Genomic epidemiology of West Nile virus in Europe

First Detection of West Nile Virus Lineage 2 in Culex pipiens Vectors in Croatia

The West Nile virus (WNV) has recently become more widespread, posing a threat to both human and animal health. In Western Europe, most outbreaks have been caused by WNV lineage 1, while in Eastern Europe, WNV lineage 2 has led to human and bird mortality. The ability to appropriately manage this threat is dependent on integrated surveillance and early detection. This study aimed to quantify the prevalence of WNV infection in mosquitoes and to identify the circulating viral lineage in eastern Croatia. Mosquito traps were set up in rural and urban areas during the 2021-2023 seasons, and the collected specimens were identified morphologically. Mosquito species Culex pipiens and Aedes albopictus were tested for Flaviviruses using conventional PCR in a heminested system. The positive samples were then subjected to a specific real-time PCR designed to detect WNV. A total of 385 mosquito pools were tested, and positive pools were found in samples from Osijek-Baranja and Vukovar-Srijem, both of which contained Cx. pipiens mosquitoes. Sequencing of amplicons revealed WNV lineage 2 partial NS5 gene sequences. Phylogenetic analysis suggests the Hungarian origin of strain, which complements birds' migratory routes. These findings indicate the first detection of WNV in mosquitoes in Croatia. This suggests that human cases in this region are likely due to infections with lineage 2 transmitted by local Culex mosquitoes.

An Inactivated West Nile Virus Vaccine Candidate Based on the Lineage 2 Strain

Background: West Nile virus (WNV) is a rapidly growing problem worldwide. The lack of emergency treatment and a safe licensed vaccine against WNV allows the virus to cause sporadic outbreaks of human disease, including fatal cases. Formalin-inactivated vaccines have been used for a long time and have been shown to be very safe and effective, especially in susceptible populations. Methods: By adapting tick-borne encephalitis vaccine production technology, we produced a laboratory-inactivated vaccine against WNV based on the strain SHUA, isolated from humans with a lethal WNV infection in the year 2021. Results: The potential vaccine was tested for safety in vitro and in vivo in outbred SHK mice of different ages, including PCR analysis of the brains of these mice to test for the absence of viral RNA after intracerebral injection. Conclusions: The inactivated whole-virion laboratory vaccine showed 100% seroconversion and immunogenicity against WNV strain SHUA-1, isolated from a lethal human case, and provided the mice with 100% protection from disease and death.

The European Union One Health 2023 Zoonoses report

This report by the European Food Safety Authority and the European Centre for Disease Prevention and Control presents the results of zoonoses monitoring and surveillance activities carried out in 2023 in 27 Member States (MSs), the United Kingdom (Northern Ireland) and 10 non-MSs. Key statistics on zoonoses and zoonotic agents in humans, food, animals and feed are provided and interpreted historically. In 2023, the first and second most reported zoonoses in humans were campylobacteriosis and salmonellosis, respectively. For both agents, an increase in the absolute number of cases was observed in comparison with 2022. Fifteen MSs and the United Kingdom (Northern Ireland) reached all the established targets in poultry populations with regard to the reduction in Salmonella prevalence for the relevant serovars. Salmonella samples from carcases of various animal species, and samples for Campylobacter quantification from broiler carcases, were more frequently positive when performed by the competent authorities than when own-checks were conducted. Shiga toxin-producing Escherichia coli (STEC) was the third most reported zoonotic agent in humans, followed by Yersinia enterocolitica and Listeria monocytogenes. L. monocytogenes and West Nile virus infections were the most severe zoonotic diseases, with the highest percentage of hospitalisations among cases and the highest case fatality rates. Twenty-seven MSs and the United Kingdom (Northern Ireland) reported a slight decrease in food-borne outbreaks in 2023 overall in comparison with 2022, although the overall number of reported human cases and hospitalisations increased. Salmonella Enteritidis remained the most frequently reported causative agent for reported cases and food-borne outbreaks. Salmonella in 'eggs and egg products' was the agent/food pair of most concern. In 2023 this combination caused the largest number of outbreaks and cases among all agent/food combination and ranked second in number of hospitalisations. Salmonella was also the causative agent associated with the majority of multi-country outbreaks reported in the EU in 2023. This report also provides updates on brucellosis, echinococcosis, Q fever, rabies, toxoplasmosis, trichinellosis, tuberculosis due to Mycobacterium bovis or M. caprae, and tularaemia.

