West Nile virus population genetics and evolution

Analysis of highly frequent point mutations in glycoprotein C, glycoprotein N, and nucleoprotein of CCHFV

Crimean-Congo hemorrhagic fever virus (CCHFV) is classified among top 10 priority pathogens by World Health Organization. CCHFV belongs to Bunyaviridae family and negative sense ssRNA genome composed of three RNA segments: L, M, and S. RNA viruses show higher mutation rate as compared to DNA viruses. To gain deeper understanding of impact of point mutations in CCHFV M and S segment, mutation profiling, homology modeling, and molecular dynamic (MD) simulation were performed. Structural glycoproteins (glycoprotein C [Gc] and glycoprotein N [Gn]) of CCHFV are important for host-virus interaction and genome packaging, whereas CCHFV nucleoprotein (NP) is crucial for viral replication. Hence, current study is focused on evaluation of eight mutations in structural glycoproteins (Gc: 7 and Gn: 1) of M segment and seven mutations in NP of S segment. All these mutations were highly frequent, with mutation frequency between 0.81 and 1.0 and found to be persistent in the recent strains of CCHFV. Solubility analysis predicted that selected point mutations reduce solubility of Gc protein and increase solubility of Gn and NP proteins. MD simulation study deciphered that A1046V and G1158E in Gc protein, I778T in Gn protein, and H195R in NP protein displayed large deviation and fluctuation, and affected intramolecular interactions. In conclusion, we observed that point mutations could impact structure, stability, and host-virus interaction of protein, and might lead to evolution of new strains for better survival and drug resistance.

Novel tools to study West Nile virus NS3 protease activity

West Nile Virus (WNV) belongs to a group of pathogenic viruses called flaviviruses. West Nile virus infection can be mild, causing so-called West Nile Fever (WNF) or severe neuroinvasive form of the disease (WNND), and ultimately even death. There are currently no known medications to prevent West Nile virus infection. Only symptomatic treatment is used. To date, there are no unequivocal tests enabling a quick and unambiguous assessment of WN virus infection. The aim of the research was to obtain specific and selective tools for determining the activity of the West Nile virus serine proteinase. Using the methods of combinatorial chemistry with iterative deconvolution, the substrate specificity of the enzyme in non-primed and primed positions was determined. The FRET ABZ-Ala-Lys-Gln-Arg-Gly-Gly-Thr-Tyr(3-NO₂)-NH₂ substrate was obtained, characterized by kinetic parameters (KM = 4.20 ± 0.32 × 10^-5 M) as for the majority of proteolytic enzymes. The obtained sequence was used to develop and synthesize highly sensitive functionalized quantum dot-based protease probes (QD). A QD WNV NS3 protease probe was obtained to detect an increase in fluorescence of 0.05 nmol enzyme in the assay system. This value was at least 20 times lower than that observed with the optimized substrate. The obtained result may be the basis for further research on the potential use of the WNV NS3 protease in the diagnosis of West Nile virus infection.

Intracellular diversity of WNV within circulating avian peripheral blood mononuclear cells reveals host-dependent patterns of polyinfection

Error-prone replication of RNA viruses generates the genetic diversity required for adaptation within rapidly changing environments. Thus, arthropod-borne virus (arbovirus) populations exist in nature as mutant swarms that are maintained between arthropods and vertebrates. Previous studies have demonstrated that West Nile virus (WNV) population dynamics are host dependent: In American crows, which experience extremely high viremia, purifying selection is weak and population diversity is high compared to American robins, which have 100 to 1000-fold lower viremia. WNV passed in robins experiences fitness gains, whereas that passed in crows does not. Therefore, we tested the hypothesis that high crow viremia allows higher genetic diversity within individual avian peripheral-blood mononuclear cells (PBMCs), reasoning that this could have produced the previously observed host-specific differences in genetic diversity and fitness. Specifically, we infected cells and birds with a novel, barcoded version of WNV and sequenced viral RNA from single cells to quantify the number of WNV barcodes that each contained. Our results demonstrate that the richness of WNV populations within crows far exceeds that in robins. Similarly, rare WNV variants were maintained by crows more frequently than by robins. Our results suggest that increased viremia in crows relative to robins leads to maintenance of defective genomes and less prevalent variants, presumably through complementation. Our findings further suggest that weaker purifying selection in highly susceptible crows is attributable to this higher viremia, polyinfections and complementation. These studies further document the role of particular, ecologically relevant hosts in shaping virus population structure.

Author Summary

WNV mutational diversity in vertebrates is species-dependent. In crows, low frequency variants are common, and viral populations are more diverse. In robins, fewer mutations become permanent fixtures of the overall viral population. We infected crows, robins and a chicken cell line with a genetically marked (barcoded) WNV. Higher levels of virus led to multiple unique WNV genomes infecting individual cells, even when a genotype was present at low levels in the input viral stock. Our findings suggest that higher levels of circulating virus in natural hosts allow less fit viruses to survive in RNA virus populations through complementation by more fit viruses. This is significant as it allows less represented and less fit viruses to be maintained at low levels until they potentially emerge when virus environments change. Overall our data reveal new insights on the relationships between host susceptibility to high viremia and virus evolution.

West Nile Virus Lineage 1 in Italy: Newly Introduced or a Re-Occurrence of a Previously Circulating Strain?

In Italy, West Nile virus (WNV) appeared for the first time in the Tuscany region in 1998. After 10 years of absence, it re-appeared in the areas surrounding the Po River delta, affecting eight provinces in three regions. Thereafter, WNV epidemics caused by genetically divergent isolates have been documented every year in the country. Since 2018, only WNV Lineage 2 has been reported in the Italian territory. In October 2020, WNV Lineage 1 (WNV-L1) re-emerged in Italy, in the Campania region. This is the first occurrence of WNV-L1 detection in the Italian territory since 2017. WNV was detected in the internal organs of a goshawk (Accipiter gentilis) and a kestrel (Falco tinnunculus). The RNA extracted in the goshawk tissue samples was sequenced, and a Bayesian phylogenetic analysis was performed by a maximum-likelihood tree. Genome analysis, conducted on the goshawk WNV complete genome sequence, indicates that the strain belongs to the WNV-L1 Western-Mediterranean (WMed) cluster. Moreover, a close phylogenetic similarity is observed between the goshawk strain, the 2008-2011 group of Italian sequences, and European strains belonging to the Wmed cluster. Our results evidence the possibility of both a new re-introduction or unnoticed silent circulation in Italy, and the strong importance of keeping the WNV surveillance system in the Italian territory active.

Global emergence of West Nile virus: Threat & preparedness in special perspective to India

West Nile virus (WNV) is a mosquito-borne single-stranded RNA neurotropic virus within the family Flaviviridae. The virus was first reported in the West Nile province of Uganda in 1937. Since then, sporadic cases have been reported until the last two decades when it has emerged as a threat to public health. The emergence of WNV with more severity in recent times is intriguing. Considering this phenomenon, the WNV-affected areas of the world were distinguished as old versus new in a depicted world map. The present review showcases the historical and epidemiological perspectives of the virus, genetic diversity of prevailing lineages and clinical spectrum associated with its infection. Emergence of the virus has been discussed in special context to India because of co-circulation of different WNV lineages/strains along with other flaviviruses. Recent laboratory diagnostics, vaccine development and clinical management associated with WNV infection have also been discussed. Further, the research gaps, especially in context to India have been highlighted that may have a pivotal role in combating the spread of WNV.

Evolution-Driven Attenuation of Alphaviruses Highlights Key Glycoprotein Determinants Regulating Viral Infectivity and Dissemination

Understanding the fundamental mechanisms of arbovirus transmission and pathogenesis is essential to develop strategies for treatment and prevention. We previously took an in vivo evolution-based approach and identified the chikungunya virus E1 glycoprotein residue 80 to play a critical role in viral transmission and pathogenesis. In this study, we address the genetic conservation and function of position 80 and demonstrate that this residue is a key determinant in alphavirus infectivity and dissemination through modulation of viral fusion and cholesterol dependence. In addition, in studying the evolution of position 80, we identified a network of glycoprotein residues, including epidemic determinants, that regulate virus dissemination and infectivity. These studies underscore the importance of taking evolution-based approaches to not only identify key viral determinants driving arbovirus transmission and pathogenesis but also to uncover fundamental aspects of arbovirus biology.

