A novel twelve class fluctuation test reveals higher than expected mutation rates for influenza A viruses.

Megan C Procario,Adam S Lauring,Matthew D Pauly

doi:10.7554/elife.26437

Abstract

Influenza virus' low replicative fidelity contributes to its capacity for rapid evolution. Clonal sequencing and fluctuation tests have suggested that the influenza virus mutation rate is 2.7 × 10-6 - 3.0 × 10-5 substitutions per nucleotide per strand copied (s/n/r). However, sequencing assays are biased toward mutations with minimal fitness impacts and fluctuation tests typically investigate only a subset of all possible single nucleotide mutations. We developed a fluctuation test based on reversion to fluorescence in a set of virally encoded mutant green fluorescent proteins, which allowed us to measure the rates of selectively neutral mutations representative of the twelve different mutation types. We measured an overall mutation rate of 1.8 × 10-4 s/n/r for PR8 (H1N1) and 2.5 × 10-4 s/n/r for Hong Kong 2014 (H3N2) and a transitional bias of 2.7-3.6. Our data suggest that each replicated genome will have an average of 2-3 mutations and highlight the importance of mutational load in influenza virus evolution.

Highlights

The rapid evolution of influenza virus has led to reduced vaccine efficacy, widespread drug resistance, and the annual emergence of novel strains
We find that the influenza virus mutation rate is much higher than previously reported and is consistent across two distinct strains and a range of temperatures
We developed a Luria-Delbrück fluctuation test for influenza virus mutation rates that scores reversion to fluorescence in a set of 12 mutant green fluorescent proteins (GFP)

Summary

Introduction

The rapid evolution of influenza virus has led to reduced vaccine efficacy, widespread drug resistance, and the annual emergence of novel strains. Environmental, and host demographic factors influence the evolutionary dynamics of influenza virus, the virus’ adaptability is driven in large part by its capacity to generate genetic diversity through mutation and reassortment [1]. An accurate accounting of influenza virus’ mutation rate and mutational bias is essential for defining its evolutionary dynamics and for informing control efforts. The mutation rate will determine the probability that a mutation conferring drug resistance, antibody escape, or broadened host range will be generated within a given virus population.

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