Population genomics of louping ill virus provide new insights into the evolution of tick-borne flaviviruses.

Jordan J Clark,Nicholas Johnson,Gavin Wilkie,Roman Biek,Alain Kohl,Richard J Orton,Margaret Baird,Ana Da Silva Filipe,Janice Gilray,Colin J Mcinnes,Michael R Holbrook

doi:10.1371/journal.pntd.0008133

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.

Highlights

The tick-borne encephalitis sub-complex of the genus Flavivirus is composed of several closely related arboviruses, all of which possess a single-stranded, positive sense, RNA genome of ~12kb [1]
louping ill virus (LIV) is a neglected virus endemic to the United Kingdom (UK) and Ireland which is closely related to the major human pathogen tick-borne encephalitis virus (TBEV), but predominantly causes disease in sheep and grouse
We were unable to estimate a reliable molecular clock rate for LIV and found that this problem extends to a larger phylogeny of TBEV sequences

Summary

Introduction

The tick-borne encephalitis sub-complex of the genus Flavivirus (family Flaviviridae) is composed of several closely related arboviruses, all of which possess a single-stranded, positive sense, RNA genome of ~12kb [1]. Members of this subcomplex are found across the northern hemisphere [2,3] and include several zoonotic viruses, such as tick-borne encephalitis virus (TBEV), of which there are three predominant subtypes: European (TBEV-Eu), Siberian (TBEV-Sib) and Far-Eastern (TBEV-FE). Louping ill virus (LIV), which is closely related to TBEV, is predominantly associated with disease in ruminants and birds, whereas human cases are rare [6,7]. Only four complete LIV genomes are available, which has prevented a meaningful analysis of LIV genomic diversity and evolution and their comparison with other flaviviruses

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Discussion

Conclusion