Figure 1.
Analysis of Halastavi árva RNA virus (HalV) complete genome (9565 nt) for putative open reading frames.
In the ORF map (Fig. 1A) for each reading frame (1, 2 and 3), potential start codons (AUG) are shown with a half-height line and stop codons (UGA, UAA, UAG) are shown by full-height lines. Predicted and recognizable viral proteins and other genomic features (UTR = untranslated region; IGR = intergenic region) are noted (Fig. 1B). Numbers for nucleotide (nt; upper number) and amino acid (aa; lower number) sequences indicate the first sequence positions of the next regions. Cleavage sites were not experimentally determined but estimated by alignment of deduced amino acid sequences (see text for more detail). Fig. 1C shows the genome acquisition strategy using 3′/5′-RACE method.
Table 1.
List of primers used in this study for detection and characterization.
Table 2.
Percental amino acid identity of the Halastavi árva RNA virus protein regions compared to the GenBank sequences using blastp (see details in Materials).
Figure 2.
Phylogenetic tree of nonstructural region.
Phylogenetic analysis based upon the amino acid sequences of complete nonstructural region (including 2C-like helicase, 3C-like protease and 3D-like RNA dependent RNA-polymerase) between the members of the order Picornavirales (Dicistroviridae, Iflaviridae, Marnaviridae, Picornaviridae and Secoviridae), marine positive-sense single-stranded RNA (+ssRNA) viruses with di-cistronic genome organization and Halastavi árva RNA virus (JN000306) identified in intestinal content of freshwater carp (Cyprinus carpio) in Hungary. Black (•) and white (○) circles represent viruses with di- and mono-cistronic genome structure. Specific hosts – if known - are shown in relation with the virus family name. Halastavi árva RNA virus is indicated by black arrow.
Figure 3.
Phylogenetic tree of structural region.
Phylogenetic analysis of amino acid sequences of complete capsid (VP2/VP4/VP3/VP1) region of representative members in the order Picornavirales. The accession numbers of the reference strains are showed in Figure 2. Halastavi árva RNA virus (JN000306) is indicated by black arrow.
Figure 4.
Nucleotide composition analysis of Halastavi árva RNA virus.
(A) Frequencies of CpG and UpA dinucleotides in picorna-like viruses from different hosts expressed as observed-to-expected ratios (y-axis). (B) Projections of the first three (most significant) canonical factors that differentiate host origins of the control sequences using mononucleotide dinucleotide frequencies. Points represent values for individual sequences, with 95% confidence ellipses positioned around the centroid of each group [17]. Halastavi árva RNA virus (JN000306) is labeled by black arrows.