The porcine epidemic diarrhea virus (PEDV) that emerged and spread throughout Taiwan in 2014 triggered significant concern in the country’s swine industry. Acknowledging the absence of a thorough investigation at the geographic level, we used 2014 outbreak sequence information from the Taiwan government’s open access databases plus GenBank records to analyze PEDV dissemination among Taiwanese pig farms. Genetic sequences, locations, and dates of identified PEDV-positive cases were used to assess spatial, temporal, clustering, GIS, and phylogeographic factors affecting PEDV dissemination. Our conclusion is that S gene sequences from 2014 PEDV-positive clinical samples collected in Taiwan were part of the same Genogroup 2 identified in the US in 2013. According to phylogenetic and phylogeographic data, viral strains collected in different areas were generally independent of each other, with certain clusters identified across different communities. Data from GIS and multiple potential infection factors were used to pinpoint cluster dissemination in areas with large numbers of swine farms in southern Taiwan. The data indicate that the 2014 Taiwan PEDV epidemic resulted from the spread of multiple strains, with strong correlations identified with pig farm numbers and sizes (measured as animal concentrations), feed mill numbers, and the number of slaughterhouses in a specifically defined geographic area.
Canine parvovirus type 2 (CPV-2) is a severe enteric pathogen mainly affecting dogs. CPV-2 contains three antigenic variants (2a, 2b, and 2c) that are distributed internationally. Detection and characterization of the currently circulating CPV-2 strains are vital for the understanding of viral evolution, transmission, and the development of methods to control its spreading. Herein, we analyzed the strains in central Taiwan to provide information of local viral evolution, diversity, and epidemiology. Stool and blood samples from 24 dogs and 2 cats were genotyped by PCR amplification of strain-specific VP2 sequence collected during 2011–2013. 60% (16/26) of them were positive and 100% (16/16) of these positive samples were type 2b. Then, the full length VP2 gene was sequenced in 6 CPV-positive samples and a maximum-likelihood phylogenetic tree was constructed using both Taiwan and other strains worldwide. Surprisingly, all Taiwan CPVs showed high relatedness to type 2a. Recombination analysis revealed a recombination of VP2 gene between type 2a and 2b. This study demonstrates a recombination between CPV-2a and 2b in nature that contributes to the genetic diversity and evolution of CPV-2.
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