The influenza virus hemagglutinin head evolves faster than the stalk domain

Ericka Kirkpatrick,Justin Bahl,Patrick C Wilson,Florian Krammer,Xueting Qiu

doi:10.1038/s41598-018-28706-1

Abstract

The limited ability of current influenza virus vaccines to protect from antigenically drifted or shifted viruses creates a public health problem that has led to the need to develop effective, broadly protective vaccines. While current influenza virus vaccines mostly induce an immune response against the immunodominant and variable head domain of the hemagglutinin, the major surface glycoprotein of the virus, the hemagglutinin stalk domain has been identified to harbor neutralizing B-cell epitopes that are conserved among and even between influenza A virus subtypes. A complete understanding of the differences in evolution between the main target of current vaccines and this more conserved stalk region are missing. Here, we performed an evolutionary analysis of the stalk domains of the hemagglutinin of pre-pandemic seasonal H1N1, pandemic H1N1, seasonal H3N2, and influenza B viruses and show quantitatively for the first time that the stalk domain is evolving at a rate that is significantly slower than that of the head domain. Additionally, we found that the cross-reactive epitopes in the stalk domain targeted by broadly neutralizing monoclonal antibodies are evolving at an even slower rate compared to the full head and stalk regions of the protein. Finally, a fixed-effects likelihood selection analysis was performed for these virus groups in both the head and stalk domains. While several positive selection sites were found in the head domain, only a single site in the stalk domain of pre-pandemic seasonal H1 hemagglutinin was identified at amino acid position 468 (H1 numbering from methionine). This site is not located in or close to the epitopes of cross-reactive anti-stalk monoclonal antibodies. Furthermore, we found that changes in this site do not significantly impact virus binding or neutralization by human anti-stalk antibodies, suggesting that some positive selection in the stalk domain is independent of immune pressures. We conclude that, while the stalk domain does evolve over time, this evolution is slow and, historically, is not directed to aid in evading neutralizing antibody responses.

Highlights

Whole data sets were subsampled by year, using a random number generator, to contain a total number of sequences that was less than 1000 and to ensure a minimum of 35 sequences per year
The head and stalk domains were determined based on a multiple sequence alignment to the A/South Carolina/1/1918 strain for H1N1, A/Aichi/2/1968 for H3N2, and B/Yamagata/16/1988 for influenza B viruses and their previously defined regions, with numbering beginning from methionine[24] For the head and stalk partitions, we applied the SRD06 approximate codon model (which applies a Hasegawa-Kishono-Yano (HKY) model to codon position 1 + 2 and a HKY model to position 3, separately) and for the STC region we applied an HKY model
The data sets were randomly sub-sampled by year, using a random number generator, so that the total number of sequences in each sub-sample was less than 500 and ensured a minimum of 20 sequences per year

Summary

Introduction

Whole data sets were subsampled by year, using a random number generator, to contain a total number of sequences that was less than 1000 and to ensure a minimum of 35 sequences per year (if available). A sampling of 500 trees selected from the output generated above was used as an empirical set in order to estimate evolutionary rates of the head antigenic sites or the approximate stalk mAb footprints of F10, CR6261, CR9114 and FI6v3 (for H1 viruses) or CR8043, CR8020 (residue R25 in HA2 numbering was omitted from the CR8020 and CR8043 epitopes), CR9114, MEDI8852 and FI6v3 for H3 viruses)[12,13,14,20,26,29]. The amino acids were mapped onto the nucleotide trees and the amino acid substitution rates for each antigenic site or mAb was estimated from repeated sampling of this empirical tree space.

Results

Conclusion