Lara S. U. Schwab1, Ruopeng Xie2,3, Ellie Reilly1, Malet Aban4, Shu Hu2,3, Natalie Spirason4, Yi-Mo Deng4, Randy Suryadinata5,6, Monica Galiano7, Matthew J. Gartner1, Kanta Subbarao1,8, Karen Laurie9, Steve Rockman1, Stephen J. Kent1,10, Adam K. Wheatley1, Ian G. Barr1,4, Vijaykrishna Dhanasekaran2,3, Marios Koutsakos1#
1 Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
2 School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
3 HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
4 WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
5 Department of Respiratory Medicine, Royal Children's Hospital, Parkville, Australia
6 Infection, Immunity and Global Health, Murdoch Children's Research Institute, Parkville, Australia
7 WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, London, UK
8 Department of Microbiology, Infectiology and Immunology, Centre de recherche du CHU de Québec, Laval University, Quebec, Canada
9 Seqirus Ltd, Parkville, Victoria, Australia
10 Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
The antigenic drift of viral glycoproteins must be balanced by purifying selection pressure to maintain functionality. Understanding these evolutionary processes is key to predicting and combating viral evolution but is primarily based on influenza A(H3N2), which may limit generalisability. By characterising the influenza B virus haemagglutinin (HA) over 8 decades of circulation in humans, we found continuous genetic diversification, punctuated with antigenic changes that did not follow a linear path in antigenic space. Antigenic change is primarily underpinned by re-occurring mutations and deletions at positions 136, 150, 162-165, 197 and 203. These residues form complex epistatic networks that modulate the antigenic impact of mutation recycling. They also generate permissive backbones on which immune escape can emerge with limited replicative fitness cost. Our study identifies critical similarities and differences with A(H3N2) evolution and demonstrates the role of epistasis in balancing antigenic novelty with viral fitness. Our findings and genetic, antigenic and phenotypic datasets support the development of genotype-to-phenotype prediction tools, but such predictions need to capture the complex outcomes of epistasis.