Abstract
The epidemiology and genetic diversity of transmissible gastroenteritis virus (TGEV) in the United States (US) was investigated by testing clinical cases for TGEV by real time RT-PCR between January 2008 and November 2016. Prevalence of TGEV ranged between 3.8–6.8% and peaked during cold months until March 2013, in which prevalence decreased to < 0.1%. Nineteen complete TGEV genomes and a single strain of porcine respiratory coronavirus (PRCV) from the US were generated and compared to historical strains to investigate the evolution of these endemic coronaviruses. Sixteen of our TGEV strains share 8 unique deletions and 119 distinct amino acid changes, which might greatly affect the biological characteristics of the variant TGEV, and resulted in a “variant” genotype of TGEV. The “variant” genotype shared similar unique deletions and amino acid changes with the recent PRCV strain identified in this study, suggesting a recombination event occurred between the ‘‘variant’’ TGEV and PRCV. Moreover, the results indicate the “variant” genotype is the dominant genotype circulating in the US. Therefore, this study provides insight into the occurrence, origin, genetic characteristics, and evolution of TGEV and PRCV circulating in the US.
Highlights
Transmissible gastroenteritis virus (TGEV) belongs to the genus Alphacoronavirus, family Coronaviridae and contains a single-stranded, positive-sense RNA genome of approximately 28.5 kb in length
The percent of positive transmissible gastroenteritis virus (TGEV) cases per state ranged between 0.4–20.6%, with the highest percentage found in Tennessee
While global historical strains of TGEV caused severe enteritis and porcine respiratory coronavirus (PRCV) is endemic in Europe, Asia, and the United States (US), the mortality rate due to TGEV infections has declined in these countries[3,44,45]
Summary
Transmissible gastroenteritis virus (TGEV) belongs to the genus Alphacoronavirus, family Coronaviridae and contains a single-stranded, positive-sense RNA genome of approximately 28.5 kb in length. In 1946, TGEV was first reported in the United States (US)[5] and was later identified in Europe (Belgium[6], England[2], France[7], Germany[8], The Netherlands[6], and Spain9), Asia (China[10] and Japan11), Africa (South Africa[4] and Uganda12), and South America (Brazil[13]). While the decline of TGEV is believed to occur in response to partial immunity from PRCV infections[29,30,31,32], the United States swine industry made significant changes (increased biosecurity, 3 site production model, etc.) to raise healthier pigs, which may have contributed to the reduction of TGEV infections as well. The porcine enteric coronaviruses (including TGEV, porcine epidemic diarrhea virus [PEDV], and porcine deltacoronavirus [PDCoV]) cause similar clinical presentation, and co-infection of these enteric coronaviruses can occur[33]. Within the past couple of years, a chimeric TGEV and PEDV virus (consisting of a TGEV backbone and the spike of PEDV) was identified in multiple countries in Europe[40,41,42], illustrating the potential emergence of a chimeric TGEV and PEDV virus in the US
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