Phylodynamic and phylogeographic analysis of the complete genome of the West Nile virus lineage 2 (WNV-2) in the Mediterranean basin

Tracking the Pathways of West Nile Virus: Phylogenetic and Phylogeographic Analysis of a 2024 Isolate from Portugal

Birds are natural hosts for numerous zoonotic viral pathogens, including West Nile virus, which is transmitted by mosquitoes. During migration, birds can act as vectors for the geographic spread of viruses. WNV is endemic in Portugal, causing annual outbreaks, particularly in horses. Here, we report the first detection of an avian WNV strain isolated from a wild bird (Astur gentilis) collected in Portugal in mid-September 2024. Phylogenetic and phylogeographic analyses were conducted to trace the virus's origin and potential transmission routes, integrating the obtained full-length genomic sequence with a dataset of WNV strains from Africa and Europe (1951-2024). Phylogenetic analysis of 92 WNV sequences spanning lineages 1-5 positioned the 2024 isolate within lineage 1a. Results obtained using phylodynamics-based analysis showed that this isolate likely originated in Africa and reached Portugal via Spain's Cádiz coast, confirming previously described WNV dispersal patterns between Africa and Europe. The data suggest a migratory route from West Africa to Europe, extending through countries such as Senegal, Mauritania, Morocco, Portugal, Spain, Italy, and France, indicating a reciprocal flow of the virus back into Africa. These transmission routes match the migratory paths of Afro-Palearctic bird species, emphasizing the role of migratory birds in the long-distance spread of WNV.

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.

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.

Seroprevalence of West Nile Virus among Equids in Bulgaria in 2022 and Assessment of Some Risk Factors

The aim of this study was to analyze the seroprevalence of West Nile virus (WNV) among equids in Bulgaria, confirm the results of a competitive ELISA versus the virus neutralization test (VNT) and investigate some predisposing factors for WNV seropositivity. A total of 378 serum samples from 15 provinces in northern and southern Bulgaria were tested. The samples originated from 314 horses and 64 donkeys, 135 males and 243 females, aged from 1 to 30 years. IgG and IgM antibodies against WNV protein E were detected by ELISA. ELISA-positive samples were additionally tested via VNT for WNV and Usutu virus. Thirty-five samples were WNV-positive by ELISA (9.26% [CI = 6.45-12.88]), of which 15 were confirmed by VNT; hence, the seroprevalence was 3.97% (CI = 2.22-6.55). No virus-neutralizing antibodies to Usutu virus were detected among the 35 WNV-ELISA-positive equids in Bulgaria. When compared with VNT, ELISA showed 100.0% sensitivity and 94.5% specificity. A statistical analysis showed that the risk factors associated with WNV seropositivity were the region (p < 0.0001), altitude of the locality (p < 0.0001), type of housing (p < 0.0001) and breed (p = 0.0365). The results of the study demonstrate, albeit indirectly, that WNV circulates among equids in northern and southern Bulgaria, indicating that they could be suitable sentinel animals for predicting human cases and determining the risk in these areas or regions of the country.

Circulation of West Nile Virus and Usutu Virus in Europe: Overview and Challenges

West Nile Virus (WNV) and Usutu Virus (USUV) are both neurotropic mosquito-borne viruses belonging to the Flaviviridae family. These closely related viruses mainly follow an enzootic cycle involving mosquitoes as vectors and birds as amplifying hosts, but humans and other mammals can also be infected through mosquito bites. WNV was first identified in Uganda in 1937 and has since spread globally, notably in Europe, causing periodic outbreaks associated with severe cases of neuroinvasive diseases such as meningitis and encephalitis. USUV was initially isolated in 1959 in Swaziland and has also spread to Europe, primarily affecting birds and having a limited impact on human health. There has been a recent expansion of these viruses' geographic range in Europe, facilitated by factors such as climate change, leading to increased human exposure. While sharing similar biological traits, ecology, and epidemiology, there are significant distinctions in their pathogenicity and their impact on both human and animal health. While WNV has been more extensively studied and is a significant public health concern in many regions, USUV has recently been gaining attention due to its emergence in Europe and the diversity of its circulating lineages. Understanding the pathophysiology, ecology, and transmission dynamics of these viruses is important to the implementation of effective surveillance and control measures. This perspective provides a brief overview of the current situation of these two viruses in Europe and outlines the significant challenges that need to be addressed in the coming years.

