Direct RNA-seq of Type I PRRSV isolated from pig tissues

We report on the micro-evolutionary events taking place within the viral quasispecies population following experimental in vivo infection with the prototypical Lelystad PRRSV in lung and lymph node 3 dpi. A total of 16 high frequency single nucleotide variants (SNV) representative of the consensus inoculum genome were first identified when compared with the reference LV genome. Additionally, 49 other low frequency SNVs were also found in the inoculum population. At 3 days post infection (dpi), a total of 9 and 10 SNVs of varying frequencies could already be detected in the LV population infecting the lung and lymph nodes respectively. Interestingly, of these, three and four novel SNVs have emerged independently in the two respective tissues when compared to the inoculum. The remaining, though already present at lower frequencies in the inoculum, were positively selected and saw their frequency increased within the quasispecies population. The data suggest that microevolution of the viral variants is rapid and some are likely to be tissue-specific.