Evolutionary trajectory of fish Piscine novirhabdovirus (=Viral Hemorrhagic Septicemia Virus) across its Laurentian Great Lakes history: Spatial and temporal diversification

Piscine novirhabdovirus = Viral Hemorrhagic Septicemia Virus (VHSV) first appeared in the Laurentian Great Lakes with large outbreaks from 2005 to 2006, as a new and novel RNA rhabdovirus subgenogroup (IVb) that killed >30 fish species. Interlude periods punctuated smaller more localized outbreaks in 2007, 2010, and 2017, although some fishes tested positive in the intervals. There have not been reports of outbreaks or positives from 2018, 2019, or 2020. Here, we employ a combined population genetics and phylogenetic approach to evaluate spatial and temporal evolutionary trajectory on its G-gene sequence variation, in comparison with whole-genome sequences (11,083 bp) from a subset of 44 individual isolates (including 40 newly sequenced ones). Our results show that IVb (N = 184 individual fish isolates) diversified into 36 G-gene haplotypes from 2003 to 2017, stemming from two originals ("a" and "b"). G-gene haplotypes "a" and "b" differed by just one synonymous single-nucleotide polymorphism (SNP) substitution, remained the most abundant until 2011, then disappeared. Group "a" descendants (14 haplotypes) remained most prevalent in the Upper and Central Great Lakes, with eight (51%) having nonsynonymous substitutions. Group "b" descendants primarily have occurred in the Lower Great Lakes, including 22 haplotypes, of which 15 (68%) contained nonsynonymous changes. Evolutionary patterns of the whole-genome sequences (which had 34 haplotypes among 44 isolates) appear congruent with those from the G-gene. Virus populations significantly diverged among the Upper, Central, and Lower Great Lakes, diversifying over time. Spatial divergence was apparent in the overall patterns of nucleotide substitutions, while amino acid changes increased temporally. VHSV-IVb thus significantly differentiated across its less than two decades in the Great Lakes, accompanied by declining outbreaks and virulence. Continuing diversification likely allowed the virus to persist at low levels in resident fish populations, and may facilitate its potential for further and future spread to new habitats and nonacclimated hosts.

Long-term, West Nile virus-induced neurological changes: A comparison of patients and rodent models

West Nile virus (WNV) is a mosquito-borne virus that can cause severe neurological disease in those infected. Those surviving infection often present with long-lasting neurological changes that can severely impede their lives. The most common reported symptoms are depression, memory loss, and motor dysfunction. These sequelae can persist for the rest of the patients’ lives. The pathogenesis behind these changes is still being determined. Here, we summarize current findings in human cases and rodent models, and discuss how these findings indicate that WNV induces a state in the brain similar neurodegenerative diseases. Rodent models have shown that infection leads to persistent virus and inflammation. Initial infection in the hippocampus leads to neuronal dysfunction, synapse elimination, and astrocytosis, all of which contribute to memory loss, mimicking findings in neurodegenerative diseases such as Alzheimer’s disease (AD) and Parkinson’s disease (PD). WNV infection acts on pathways, such as ubiquitin-signaled protein degradation, and induces the production of molecules, including IL-1β, IFN-γ, and α-synuclein, that are associated with neurodegenerative diseases. These findings indicate that WNV induces neurological damage through similar mechanisms as neurodegenerative diseases, and that pursuing research into the similarities will help advance our understanding of the pathogenesis of WNV-induced neurological sequelae.

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In patients with and without diagnosed WNND, there are long-lasting neurological sequelae that can mimic neurodegenerative diseases.

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Some rodent models of WNV reproduce some of these changes with mechanisms similar to neurodegenerative diseases.

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There is significant overlap between WNV and ND pathogenesis and this has been understudied.

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Further research needs to be done to determine accuracy of animal models compared to human patients.

High Transmission Potential of West Nile Virus Lineage 1 for Cx. pipiens s.l. of Iran

: Vector competence is an important parameter in evaluating whether a species plays a role in transmission of an arbovirus. Although the protocols are similar, interpretation of results is unique given the specific interactions that exist between a mosquito population and a viral genotype. Here, we assessed the infection (IR), dissemination (DR), and transmission (TR) rates of Cx. pipiens s.l., collected from Iran, for West Nile virus (WNV) lineage 1a. We showed that Cx. pipiens s.l. mosquitoes in Iran were susceptible to WNV with IR up to 89.7%, 93.6%, and 83.9% at 7, 14, and 21 days post-infection (dpi) respectively. In addition, DR and TR reached respectively 92.3% and 75.0% at 21 dpi, and the number of viral particles delivered with saliva reached up to 1.33 × 105 particles. Therefore, an unexpected high risk of WNV dissemination in the region where Cx. pipiens s.l. mosquitoes are well established should be considered carefully and surveillance measures implemented accordingly.

Multiscale analysis for patterns of Zika virus genotype emergence, spread, and consequence

The question of how Zika virus (ZIKV) changed from a seemingly mild virus to a human pathogen capable of microcephaly and sexual transmission remains unanswered. The unexpected emergence of ZIKV's pathogenicity and capacity for sexual transmission may be due to genetic changes, and future changes in phenotype may continue to occur as the virus expands its geographic range. Alternatively, the sheer size of the 2015-16 epidemic may have brought attention to a pre-existing virulent ZIKV phenotype in a highly susceptible population. Thus, it is important to identify patterns of genetic change that may yield a better understanding of ZIKV emergence and evolution. However, because ZIKV has an RNA genome and a polymerase incapable of proofreading, it undergoes rapid mutation which makes it difficult to identify combinations of mutations associated with viral emergence. As next generation sequencing technology has allowed whole genome consensus and variant sequence data to be generated for numerous virus samples, the task of analyzing these genomes for patterns of mutation has become more complex. However, understanding which combinations of mutations spread widely and become established in new geographic regions versus those that disappear relatively quickly is essential for defining the trajectory of an ongoing epidemic. In this study, multiscale analysis of the wealth of genomic data generated over the course of the epidemic combined with in vivo laboratory data allowed trends in mutations and outbreak trajectory to be assessed. Mutations were detected throughout the genome via deep sequencing, and many variants appeared in multiple samples and in some cases become consensus. Similarly, amino acids that were previously consensus in pre-outbreak samples were detected as low frequency variants in epidemic strains. Protein structural models indicate that most of the mutations associated with the epidemic transmission occur on the exposed surface of viral proteins. At the macroscale level, consensus data was organized into large and interactive databases to allow the spread of individual mutations and combinations of mutations to be visualized and assessed for temporal and geographical patterns. Thus, the use of multiscale modeling for identifying mutations or combinations of mutations that impact epidemic transmission and phenotypic impact can aid the formation of hypotheses which can then be tested using reverse genetics.

West Nile Virus and Usutu Virus Co-Circulation in Europe: Epidemiology and Implications

West Nile virus (WNV) and Usutu virus (USUV) are neurotropic mosquito-borne flaviviruses that may infect humans. Although WNV is much more widespread and plays a much larger role in human health, the two viruses are characterized by similar envelope antigens, clinical manifestations, and present overlapping in terms of geographic range of transmission, host, and vector species. This review highlights some of the most relevant aspects of WNV and USUV human infections in Europe, and the possible implications of their co-circulation.

West Nile virus infections are here! Are we prepared to face another flavivirus epidemic?

