Characterization and evolution of porcine deltacoronavirus in the United States

Abstract

Porcine deltacoronavirus (PDCoV) was identified in multiple states across the United States (US) in 2014. In this study, we investigate the presence of PDCoV in diagnostic samples, which were further categorized by case identification (ID), and the association between occurrence, age, specimen and location between March and September 2014. Approximately, 7% of the case IDs submitted from the US were positive for PDCoV. Specimens were categorized into eight groups, and the univariate analysis indicated that oral fluids had 1.89 times higher odds of detecting PDCoV compared to feces. While the 43-56 day age group had the highest percentage of PDCoV positives (8.4%), the univariate analysis indicated no significant differences between age groups. However, multivariable analysis for age adjusted by specimen indicated the >147 day age group had 59% lower odds than suckling pigs of being positive for PDCoV. The percentage of PDCoV in diagnostic samples decreased to <1% in September 2014. In addition, 19 complete PDCoV genomes were sequenced, and Bayesian analysis was conducted to estimate the emergence of the US clade. The evolutionary rate of the PDCoV genome is estimated to be 3.8×10(-4) substitutions/site/year (2.3×10(-4)-5.4×10(-4), 95% HPD). Our results indicate that oral fluids continue to be a valuable specimen to monitor swineherd health, and PDCoV has been circulating in the US prior to 2014.

Porcine deltacoronavirus: Overview of infection dynamics, diagnostic methods, prevalence and genetic evolution

“…Among the structural proteins, the S glycoprotein of CoVs generally functions in receptor binding, cell membrane fusion and entry; in addition, the S protein is postulated to harbor epitopes to induce neutralizing antibodies. In regards to molecular characterization of PDCoV, the whole genome sequences and/or S and N gene sequences have been frequently used for phylogenetic analysis (Homwong et al, 2016;Janetanakit et al, 2016;Lee et al, 2016;Song et al, 2015;Wang et al, 2014a). The S, M and N protein genes have also been targeted for the development of virological and serological diagnostic assays for PDCoV (Chen et al, 2015b;Ma et al, 2015;Marthaler et al, 2014b;Song et al, 2015;Su et al, 2015;Thachil et al, 2015;Wang et al, 2014a).…”

Isolation, genomic characterization, and pathogenicity of a Chinese porcine deltacoronavirus strain CHN-HN-2014

“…PDCoV was first detected in farmed pig with diarrhea in February 2014 in Ohio, USA (Wang et al, 2014a). To date, it has been reported in at least 18 states of the United States, Canada, South Korea, China, Mexico, and Thailand (Wang et al, 2014b;Ma et al, 2015;Homwong et al, 2016;Janetanakit et al, 2016;Jung et al, 2016;Lee et al, 2016;Zhang, 2016). A retrospective epidemiological study showed that PDCoV was detected in pig samples as early as August 2013 in the United States (McCluskey et al, 2015) and in pig samples in South Korea in May 2014 .…”

The detection and phylogenetic analysis of porcine deltacoronavirus from Guangdong Province in Southern China

“…The emergence of PDCoV was most often associated with clinical infection symptoms including diarrhoea, vomiting and dehydration in pigs, especially in sucking and nursing piglets (Janetanakit et al., ; Ma et al., ; Marthaler, Raymond et al ; Song et al., ). These worldwide outbreaks of PDCoV have caused economic losses to the global commercial swine industry (Chen, Gauger et al., ; Chen, Zhu et al., ; Homwong et al., ; Song et al., ; Wang et al., ).…”