Biology subjects

Sikkema, R.

Publications and source records attributed to Sikkema, R..

5 recordsLinked to original sources

bioRxiv2026

Quantifying circulation and antibody cross-reactivity for co-circulating flaviviruses: the case of Usutu and West Nile virus in blackbirds

Serological testing is important for assessing past exposure and immunity, but interpretation can be complicated by antibody cross-reactivity between closely related viruses. We assess this challenge for Usutu virus (USUV) and West Nile virus (WNV), flaviviruses that recently emerged in Europe. We analysed samples from wild blackbirds collected in the Netherlands between 2016-2022. Samples (N=1742) were screened using an NS1-based protein micro-array, with positives confirmed by Focus Reduction Neutralization Tests (FRNT). We jointly estimated seroprevalence and antibody responses by fitting a Bayesian latent-variable model to FRNT values. Estimates of homologous and cross-reactive antibody responses were used to improve interpretation of observed titres for serosurveillance. Estimated seroprevalence varied across time and regions between 4.9% (95%CrI 3.5-6.7) to 18.5% (95%CrI 14.9-22.7) for USUV and between 2.4% (95%CrI 1.3-3.8) to 6.4% (95%CrI 3.9-9.6) for WNV. These were 1.5 (USUV) to 2.4 times (WNV) higher than estimates based on the current threshold-based algorithm. USUV induced a higher antibody response and was more likely to induce a cross-reactive response than WNV. Our classification algorithm informed by these estimates showed high sensitivity (WNV: 0.88, USUV: 0.97) and specificity (both: >0.99). Our results illustrate how quantitative frameworks can improve serological interpretation in settings with co-circulating pathogens.

ecology↗

bioRxiv2024

Silent reservoirs are shaping disease emergence: the case of Usutu virus in the Netherlands

Disentangling contributions of different hosts to disease transmission is highly complex, but critical for improving predictions, surveillance, and response. This is particularly challenging in wildlife, with pathogens often infecting multiple species and data collection being difficult. Using the emergence of Usutu virus (USUV) in the Netherlands as a case study, we demonstrate the use of an Approximate Bayesian Computation framework on diverse data sources to uncover drivers of spatio-temporal wildlife disease emergence. We calibrated single- and multi-host mechanistic transmission models to five types of wildlife surveillance and research data, describing molecular and serological evidence of USUV in birds. Although Eurasian blackbirds, the primary target species for surveillance, were most severely affected, our models indicated that USUV could not persist in blackbirds alone. Our framework provided statistical support for additional, unobserved bird species to have contributed to transmission. This population of bird species is characterised by limited infection mortality, a longer lifespan, and likely further dispersal than blackbirds. Immunity in this population appears to have protected blackbirds from further USUV-related population decline. Our results underscore the importance of considering multiple host populations to understand outbreak dynamics. Neglecting the multi-host context of transmission can impact the reliability of predictions and projected impact of interventions.

ecology↗

bioRxiv2022

West Nile Virus spread in Europe - phylogeographic pattern analysis and key drivers

Spread and emergence of West Nile virus (WNV) in Europe have been very different from those observed in North America. Here, we describe key drivers by combining viral genome sequences with epidemiological data and possible factors of spread into phylodynamic models. WNV in Europe has greater lineage diversity than other regions of the world, suggesting repeated introductions and local amplification. Among the six lineages found in Europe, WNV-2a is predominant, has spread to at least 14 countries and evolved into two major co-circulating clusters (A and B). Both of these seem to originate from regions of Central Europe. Viruses of Cluster A emerged earlier and have spread towards the west of Europe with higher genetic diversity. Amongst multiple drivers, high agriculture activities were associated with both spread direction and velocity. Our study suggests future surveillance activities should be strengthened in Central Europe and Southeast European countries, and enhanced monitoring should be targeted to areas with high agriculture activities.

evolutionary biology↗

bioRxiv2020

SARS-CoV2 infection in farmed mink, Netherlands, April 2020

In April 2020, respiratory disease and increased mortality were observed in farmed mink on two farms in the Netherlands. In both farms, at least one worker had been found positive for SARS-CoV-2. Necropsies of the mink revealed interstitial pneumonia, and organ and swab samples tested positive for SARS-CoV-2 RNA by qPCR. Variations in viral genomes point at between-mink transmission on the farms and lack of infection link between the farms. Inhalable dust in the mink houses contained viral RNA, indicating possible exposure of workers.

microbiology↗

bioRxiv2020

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

SARS-CoV-2 is a novel coronavirus that has rapidly spread across the globe. In the Netherlands, the first case of SARS-CoV-2 has been notified on the 27th of February. Here, we describe the first three weeks of the SARS-CoV-2 outbreak in the Netherlands, which started with several different introductory events from Italy, Austria, Germany and France followed by local amplification in, and later also, outside the South of the Netherlands. The timely generation of whole genome sequences combined with epidemiological investigations facilitated early decision making in an attempt to control local transmission of SARS-CoV-2 in the Netherlands.

genomics↗