Emerging arthropod-borne viruses (arboviruses), such as chikungunya and Zika viruses, are a major threat to public health in countries like Brazil where biodiversity is high and medical care is sometimes precarious. West Nile fever is a disease caused by the West Nile Virus (WNV), an RNA virus belonging to the Flaviviridae family. It is transmitted by infected mosquitoes to numerous animals like birds, reptiles and mammals, including human and non-human primates. In the last decade, the number of reported cases of WNV infection in humans and animals has increased in the Americas. Circulation of WNV in forests and rural areas in Brazil has been detected based on serological surveys and, in 2014, the first case of West Nile fever was confirmed in a patient from Piauí State. In 2018, the virus was isolated for the first time from a horse from a rural area in the state of Espírito Santo presenting with a neurological disorder; this raises the possibility that other cases of WNV encephalitis may have occurred without clinical recognition and without laboratory diagnosis by specific assays. The imminent WNV outbreak poses a challenge for Brazilian clinicians and researchers. In this review, we summarize the basic biological and ecological characteristics of this virus and the clinical presentation and treatment of febrile illnesses caused by WNV. We also discuss the epidemiological aspects, prophylaxis of WNV infections, and monitoring strategies that could be applied in the possibility of a WNV outbreak in Brazil.

Co-circulation dynamics and persistence of newly introduced clades of 2012 outbreak associated West Nile Virus in Texas, 2012-2015

The second largest outbreak of West Nile encephalitis and West Nile fever ever recorded occurred in the United States (U.S) in the summer of 2012. The outbreak was related to the widespread circulation of closely related clades, or groups, of West Nile virus (WNV) into multiple states where they were not previously found. Whether the invading 2012 strains were able to circulate and overwinter in states with their own endemic population of WNV is unknown and the effect of viral genetics on adaptation and persistence in a new ecological niche is unclear. In this study, we sequenced 70 mosquito isolates from multiple counties throughout Texas in 2012-2015. We identified isolates representative of previously described 2012 WNV groups (Groups 8-10) and discovered a novel group which we called Group 11. Although we identified isolates representative of WNV endemic (2/70) to Texas, most isolates (68/70) were related to the invading 2012 strains, and of these Group 10 (45/68) was predominant. We also observed differences among the 2012 WNV groups correlating to their genotype. Group 10 WNV in Texas, which carry two putative positively selected variants, had limited introductions into Texas, wide circulation, and strong evidence of continued persistence perhaps indicative of overwintering. In contrast, Groups 8 and 11, without positively selected variants, had multiple introductions into Texas, limited circulation, and limited persistence. Lastly, we identified a potential transmission source in New York for incoming Group 8 WNV into Texas. Altogether our study suggests that mutations in the WNV genome may influence the range and dynamics of WNV circulation, and the ability of different strains to persist in new ecological niches.

Comparative Vector Competence of North American Culex pipiens and Culex quinquefasciatus for African and European Lineage 2 West Nile Viruses

West Nile virus (WNV) is a mosquito-borne flavivirus that is phylogenetically separated into distinct lineages. Lineage 1 (L1) and lineage 2 (L2) encompass all WNV isolates associated with human and veterinary disease cases. Although L1 WNV is globally distributed, including North America, L2 WNV only recently emerged out of sub-Saharan Africa into Europe and Russia. The spread of L2 WNV throughout and beyond Europe depends, in part, on availability of competent vectors. The vector competence of mosquitoes within the Culex genus for WNV is well established for L1 WNV but less extensively studied for L2 WNV. Assessing the vector competence of North American Culex mosquitoes for L2 WNV will be critical for predicting the potential for L2 WNV emergence in North America. We address the vector competence of North American Culex pipiens and Culex quinquefasciatus for L2 WNV. Both mosquito species were highly competent for each of the L2 WNV strains assessed, but variation in infection, dissemination, and transmission was observed. An L2 WNV strain (NS10) isolated during the Greek outbreak in 2010 exhibited a reduced capacity to infect Cx. pipiens compared with other L2 WNV strains. In addition, a South African L2 WNV strain (SA89) displayed a significantly shorter extrinsic incubation period in Cx. quinquefasciatus compared with other L2 WNV strains. These results demonstrate that North American Culex mosquito species are competent vectors of African and European L2 WNV and that emergence of L2 WNV is unlikely to be hindered by poor competence of North American vectors.

Selective constraint and adaptive potential of West Nile virus within and among naturally infected avian hosts and mosquito vectors

Arthropod-borne viruses are among the most genetically constrained RNA viruses, yet they have a remarkable propensity to adapt and emerge. We studied wild birds and mosquitoes naturally infected with West Nile virus (WNV) in a 'hot spot' of virus transmission in Chicago, IL, USA. We generated full coding WNV genome sequences from spatiotemporally matched bird and mosquito samples using high-throughput sequencing, allowing a molecular evolutionary assessment with deep coverage. Mean FST among samples was 0.66 (±0.02 SE) and was bimodal, with mean nucleotide diversity being higher between samples (interhost πN = 0.001; πS = 0.024) than within them (intrahost πN < 0.0001; πS < 0.001). Eight genomic sites with FST > 1.01 (in the PrM, NS2a, NS3, NS4b, and 5'-noncoding genomic regions) showed bird versus mosquito variant frequency differences of >30 per cent and/or polymorphisms fixed in ≥5 host or vector individuals, suggesting host tropism for these variants. However, phylogenetic analyses demonstrated a lack of grouping by bird or mosquito, most inter-sample differences were synonymous (mean interhost πN/πS = 0.04), and there was no significant difference between hosts and vectors in either their nucleotide diversities or levels of purifying selection (mean intrahost πN/πS = 0.28 in birds and πN/πS = 0.21 in mosquitoes). This finding contrasts with the 'trade-off' and 'selective sieve' hypotheses that have been proposed and tested in the laboratory, which predict strong host versus vector effects on WNV genetic variation, with heightened selective constraint in birds alternating with heightened viral diversity in mosquitoes. Overall, our data show WNV to be highly selectively constrained within and between both hosts and vectors but still able to vary at a limited number of sites across the genome. Such site-specific plasticity in the face of overall selective constraint may offer a mechanism whereby highly constrained viruses such as WNV and its relatives can still adapt and emerge.

Evolution and Emergence of Pathogenic Viruses: Past, Present, and Future

Incidences of emerging/re-emerging deadly viral infections have significantly affected human health despite extraordinary progress in the area of biomedical knowledge. The best examples are the recurring outbreaks of dengue and chikungunya fever in tropical and sub-tropical regions, the recent epidemic of Zika in the Americas and the Caribbean, and the SARS, MERS, and influenza A outbreaks across the globe. The established natural reservoirs of human viruses are mainly farm animals, and, to a lesser extent, wild animals and arthropods. The intricate "host-pathogen-environment" relationship remains the key to understanding the emergence/re-emergence of pathogenic viruses. High population density, rampant constructions, poor sanitation, changing climate, and the introduction of anthropophilic vectors create selective pressure on host-pathogen reservoirs. Nevertheless, the knowledge and understanding of such zoonoses and pathogen diversity in their known non-human reservoirs are very limited. Prevention of arboviral infections using vector control methods has not been very successful. Currently, new approaches to protect against food-borne infections, such as consuming only properly cooked meats and animal products, are the most effective control measures. Though significant progress in controlling human immunodeficiency virus and hepatitis viruses has been achieved, the unpredictable nature of evolving viruses and the rare occasions of outbreaks severely hamper control and preventive modalities.

West Nile virus and its vectors

West Nile virus (WNV Flaviviridae; Flavivrus) is the most geographically widespread arbovirus in the world and the leading cause of arboviral encephalitis globally. Worldwide, WNV is maintained in an enzootic cycle between primarily Culex spp. mosquitoes and birds, with human infection and disease resulting from enzootic spillover. Dynamic and complex intrinsic and extrinsic factors contribute to the temporal and spatial variability in WNV transmission. The most current information on the relative contribution of each of these factors is reviewed and a case to incorporate detailed and localized environmental and genetic data into predictive models is presented.

