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Genome of Cowpox Virus

#3273


Study of the Cowpox Virus Genome Variability

Tech Area / Field

  • BIO-CGM/Cytology, Genetics and Molecular Biology/Biotechnology
  • BIO-INF/Bioinformatics/Biotechnology
  • MED-DID/Diagnostics & Devices/Medicine
  • MED-DIS/Disease Surveillance/Medicine
  • BIO-MIB/Microbiology/Biotechnology

Status
3 Approved without Funding

Registration date
25.04.2005

Leading Institute
State Research Center of Virology and Biotechnology VECTOR, Russia, Novosibirsk reg., Koltsovo

Collaborators

  • Centers for Disease Control and Prevention (CDC) / Centers for Disease Control and Prevention, USA, GA, Atlanta\nRobert-Koch-Institute, Germany, Berlin\nInstitute of Microbiology of the German Army, Germany, Munich

Project summary

The main goal of the project is to study the genomic structures of cowpox virus (CPXV) in order to detect the variation of CPXV strains and limits of variability of viral genomes using LPCR–RFLP assay and comparative phylogenetic study of various orthopoxvirus strains.

The project comprises the following tasks:

  1. Preparative production and characterization of 15-20 CPXV strains, isolation of the viral DNAs, and their characterization;
  2. LPCR amplification of the overlapping segments of viral DNAs of complete CPXV genome;
  3. RFLP assay of the amplicons obtained to study the genomic organization of 15-20 CPXV strains using four-letter restriction endonucleases;
  4. Phylogenetic analysis of the data obtained;
  5. PCR amplification, sequencing, and analysis of organization of inpidual loci of 15-20 CPXV strains;
  6. Determination using computer analysis of previously non-described loci promising for species-specific identification of CPXV by PCR; and experiments on development of such method for rapid assay.

In the project the exchange of not infectious DNA preparations of various CPXV strains between Institute of Microbiology of the German Armed Forces and "Vector" is supposed. We will transfer 7-10 DNA preparations and the same quantity of CPXV DNA preparations from the collection of Institute of Microbiology will be received. Search for new CPXV strains using a species-level rapid CPXV diagnostics is also planned. As a result of project implementation, data of comparative DNA restriction analysis of the CPXV strains studied will be obtained as well as data on nucleotide sequences of selected genetic loci of 15-20 CPXV strains (totally, 100–200 kbp). This will allow us to make inference on CPXV genetic organization, find out the patterns of recombinational rearrangement of the viral genome, and reveal the evolutionary relationships between CPXV and other orthopoxviruses. Information will be collaboratively used amongst investigators so as to make timely progress in evaluation of pergence as well as diagnostic advances. Comparative analysis of genomic organization of CPXV strains will allow for determining the limits of their variation, detecting the regions of rearrangements, and answering the question on the presence of CPXV subspecies. The evolutionary potential of CPXV and the probability of emergence of a new variola-like virus will be estimated. The totality of the data obtained will form the background for development of a method for species-specific detection of CPXV.


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