Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes

Gardner, Shea N.; Jaing, Crystal J.; Elsheikh, Maher M.; Peña, José; Hysom, David A.; Borucki, Monica K.

Run tiled primers was used to design primers for selected regions of the coronavirus murine hepatitis virus (strain MHV-1) genome following passage in the lab, for a separate project in which deep sequencing of selected regions following lab passage was performed. In other work attempting to amplify passaged RNA viruses, finding robust primers based on the original genome was difficult due to mutations which modified primer binding sites [8] . It was hoped that run tiled primers would help avoid selecting primers in mutational hotspots by taking into account strain variation across multiple available genomes for the species, since run tiled primers seeks maximally conserved primers in the available sequences.