Influenza A Hemagglutinin Passage Bias Sites and Host Specificity Mutations.

Raphael T C Lee,Hsiao-Han Chang,Marc Lipsitch,Sebastian Maurer-Stroh,Colin A Russell

doi:10.3390/cells8090958

Abstract

Animal studies aimed at understanding influenza virus mutations that change host specificity to adapt to replication in mammalian hosts are necessarily limited in sample numbers due to high cost and safety requirements. As a safe, higher-throughput alternative, we explore the possibility of using readily available passage bias data obtained mostly from seasonal H1 and H3 influenza strains that were differentially grown in mammalian (MDCK) and avian cells (eggs). Using a statistical approach over 80,000 influenza hemagglutinin sequences with passage information, we found that passage bias sites are most commonly found in three regions: (i) the globular head domain around the receptor binding site, (ii) the region that undergoes pH-dependent structural changes and (iii) the unstructured N-terminal region harbouring the signal peptide. Passage bias sites were consistent among different passage cell types as well as between influenza A subtypes. We also find epistatic interactions of site pairs supporting the notion of host-specific dependency of mutations on virus genomic background. The sites identified from our large-scale sequence analysis substantially overlap with known host adaptation sites in the WHO H5N1 genetic changes inventory suggesting information from passage bias can provide candidate sites for host specificity changes to aid in risk assessment for emerging strains.

Highlights

Influenza pandemics typically occur when an influenza virus from animals infects humans and evolves the capacity for human-to-human transmission [1,2,3,4,5]
Passage bias sites were frequently shared between different influenza subtypes
In hemagglutinin, overlap of antigenic regions and passage sites might lead to reduced efficacy of egg-grown vaccines [12,29]

Summary

Introduction

Influenza pandemics typically occur when an influenza virus from animals infects humans and evolves the capacity for human-to-human transmission [1,2,3,4,5]. Previous studies in ferrets have shown that as few as 3–4 HA mutations (along with a mutation in the influenza virus polymerase complex) can be sufficient to enable a highly pathogenic A/H5N1 avian influenza virus to become mammal-to-mammal transmissible [7,8] Such experiments are controversial [9] and cannot be performed on a wide variety of strains due to cost and ethical issues; such experiments produce results which cannot be extrapolated across relatively small changes in the genetic background [10]. Observed in laboratory practice, influenza viruses mutate at specific positions when cultured or passaged in different cell types (e.g., from different species). These passage bias mutations are assumed to increase fitness of the virus in the respective species and are sometimes necessary to grow in culture at all. Since passage annotation data is available for tens of thousands of viruses, we wanted to investigate systematically over common subtypes which positions in HA show passage bias and if this information could be linked to host specificity mutations which could aid in pandemic risk assessment in the future [13,14,15,16,17]

Objectives

Methods

Results

Conclusion