Decline of transmissible gastroenteritis virus and its complex evolutionary relationship with porcine respiratory coronavirus in the United States

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.

Figure 1

Distribution of TGEV cases. (A) The geographical distribution of positive TGEV cases in the US. (B) The temporal distribution of positive TGEV cases per month between 2008 to 2016. The black dots represent the percentage of TGEV positive cases per month. A LOESS regression model was fitted to the data (red line), and the shaded area represents the 95% confidence interval. The light red shaded areas represent the cold months of November to April. The blue vertical dotted line represents the introduction of PEDV in April 2013.

Figure 2

Genomic insertion-deletions (INDELs) within TGEV and PRCV strains. (A) Variation within the 30 TGEV and 3 PRCV strains. Thin horizontal dash lines represent deletion in the alignment nucleotides. The vertical black bars represent the differences from consensus sequence. The organization of the genome is listed below (B). Visualization of insertion and deletion region of the 30 TGEV and 3 PRCV strains. The dashed lines represent absent nucleotides. The US TGEV strains are colored red. The US PRCV strains are colored purple. The Chinese TGEV strains are colored blue. The Mexican TGEV strain is colored black.

Figure 3

Nucleotide (A) and amino acid (B) entropy analysis of TGEV strains. The x-axis represents nucleotide or amino acid position while the y-axis represents entropy level. The TGEV non-structural and structural proteins are annotated below each plot. Black line represents the variance threshold of 0.7 for nucleotide and amino acid sequences.

Figure 4

Recombination analysis of the variant TGEV strain Oklahoma147 with Minnesota141/2007 (red colored line) and Minnesota155/2016 (blue colored line). The x and y axes indicate the genomic nucleotide position and genetic identity, respectively. Possible recombination position is shaded with light red, and the breakpoint is marked with nucleotide position number (19,941).

Figure 5

Phylogenetic trees of the TGEV and PRCV strains based on the whole genome (n = 40) (A), the whole S gene (n = 56) (B), and partial S gene (n = 70) (C). The scale bar represents nucleotide substitutions per site. The red color represents the US TGEV strains. The purple color represents the US PRCV strains. The blue color represents Chinese TGEV isolates. The black color represents strains from other countries. Our TGEV or PRCV strains were highlighted by solid circle.

Figure 6

Protein alignment and modeling of S1 domain receptor-binding domain RBD, S protein monomer and trimer. (A) The RBD alignment of the 37 whole genome strains and 3 PRCV strains. Identical residues to the consensus sequence are shown as dots while residues that differ from the consensus are highlighted in different colors. (B,C) The monomer and trimer theoretical protein model of the RBD region, with 4 of the 8 major substitutions highlighted in red. (D) Trimer theoretical structure model of RBD, with 2 of the 4 of the TGEV S protein trimer in pink. The body of S protein and the RBD region are highlighted in slate blue and grey.