Arbovirus Sequencing Project

The complete genomes of several strains of three different neurotropic arboviruses will be sequenced to understand their pathogenicity and virulence mechanisms. The viruses include Japanese encephalitis virus (JEV), Yellow fever virus (YFV) and Venezuelan equine encephalitis virus (VEEV).

Venezuelan equine encephalitis virus (alphavirus genus) has caused massive outbreaks in humans, equids, and other domestic animals. VEEV is also a well developed biological weapon that is highly infectious via the aerosol route and is classified as a select agent on the NIAID category B list of priority pathogens. VEEV is the most important emerging alphavirus pathogen of the Americas, and has affected hundreds-of-thousands of people since its discovery in 1938. VEEV emerges naturally when sylvatic, enzootic strains mutate to become capable of amplifying in equids and/or of infecting epidemic mosquito vectors. The identification of some of the mutations responsible for these host range changes have been identified phylogenetically. Reverse genetic studies imply that mutations in the E2 envelope glycoprotein gene are major determinants of adaptation to both equines and mosquito vectors. There may be additional contributing mutations from nonstructural proteins that remain to be determined.

Japanese encephalitis virus, a member of the flavivirus genus, is one of the most prevalent causes of viral encephalitis in the world and the leading cause of childhood encephalitis in Asia. It is also classified as a NIAID category B select agent and is also transmitted to humans through mosquitoes. JE has been divided into four distinct genotypes with a maximum divergence of 21% among the isolates. Little is known about the molecular basis of neurovirulance of JEV or the biological differences between genotypes, which will be necessary for development of improved vaccines against the virus.

Yellow fever virus is another mosquito-borne member of the flavivirus genus responsible for epidemics of hemorrhagic fever in sub-Saharan Africa and tropical South America for hundreds of years. Yellow fever is considered to be a re-emerging infectious disease and the causative agent YFV is classified as a NIAID category C priority pathogen. Complete genomes for only 10 isolates of wild-type YFV have been determined. The identification of genetic variation in numerous isolates will help to identify proteins to be considered as potential drug targets and possibly a pan-flavivirus drug.

Material for the study of these viruses will be obtained from the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA), which contains over 1000 isolates from mosquitoes, birds, pigs, and humans from over a period of more than 70 years. This collection will be used to identify 100 strains each of JEV, YFV, VEEV and 100 unknowns (400 total) for complete genome sequencing. Strains will span various hosts, geographic regions, and time periods to provide a broad diversity of genomes for study. The sequencing data generated from these projects will be used to identify potential determinants of pathogenesis, virulence, immunologic response to infection, and improved vaccines or drug targets, as well as to provide new insight into the ecology, evolution and emergence of these viral agents of infectious disease.


This project has been funded in whole or part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services under contract numbers N01-AI30071 and/or HHSN272200900007C.


David Wentworth, PhD
Director Viral Programs

Alan Barrett, PhD
Robert B. Tesh, PhD
Scott Weaver, PhD
University of Texas Medical Branch

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