Novel G9 rotavirus strains co-circulate in children and pigs, Taiwan

Figures

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  Figure 1. Map of locations in which G9 positive pig farms and residences of patients are located. Map modified from Google Maps: Map data ©2015 Google, ZENRIN, with Adobe Photoshop CS 8.0

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  Figure 2. Genotype constellations of Taiwanese porcine and human G9 RVA strains. Human and porcine strains with similar genotype constellations are included for comparison. Wa-like genotypes are indicated in shades of green, typical porcine genotypes are indicated in shades of blue, and grey represent genotypes that are unusual in human or porcine strains. Strains characterized in this study are indicated in boldface. Roman numerals in parentheses after genotype in strains from this study represent the cluster as identified in phylogenetic trees in Figs 4 and 5. Asterisks indicate rearranged NSP54041.

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  Figure 3. Structure of normal and rearranged NSP5 in (A). Taiwanese porcine strains 3-20, 2-1 and human strains D152, D210 compared to (B). Thai human strains Mc 323 and Mc345, and (C) porcine strains Gottfried and BE2001. Start and stop codons are in bold, YUU and direct repeat motifs are underlined, and beginning of duplicated sequence in red italics. Accession numbers for NSP5 sequences used: 3-20: KU739956, 2-1: KU739916, D152: KU740018, D120: KU740026, Mc323: JN872347, Mc345: JN872348, Gottfried: GU199491, BE2001: JQ993328.

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  Figure 4. Maximum likelihood phylogenetic tree the VP7 gene (A) and the VP4 gene (B) of Taiwanese G9 strains identified in humans and pigs. The G9 VP7 tree was reconstructed using partial gene sequences (VP7, nt 56–1009; VP4, nt 156–883). In both reconstructions the Tamura 3-parameter substitution model with gamma and invariant sites was used with 1,000 bootstrap replicates. Only >75% bootstrap values are shown. Closed circles indicate Taiwanese porcine strains from 2015; open circles indicate Taiwanese human strains; open diamonds denote Taiwanese porcine strains from 2014 used here as reference.

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  Figure 5. Condensed phylogenetic trees of (A) VP1, (B) VP2, (C) VP3, (D) VP6, (E) NSP1, (F) NSP2, (G) NSP3, (H) NSP4, and (I) NSP5 were constructed with MEGA6 using neighbor-joining (maximum composite likelihood) or maximum likelihood method with 1,000 bootstrap replicates using the best-fit substitution models determined by the built-in model test application: GTR = General Time Reversible, T92 = Tamura 92, HKY = Hasegawa-Kishino-Yano 85, TN93 = Tamura-Nei 93, G = gamme sites, I = invariant sites. The region within each of the gene segment used for each analysis is also shown. Open circles indicate Taiwanese human strains, closed circles denote Taiwanese porcine strains from 2015, open diamonds denote Taiwanese porcine strains from 2014.

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  Figure 6. Amino acid variable positions of VP1, VP2, and VP3 in samples from this study and reference typical and unusual strains.

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  Figure 7. Amino acid variable positions of NSP2 and NSP3 in samples from this study and reference typical and unusual strains.