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In Silico Biology 5, 0048 (2005); ©2005, Bioinformation Systems e.V.  



Molecular analysis of a 348 base-pair segment of open reading frame 2 of human astrovirus. A characterization of Colombian isolates

Juan Carlos Ulloa1, Adriana Matiz1, Leonardo Lareo2 and Maria Fernanda Gutiérrez1*

1 Microbiology Department, Universidad Javeriana, Bogotá, Colombia
2 Biochemistry and Nutrition Department, Universidad Javeriana, Bogotá, Colombia

* Corresponding author
   Email: mfgutier@javeriana.edu.co


Edited by E. Wingender; received June 10, 2005; revised September 23; accepted September 24, 2005; published October 15, 2005


Abstract

We are reporting computational studies of several genotyped strains of astrovirus isolated in Colombia which we have genotyped using the 348-bp segment located between nucleotides 258 and 606 close to the amino terminal region of the complete ORF 2. By biocomputational techniques this 348-bp segment from the different strains was translated into an amino acid sequence. The sequences were aligned and compared in order to build a dendrogram. Our results show that the 348 bp and the 116 amino acid peptides cluster in a very conservative way, showing slight genetic variations between them. This slight sequence variability does not allow us to identify common amino acid substitution patterns shared by all members of each HAstV specific type, thus suggesting that antigenic epitopes are probably located outside the 116 peptide fragment of this capsid protein. These results show that there is little recombination among different regions of the ORF2, thus suggesting that this genotyping method should continue to be useful for serotyping HAstV isolates.


Keywords: human diarrhea, human astrovirus, ORF 2 of human astrovirus