High levels of local inter- and intra-host genetic variation of West Nile virus and evidence of fine-scale evolutionary pressures

West Nile virus (WNV; Flaviviridae, Flavivirus) has been endemic in New York State (NYS) since its 1999 introduction, yet prevalence in Culex mosquitoes varies substantially over small spatial and temporal scales. It is unclear if viral genetics plays a role in this variability, as genetic and phenotypic characterization on local scales has generally been lacking. In addition, intrahost diversity of circulating strains have not been fully characterized despite the documented role of minority variants in viral fitness and virulence. In an effort to characterize WNV variability within epidemiologically relevant scales, we performed phylogenetic analyses on NYS isolates from 1999 to 2012. In addition, we performed full-genome, deep-sequencing and genetic analyses on 15 WNV strains isolated in 2012 from Cx. pipiens in an endemic focus of Suffolk County, NY. Our results indicate continued evolution and seasonal maintenance in NYS, yet also widespread mixing and high levels of genetic diversity within geographic foci and individual seasons. Well supported local clusters with shared amino acid differences were identified and suggest local evolutionary pressures and the potential for phenotypic variability. Intrahost diversity of focal isolates was also high, with polymorphism at levels >1.0% identified in approximately 10% of the WNV genome. Although most minority mutations were unique, mutational hotspots shared among local isolates were identified, particularly in C, NS1 and NS2A genes. The most polymorphic region, positions 3198-3388 of the NS1 gene, was comprised predominately of non-synonymous mutations, suggesting a selective advantage for amino acid diversity in this region.

Dynamics of West Nile virus evolution in mosquito vectors

West Nile virus remains the most common cause of arboviral encephalitis in North America. Since it was introduced, it has undergone adaptive genetic change as it spread throughout the continent. The WNV transmission cycle is relatively tractable in the laboratory. Thus the virus serves as a convenient model system for studying the population biology of mosquito-borne flaviviruses as they undergo transmission to and from mosquitoes and vertebrates. This review summarizes the current knowledge regarding the population dynamics of this virus within mosquito vectors.

Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses?

We propose that predominant clonal evolution (PCE) in microbial pathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure. The main features of PCE are (1) strong linkage disequilibrium, (2) the widespread occurrence of stable genetic clusters blurred by occasional bouts of genetic exchange ('near-clades'), (3) the existence of a "clonality threshold", beyond which recombination is efficiently countered by PCE, and near-clades irreversibly diverge. We hypothesize that the PCE features are not mainly due to natural selection but also chiefly originate from in-built genetic properties of pathogens. We show that the PCE model obtains even in microbes that have been considered as 'highly recombining', such as Neisseria meningitidis, and that some clonality features are observed even in Plasmodium, which has been long described as panmictic. Lastly, we provide evidence that PCE features are also observed in viruses, taking into account their extremely fast genetic turnover. The PCE model provides a convenient population genetic framework for any kind of micropathogen. It makes it possible to describe convenient units of analysis (clones and near-clades) for all applied studies. Due to PCE features, these units of analysis are stable in space and time, and clearly delimited. The PCE model opens up the possibility of revisiting the problem of species definition in these organisms. We hypothesize that PCE constitutes a major evolutionary strategy for protozoa, fungi, bacteria, and viruses to adapt to parasitism.

West Nile Virus Temperature Sensitivity and Avian Virulence Are Modulated by NS1-2B Polymorphisms

West Nile virus (WNV) replicates in a wide variety of avian species, which serve as reservoir and amplification hosts. WNV strains isolated in North America, such as the prototype strain NY99, elicit a highly pathogenic response in certain avian species, notably American crows (AMCRs; Corvus brachyrhynchos). In contrast, a closely related strain, KN3829, isolated in Kenya, exhibits a low viremic response with limited mortality in AMCRs. Previous work has associated the difference in pathogenicity primarily with a single amino acid mutation at position 249 in the helicase domain of the NS3 protein. The NY99 strain encodes a proline residue at this position, while KN3829 encodes a threonine. Introduction of an NS3-T249P mutation in the KN3829 genetic background significantly increased virulence and mortality; however, peak viremia and mortality were lower than those of NY99. In order to elucidate the viral genetic basis for phenotype variations exclusive of the NS3-249 polymorphism, chimeric NY99/KN3829 viruses were created. We show herein that differences in the NS1-2B region contribute to avian pathogenicity in a manner that is independent of and additive with the NS3-249 mutation. Additionally, NS1-2B residues were found to alter temperature sensitivity when grown in avian cells.

West Nile virus (WNV) is a mosquito-borne virus that has caused outbreaks in humans in many regions of the world. Birds are the natural hosts for WNV. However, different strains of WNV cause different disease outcomes in birds. Here, we compared two WNV strains, one of which causes higher mortality and generates more virus in American crows than the other. Previous research has shown that this difference is due in large part to a difference between the two strains at a single amino acid in the NS3 gene; however, this difference does not completely explain the observed effect. Here we show that another region of the viral genome also affects disease outcomes in American crows, and changes the sensitivity of the virus to temperature when grown in bird cells. These findings help us to understand the genetic features that affect WNV infection and disease outcomes in its natural host. Detection of such features in new strains of WNV and related viruses could help to understand and predict future outbreaks.

Epidemiological and clinical aspects on West Nile virus, a globally emerging pathogen

BACKGROUND

Since the isolation of West Nile virus (WNV) in 1937, in Uganda, it has spread globally, causing significant morbidity and mortality. While birds serve as amplifier hosts, mosquitoes of the Culex genus function as vectors. Humans and horses are dead end hosts. The clinical manifestations of West Nile infection in humans range from asymptomatic illness to West Nile encephalitis.

METHODS

The laboratory offers an array of tests, the preferred method being detection of RNA and serum IgM for WNV, which, if detected, confirms the clinical diagnosis. Although no definitive antiviral therapy and vaccine are available for humans, many approaches are being studied.

STUDY

This article will review the current literature of the natural cycle, geographical distribution, virology, replication cycle, molecular epidemiology, pathogenesis, laboratory diagnosis, clinical manifestations, blood donor screening for WNV, treatment, prevention and vaccines.

Genetic Variability of West Nile Virus in U.S. Blood Donors from the 2012 Epidemic Season

West Nile virus (WNV) is an arbovirus maintained in nature in a bird-mosquito enzootic cycle which can also infect other vertebrates including humans. WNV is now endemic in the United States (U.S.), causing yearly outbreaks that have resulted in an estimated total of 4-5 million human infections. Over 41,700 cases of West Nile disease, including 18,810 neuroinvasive cases and 1,765 deaths, were reported to the CDC between 1999 and 2014. In 2012, the second largest West Nile outbreak in the U.S. was reported, which caused 5,674 cases and 286 deaths. WNV continues to evolve, and three major WNV lineage I genotypes (NY99, WN02, and SW/WN03) have been described in the U.S. since introduction of the virus in 1999. We report here the WNV sequences obtained from 19 human samples acquired during the 2012 U.S. outbreak and our examination of the evolutionary dynamics in WNV isolates sequenced from 1999-2012. Maximum-likelihood and Bayesian methods were used to perform the phylogenetic analyses. Selection pressure analyses were performed with the HyPhy package using the Datamonkey web-server. Using different codon-based and branch-site selection models, we detected a number of codons subjected to positive pressure in WNV genes. Thirteen of the 19 completely sequenced isolates from 10 U.S. states were genetically similar, sharing up to 55 nucleotide mutations and 4 amino acid substitutions when compared with the prototype isolate WN-NY99. Overall, these analyses showed that following a brief contraction in 2008-2009, WNV genetic divergence in the U.S. continued to increase in 2012, and that closely related variants were found across a broad geographic range of the U.S., coincident with the second-largest WNV outbreak in U.S.

