Use of nucleotide composition analysis to infer hosts for three novel picorna-like viruses.
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.
Kapoor
A
A
Blood Systems Research Institute, San Francisco, CA 94118, USA.
Simmonds
P
P
Lipkin
W I
WI
Zaidi
S
S
Delwart
E
E
D000346:Afghanistan; D000595:Amino Acid Sequence; D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D017931:DNA Primers / Q000235:genetics; D005516:Food Microbiology; D014644:Genetic Variation; D016679:Genome, Viral; D054884:Host-Pathogen Interactions; D006801:Humans; D007313:Insecta / Q000821:virology; D008969:Molecular Sequence Data; D010802:Phylogeny; D010849:Picornaviridae / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics; D057057:Serine Proteases / Q000235:genetics; D013045:Species Specificity; D020506:Untranslated Regions; D017361:Viral Nonstructural Proteins / Q000235:genetics; D015678:Viral Structural Proteins / Q000235:genetics
D017931:DNA Primers; D012367:RNA, Viral; D020506:Untranslated Regions; D017361:Viral Nonstructural Proteins; D015678:Viral Structural Proteins; D057057:Serine Proteases