Detection and Complete Genome Analysis of Porcine Circovirus 2 (PCV2) and an Unclassified CRESS DNA Virus from Diarrheic Pigs in the Dominican Republic: First Evidence for Predominance of PCV2d from the Caribbean Region

Figures

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  Figure 1. Multiple alignment of the partial origin of replication (ori) sequences (downstream of the putative nick site) of porcine circovirus 2 (PCV2) strains from the Dominican Republic (host/virus species/country/virus name/year) with those of reference PCV2 strains (host/PCV2 genotype/GenBank accession number). The four hexamer repeats, H1-4, are highlighted with orange, yellow, pink, and gray, respectively. A unique 11-nucleotide (nt) deletion (shown with red) was observed in the putative ori sequences of PCV2 strain GES7 (shown with blue) from the Dominican Republic and PCV2a strain Belgorod RA18 (GenBank accession number MZ511700, shown with green) from Russia. A ‘*’ denotes an identical nt residue, whilst ‘-’ indicates absence of an nt residue. Numbers to the right indicate the positions of the nt for respective sequences.

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  Figure 2. Phylogenetic analyses of the nucleotide sequences of open reading frame 2 (A) and complete genomes (B) of porcine circovirus 2 (PCV2) strains from the Dominican Republic with those of viruses belonging to the eight PCV2 genotypes (PCV2a-PCV2h). The trees were constructed using the maximum-likelihood method. The host/virus species/country/virus name/year are shown for the PCV2 strains from the Dominican Republic, whilst the host/PCV2 genotype/country/virus name/year of detection, or year of GenBank submission/GenBank accession number have been mentioned for the other PCV2 strains. Red and black circles indicate the PCV2 strains detected in vaccinated animals during 2021 and in unvaccinated animals during 2020, respectively, from the Dominican Republic. In (B), porcine circovirus 1 strain Po/PCV1/UK/PCV1-Eng-1970/1970/KJ408798 was used as the outgroup sequence (not shown here due to space constraints). Bootstrap values < 65% are not shown. Scale bar, 0.01 substitutions per nucleotide. Phylogenetic analyses performed using the neighbor-joining method are shown in Supplementary Material S4.

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  Figure 3. Genome organization of porcine-associated circular Rep-encoding single-stranded (CRESS) DNA virus CRESSV2/ENG22. The nonanucleotide motif at the apex of a putative stem-loop structure (marked in the large intergenic region) and the three predicted open reading frames (ORFs) were located on the genome-sense strand of CRESSV2/ENG22. The ORF encoding the putative replication associated (Rep) protein is shown with red, whilst ORF1 (speculated to encode the putative capsid (Cp) protein) and ORF2 is shown with blue and green, respectively (A). Presence of the conserved rolling circle replication (motifs I through III) and superfamily 3 helicase (Walker A and B, and motif C) motifs in the putative Rep proteins of CRESSV2/ENG22, other porcine-associated CRESS DNA viruses, and porcine circovirus 2. The number below the motif denotes the position of the amino acid (aa) residue in the respective Rep protein. Sample ENG22 also tested positive for porcine circovirus 2d. The GenBank accession numbers are shown in parentheses (B). The putative nonanucleotide motif (highlighted with blue), complementary sequences flanking the nonanucleotide motif (underlined), and repeat sequences (shown with…

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  Figure 4. Phylogenetic analysis of the putative replication associated (Rep) protein of porcine-associated circular Rep-encoding single-stranded (CRESS) DNA virus CRESSV2/ENG22 (shown with black circle) with those of viruses belonging to the orders Cremevirales and Cirlivirales. The virus name/source: animal/sample/country/year/GenBank accession number are shown for the CRESSV2 DNA viruses. Scale bar, 0.5 substitutions per amino acid residue. Bootstrap values of <70 are not shown.