Research Article: Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody

Date Published: June 28, 2016

Publisher: Public Library of Science

Author(s): Ning Chai, Lee R. Swem, Mike Reichelt, Haiyin Chen-Harris, Elizabeth Luis, Summer Park, Ashley Fouts, Patrick Lupardus, Thomas D. Wu, Olga Li, Jacqueline McBride, Michael Lawrence, Min Xu, Man-Wah Tan, Peter Palese.


Broadly neutralizing antibodies targeting the stalk region of influenza A virus (IAV) hemagglutinin (HA) are effective in blocking virus infection both in vitro and in vivo. The highly conserved epitopes recognized by these antibodies are critical for the membrane fusion function of HA and therefore less likely to be permissive for virus mutational escape. Here we report three resistant viruses of the A/Perth/16/2009 strain that were selected in the presence of a broadly neutralizing stalk-binding antibody. The three resistant viruses harbor three different mutations in the HA stalk: (1) Gln387Lys; (2) Asp391Tyr; (3) Asp391Gly. The Gln387Lys mutation completely abolishes binding of the antibody to the HA stalk epitope. The other two mutations, Asp391Tyr and Asp391Gly, do not affect antibody binding at neutral pH and only slightly reduce binding at low pH. Interestingly, they enhance the fusion ability of the HA, representing a novel mechanism that allows productive membrane fusion even in the presence of antibody and hence virus escape from antibody neutralization. Therefore, these mutations illustrate two different resistance mechanisms used by IAV to escape broadly neutralizing stalk-binding antibodies. Compared to the wild type virus, the resistant viruses release fewer progeny viral particles during replication and are more sensitive to Tamiflu, suggesting reduced viral fitness.

Partial Text

Each year influenza virus causes 3 to 5 million cases of severe illness and around half million deaths worldwide [1], with more than 200,000 hospitalizations and approximately 36,000 deaths in the United States alone [2,3]. Beyond causing seasonal flu and epidemics, influenza A virus (IAV) has the potential to generate large pandemics and kill millions of people [4]. Although influenza vaccines are available, they typically elicit strain-specific antibody responses and are thus ineffective against serologically distinct new viral variants. This is exemplified by the mismatch between the 2014 vaccine and the actual H3N2 IAV strain circulating during the 2014/15 winter season [5]. The current standards of treatment for influenza A infection are neuraminidase inhibitors such as oseltamivir phosphate (Tamiflu) and zanamivir (Relenza) that block the function of the viral neuraminidase (NA) protein, thereby blocking efficient viral release from infected cells. Other antiviral drugs such as amantadine, an inhibitor of the viral ion channel M2, have also been used. While these small-molecule inhibitors are effective against susceptible strains, high resistance frequency limits their clinical use. [6,7]. Antiviral resistance and vaccine mismatch can be attributed to the highly error-prone nature of the viral RNA-dependent RNA polymerase, which constantly introduces polymorphisms to viral proteins [8].

Broadly neutralizing stalk-binding mAbs (bnAbs) hold high promise in influenza therapy and the potential of developing a universal flu vaccine. These bnAbs fall into three classes: a) Group 1-specific bnAbs, b) Group 2-specific bnAbs, and c) pan-IAV bnAbs. The epitopes of these bnAbs have been defined. However, extensive studies on the frequency of escape variants and the underlying mechanism of resistance are still needed to address potential liabilities of these antibodies as therapeutics and these epitopes for vaccine development. To-date, antibody-resistant variants have been isolated and characterized only for anti-IAV group 1 and group 2 bnAbs [20–23,27]. Here we report for the first time the isolation of three escape variants to a pan-IAV bnAb. The three variants represent two different escape mechanisms: (a) abolishing antibody binding, which is a common virus escape mechanism, and (b) enhanced membrane fusion ability of HA in conjunction with reduced antibody binding at low pH. To our knowledge, our study is the first report of IAV variants that can escape stalk-binding bnAb by increasing their fusogenic ability to counteract a fusion-inhibiting antibody.




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