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. 2015 Nov 20;4(4):816-25.
doi: 10.3390/pathogens4040816.

Full Genomic Characterization of a Saffold Virus Isolated in Peru

Mariana Leguia  1 , Steev Loyola  2 , Jane Rios  3 , Diana Juarez  4 , Carolina Guevara  5 , Maria Silva  6 , Karla Prieto  7 , Michael Wiley  8 , Matthew R Kasper  9 , Gustavo Palacios  10 , Daniel G Bausch  11
Affiliations

Full Genomic Characterization of a Saffold Virus Isolated in Peru

Mariana Leguia et al. Pathogens. .

Abstract

While studying respiratory infections of unknown etiology we detected Saffold virus in an oropharyngeal swab collected from a two-year-old female suffering from diarrhea and respiratory illness. The full viral genome recovered by deep sequencing showed 98% identity to a previously described Saffold strain isolated in Japan. Phylogenetic analysis confirmed the Peruvian Saffold strain belongs to genotype 3 and is most closely related to strains that have circulated in Asia. This is the first documented case report of Saffold virus in Peru and the only complete genomic characterization of a Saffold-3 isolate from the Americas.

Keywords: Cardiovirus; Peru; Saffold virus; full genome.

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Figures

Figure 1
Figure 1
Schematic representation of the genomic organization of the SAFV polyprotein, including all genes (L, VP1, VP2, VP3, VP4, 2A, 2B, 2C, 3A, 3B, 3C, and 3D) drawn to approximate scale (top), followed by the corresponding coverage depth by Illumina sequencing (bottom).
Figure 2
Figure 2
Phylogenetic analyses of SAFV full genome (A) and complete VP1 (B) sequences. Each strain is labeled using standard identifiers, including virus type, country of isolation (using ISO country codes), isolate name (if any), year of isolation, and GenBank accession number. Additionally, SAFV1-11 serotypes are color-coded for easy viewing. The Peruvian isolate described here is highlighted in bold and with an arrow. Full genome trees were constructed using a total of 36 publicly available complete genome sequences covering serotypes 1–11. Full VP1 trees were constructed using those same sequences plus 17 additional sequences containing complete VP1 genes. Scale bars represent the number of substitutions per site.
Figure 2
Figure 2
Phylogenetic analyses of SAFV full genome (A) and complete VP1 (B) sequences. Each strain is labeled using standard identifiers, including virus type, country of isolation (using ISO country codes), isolate name (if any), year of isolation, and GenBank accession number. Additionally, SAFV1-11 serotypes are color-coded for easy viewing. The Peruvian isolate described here is highlighted in bold and with an arrow. Full genome trees were constructed using a total of 36 publicly available complete genome sequences covering serotypes 1–11. Full VP1 trees were constructed using those same sequences plus 17 additional sequences containing complete VP1 genes. Scale bars represent the number of substitutions per site.
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