Molecular Xenomonitoring (MX) allows real-time surveillance of West Nile and Usutu virus in mosquito populations

West Nile Virus (WNV) and Usutu virus (USUV) circulate through complex cryptic transmission cycles involving mosquitoes as vectors, birds as amplifying hosts and several mammal species as dead-end hosts. Both viruses can be transmitted to humans through mosquito bites, which can lead to neuroinvasive and potentially fatal disease. Notably, WNV can also be transmitted through blood donations and organ transplants. The high proportion of asymptomatic infections caused by these viruses and their cryptic enzootic circulation make their early detection in the environment challenging. Viral surveillance in France still heavily relies on human and animal surveillance, i.e. late indicators of viral circulation. Entomological surveillance is a method of choice for identifying virus circulation ahead of the first human and animal cases and to reveal their genetic identity, but performing molecular screening of vectors is expensive, and time-consuming. Here we show substantial WNV and USUV co-circulation in Atlantic seaboard of France between July and August 2023 using a non-invasive MX (Molecular Xenomonitoring) method that use trapped mosquito excreta. MX offers significant advantages over traditional entomological surveillance: it is cost-effective and efficient, enabling viral RNA screening from a community of trapped mosquitoes via their excreta, which can be transported at room temperature. Additionally, MX extends the longevity of trapped mosquitoes, enhancing virus detection and simplifying logistics, and is easy to implement without requiring specialized skills. At the crossroads between entomological and environmental surveillance, MX can detect the circulation of zoonotic pathogens in the environment before cases are observed in humans and horses, enabling the timely alerts to health policy makers, allowing them to take suitable control measures.

Modelling the temperature dependent extrinsic incubation period of West Nile Virus using Bayesian time delay models

West Nile Virus (WNV) is a mosquito-borne pathogen that primarily infects birds. Infections can spillover to humans and cause a spectrum of clinical symptoms, including WNV neuroinvasive disease. The extrinsic incubation period (EIP) is the time taken for a mosquito to become infectious following the ingestion of an infected blood meal. Characterising how the EIP varies with temperature is an essential part of predicting the impact and transmission dynamics of WNV. We re-analyse existing experimental data using Bayesian time delay models, allowing us to account for variation in how quickly individual mosquitoes developed disseminated WNV infections. In these experiments, cohorts of Culex pipiens mosquitoes were infected with WNV and kept under different temperature conditions, being checked for disseminated infection at defined timepoints. We find that EIPs are best described with a Weibull distribution and become shorter log-linearly with temperature. Under 18°C, less than 1% of infected Cx. pipiens had a disseminated infection after 5 days, compared to 9.73% (95% CrI: 7.97 to 11.54) at 25°C and 42.20% (95% CrI: 38.32 to 46.60) at 30°C. In the hottest experimental temperature treatment (32°C), the EIP50 was estimated at 3.78 days (CrI: 3.42 to 4.15) compared to over 100 days in the coolest treatment (15°C). The variance of EIPs was found to be much larger at lower temperatures than higher temperatures, highlighting the importance of characterising the time delay distribution associated with the EIP. We additionally demonstrate a competitive advantage of WNV strain WN02 over NY99, where the former infects mosquitoes more quickly at colder temperatures than the latter. This research contributes crucial parameters to the WNV literature, providing essential insights for modellers and those planning interventions.

Advancing West Nile virus monitoring through whole genome sequencing: Insights from a One Health genomic surveillance study in Romagna (Italy)

In the last 6 years, Italy accounted for 36 % of the total autochthonous European West Nile virus (WNV) cases reported to ECDC. Since 2001, the country put in place a multi-species national surveillance plan. The plan was enhanced in 2020 by adopting a fully integrated "One Health" approach, including human, wild bird, equine, and mosquito surveillance for the early detection of WNV. In this context, the systematic acquisition of whole viral genetic information from human patients and animals is fundamental to obtain an in-depth knowledge on the patterns of virus evolution and transmission and to gain insights on the role virus genetics in morbidity and mortality, The purpose of this pilot study was thus to design a One-Health surveillance framework based on the genomic surveillance of WNV circulating at the vector-human-animal interface, in the endemic territory of Romagna (North-Eastern Italy) during the 2023 transmission season. Whole genome sequencing (WGS) analyses confirmed the circulation of WNV lineage 2 showing high nucleotide and amino acid identity of 99.82 % and 99.92 % respectively among viral sequences from human patients, vectors and birds. All the sequences clustered with other Italian strains in the Central and Southern European clade with robust bootstrap support and BLASTn identity exceeding 99.7 %. The highest nucleotide identity was observed with sequences from Emilia-Romagna and Veneto regions (Italy), confirming a local virus circulation and overwintering of WNV lineage 2 with a confined virus spread and no (or limited) external introduction of viral strains. Our results, support the adoption of a One Health approach to WNV surveillance, based on WGS and integrating the clinical diagnosis, epidemiology, and genomic characterisation, to create a suitable operational process for the characterisation of autochthonous and imported Arboviruses circulating in Romagna to effectively integrate the already established surveillance plan.

Complex patterns of WNV evolution: a focus on the Western Balkans and Central Europe

Introduction

West Nile Virus, an emerging zoonotic pathogen, has been circulating in Serbia for over a decade, with its first detection in mosquitoes in 2010. Since then, the virus has led to increasing cases in both animals and humans, peaking in 2018 with 415 human cases and 36 fatalities. This study aimed to explore the phylogenetic relationships between previously sequenced West Nile virus strains from Serbia and those sequenced in this study, while also identifying possible virulence factors.

