Clark, J. J., Gilray, J., Orton, R. J. , Baird, M., Wilkie, G., da Silva Filipe, A. , Johnson, N., McInnes, C. J., Kohl, A. and Biek, R. (2020) Population genomics of louping ill virus provide new insights into the evolution of tick-borne flaviviruses. PLoS Neglected Tropical Diseases, 14(9), e0008133. (doi: 10.1371/journal.pntd.0008133) (PMID:32925939) (PMCID:PMC7515184)
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Abstract
The emergence and spread of tick-borne arboviruses pose an increased challenge to human and animal health. In Europe this is demonstrated by the increasingly wide distribution of tick-borne encephalitis virus (TBEV, Flavivirus, Flaviviridae), which has recently been found in the United Kingdom (UK). However, much less is known about other tick-borne flaviviruses (TBFV), such as the closely related louping ill virus (LIV), an animal pathogen which is endemic to the UK and Ireland, but which has been detected in other parts of Europe including Scandinavia and Russia. The emergence and potential spatial overlap of these viruses necessitates improved understanding of LIV genomic diversity, geographic spread and evolutionary history. We sequenced a virus archive composed of 22 LIV isolates which had been sampled throughout the UK over a period of over 80 years. Combining this dataset with published virus sequences, we detected no sign of recombination and found low diversity and limited evidence for positive selection in the LIV genome. Phylogenetic analysis provided evidence of geographic clustering as well as long-distance movement, including movement events that appear recent. However, despite genomic data and an 80-year time span, we found that the data contained insufficient temporal signal to reliably estimate a molecular clock rate for LIV. Additional analyses revealed that this also applied to TBEV, albeit to a lesser extent, pointing to a general problem with phylogenetic dating for TBFV. The 22 LIV genomes generated during this study provide a more reliable LIV phylogeny, improving our knowledge of the evolution of tick-borne flaviviruses. Our inability to estimate a molecular clock rate for both LIV and TBEV suggests that temporal calibration of tick-borne flavivirus evolution should be interpreted with caution and highlight a unique aspect of these viruses which may be explained by their reliance on tick vectors.
| Item Type: | Articles |
|---|---|
| Additional Information: | This work was also supported by the UK Medical Research Council with grant MC_UU_12014/12). |
| Status: | Published |
| Refereed: | Yes |
| Glasgow Author(s) Enlighten ID: | Orton, Dr Richard and Wilkie, Dr Gavin and Da Silva Filipe, Dr Ana and Biek, Professor Roman and Baird, Mrs Margaret and CLARK, Jordan and Kohl, Professor Alain |
| Creator Roles: | Clark, J. J.Data curation, Formal analysis, Investigation, Methodology, Validation, Writing – original draft, Writing – review and editing Orton, R. J.Resources, Writing – review and editing Baird, M.Resources Wilkie, G.Resources da Silva Filipe, A.Resources, Writing – review and editing Kohl, A.Conceptualization, Funding acquisition, Supervision, Writing – review and editing Biek, R.Conceptualization, Formal analysis, Funding acquisition, Methodology, Supervision, Validation, Writing – original draft, Writing – review and editing |
| Authors: | Clark, J. J., Gilray, J., Orton, R. J., Baird, M., Wilkie, G., da Silva Filipe, A., Johnson, N., McInnes, C. J., Kohl, A., and Biek, R. |
| College/School: | College of Medical Veterinary and Life Sciences > School of Infection & Immunity College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine |
| Journal Name: | PLoS Neglected Tropical Diseases |
| Publisher: | Public Library of Science |
| ISSN: | 1935-2727 |
| ISSN (Online): | 1935-2735 |
| Copyright Holders: | Copyright © 2020 Clark et al. |
| First Published: | First published in PLoS Neglected Tropical Diseases 14(9): e0008133 |
| Publisher Policy: | Reproduced in accordance with the publisher copyright policy |
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