Development and evaluation of an easy to use real-time reverse-transcription loop-mediated isothermal amplification assay for clinical diagnosis of West Nile virus

West Nile Virus (WNV) causes a serious public health concern in many countries around the world. Virus detection in pathological samples is a key component of WNV infection diagnostic, classically performed by real-time PCR. In outbreak situation, rapid detection of the virus, in peripheral laboratories or at point of care, is crucial to guide decision makers and for the establishment of adequate action plans to prevent virus dissemination. Here, we evaluate a Loop-mediated isothermal amplification (LAMP) tool for WNV detection. Amplifications were performed comparatively on extracted viral RNA and on crude samples using a classical thermal cycler and a portable device (pebble device). qRT-PCR was used as gold standard and two sets of urine samples (n = 62 and n = 74) were used to evaluate the retained amplification protocols and assess their sensitivity and specificity. RT-LAMP on RNA extracts and crude samples showed a sensitivity of 90 % and 87 %, respectively. The specificity was 100 % for extracts and 97 % for crude samples. Using the device, the RT-LAMP on extracted RNA was comparable to the gold standard results (100 % sensitivity and specificity) and it was a bit lower on crude samples (65 % sensitivity and 94 % specificity). These results show that RT-LAMP is an efficient technique to detect WNV. RT-LAMP provides a rapid, sensitive, high-throughput and portable tool for accurate WNV detection and has potentials to facilitate diagnostic and surveillance efforts both in the laboratory and in the field, especially in developing countries.

West Nile virus spread in Europe: Phylogeographic pattern analysis and key drivers

BACKGROUND

West Nile virus (WNV) outbreaks in birds, humans, and livestock have occurred in multiple areas in Europe and have had a significant impact on animal and human health. The patterns of emergence and spread of WNV in Europe are very different from those in the US and understanding these are important for guiding preparedness activities.

METHODS

We mapped the evolution and spread history of WNV in Europe by incorporating viral genome sequences and epidemiological data into phylodynamic models. Spatially explicit phylogeographic models were developed to explore the possible contribution of different drivers to viral dispersal direction and velocity. A "skygrid-GLM" approach was used to identify how changes in environments would predict viral genetic diversity variations over time.

FINDINGS

Among the six lineages found in Europe, WNV-2a (a sub-lineage of WNV-2) has been predominant (accounting for 73% of all sequences obtained in Europe that have been shared in the public domain) and has spread to at least 14 countries. In the past two decades, WNV-2a has evolved into two major co-circulating clusters, both originating from Central Europe, but with distinct dynamic history and transmission patterns. WNV-2a spreads at a high dispersal velocity (88km/yr-215 km/yr) which is correlated to bird movements. Notably, amongst multiple drivers that could affect the spread of WNV, factors related to land use were found to strongly influence the spread of WNV. Specifically, the intensity of agricultural activities (defined by factors related to crops and livestock production, such as coverage of cropland, pasture, cultivated and managed vegetation, livestock density) were positively associated with both spread direction and velocity. In addition, WNV spread direction was associated with high coverage of wetlands and migratory bird flyways.

CONCLUSION

Our results suggest that-in addition to ecological conditions favouring bird- and mosquito- presence-agricultural land use may be a significant driver of WNV emergence and spread. Our study also identified significant gaps in data and the need to strengthen virological surveillance in countries of Central Europe from where WNV outbreaks are likely seeded. Enhanced monitoring for early detection of further dispersal could be targeted to areas with high agricultural activities and habitats of migratory birds.

