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Nearly complete genome sequences of three novel RNA viruses were acquired from the stool of an Afghan child. Phylogenetic analysis indicated that these viruses belong to the picorna-like virus superfamily. Because of their unique genomic organization and deep phylogenetic roots, we propose these viruses, provisionally named calhevirus, tetnovirus-1, and tetnovirus-2, as prototypes of new viral families. A newly developed nucleotide composition analysis (NCA) method was used to compare mononucleotide and dinucleotide frequencies for RNA viruses infecting mammals, plants, or insects. Using a large training data set of 284 representative picornavirus-like genomic sequences with defined host origins, NCA correctly identified the kingdom or phylum of the viral host for >95% of picorna-like viruses. NCA predicted an insect host origin for the 3 novel picorna-like viruses. Their presence in human stool therefore likely reflects ingestion of insect-contaminated food. As metagenomic analyses of different environments and organisms continue to yield highly divergent viral genomes NCA provides a rapid and robust method to identify their likely cellular hosts.

Original publication

DOI

10.1128/JVI.00601-10

Type

Journal article

Journal

J Virol

Publication Date

10/2010

Volume

84

Pages

10322 - 10328

Keywords

Afghanistan, Amino Acid Sequence, Animals, Base Composition, Base Sequence, DNA Primers, Food Microbiology, Genetic Variation, Genome, Viral, Host-Pathogen Interactions, Humans, Insecta, Molecular Sequence Data, Phylogeny, Picornaviridae, RNA, Viral, Serine Proteases, Species Specificity, Untranslated Regions, Viral Nonstructural Proteins, Viral Structural Proteins