Deep-sequencing profile of the distinguishing nucleotides between CPV-2a (KM457143) and 364-rec recombinant (KM457139) strains in sample 364.

a<p> The left fragment (NS gene) of the 364-rec strain was derived from a CPV-2c strain, and the right fragment was from a CPV-2a strain.</p>b<p> Coverage: number of times a nucleotide is read during the sequencing process.</p>c<p> The recombination breakpoint in the 364-rec recombinant strain falls in a 117-nt region between two constant parental markers (positions 2433 and 2549).</p>d<p> The difference in the 2907 position corresponds to a single-nucleotide polymorphism in the 2a homologous region of the co-infecting strains.</p><p>Deep-sequencing profile of the distinguishing nucleotides between CPV-2a (KM457143) and 364-rec recombinant (KM457139) strains in sample 364.</p

CPV recombination network.

<p>The phylogenetic network was generated from alignment of 42 complete CPV genome sequences. There are two main clades encompassing CPV-2c and CPV-2a strains (circles), and an edge (split) that reveals a possible recombination event involving strain 364-rec (KM457139). The Phi test for recombination was significant at p = 0.003.</p

Deep-sequencing profile of the distinguishing nucleotides between CPV-2a (KM457141) and CPV-2c (KM457142) strains in sample 370.

a<p>Coverage: number of times a nucleotide is read during the sequencing process.</p><p>Deep-sequencing profile of the distinguishing nucleotides between CPV-2a (KM457141) and CPV-2c (KM457142) strains in sample 370.</p

Uruguayan dog fecal samples used in this study.

a<p> (C) Capital city (Montevideo); (P) Periphery: cities/regions located in or near (within 15 km) the boundary of Montevideo; (I) Interior (remainder of the country). The VP2 gene sequences for some of these strains have been previously reported <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111779#pone.0111779-Maya1" target="_blank">[31]</a>.</p><p>Uruguayan dog fecal samples used in this study.</p

Phylogenetic incongruence analysis.

<p>Phylogenetic reconstructions were performed with non-recombinant fragments of the 4269-bp CPV coding region containing nt 1–2500 (A), and nt 2501–4269 (B). The 364-rec strain (arrowhead) associates with both the CPV-2c (A) and CPV-2a (B) clades. 2a-UY: Uruguayan CPV-2a clade; 2c-UY: Uruguayan CPV-2c clade; FPV-US.06: feline panleukopenia virus (EU659115); MEV-CH.09: mink enteritis virus (FJ592174); CPV2-US.79: Canine parvovirus type 2 (M38245); CPV2a-15 United States 2a isolate (M24003); CPV2a-s5/2010 Chinese 2a isolate (KF638400.1). CPV2c-56/00 Italian 2c isolate. CH: China; US: United States; UY: Uruguay.</p

Nucleotide and amino acid differences along the coding sequences of all the Uruguayan CPV-2c and CPV-2a strains, and recombinant 364-rec strain (KM457139).

a<p>VP1 Intron. Nucleotides in bold represent identical sequences. Amino acids before and after positions correspond to the CPV-2a and CPV-2c strains, respectively.</p><p>Nucleotide and amino acid differences along the coding sequences of all the Uruguayan CPV-2c and CPV-2a strains, and recombinant 364-rec strain (KM457139).</p