Phylogenetic characterization of Central/Southern European lineage 2 West Nile virus: analysis of human outbreaks in Italy and Greece, 2013-2014

In recent years, West Nile virus (WNV) lineage 2 has been spreading and causing disease outbreaks in humans and animals in Europe. In order to characterize viral diversity, we performed full-length genome sequencing of WNV lineage 2 from human samples collected during outbreaks in Italy and Greece in 2013 and 2014. Phylogenetic analysis showed that these WNV lineage 2 genomes belonged to a monophyletic clade derived from a single introduction into Europe of the prototype Hungarian strain. Correlation of phylogenetic data with geospatial information showed geographical clustering of WNV genome sequences both in Italy and in Greece, indicating that the virus had evolved and diverged during its dispersal in Europe, leading to the emergence of novel genotypes, as it adapted to local ecological niches. These genotypes carried divergent conserved amino acid substitutions, which might have been relevant for viral adaptation, as suggested by selection pressure analysis and in silico and experimental modelling of sequence changes. In conclusion, the results of this study provide further information on WNV lineage 2 transmission dynamics in Europe, and emphasize the need for WNV surveillance activities to monitor viral evolution and diversity.

The challenge of West Nile virus in Europe: knowledge gaps and research priorities

West Nile virus (WNV) is continuously spreading across Europe, and other continents, i.e. North and South America and many other regions of the world. Despite the overall sporadic nature of outbreaks with cases of West Nile neuroinvasive disease (WNND) in Europe, the spillover events have increased and the virus has been introduced into new areas. The high genetic diversity of the virus, with remarkable phenotypic variation, and its endemic circulation in several countries, require an intensification of the integrated and multidisciplinary research efforts built under the 7th Framework Programme of the European Union (FP7). It is important to better clarify several aspects of WNV circulation in Europe, including its ecology, genomic diversity, pathogenicity, transmissibility, diagnosis and control options, under different environmental and socio-economic scenarios. Identifying WNV endemic as well as infection-free areas is becoming a need for the development of human vaccines and therapeutics and the application of blood and organs safety regulations. This review, produced as a joint initiative among European experts and based on analysis of 118 scientific papers published between 2004 and 2014, provides the state of knowledge on WNV and highlights the existing knowledge and research gaps that need to be addressed with high priority in Europe and neighbouring countries.

Latest developments and challenges in the diagnosis of human West Nile virus infection

West Nile virus (WNV) is a mosquito-borne flavivirus responsible for an increasing number of human outbreaks of neuroinvasive disease in Europe and in North America. Notwithstanding the improvements in the knowledge of virus epidemiology and clinical course of infection and the development of new laboratory tests, the diagnosis of WNV infection remains challenging and many cases still remain unrecognized. WNV genome diversity, transient viremia with low viral load and cross-reactivity with other flaviviruses of the antibodies induced by WNV infection are important hurdles that require the diagnosis to be performed by experienced laboratories. Herein, we present and discuss the novel findings on the molecular epidemiology and clinical features of WNV infection in humans with special focus on Europe, the performance of diagnostic tests and the novel methods that have been developed for the diagnosis of WNV infection. A view on how the field might evolve in the future is also presented.

Oxidative stress influences positive strand RNA virus genome synthesis and capping

Flaviviruses are 5′ capped positive-stranded RNA viruses that replicate their genomes within endoplasmic reticulum-derived vesicles. Flaviviruses are well known to induce oxidative stress late in infection but it is unknown if oxidative stress plays a positive role in the viral RNA replication cycle. We therefore examined how oxidation affects flavivirus RNA replication. We found that antioxidant treatment reduced virus production, reduced the viral positive-to-negative strand RNA ratio, and resulted in the accumulation of uncapped positive-sense viral RNAs. Treatment of the NS5 RNA capping enzyme in vitro with oxidizing agents enhanced guanylyltransferase activity, indicating that the guanylyltransferase function of the flavivirus NS5 RNA capping enzyme is activated by oxidative conditions. Antioxidant treatment also reduced alphavirus RNA replication and protein expression while enhancing nsP1 capping activity. These findings suggest that RNA viruses may utilize oxidative stress induced during infection to help temporally control genome RNA capping and genome replication.

Vaccine-induced protection of rhesus macaques against plasma viremia after intradermal infection with a European lineage 1 strain of West Nile virus

The mosquito-borne West Nile virus (WNV) causes human and animal disease with outbreaks in several parts of the world including North America, the Mediterranean countries, Central and East Europe, the Middle East, and Africa. Particularly in elderly people and individuals with an impaired immune system, infection with WNV can progress into a serious neuroinvasive disease. Currently, no treatment or vaccine is available to protect humans against infection or disease. The goal of this study was to develop a WNV-vaccine that is safe to use in these high-risk human target populations. We performed a vaccine efficacy study in non-human primates using the contemporary, pathogenic European WNV genotype 1a challenge strain, WNV-Ita09. Two vaccine strategies were evaluated in rhesus macaques (Macaca mulatta) using recombinant soluble WNV envelope (E) ectodomain adjuvanted with Matrix-M, either with or without DNA priming. The DNA priming immunization was performed with WNV-DermaVir nanoparticles. Both vaccination strategies successfully induced humoral and cellular immune responses that completely protected the macaques against the development of viremia. In addition, the vaccine was well tolerated by all animals. Overall, The WNV E protein adjuvanted with Matrix-M is a promising vaccine candidate for a non-infectious WNV vaccine for use in humans, including at-risk populations.

Programmed ribosomal frameshift alters expression of west nile virus genes and facilitates virus replication in birds and mosquitoes

West Nile virus (WNV) is a human pathogen of significant medical importance with close to 40,000 cases of encephalitis and more than 1,600 deaths reported in the US alone since its first emergence in New York in 1999. Previous studies identified a motif in the beginning of non-structural gene NS2A of encephalitic flaviviruses including WNV which induces programmed −1 ribosomal frameshift (PRF) resulting in production of an additional NS protein NS1′. We have previously demonstrated that mutant WNV with abolished PRF was attenuated in mice. Here we have extended our previous observations by showing that PRF does not appear to have a significant role in virus replication, virion formation, and viral spread in several cell lines in vitro. However, we have also shown that PRF induces an over production of structural proteins over non-structural proteins in virus-infected cells and that mutation abolishing PRF is present in ∼11% of the wild type virus population. In vivo experiments in house sparrows using wild type and PRF mutant of New York 99 strain of WNV viruses showed some attenuation for the PRF mutant virus. Moreover, PRF mutant of Kunjin strain of WNV showed significant decrease compared to wild type virus infection in dissemination of the virus from the midgut through the haemocoel, and ultimately the capacity of infected mosquitoes to transmit virus. Thus our results demonstrate an important role for PRF in regulating expression of viral genes and consequently virus replication in avian and mosquito hosts.

Programmed ribosomal frameshift (PRF) is a strategy used by some viruses to regulate expression of viral genes and/or generate additional gene products for the benefit of the virus. Encephalitic flaviruses from Japanese encephalitis virus serogroup encode PRF motif in the beginning of nonstructural gene NS2A that results in production of an additional nonstructural protein NS1′ which for West Nile virus (WNV) consists of NS1 protein with 52 amino acid addition at the C terminus. Our previous studies showed that abolishing PFR and NS1′ production attenuated WNV virulence in mice. Here we show by using wild type and PRF-deficient WNV mutant that PRF induces overproduction of structural proteins, which facilitates virus replication in birds and mosquitoes while having no advantage for virus replication in cell lines in vitro. Presence of PRF/NS1′ allowed more efficient virus dissemination in the body of mosquitoes after taking infected blood meal and subsequent accumulation of the virus in saliva to facilitate transmission. Combined with our previous data in mice, the results obtained in this study demonstrate that while having no advantage for WNV replication in vitro, PRF provides advantage for WNV replication in vivo in mammalian, avian and mosquito hosts most likely by overproducing viral structural proteins and generating NS1′.

Review of West Nile virus epidemiology in Italy and report of a case of West Nile virus encephalitis

West Nile virus (WNV) is a flavivirus that causes neurological disorders in less than 1 % of infected subjects. Human cases of WNV-associated fever and/or neurological disorders have been reported in Italy since 2008. The first outbreak occurred in the northeastern region of Italy surrounding the Po River and was caused by the Po River lineage 1 strain, and since then, WNV infections have been reported in several regions of central Italy. Although the virus is highly genetically conserved, stochastic mutations in its genome may lead to the emergence of new strains, as was observed in Italy in 2011 with the identification of two new lineage 1 strains, the WNV Piave and WNV Livenza strains. To help further define WNV epidemiology in Italy, we describe a case of an Italian man living in the Po River area who developed fatal encephalitis in 2009 due to infection with the WNV Piave strain. This finding supports the notion that the Piave strain has been circulating in this area of Italy for 2 years longer than was previously believed.

