The Prime-and-Realign Process of the Influenza A Virus Occurs to Rescue Cap-Snatched Primers on the Basis of Length and RNA Duplex Stability

Abstract

Cap-snatching by the influenza A virus (IAV) RNA-dependant RNA polymerase (RdRp) is driven by the abundance of transcripts being actively transcribed by host RNA polymerase II (Pol II)[1]–[3]. Deviations from a direct correlation with abundance do arise, due to selective cleavage of transcripts with a compatible length (10 to 13 nucleotides) and nucleotide sequence (ending in 3’AG)[4]–[7]. Some cap-snatched primers are not directly used to transcribe mRNA, but instead undergo a prime-and-realign mechanism (PAR). As of yet it is unknown why this process occurs. My hypothesis is that the prime-and-realign process is related to the physical characteristics of the primers and their interactions with RdRp and the vRNA template. Here, I used four published deep sequencing datasets of the 5’ ends of IAV mRNA obtained from IAV infected A549 cells to examine PAR[1], [7]–[9]. Primers are biased towards PAR on the basis of length (<12 nucleotides) and RNA duplex stability (mediated by the base directed at 3’U1 and the pyrimidine-purine base pair at position four). PAR typically adds a GCA addition resulting in a primer three nucleotides longer ending in a compatible nucleotide sequence with 3’U1. Prime-and-realign converts poor primers on the basis of length and sequence compatibility with the 3’ end of the vRNA into one that can efficiently undergo transcription of the critical conserved sequence without errors, or failure. Prime-and-realign, therefore, affords tremendous flexibility to RdRp in cap snatched primer length and sequence compatibility.