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West Nile Virus

Background

As an emerging disease in the public eye, WNV continues to generate scientific interest as well. Researchers are exploring questions about its origin, evolution, transmission by multiple vectors and host tissues, replication in multiple hosts, viremic period, viral loads, seroconversion and antibody production, detection, vaccine potential, etc. Central to these investigations are the use of molecular data including nucleic acid sequences and the use of bioinformatics.

WNV is a small, enveloped virus with a positive sense single stranded RNA. This strand can act directly as mRNA and its genome consists of a single open reading frame.

WNV is a member of the Flaviviridae related to yellow fever. It is an arborvirus ( ar thropod bo rne) that arrived in New York City in 1999 and has been spreading across the US, Canada, and Mexico ever since. West Nile is transmitted primarily by mosquitoes that feed on birds. High viral titers found in many bird species make them reservoir hosts for this disease. Other vertebrates often serve as incidental hosts. Variations in enzootic vectors, bridging vectors, avian hosts, climate, and behavior all influence the likelihood that the human population is at risk. Many intriguing research data sets exist for questions raised about tracking the virus.

In humans, symptoms of WNV are subclinical in 80% of those infected. About 1 in 150 ends up with encephalitis. Viremia, the period of time that the virus is active, is usually quite short - six days or less. The amount of genetic material produced from the virus (viral titer) is also quite low less than 5,000 copies per ml of blood. Other viral encephalitis patients have up to 25,000,000 copies per ml of blood. Nevertheless, human to human transmission through blood and organ donation as well as during pregnancy or nursing has been reported. Screening tests including nucleic acid amplification as well as antibody detection have been developed.

Medical research data add to the rich problem space that is available for investigating WNV. In addition to sequence information, images, maps, epidemiological reports, bird counts, etc. are easily accessible on line. Global and historical data since WNV was first isolated in Uganda in 1937 extend the possibilities for working with WNV.

http://www.cdc.gov/ncidod/dvbid/westnile/
CDC: West Nile Virus Homepage

http://www.audubon.org/bird/wnv/
Audubon fact pages.

Goals

  1. Incorporate the use of bioinformatics into your repertoire of problem posing, problem solving, and peer persuasion strategies.
  2. Become familiar with Biology WorkBench including the use of Nucleic Acid Tools such as ClustalW and SixFrame as well as Alignment Tools such as DrawGram, BoxShade, and MView, etc.
  3. Locate and download sequence data on line using Biology WorkBench, NCBI, and more. Edit your sequences for comparing sequence data obtained from multiple sources and/or for making shorter labels.
  4. Learn more about the West Nile Virus.
    • Structure of the virus
    • Transmission cycle
    • Replication cycle
    • Reservoir and incidental hosts (viremia, blood titers, and disease)
    • Vectors for this arbovirus ( arthropod borne)
    • Natural history(in the US and global)
    • Testing for WNV to include Nucleic Acid Amplification Test (NAAT) and ELISA

Tools

Orientation to the Biology Workbench (pdf)
The Biology Workbench is a free and web-accessible collection of tools for exploring and analyzing molecular sequence data. This document provides a quick introduction to using the Biology Workbench. Copyright ©2003 BioQUEST Curriculum Consortium, All Rights Reserved.

http://workbench.sdsc.edu/
Biology WorkBench

http://www.ncbi.nlm.nih.gov/
National Center for Biotechnology Information

Potential Investigations

Tracking West Nile Virus - NYC
Sequences in the strain of WNV introduced in New York City in 1999 can be compared to the sequences found in other strains identified worldwide since 1937 when WNV was first isolated from a woman in Uganda. Using the sequence data set provided and tools from the Biology WorkBench, run a ClustalW to produce a rooted tree in order to examine phylogenetic distances.

Tracking West Nile Virus Israel
How were penned domestic geese in Israel exposed to WNV? Did the stork bring it? Explore bird migrations and the spread of WNV.

Tracking West Nile Virus Regional Differences in the US
Are there transmission factors involved in the differences observed between Eastern, Midwestern, and Western regions of the US? What organisms are involved? How might sequence information help us predict and control future WNV outbreaks?

Evolution of WNV in North America

Throughout 1999 and 2000, WNV spread through northeastern states of the U.S., yet little genetic divergence was observed. The sequence of nucleotides making up its RNA molecule remained pretty much the same. Yet WNV from different regions of the U.S. since 2001 indicate that WNV is evolving. Mutations are incorporated into WNV genetic material and different variants with similar genetic structure tend to occur in the same geographic area.

  • Identify strains associated with specific areas of the US. How might this be helpful to health agencies?
  • Compare WNV strains in Mexico with those in the US and Canada. Which are thought to be here the longest? Why?

Characterize variations in WNV sequences
The viral genome behaves as a single ORF (Open Reading Frame). The single stranded RNA acts as mRNA to produce a protein complex that is digested.

  • Can you identify specific substitutions, deletions, insertions, etc. What percent of these are silent?
  • Can you identify potential changes in viral actions such as infectivity and virulence associated with specific sequence variations.

Testing for WNV
How do we test patients for WNV? How do we screen blood and organ donations?

and more!

Data

West Nile Virus Sequences from Microbes Count!
banet_03
jia_99
lanciotti_03
lanciotti_99
malkinson_02
 

White stork info:
http://www.ooievaars.vlaanderen.be/en/whitestorkframe.html

Structure

Maps

Transmission

Replication and production

Papers