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

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.Usutu virus (USUV) is a mosquito-borne arbovirus of the genus Flavivirus. The virus has a positive-stranded RNA genome with a genome length of around 11,000 nucleotides which encodes a single polyprotein. The polyprotein is processed by viral and host proteases into structural and non-structural proteins 1 . The life cycle of USUV involves mosquitoes (mainly Culex sp. 2,3 ) as vectors and wild birds as the main amplifying hosts. Humans and other mammals can be infected by mosquito bites and are generally considered dead-end hosts. Recent studies revealed that USUV can also be detected in small mammals such as bats 4 , rodents and shrews 5 .USUV was first identified from a Culex neavei mosquito in South Africa in 1959 6 . Over subsequent decades, it was sporadically reported in several mosquito and bird species, and twice in a human patient with fever and rash in African countries 7 . USUV was for first identified in Europe in 2001, when it was determined to be the causative agent of a mass mortality event in several bird species in Austria 8 . This prompted retrospective analysis of archived tissue samples from dead wild birds in Italy in 1996, which revealed an earlier presence of the virus in Europe 9 . Our understanding of the USUV geographical range has since expanded to include the majority of European countries 10 , where outbreaks are marked by mass die-offs of wild birds, with the heaviest toll on common blackbird (Turdus merula) populations. In Germany, it has been demonstrated that five years after the first detection of USUV in the southwest of the country, circulation of the virus was associated with a 15.7% decline in the common blackbird population in USUV-suitable areas 11 .The recent emergence of USUV epizootics among wild bird populations in Europe has been accompanied by reports of USUV infections in humans. Pathogenicity in humans appears to range from asymptomatic or mild symptoms, as shown in seroprevalence studies among healthy blood donors in Italy 12 , Germany 13 , Austria 14 and the Netherlands 15 to neuroinvasive infections associated with encephalitis or meningo-encephalitis, m...

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“…Extensive surveillance of mosquitoes, dead and live birds was set up in 2016 to monitor the introduction and spread of a selection of high-risk arboviruses in the Netherlands. The presence of Usutu virus (USUV) infections was confirmed first in 2016, and genomic sequencing provided evidence for continued enzootic presence of USUV in subsequent years [1,2]. West Nile virus (WNV), however, had so far not been detected.…”

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“…Whole genome sequencing (WGS) can be used to monitor the emergence and spread of pathogens (34)(35)(36)(37). As part of the surveillance effort in the Netherlands over 1,750 SARS-CoV-2 viruses have been sequenced to date from patients from different parts of the Netherlands (38).…”

Rapid SARS-CoV-2 whole genome sequencing for informed public health decision making in the Netherlands

“…Whole genome sequencing (WGS) is a powerful tool to understand transmission dynamics of (viral) outbreaks. Recently, several outbreaks of zoonotic viral pathogens have been reconstructed using genomic information [4][5][6][7] . Equally, WGS can be used to inform outbreak control decisions.…”

“…Therefore, whole genome sequencing for outbreak support is an active area of research. Nanopore sequencing has been employed in recent outbreaks of Usutu, Ebola, Zika and Yellow fever virus owing to the ease of use and relatively low start-up cost [4][5][6][7] . The robustness of this method has recently been validated using Usutu virus 13,14 .…”