Porcine Respiratory Coronavirus (PRCV): Isolation and Characterization of a Variant PRCV from USA Pigs

Abstract

Porcine respiratory coronavirus (PRCV), a mutant of the transmissible gastroenteritis virus (TGEV), was first reported in Belgium in 1984. PRCV typically replicates and induces mild lesions in the respiratory tract, distinct from the enteric tropism of TGEV. In the past 30 years, PRCV has rarely been studied, and most cited information is on traditional isolates obtained during the 1980s and 1990s. Little is known about the genetic makeup and pathogenicity of recent PRCV isolates. The objective of this study was to obtain a contemporary PRCV isolate from US pigs for genetic characterization. In total, 1245 lung homogenate samples from pigs in various US states were tested via real-time PCR targeting PRCV and TGEV RNA. Overall, PRCV RNA was detected in five samples, and a single isolate (ISU20-92330) was successfully cultured and sequenced for its full-length genome. The isolate clustered with a new group of variant TGEVs and differed in various genomic regions compared to traditional PRCV isolates. Pathogens, such as PRCV, commonly circulate in pig herds without causing major disease. There may be value in tracking genomic changes and regularly updating the diagnostic methods for such viruses to be better prepared for the emergence of variants in ecology and pathogenicity.

Keywords: PRCV/TGEV/XIPC 3-plex RT PCR; genomic analysis; porcine respiratory coronavirus (PRCV); prevalence; transmissible gastroenteritis virus (TGEV).

Figure 1

Multi-step growth curve of a contemporary PRCV isolate (ISU20-92330) and a traditional PRCV isolate (AR310) in ST cells. The mean titers log₁₀ (TCID₅₀/_mL) at each time point are shown. Asterisks indicate significant differences between the two virus strains at certain time points.

Figure 2

Phylogenetic trees based on whole-genome sequences (A) and full-length spike gene (B) sequences of TGEV (n = 34) and PRCV (n = 11). The variant TGEV group and traditional TGEV group are labeled in the trees. Three PRCV sequences closely clustered with the variant TGEV group are denoted with circles, two previously reported sequences are shown by a black circle, and one sequence determined in this study (PRCV_USA/ISU20-92330/2020) is shown in a red circle. Other traditional PRCV sequences are shown in triangles.

Figure 3

Summary of TGEV and PRCV sequence comparisons across the genome. On top, the schematic diagram shows the organization of the TGEV and PRCV genome, which includes ORF1a, ORF1b, spike (S), ORF3a, ORF3b, envelope (E), membrane (M), nucleocapsid (N), and ORF7. At the bottom, the length of each gene, as well as the intergenic region between S and ORF3a and the intergenic region between ORF3a and ORF3b, is provided. Thirteen representative traditional TGEVs are shown in a blue color, and nine representative variant TGEVs are shown in a red color.

Figure 4

Comparison of partial nsp3 sequences demonstrating the differences between traditional TGEVs, variant TGEVs, and PRCVs. The representative traditional TGEVs are shown in a blue color, and the representative variant TGEVs are shown in a red color. Nucleotides are numbered according to the TGEV PUR46-MAD sequence (GenBank accession number AJ271965).

Figure 5

Comparison of partial spike gene sequences demonstrating the differences between traditional TGEVs, variant TGEVs, and PRCVs. The representative traditional TGEVs are shown in a blue color, and the representative variant TGEVs are shown in a red color. Nucleotides are numbered according to the TGEV PUR46-MAD sequence (GenBank accession number AJ271965).