A review of the epidemiological and clinical aspects of West Nile virus

The resurgence of West Nile virus (WNV) in North America and Europe in recent years has raised the concerns of local authorities and highlighted that mosquito-borne disease is not restricted to tropical regions of the world. WNV is maintained in enzootic cycles involving, primarily, Culex spp. mosquitoes and avian hosts, with epizootic spread to mammals, including horses and humans. Human infection results in symptomatic illness in approximately one-fifth of cases and neuroinvasive disease in less than 1% of infected persons. The most consistently recognized risk factor for neuroinvasive disease is older age, although diabetes mellitus, alcohol excess, and a history of cancer may also increase risk. Despite the increasing public health concern, the current WNV treatments are inadequate. Current evidence supporting the use of ribavirin, interferon α, and WNV-specific immunoglobulin are reviewed. Nucleic acid detection has been an important diagnostic development, which is particularly important for the protection of the donated blood supply. While effective WNV vaccines are widely available for horses, no human vaccine has been registered. Uncertainty surrounds the magnitude of future risk posed by WNV, and predictive models are limited by the heterogeneity of environmental, vector, and host factors, even in neighboring regions. However, recent history has demonstrated that for regions where suitable mosquito vectors and reservoir hosts are present, there will be a risk of major epidemics. Given the potential for these outbreaks to include severe neuroinvasive disease, strategies should be implemented to monitor for, and respond to, outbreak risk. While broadscale mosquito control programs will assist in reducing the abundance of mosquito populations and subsequently reduce the risks of disease, for many individuals, the use of topical insect repellents and other personal protective strategies will remain the first line of defense against infection.

Alphavirus mutator variants present host-specific defects and attenuation in mammalian and insect models

Arboviruses cycle through both vertebrates and invertebrates, which requires them to adapt to disparate hosts while maintaining genetic integrity during genome replication. To study the genetic mechanisms and determinants of these processes, we use chikungunya virus (CHIKV), a re-emerging human pathogen transmitted by the Aedes mosquito. We previously isolated a high fidelity (or antimutator) polymerase variant, C483Y, which had decreased fitness in both mammalian and mosquito hosts, suggesting this residue may be a key molecular determinant. To further investigate effects of position 483 on RNA-dependent RNA-polymerase (RdRp) fidelity, we substituted every amino acid at this position. We isolated novel mutators with decreased replication fidelity and higher mutation frequencies, allowing us to examine the fitness of error-prone arbovirus variants. Although CHIKV mutators displayed no major replication defects in mammalian cell culture, they had reduced specific infectivity and were attenuated in vivo. Unexpectedly, mutator phenotypes were suppressed in mosquito cells and the variants exhibited significant defects in RNA synthesis. Consequently, these replication defects resulted in strong selection for reversion during infection of mosquitoes. Since residue 483 is conserved among alphaviruses, we examined the analogous mutations in Sindbis virus (SINV), which also reduced polymerase fidelity and generated replication defects in mosquito cells. However, replication defects were mosquito cell-specific and were not observed in Drosophila S2 cells, allowing us to evaluate the potential attenuation of mutators in insect models where pressure for reversion was absent. Indeed, the SINV mutator variant was attenuated in fruit flies. These findings confirm that residue 483 is a determinant regulating alphavirus polymerase fidelity and demonstrate proof of principle that arboviruses can be attenuated in mammalian and insect hosts by reducing fidelity.

Chikungunya (CHIKV) is a re-emerging mosquito-borne virus that constitutes a major and growing human health burden. Like all RNA viruses, during viral replication CHIKV copies its genome using a polymerase that makes an average of one mistake per replication cycle. Therefore, a single virus generates millions of viral progeny that carry a multitude of distinct mutations in their genomes. In this study, we isolated CHIKV mutators (strains that make more errors than the wildtype virus), to study how higher mutation rates affect fitness in arthropod-borne viruses (arboviruses). CHIKV mutators have reduced virulence in mice and severe replication defects in Aedes mosquito cells. However, these replication defects result in selective pressure for reversion of mutators to a wildtype polymerase in mosquito hosts. To examine how mutators would behave in an insect model in absence of this genetic instability, we isolated mutators of a related virus, Sindbis virus (SINV). SINV mutators had no replication defect in fruit fly (Drosophila) cells, and a SINV mutator strain was stable and attenuated in fruit flies. This work shows proof of principle that arbovirus mutators can exhibit attenuation in both mammalian and insect hosts, and may remain a viable vaccine strategy.

WNV Typer: a server for genotyping of West Nile viruses using an alignment-free method based on a return time distribution

West Nile virus (WNV), genus Flavivirus, family Flaviviridae, is a major cause of viral encephalitis with broad host range and global spread. The virus has undergone a series of evolutionary changes with emergence of various genotypic lineages that are known to differ in type and severity of the diseases caused. Currently, genotyping is carried out using molecular phylogeny of complete coding sequences and genotype is assigned based on proximity to reference genotypes in tree topology. Efficient epidemiological surveillance of WNVs demands development of objective criteria for typing. An alignment-free approach based on return time distribution (RTD) of k-mers has been validated for genotyping of WNVs. The RTDs of complete genome sequences at k=7 were found to be optimum for classification of the known lineages of WNVs as well as for genotyping. It provides time and computationally efficient alternative for genome based annotation of WNV lineages. The development of a WNV Typer server based on RTD is described (http://bioinfo.net.in/wnv/homepage.html). Both the method and the server have 100% sensitivity and specificity.

Vector-virus interactions and transmission dynamics of West Nile virus

West Nile virus (WNV; Flavivirus; Flaviviridae) is the cause of the most widespread arthropod-borne viral disease in the world and the largest outbreak of neuroinvasive disease ever observed. Mosquito-borne outbreaks are influenced by intrinsic (e.g., vector and viral genetics, vector and host competence, vector life-history traits) and extrinsic (e.g., temperature, rainfall, human land use) factors that affect virus activity and mosquito biology in complex ways. The concept of vectorial capacity integrates these factors to address interactions of the virus with the arthropod host, leading to a clearer understanding of their complex interrelationships, how they affect transmission of vector-borne disease, and how they impact human health. Vertebrate factors including host competence, population dynamics, and immune status also affect transmission dynamics. The complexity of these interactions are further exacerbated by the fact that not only can divergent hosts differentially alter the virus, but the virus also can affect both vertebrate and invertebrate hosts in ways that significantly alter patterns of virus transmission. This chapter concentrates on selected components of the virus-vector-vertebrate interrelationship, focusing specifically on how interactions between vector, virus, and environment shape the patterns and intensity of WNV transmission.

Virus Variation Resource--recent updates and future directions

Virus Variation (http://www.ncbi.nlm.nih.gov/genomes/VirusVariation/) is a comprehensive, web-based resource designed to support the retrieval and display of large virus sequence datasets. The resource includes a value added database, a specialized search interface and a suite of sequence data displays. Virus-specific sequence annotation and database loading pipelines produce consistent protein and gene annotation and capture sequence descriptors from sequence records then map these metadata to a controlled vocabulary. The database supports a metadata driven, web-based search interface where sequences can be selected using a variety of biological and clinical criteria. Retrieved sequences can then be downloaded in a variety of formats or analyzed using a suite of tools and displays. Over the past 2 years, the pre-existing influenza and Dengue virus resources have been combined into a single construct and West Nile virus added to the resultant resource. A number of improvements were incorporated into the sequence annotation and database loading pipelines, and the virus-specific search interfaces were updated to support more advanced functions. Several new features have also been added to the sequence download options, and a new multiple sequence alignment viewer has been incorporated into the resource tool set. Together these enhancements should support enhanced usability and the inclusion of new viruses in the future.

