Analysis of NS2-dependent effects on influenza PB1 segment extends replication requirements beyond the canonical promoter

Abstract

Influenza A virus encodes conserved promoter sequences. Using minimal replication assays—transfections with viral polymerase, nucleoprotein, and a genomic template—these sequences were identified as 13nt at the 5’ end of the genomic RNA (U13) and 12nt at the 3’ end (U12). Other than the fourth 3’ nucleotide, the U12 and U13 sequences are identical between all eight RNA molecules of the segmented influenza A genome. However, individual segments can exhibit different dynamics during infection. Influenza NS2, which modulates transcription and replication differentially between genomic segments, may provide an explanation. Here, we assess how internal sequences of two genomic segments, HA and PB1, contribute to NS2-dependent replication and map such interactions down to individual nucleotides in PB1. We find that the expression of NS2 significantly alters sequence requirements for efficient replication beyond the identical U12 and U13 sequences, providing a potential mechanism for segment-specific replication dynamics across the influenza genome.

Introduction

RNA viruses are constrained in genome size as a result of limitations from packaging and mutational burden1. Due to these constraints it is quite common for viral genomes to encode multifunctional proteins to maximize their use of limited genomic real estate.

Influenza A virus (IAV) is a

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