (12108)
  • Epidemiology (2067)
  • Evolutionary Biology (15989)
  • Genetics (10927)
  • Genomics (14743)
  • Immunology (9870)
  • Microbiology (23678)
  • Molecular Biology (9486)
  • Neuroscience (50875)
  • Paleontology (369)
  • Pathology (1539)
  • Pharmacology and Toxicology (2683)
  • Physiology (4017)
  • Plant Biology (8657)
  • Scientific Communication and Education (1510)
  • Synthetic Biology (2397)
  • Systems Biology (6436)
  • Zoology (1346)