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

Abstract

Porcine deltacoronavirus (PDCoV) was first reported in Hong Kong, China in 2012 and reported in United States swine in February 2014. PDCoV has subsequently been detected in South Korea, mainland China, and Thailand. PDCoV has been experimentally confirmed to cause diarrhea in inoculated pigs and need to be differentially diagnosed from porcine epidemic diarrhea virus and transmissible gastroenteritis virus in the field. Rapid diagnosis is critical for the implementation of efficient control strategies against PDCoV. Developing high-quality diagnostic methods and understanding PDCoV infection dynamics to collect appropriate specimens at the appropriate time window are important to obtain reliable diagnostic results. Among the virological methods, PDCoV-specific RT-PCR remains the method of choice for the detection of PDCoV; immunohistochemistry combined with hematoxylin and eosin staining has also been commonly used to examine histopathological lesions caused by PDCoV. Serological assays can provide information about previous exposure to PDCoV and also determine antibody responses to infection or vaccination. Prevalence of PDCoV is lower compared to that of PEDV. However, among PDCoV-positive samples, co-infection with other enteric pathogen e.g. PEDV is common. It is also important to understand molecular epidemiology of PDCoV and genetic relationships of global PDCoVs. This review discusses PDCoV infection dynamics and appropriate sample collection for diagnostic testing, the commonly used virological and serological methods for PDCoV diagnosis, prevalence and genetic evolution of PDCoVs.

Keywords: Diagnostics; Genetic evolution; PDCoV; Porcine deltacoronavirus; Prevalence.

Fig. 1

Schematic diagrams of PDCoV genome organization. The PDCoV entire genome organization is depicted at the top. The 5′ untranslated region (UTR), ORFs 1a and 1b encoding replicase polyproteins, spike (S), envelope (E), membrane (M), nonstructural protein 6 (NS6), nucleocapsid (N), nonstructural protein 7 (NS7) genes, and 3′ UTR are shown, with the ribosomal frameshift site indicated. The nucleotide locations of each ORF in the PDCoV genome are depicted at the bottom.

Fig. 2

Schematic diagram of PDCoV infection dynamics in 3-week-old weaned pigs. Time periods with clinical signs, average virus shedding levels (viral RNA as determined by PDCoV M gene-based real-time RT-PCR) in individual fecal swabs, pen-based feces, and pen-based oral fluids, and average neutralizing antibody levels in serum are indicated.

Fig. 3

Biological accessions tested for PDCoV by RT-PCR in the US. (A) Distributions of biological accessions tested and the numbers as well as the percentages of PDCoV-positive accessions by month. (B) Distributions of PDCoV-positive accessions by state from where the samples were collected during March 2014-March 2016. Figures were drawn based on the data available at www.aphis.usda.gov/animal-health/secd.

Fig. 4

Phylogenetic analysis of 50 global PDCoV complete genome sequences. The tree was constructed using the distance-based neighbor-joining method of the software MEGA6.06. Bootstrap analysis was carried out on 1000 replicate data sets, and values are indicated adjacent to the branching points. The US, Korean, Chinese, and Thailand PDCoVs are indicated by black, red, blue and purple font color, respectively.