Materials and methods

Whole genome sequencing was conducted using a targeted approach on the MinION Mk1C platform, following a two-step process involving cDNA synthesis and amplification. Bioinformatics analysis included demultiplexing, primer trimming, and sequence mapping using tools such as iVar, Minimap2, and Samtools. Phylogenetic analysis was performed using MAFFT alignment and the Maximum Likelihood method with the Tamura Nei model in MEGA X software. Virulence factors were assessed in both structural and nonstructural proteins, focusing on key glycosylation motifs and specific mutations. Homology modeling of the E protein was also performed to evaluate potential structural changes due to mutations.

Results

Phylogenetic analysis revealed two major sublineages within the E subclade, representing the majority of strains from Western and Central Europe. These sublineages likely originated from Austria, Serbia, and Hungary between 2008 and 2012. The study also identified three distinct sublineages within the D subclade, which includes more diverse strains from Southern Europe. The E protein exhibited significant variations, particularly at the E159 site, which is crucial for virulence. The EI159T aa change has become dominant in recent years, replacing the previously prevalent EI159M. Additionally, changes in the NS1 glycoprotein and NS3 protein, both of which are involved in immune modulation and viral replication, were identified, with potential implications for the virus's virulence.

Conclusion

The study's findings highlight the Western Balkans and Central Europe as key regions for the mixing and dissemination of West Nile virus strains from both Western-Central and Southern Europe. These results underscore the importance of continuous surveillance and phylogenetic analysis to monitor the evolution and spread of West Nile virus, particularly in light of the frequent mutations observed in virulence-associated sites.

Continuous and Dynamic Circulation of West Nile Virus in Mosquito Populations in Bucharest Area, Romania, 2017-2023

West Nile virus (WNV) is a mosquito-borne pathogen with a worldwide distribution. Climate change and human activities have driven the expansion of WNV into new territories in Europe during the last two decades. Romania is endemic for WNV circulation since at least 1996 when the presence of lineage 1 was documented during an unprecedented outbreak. Lineage 2 was first identified in this country during a second significant human outbreak in 2010. Its continuous circulation is marked by clade replacement, and even co-circulation of different strains of the same clade was observed until 2016. The present study aims to fill the information gap regarding the WNV strains that were circulating in Romania between 2017 and 2023, providing chiefly viral sequences obtained from mosquito samples collected in the Bucharest metropolitan area, complemented by human and bird viral sequences. WNV was detected mainly in Culex pipiens mosquitoes, the vectors of this virus in the region, but also in the invasive Aedes albopictus mosquito species. Lineage 2 WNV was identified in mosquito samples collected between 2017 and 2023, as well as in human sera from patients in southern and central Romania during the outbreaks of 2017 and 2018. Both 2a and 2b sub-lineages were identified, with evidence of multiple clusters and sub-clusters within sub-lineage 2a, highlighting the complex and dynamic circulation of WNV in Romania, as a consequence of distinct introduction events from neighboring countries followed by in situ evolution.

Drivers and epidemiological patterns of West Nile virus in Serbia

Background

West Nile virus (WNV) is an emerging mosquito-borne pathogen in Serbia, where it has been detected as a cause of infection in humans since 2012. We analyzed and modelled WNV transmission patterns in the country between 2012 and 2023.

Methods

We applied a previously developed modelling approach to quantify epidemiological parameters of interest and to identify the most important environmental drivers of the force of infection (FOI) by means of statistical analysis in the human population in the country.

Results

During the study period, 1,387 human cases were recorded, with substantial heterogeneity across years. We found that spring temperature is of paramount importance for WNV transmission, as FOI magnitude and peak timing are positively associated with it. Furthermore, FOI is also estimated to be greater in regions with a larger fraction of older adult people, who are at higher risk to develop severe infections.

Conclusion

Our results highlight that temperature plays a key role in shaping WNV outbreak magnitude in Serbia, confirming the association between spring climatic conditions and WNV human transmission risk and thus pointing out the importance of this factor as a potential early warning predictor for timely application of preventive and control measures.

Mechanistic models for West Nile virus transmission: a systematic review of features, aims and parametrization

Mathematical models within the Ross-Macdonald framework increasingly play a role in our understanding of vector-borne disease dynamics and as tools for assessing scenarios to respond to emerging threats. These threats are typically characterized by a high degree of heterogeneity, introducing a range of possible complexities in models and challenges to maintain the link with empirical evidence. We systematically identified and analysed a total of 77 published papers presenting compartmental West Nile virus (WNV) models that use parameter values derived from empirical studies. Using a set of 15 criteria, we measured the dissimilarity compared with the Ross-Macdonald framework. We also retrieved the purpose and type of models and traced the empirical sources of their parameters. Our review highlights the increasing refinements in WNV models. Models for prediction included the highest number of refinements. We found uneven distributions of refinements and of evidence for parameter values. We identified several challenges in parametrizing such increasingly complex models. For parameters common to most models, we also synthesize the empirical evidence for their values and ranges. The study highlights the potential to improve the quality of WNV models and their applicability for policy by establishing closer collaboration between mathematical modelling and empirical work.