title: Comparison of genome sequences of single-stranded RNA viruses infecting the bivalve-killing dinoflagellate Heterocapsa circularisquama.
abstract: Heterocapsa circularisquama RNA virus (HcRNAV) has at least two ecotypes (types UA and CY) that have intraspecies host specificities which are complementary to each other. We determined the complete genomic RNA sequence of two typical HcRNAV strains, HcRNAV34 and HcRNAV109, one of each ecotype. The nucleotide sequences of the viruses were 97.0% similar, and each had two open reading frames (ORFs), ORF-1 coding for a putative polyprotein having protease and RNA-dependent RNA polymerase (RdRp) domains and ORF-2 encoding a single major capsid protein. Phylogenetic analysis of the RdRp amino acid sequence suggested that HcRNAV belongs to a new previously unrecognized virus group. Four regions in ORF-2 had amino acid substitutions when HcRNAV34 was compared to HcRNAV109. We used a reverse transcription-nested PCR system to amplify the corresponding regions and also examined RNAs purified from six other HcRNAV strains with known host ranges. We also looked at natural marine sediment samples. Phylogenetic dendrograms for the amplicons correlated with the intraspecies host specificities of the test virus strains. The cloned sequences found in sediment also exhibited considerable similarities to either the UA-type or CY-type sequence. The tertiary structure of the capsid proteins predicted using computer modeling indicated that many of the amino acid substitutions were located in regions on the outside of the viral capsid proteins. This strongly suggests that the intraspecies host specificity of HcRNAV is determined by nanostructures on the virus surface that may affect binding to suitable host cells. Our study shows that capsid alterations can change the phytoplankton-virus (host-parasite) interactions in marine systems.
authors.affiliation: National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan. nagasaki@affrc.go.jp
authors.forename: Keizo
authors.initials: K
authors.lastname: Nagasaki
authors.forename: Yoko
authors.initials: Y
authors.lastname: Shirai
authors.forename: Yoshitake
authors.initials: Y
authors.lastname: Takao
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Mizumoto
authors.forename: Kensho
authors.initials: K
authors.lastname: Nishida
authors.forename: Yuji
authors.initials: Y
authors.lastname: Tomaru
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D049872:Bivalvia / Q000821:virology*; D002213:Capsid / Q000737:chemistry / Q000378:metabolism; D017753:Ecosystem; D016679:Genome, Viral; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D012328:RNA Viruses / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D012367:RNA, Viral / Q000235:genetics*; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid
chemical_list: D012367:RNA, Viral