sh.sePublications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • harvard-anglia-ruskin-university
  • apa-old-doi-prefix.csl
  • sodertorns-hogskola-harvard.csl
  • sodertorns-hogskola-oxford.csl
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Revisiting Recombination Signal in the Tick-Borne Encephalitis Virus: A Simulation Approach
Science and Historical Investigations of Evolution Laboratory of Dubá, Dubá, Czech Republic.ORCID iD: 0000-0001-6593-6959
Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology. Örebro University.
Sahlgrenska University.
2016 (English)In: PLOS ONE, E-ISSN 1932-6203, Vol. 11, no 10, article id e0164435Article in journal (Refereed) Published
Abstract [en]

The hypothesis of wide spread reticulate evolution in Tick-Borne Encephalitis virus (TBEV) has recently gained momentum with several publications describing past recombination events involving various TBEV clades. Despite a large body of work, no consensus has yet emerged on TBEV evolutionary dynamics. Understanding the occurrence and frequency of recombination in TBEV bears significant impact on epidemiology, evolution, and vaccination with live vaccines. In this study, we investigated the possibility of detecting recombination events in TBEV by simulating recombinations at several locations on the virus' phylogenetic tree and for different lengths of recombining fragments. We derived estimations of rates of true and false positive for the detection of past recombination events for seven recombination detection algorithms. Our analytical framework can be applied to any investigation dealing with the difficult task of distinguishing genuine recombination signal from background noise. Our results suggest that the problem of false positives associated with low detection P-values in TBEV, is more insidious than generally acknowledged. We reappraised the recombination signals present in the empirical data, and showed that reliable signals could only be obtained in a few cases when highly genetically divergent strains were involved, whereas false positives were common among genetically similar strains. We thus conclude that recombination among wild-type TBEV strains may occur, which has potential implications for vaccination with live vaccines, but that these events are surprisingly rare.

Place, publisher, year, edition, pages
2016. Vol. 11, no 10, article id e0164435
National Category
Biological Sciences
Research subject
Baltic and East European studies
Identifiers
URN: urn:nbn:se:sh:diva-31079DOI: 10.1371/journal.pone.0164435ISI: 000386204000036PubMedID: 27760182Scopus ID: 2-s2.0-84992395862OAI: oai:DiVA.org:sh-31079DiVA, id: diva2:1044535
Part of project
Molecular epidemiology, molecular evolution and vaccine development of Tick-borne encephalitis virus within the Baltic Sea region., The Foundation for Baltic and East European Studies
Funder
The Foundation for Baltic and East European Studies, A046-2010Knowledge Foundation, 20150201Available from: 2016-11-03 Created: 2016-11-03 Last updated: 2022-07-04Bibliographically approved

Open Access in DiVA

No full text in DiVA

Other links

Publisher's full textPubMedScopusPMC Full text

Authority records

Bertrand, Yann J.Johansson, Magnus

Search in DiVA

By author/editor
Bertrand, Yann J.Johansson, Magnus
By organisation
Biology
In the same journal
PLOS ONE
Biological Sciences

Search outside of DiVA

GoogleGoogle Scholar

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 316 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • harvard-anglia-ruskin-university
  • apa-old-doi-prefix.csl
  • sodertorns-hogskola-harvard.csl
  • sodertorns-hogskola-oxford.csl
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf