Detection of West Nile virus

Evolution and emergence of mosquito-borne viruses of medical importance: towards a routine metagenomic surveillance approach

During the last two decades, the world has witnessed the emergence and re-emergence of arthropod-borne viruses, better known as arboviruses. The close contact between sylvatic, rural and peri-urban vector species and humans has been mainly determined by the environment-modifying human activity. The resulting interactions have led to multiple dead-end host infections and have allowed sylvatic arboviruses to eventually adapt to new vectors and hosts, contributing to the establishment of urban transmission cycles of some viruses with enormous epidemiologic impact. The metagenomic next-generation sequencing (NGS) approach has allowed obtaining unbiased sequence information of millions of DNA and RNA molecules from clinical and environmental samples. Robust bioinformatics tools have enabled the assembly of individual sequence reads into contigs and scaffolds partially or completely representing the genomes of the microorganisms and viruses being present in biological samples of clinical relevance. In this review, we describe the different ecological scenarios for the emergence of viral diseases, the virus adaptation process required for the establishment of a new transmission cycle and the usefulness of NGS and computational methods for the discovery and routine genomic surveillance of mosquito-borne viruses in their ecosystems.

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.

Viral Enrichment Methods Affect the Detection but Not Sequence Variation of West Nile Virus in Equine Brain Tissue

West Nile virus (WNV), a small, positive sense, single stranded RNA virus continues to encroach into new locales with emergence of new viral variants. Neurological disease in the equine can be moderate to severe in the face of low to undetectable virus loads. Physical methods of virus enrichment may increase sensitivity of virus detection and enhance analysis of viral diversity, especially for deep sequencing studies. However, the use of these techniques is limited mainly to non-neural tissues. We investigated the hypothesis that elimination of equine brain RNA enhances viral detection without limiting viral variation. Eight different WNV viral RNA enrichment and host RNA separation methods were evaluated to determine if elimination of host RNA enhanced detection of WNV and increase the repertoire of virus variants for sequencing. Archived brain tissue from 21 different horses was inoculated with WNV, homogenized, before enrichment and separation. The protocols utilized combinations of low-speed centrifugation, syringe filtration, and nuclease treatment. Viral and host RNA were analyzed using real-time PCR targeting the WNV Envelope (E) protein and equine G3PDH to determine relative sensitivity for WNV and host depletion, respectively. To determine the effect of these methods on viral variation, deep sequencing of the E protein was performed. Our results demonstrate that additional separation and enrichment methods resulted in loss of virus in the face of host RNA depletion. DNA sequencing showed no significant difference in total sequence variation between the RNA enrichment protocols. For equine brain infected with WNV, direct RNA extraction followed by host RNA depletion was most suitable. This study highlights the importance of evaluating viral enrichment and separation methods according to tissue type before embarking on studies where quantification of virus and viral variants is essential to the outcome of the study.

A Mouse Model of West Nile Virus Infection

The use of a mouse model to study the breadth of symptoms and disease severity seen in human West Nile virus (WNV) infection can provide insight into the kinetics of the immune response and the specific pathways responsible for control of WNV infection and viral clearance. Here, we provide protocols for performing WNV infection of mice, as well as complete immunophenotyping analysis of the cellular immune response to infection in both the periphery and the central nervous system in a mouse model of WNV infection. © 2017 by John Wiley & Sons, Inc.

Seroprevalence of anti-WNV IgG antibodies and WNV-RNA in Egyptian blood donors

Transmission of West Nile virus (WNV) from asymptomatic donors has been reported during blood transfusions and organ transplants in humans. In this work, we aimed to investigate the presence of WNV antibody and WNV RNA in blood donors to evaluate the sero-prevalence of WNV and risk for WNV transmission. One hundred and sixty blood donors were tested for the presence of anti-WNV IgG by ELISA and for WNVs 1 and 2 RNA by RT-PCR. About 55% of blood donors were seropositive for WNV IgG antibodies, with significantly higher percentage of positive donors coming from rural areas and Nile Delta region compared to other donors. Using RT-PCR all donors were negative for viral RNA of both WNV lineages 1 and 2. High sero-prevelance of WNV antibodies in asymptomatic blood donors denotes endemicity of the WNV in Egypt and points to the importance of routine screening of blood donors for WNV RNA. On the other hand the absence of WNV RNA by RT-PCR indicates apparent low risk of the blood products as regards WNV transmission. Further studies into significance of WNV seronegativity among Rh negative donors and into the use of WNV seropositive blood in prophylaxis or treatment of WNV neuroinvasive disease are recommended. J. Med. Virol. 89:1323-1329, 2017. © 2017 Wiley Periodicals, Inc.

