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Research Project: Development of a Population Genetics Pipeline for Characterizing Viral and Vector Population Diversity

Location:

Project Number: 3022-32000-012-03-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Jul 1, 2020
End Date: Jun 30, 2023

Objective:
The objective of this research is to develop a computational pipeline for analysis of genetic population diversity. This pipeline will be applicable across disciplines but will initially be focused on viral population genetic diversity selected by host source using datasets already planned to be developed in ARS research projects through the following aims: Aim 1: Develop comparative next generations sequence datasets for JEV isolated from invertebrate and vertebrate cell lines and organisms. Aim 2: Establish a computational pipeline to provide quantitative analysis of the genetic diversity between virus populations from various sources. Aim 3: Integrate the virus populations genetics into epidemiology models to provide insight on how viruses may evolve when introduced into new environments.

Approach:
Objective 1: A. Establish assay standards, controls and methods for antibody-mediated virus neutralization for selected Flavivirus and Orbivirus agents. This work will include supportive immunological assays as needed. Reagents will come from existing stocks of viruses, sera and other materials as well as from animal studies to be completed as parts of other studies and through multiple collaborations. B. Evaluate potential neutralization determinants of the selected viruses that may be generated via computational platforms, genetic analysis, immunoprecipitation or other methods. The specific goals will be to identify primary/linear and secondary/conformational epitopes associated with antibody-mediated neutralization.