Genotyping and origin of the emergent U. S

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Genotyping and origin of the emergent U. S Genotyping and origin of the emergent U.S. PEDV strains based on full-length genomic sequence analyses. Genotyping and origin of the emergent U.S. PEDV strains based on full-length genomic sequence analyses. (A) Phylogeny-based genotyping of 26 PEDV strains with available complete genomic sequences, including the 3 U.S. PEDV strains. The tree was constructed by the neighbor-joining method, based upon the full-length genomic nucleotide sequences using the bat coronavirus BtCoV/512/2005 sequence as an outgroup. Bootstrap values are indicated for each node from 1,000 resamplings. The names of the strains, years and places of isolation, GenBank accession numbers, and genogroups and subgroups proposed in this study are shown. (An asterisk indicates that the isolation year of LZC is unknown but should be before 2006 according to the GenBank submission date.) Red solid circles, the three U.S. PEDV strains; purple solid triangles, cell-culture-adapted PEDV strains or vaccines; green solid diamonds, bat coronavirus BtCoV/512/2005. (B) Phylogeny-based geographical dissection of genogroup 2 Chinese PEDV strains. The map of China shows all of the provinces where genogroup 2 PEDV strains with the available complete genomic sequences were isolated. The numbers in order and the colors for PEDV strains correspond to those labeled in panel A: genogroup 2a strains are in red, and genogroup 2b strains are in blue. The coverage area for each subgroup (depicted by the red or the blue oval) is deduced based on the distributions of the strains. XS indicates a representative strain (XS2012) isolated in Zhejiang Province of eastern China that belongs to genogroup 2a based on the sequence of the S gene from this study. The yellow shaded circle indicates the hypothetical location of the origin of the U.S. PEDV, where the closely related AH2012 strain was identified. The two early PEDV strains CH/S and LZC and their locations are also shown. Five provinces where bat coronaviruses phylogenetically related to PEDV were isolated (10) are also marked by the “bat” symbols. In particular, the BtCoV/512/2005 strain, isolated in Hainan Province, is marked in green. (C) Bootscan analysis for possible recombination events of lineage US-AH strains (three U.S. strains plus the AH2012 strain) in subgroup 2a as the query group throughout the genome compared to the other two lineages. 2a-BJ/JS/GD includes strains BJ-2011-1, GD-B and JS-HZ2012 (denoted by the brown line), and “2a-others” includes CH/ZMDZY/11, CH/FJND-3/2011, and CH/FLZZ-9/2012 (denoted by the yellow line) in the same subgroup (based upon the phylogenetic tree constructed in panel A), subgroup 1a (green line), 1b (red line), R (cyan line), 2b (purple line), and BtCoV/512/2005 (accession no. DQ648858 [blue line]). Bootscanning was conducted by SimPlot (version 3.5.1; window size: 1,000 bp; step, 200 bp), and the cutoff value of bootstrap support for clustering was set to 70. The putative recombinant regions corresponding to functional domains in the PEDV genome are shown at the top. Yao-Wei Huang et al. mBio 2013; doi:10.1128/mBio.00737-13