Geography and Timing of Cases of Eastern Equine Encephalitis in New York State from 1992 to 2012

INTRODUCTION

In New York State (NYS), Eastern equine encephalitis (EEE) was first reported in a human in 1971, in horses in 1970, and in pheasants in 1952.

MATERIAL AND METHOD

Following work for the interval from 1970 to 1991, we identified cases in vertebrates from 1992 to 2012, through a passive surveillance system involving veterinarians in clinical practice, county health departments, and the Departments of Agriculture and Markets, Environmental Conservation, and Health, of the State of New York.

RESULT

During an 11-year hiatus, from 1992 to 2002, no case in any vertebrate was observed. In a re-emergence, from 2003 to 2012, disease occurred in 12 counties, including 7 counties where disease had never been documented. Vertebrate cases included 4 cases in humans and 77 nonhuman occurrences; in 58 horses, Equus ferus caballus L.; 2 deer, Odocoileus virginianus Zimmermann; 6 dogs, Canis familiaris; 10 birds; and 1 flock of pheasants, Phasianus colchicus L. These were the first reported cases in NYS in white-tailed deer, the domestic dog, and in five species of birds: American crow, Corvus brachyrhynchos Brehm; American goldfinch, Carduelis tristis L.; bald eagle, Haliaeetus leucocephalus L.; blue jay, Cyanocitta cristata (L.); and red-tailed hawk, Buteo jamaicensis Gmelin. One crow was dually infected with EEE virus and West Nile virus. The northern, southern, and southeastern borders of the state were newly affected.

CONCLUSION

The geographic area, time periods, and vertebrate species with risk of EEE disease expanded from 1992 to 2012.

Genetic analysis of West Nile virus isolates from an outbreak in Idaho, United States, 2006-2007

West Nile virus (WNV) appeared in the U.S. in 1999 and has since become endemic, with yearly summer epidemics causing tens of thousands of cases of serious disease over the past 14 years. Analysis of WNV strains isolated during the 2006–2007 epidemic seasons demonstrates that a new genetic variant had emerged coincidentally with an intense outbreak in Idaho during 2006. The isolates belonging to the new variant carry a 13 nt deletion, termed ID-Δ13, located at the variable region of the 3′UTR, and are genetically related. The analysis of deletions and insertions in the 3′UTR of two major lineages of WNV revealed the presence of conserved repeats and two indel motifs in the variable region of the 3′UTR. One human and two bird isolates from the Idaho 2006–2007 outbreaks were sequenced using Illumina technology and within-host variability was analyzed. Continued monitoring of new genetic variants is important for public health as WNV continues to evolve.

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.

Development and characterization of West Nile virus replicon expressing secreted Gaussia luciferase

We developed a Gaussia luciferase (Gluc) reporter replicon of West Nile virus (WNV) and used it to quantify viral translation and RNA replication. The advantage of the Gluc replicon is that Gaussia luciferase is secreted into the culture medium from cells transfected with Gluc replicon RNA, and the medium can be assayed directly for luciferase activity. Using a known Flavivirus inhibitor (NITD008), we demonstrated that the Gluc-WNV replicon could be used for antiviral screening. The Gluc-WNV-Rep will be useful for research in antiviral drug development programs, as well as for studying viral replication and pathogenesis of WNV.

Molecular diagnosis of flaviviruses

The genus Flavivirus includes major pathogens such as dengue, yellow fever, Japanese encephalitis, West Nile and tick-borne encephalitis viruses. Molecular amplification assays for the diagnosis of flaviviruses have been developed in the last decades. These assays were formerly based on reverse transcriptase PCR, while in recent years the real-time reverse transcriptase PCR format has taken a predominant role. In this article, we focus on the more recent developments for the molecular diagnosis of flaviviruses, with special attention to those based on new methodologies such as nucleic acid sequence-based amplification or loop-mediated isothermal amplification techniques. These new approaches may provide a good profile of sensitivity and specificity and offer a real chance to implement flavivirus molecular diagnosis in clinical and point-of-care settings.