West Nile virus state of the art report of MALWEST Project

During the last three years Greece is experiencing the emergence of West Nile virus (WNV) epidemics. Within this framework, an integrated surveillance and control programme (MALWEST project) with thirteen associate partners was launched aiming to investigate the disease and suggest appropriate interventions. One out of seven work packages of the project is dedicated to the State of the Art report for WNV. Three expert working groups on humans, animals and mosquitoes were established. Medical databases (PubMed, Scopus) were searched together with websites: e.g., WHO, CDC, ECDC. In total, 1,092 relevant articles were initially identified and 258 of them were finally included as references regarding the current knowledge about WNV, along with 36 additional sources (conference papers, reports, book chapters). The review is divided in three sections according to the fields of interest: (1) WNV in humans (epidemiology, molecular characteristics, transmission, diagnosis, treatment, prevention, surveillance); (2) WNV in animals (epidemiological and transmission characteristics concerning birds, horses, reptiles and other animal species) and (3) WNV in mosquitoes (control, surveillance). Finally, some examples of integrated surveillance programmes are presented. The introduction and establishment of the disease in Greece and other European countries further emphasizes the need for thorough research and broadening of our knowledge on this viral pathogen.

Characterization of West Nile virus (WNV) isolates from Assam, India: insights into the circulating WNV in northeastern India

West Nile virus (WNV) is a mosquito-borne flavivirus that causes subclinical symptoms, febrile illness with possible kidney infarction and encephalitis. Since WNV was first serologically detected in Assam during 2006, it has become recognized as an important etiological agent that causes acute encephalitis syndrome (AES) in addition to endemic Japanese encephalitis virus (JEV). Therefore, isolating and characterizing the currently circulating strain of WNV is important. The virus was isolated from the cerebrospinal fluid (CSF) of two patients that presented with AES. The genotyping of the isolates HQ246154 (WNIRGC07) and JQ037832 (WNIRTC08) based on the partial sequencing of 921 nucleotides (C-prM-E) of the genome placed them within lineage 5 along with other Indian strains isolated prior to 1982, but the present circulating virus formed a distinct subclade. The derived amino acid sequence alignment indicated substitution in A81T and A84P of the capsid region in HQ246154. A cross-neutralization assay suggested substantial antigenic variation between isolates. The pathogenesis in mice that suggested the circulating WNV was neuroinvasive and comparatively more pathogenic than previous strains from India.

Lack of identification of Flaviviruses in oral and cloacal swabs from long- and short-distance migratory birds in Trentino-Alto Adige (North-eastern Italy)

Background

West Nile virus (WNV) and Usutu virus (USUV), both belonging to the genus Flavivirus, are emerging in Italy as important human and animal pathogens. Migratory birds are involved in the spread of Flaviviruses over long distances, particularly from Africa to Europe. Once introduced, these viruses can be further be dispersed by short-distance migratory and resident bird species. Thus far, there is still a considerable knowledge gap on the role played by different bird species in the ecology and transmission mechanisms of these viruses. The Region of Trentino-Alto Adige (north-eastern Italy) is located on the migratory route of many of the short- and long-distance migratory birds that cross the Alps, connecting northern Europe and western Asia with southern Europe and Africa. Until now, only a silent circulation of WNV and USUV within the territory of the Province of Trento has been confirmed by serological screening, whilst no cases of infected humans or animals have so far been reported. However, continuous spillover events of both viruses have been reported in neighbouring Regions. The aim of this study was to monitor the circulation of WNV and USUV in Trentino-Alto Adige, in order to detect if active virus shedding occurs in migratory birds captured during their seasonal movements and to evaluate the role that different bird species could play in the spreading of these viruses.

Methods

We carried out a biomolecular survey on oral and cloacal swabs collected from migratory birds during seasonal migrations. Birds belonging to 18 transaharian and 21 intrapaleartic species were examined during spring (n = 176) and autumn (n = 146), and were tested using a generic nested-PCR.

Results

All samples tested negative for Flaviviruses. The possible causes of unapparent shedding, along with ecological and epidemiological implications are discussed.

Conclusions

The lack of detection of active virus shedding in these bird species does not exclude the circulation of these viruses within the Trentino-Alto Adige region, as reported in previous studies. The possible ecological implications are discussed.

The complex epidemiological scenario of West Nile virus in Italy

Entomological, veterinary, and human surveillance systems for West Nile virus (WNV) infection have been implemented in Italy since the first detection of the virus in 1998. These surveillance activities documented a progressive increase of WNV activity and spread in different regions and the emergence of new WNV lineages and strains. Italy is a paradigmatic example of the complex epidemiology of WNV in Europe, where sporadic cases of WNV infection, clusters, and small outbreaks have been reported in several regions. In addition, different strains of both WNV lineage 1 and lineage 2 have been identified, even co-circulating in the same area.

West Nile virus genome with glycosylated envelope protein and deletion of alpha helices 1, 2, and 4 in the capsid protein is noninfectious and efficiently secretes subviral particles

Flavivirus genomes with deletions in the capsid (C) gene are attractive vaccine candidates, as they secrete highly immunogenic subviral particles (SVPs) without generating infectious virus. Here, we report that cytomegalovirus promoter-driven cDNA of West Nile virus Kunjin (KUNV) containing a glycosylation motif in the envelope (E) gene and a combined deletion of alpha helices 1, 2, and 4 in C produces significantly more SVPs than KUNV cDNAs with nonglycosylated E and various other deletions in C.

West Nile virus surveillance, Brazil, 2008-2010

BACKGROUND

West Nile virus (WNV) is an emergent pathogen that is widely distributed in North and Central America. The recent introduction in South America has focused attention on the spread of WNV across Southern American countries. The transmission network involves mosquitoes, birds, horses and humans.

METHODS

The serological evaluation of sera from 678 equids and 478 birds was performed using a WNV-specific blocking ELISA, and only the positive results were confirmed by plaque reduction neutralisation tests (PRNTs). Molecular analysis was performed on sera from 992 healthy equids and on 63 macerates of brains from equids that died of encephalitis and had previously tested negative for other pathogens. We also tested swabs from 928 birds. The samples analysed were collected in different biomes of Brazil.

RESULTS

We identified WNV antibodies by ELISA in thirteen equids and five birds, and PRNT90 confirmed WNV positivity in four equid samples collected in 2009 in an area between the Amazon and the Pantanal. None of the ELISA positive bird samples were confirmed by PRNT90, and all samples tested by RT-PCR were negative.

CONCLUSION

WNV circulation is confirmed by this large scale survey even in the absence of detection of clinical cases.

Regulation of flavivirus RNA synthesis and capping

RNA viruses, such as flaviviruses, are able to efficiently replicate and cap their RNA genomes in vertebrate and invertebrate cells. Flaviviruses use several specialized proteins to first make an uncapped negative strand copy of the viral genome that is used as a template for the synthesis of large numbers of capped genomic RNAs. Despite using relatively simple mechanisms to replicate their RNA genomes, there are significant gaps in our understanding of how flaviviruses switch between negative and positive strand RNA synthesis and how RNA capping is regulated. Recent work has begun to provide a conceptual framework for flavivirus RNA replication and capping and shown some surprising roles for genomic RNA during replication and pathogenesis.

