RNA sequence analysis and fluorescent in situ RNA hybridisation revealed the temporal gene expression profile of the porcine reproductive and respiratory syndrome virus in Marc-145 cells

The global outbreaks of porcine reproductive and respiratory syndrome (PRRS) led to a huge loss to the swine industry. Hence, there is a need to further understand how PRRSV transcribes its genes in host cells to better control PRRSV infection. In this study, we implemented RNA-seq and fluorescent in situ RNA hybridisation techniques to determine the temporal gene expression profile of PRRSV in Marc -145 cells. The expression level of PRRSV genes increases over infection time, with a tendency of the expression level from the highest to the lowest for ORF7, ORF6, PRF5, ORF4, ORF3, ORF2, ORF1b and ORF1b, which warrant further confirmations. Next, analyses of protein interaction showed that the host may react to PRRSV infection through many genes, proteins, and pathways involved in surveillance, metabolism, regulation, binding, and splicing of RNA. Furthermore, our codon usage bias (CUB) analysis proposed the hypothesis that synonym mutations by reverse genetic tools can mutate the third letters of codons to be different from the host system, to reduce viral gene transcription and protein translation. In this way, the same amino acids or protein sequences can be produced, but with much less efficacy, and as a result, the artificially synthesised virions can be used as live attenuated vaccines with synonym mutations to stimulate host defence responses and immunity against PRRSV infection. Collectively, our findings provided meaningful information to the temporal gene expression profile of PRRSV. This will assist in filling research gaps and developing strategies for better control of PRRS.