Genomic monitoring to understand the emergence and spread of Usutu virus in the Netherlands, 2016-2018

B Bas Oude Munnink, E Münger, D F Nieuwenhuijse, R Kohl, A van der Linden, C M E Schapendonk, H van der Jeugd, M Kik, J M Rijks, C B E M Reusken, M Koopmans, B Bas Oude Munnink, E Münger, D F Nieuwenhuijse, R Kohl, A van der Linden, C M E Schapendonk, H van der Jeugd, M Kik, J M Rijks, C B E M Reusken, M Koopmans

Abstract

Usutu virus (USUV) is a mosquito-borne flavivirus circulating in Western Europe that causes die-offs of mainly common blackbirds (Turdus merula). In the Netherlands, USUV was first detected in 2016, when it was identified as the likely cause of an outbreak in birds. In this study, dead blackbirds were collected, screened for the presence of USUV and submitted to Nanopore-based sequencing. Genomic sequences of 112 USUV were obtained and phylogenetic analysis showed that most viruses identified belonged to the USUV Africa 3 lineage, and molecular clock analysis evaluated their most recent common ancestor to 10 to 4 years before first detection of USUV in the Netherlands. USUV Europe 3 lineage, commonly found in Germany, was less frequently detected. This analyses further suggest some extent of circulation of USUV between the Netherlands, Germany and Belgium, as well as likely overwintering of USUV in the Netherlands.

Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Phylogenetic analysis and geographic distribution of USUV strains detected in dead blackbirds in the Netherlands. (a) Maximum likelihood phylogeny of USUV complete coding sequences. PhyCLIP’s cluster designation is indicated in colour and asterisk indicate bootstrap scores ≥80%. (b) Geographic distribution of USUV clusters detected in dead blackbirds in the Netherlands. Dots indicate the center of municipality at which USUV positive dead birds were collected. In municipalities where more than one dead blackbird were collected, dots are dispersed and the municipality is colored according to year of most recent death. Scale bar represents units of substitutions per site.
Figure 2
Figure 2
Molecular clock phylogeny of the complete coding sequences of USUV lineages detected in dead blackbirds from the Netherlands. Annotations correspond to clusters designed by PhyCLIP. Node bars indicate 95% confidence intervals of the time of the most common ancestor.

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