Evolutionary dynamics of West Nile virus in the United States, 1999-2011: phylogeny, selection pressure and evolutionary time-scale analysis

West Nile virus (WNV), an arbovirus maintained in a bird-mosquito enzootic cycle, can infect other vertebrates including humans. WNV was first reported in the US in 1999 where, to date, three genotypes belonging to WNV lineage I have been described (NY99, WN02, SW/WN03). We report here the WNV sequences obtained from two birds, one mosquito, and 29 selected human samples acquired during the US epidemics from 2006–2011 and our examination of the evolutionary dynamics in the open-reading frame of WNV isolates reported from 1999–2011. Maximum-likelihood and Bayesian methods were used to perform the phylogenetic analyses and selection pressure analyses were conducted with the HyPhy package. Phylogenetic analysis identified human WNV isolates within the main WNV genotypes that have circulated in the US. Within genotype SW/WN03, we have identified a cluster with strains derived from blood donors and birds from Idaho and North Dakota collected during 2006–2007, termed here MW/WN06. Using different codon-based and branch-site selection models, we detected a number of codons subjected to positive pressure in WNV genes. The mean nucleotide substitution rate for WNV isolates obtained from humans was calculated to be 5.06×10⁻⁴ substitutions/site/year (s/s/y). The Bayesian skyline plot shows that after a period of high genetic variability following the introduction of WNV into the US, the WNV population appears to have reached genetic stability. The establishment of WNV in the US represents a unique opportunity to understand how an arbovirus adapts and evolves in a naïve environment. We describe a novel, well-supported cluster of WNV formed by strains collected from humans and birds from Idaho and North Dakota. Adequate genetic surveillance is essential to public health since new mutants could potentially affect viral pathogenesis, decrease performance of diagnostic assays, and negatively impact the efficacy of vaccines and the development of specific therapies.

West Nile Virus (WNV) is a mosquito-borne virus of African origin that is widespread around the world. The WNV life-cycle involves mosquitoes and birds, but humans and other animals can be infected, although they are not considered to be important players in the transmission cycle. Clinically, most WNV infections are unapparent, but the virus can disseminate to the central nervous system causing a potentially fatal neurological disease, especially in susceptible populations including elderly and immunocompromised individuals. West Nile virus can also be transmitted by organ transplant and by transfusion of blood and blood components. Like other arboviruses, WNV has the extraordinary capacity of growing in the different microenvironments represented by the invertebrate vector and the vertebrate hosts. From an evolutionary standpoint, the arrival of WNV in the US in 1999 represents a unique opportunity to explore the processes involved in the adaptation and dissemination of an arbovirus in a naïve environment. From the study of WNV sequences, we can not only learn about the evolutionary mechanisms that govern arboviruses, but also update diagnostic tests that rely on the detection of the viral genome upon the occurrence of mutations and study the existence of genetic markers that may be responsible for increases in clinical cases and their severity.

Resurgence of West Nile neurologic disease in the United States in 2012: what happened? What needs to be done?

The resurgence in cases of neurologic disease caused by West Nile virus (WNV) in the United States in 2012 came as a surprise to the general public and to many non-arbovirus researchers. Following the introduction of WNV into the US in 1999, the number of human infections rose dramatically, peaking in 2002-03. However, cases declined from 2008-11, and it was unclear if the virus would continue to have a low-level endemic transmission pattern with occasional outbreaks, like the related flavivirus, Saint Louis encephalitis virus, or a more active pattern with annual outbreaks, including occasional years with large epidemics, like Japanese encephalitis virus. The large epidemic in 2012 suggests that the United States can expect periodic outbreaks of West Nile fever and neurologic disease in the coming years. In this paper, we consider the causes of the upsurge in WNV infections during the past year and their implications for future research and disease control measures.

The evolution of virulence of West Nile virus in a mosquito vector: implications for arbovirus adaptation and evolution

BACKGROUND

Virulence is often coupled with replicative fitness of viruses in vertebrate systems, yet the relationship between virulence and fitness of arthropod-borne viruses (arboviruses) in invertebrates has not been evaluated. Although the interactions between vector-borne pathogens and their invertebrate hosts have been characterized as being largely benign, some costs of arbovirus exposure have been identified for mosquitoes. The extent to which these costs may be strain-specific and the subsequent consequences of these interactions on vector and virus evolution has not been adequately explored.

RESULTS

Using West Nile virus (WNV) and Culex pipiens mosquitoes, we tested the hypothesis that intrahost fitness is correlated with virulence in mosquitoes by evaluating life history traits following exposure to either non-infectious bloodmeals or bloodmeals containing wildtype (WNV WT) or the high fitness, mosquito-adapted strain, WNV MP20 derived from WNV WT. Our results demonstrate strain-specific effects on mosquito survival, fecundity, and blood feeding behavior. Specifically, both resistance to and infection with WNV MP20, but not WNV WT, decreased survival of Cx. pipiens and altered fecundity and bloodfeeding such that early egg output was enhanced at a later cost.

CONCLUSIONS

As predicted by the trade-off hypothesis of virulence, costs of infection with WNV MP20 in terms of survival were directly correlated to viral load, yet resistance to infection with this virulent strain was equally costly. Taken together, these results demonstrate that WNV MP20 infection decreases the transmission potential of Cx. pipiens populations despite the increased intrahost fitness of this strain, indicating that a virulence-transmission trade-off in invertebrates could contribute significantly to the adaptive and evolutionary constraint of arboviruses.

Quantifying pathogen surveillance using temporal genomic data

With the advent of deep sequencing, genomic surveillance has become a popular method for detection of infectious disease, supplementing information gathered by classic clinical or serological techniques to identify host-determinant markers and trace the origin of transmission. However, two main factors complicate genomic surveillance. First, pathogens exhibiting high genetic diversity demand higher levels of scrutiny to obtain an accurate representation of the entire population. Second, current systems of detection are nonuniform, with significant gaps in certain geographic locations and animal reservoirs. Despite past unforeseen pandemics like the 2009 swine-origin H1N1 influenza virus, there is no standardized way of evaluating surveillance. A more complete surveillance system should capture a greater proportion of pathogen diversity. Here we present a novel quantitative method of assessing the completeness of genomic surveillance that incorporates the time of sequence collection, as well as the pathogen’s evolutionary rate. We propose the q2 coefficient, which measures the proportion of sequenced isolates whose closest neighbor in the past is within a genetic distance equivalent to 2 years of evolution, roughly the median time of changing strain selection for influenza A vaccines. Easily interpretable and significantly faster than other methods, the q2 coefficient requires no full phylogenetic characterization or use of arbitrary clade definitions. Application of the q2 coefficient to influenza A virus confirmed poor sampling of swine and avian populations and identified regions with deficient surveillance. We demonstrate that the q2 coefficient can not only be applied to other pathogens, including dengue and West Nile viruses, but also used to describe surveillance dynamics, particularly the effects of different public health policies.

Surveillance programs have become key assets in determining the emergence or prevalence of pathogens circulating in human and animal populations. Genomic surveillance, in particular, provides comprehensive information on the history of isolates and potential molecular markers for infectivity and pathogenicity. Current techniques for evaluating genomic surveillance are inaccurate, ignoring the pathogen’s evolutionary rate and biodiversity, as well as the timing of sequence collection. Using sequence data, we propose the q2 coefficient as a quantitative measure of surveillance completeness that combines elements of time and evolution without defining arbitrary criteria for clades or species. Through several case studies of influenza A, dengue, and West Nile viruses, we employed the q2 coefficient to identify sampling deficiencies in different host species and locations, as well as examine the effects of different public health policies through historical records of the q2 coefficient. These results can guide public health agencies to focus resource allocation and virus collection to bolster specific problems in surveillance.

A detailed comparative analysis on the overall codon usage patterns in West Nile virus

West Nile virus (WNV) is a member of the family Flaviviridae and its genome consists of an 11-kb single-stranded, positive-sense RNA. WNV is maintained in an enzootic cycle between mosquitoes and birds, but can also infect and cause disease in horses and humans, which serve as incidental dead-end hosts. Understanding the extent and causes of biases in codon usage is essential to the comprehension of viral evolution. In this study, we performed a comprehensive analysis of 449 WNV strains, for which complete genome sequences are available. Effective number of codons (ENC) indicates that the overall codon usage among WNV strains is only slightly biased. Codon adaptation index (CAI) values found for WNV genes are different from the CAI values found for human genes. The relative synonymous codon usage among WNV strains isolated from birds, equines, humans and mosquitoes are roughly similar and are influenced by the relative dinucleotide frequencies. Taking together, the results of this work suggest that WNV genomic biases are the result of the evolution of genome composition, the need to escape the antiviral cell responses and a dynamic process of mutation and selection to re-adapt its codon usage to different environments.