Dispersion and diversification of Lyssavirus rabies transmitted from haematophagous bats Desmodus rotundus: a phylogeographical study

Rabies is worldwide zoonosis caused by Lyssavirus rabies (RABV) a RNA negative sense virus with low level of fidelity during replication cycle. Nucleoprotein of RABV is the most conserved between all five proteins of the virus and is the most used gene for phylogenetic and phylogeographic studies. Despite of rabies been very important in Public Health concern, it demands continuous prophylactic care for herbivores with economic interest, such as cattle and horses. The main transmitter of RABV for these animals in Brazil is the hematophagous bats Desmodus rotundus. The aim of this study was to determine the dispersion over time and space of RABV transmitted by D. rotundus. Samples of RABV from the State of São Paulo (SP), Southeast Brazil isolated from the central nervous system (CNS) of cattle, were submitted to RNA extraction, RT-PCR, sequencing and phylogeographic analyzes with BEAST (Bayesian Evolutionary Analysis Sampling Trees) v 2.5 software. Was possible to identify high rate of diversification in starts sublineages of RABV what are correlated with a behavior of D. rotundus, the main transmitter of rabies to cattle. This study also highlights the importance of continuous monitoring of genetic lineages of RABV in Brazil.

Spatial and temporal dynamics of West Nile virus between Africa and Europe

It is unclear whether West Nile virus (WNV) circulates between Africa and Europe, despite numerous studies supporting an African origin and high transmission in Europe. We integrated genomic data with geographic observations and phylogenetic and phylogeographic inferences to uncover the spatial and temporal viral dynamics of WNV between these two continents. We focused our analysis towards WNV lineages 1 (L1) and 2 (L2), the most spatially widespread and pathogenic WNV lineages. Our study shows a Northern-Western African origin of L1, with back-and-forth exchanges between West Africa and Southern-Western Europe; and a Southern African origin of L2, with one main introduction from South Africa to Europe, and no back introductions observed. We also noticed a potential overlap between L1 and L2 Eastern and Western phylogeography and two Afro-Palearctic bird migratory flyways. Future studies linking avian and mosquito species susceptibility, migratory connectivity patterns, and phylogeographic inference are suggested to elucidate the dynamics of emerging viruses.

Comparison of West Nile Virus Disease in Humans and Horses: Exploiting Similarities for Enhancing Syndromic Surveillance

West Nile virus (WNV) neuroinvasive disease threatens the health and well-being of horses and humans worldwide. Disease in horses and humans is remarkably similar. The occurrence of WNV disease in these mammalian hosts has geographic overlap with shared macroscale and microscale drivers of risk. Importantly, intrahost virus dynamics, the evolution of the antibody response, and clinicopathology are similar. The goal of this review is to provide a comparison of WNV infection in humans and horses and to identify similarities that can be exploited to enhance surveillance methods for the early detection of WNV neuroinvasive disease.

One Health surveillance of West Nile and Usutu viruses: a repeated cross-sectional study exploring seroprevalence and endemicity in Southern France, 2016 to 2020

BackgroundWest Nile virus (WNV) and Usutu virus (USUV), two closely related flaviviruses, mainly follow an enzootic cycle involving mosquitoes and birds, but also infect humans and other mammals. Since 2010, their epidemiological situation may have shifted from irregular epidemics to endemicity in several European regions; this requires confirmation, as it could have implications for risk assessment and surveillance strategies.AimTo explore the seroprevalence in animals and humans and potential endemicity of WNV and USUV in Southern France, given a long history of WNV outbreaks and the only severe human USUV case in France in this region.MethodsWe evaluated the prevalence of WNV and USUV in a repeated cross-sectional study by serological and molecular analyses of human, dog, horse, bird and mosquito samples in the Camargue area, including the city of Montpellier, between 2016 and 2020.ResultsWe observed the active transmission of both viruses and higher USUV prevalence in humans, dogs, birds and mosquitoes, while WNV prevalence was higher in horses. In 500 human samples, 15 were positive for USUV and 6 for WNV. Genetic data showed that the same lineages, WNV lineage 1a and USUV lineage Africa 3, were found in mosquitoes in 2015, 2018 and 2020.ConclusionThese findings support existing literature suggesting endemisation in the study region and contribute to a better understanding of USUV and WNV circulation in Southern France. Our study underlines the importance of a One Health approach for the surveillance of these viruses.