Immune Pressure on Polymorphous Influenza B Populations Results in Diverse Hemagglutinin Escape Mutants and Lineage Switching

Abstract

Mutations arise in the genomes of progeny viruses during infection. Mutations that occur in epitopes targeted by host antibodies allow the progeny virus to escape the host adaptive, B-cell mediated antibody immune response. Major epitopes have been identified in influenza B virus (IBV) hemagglutinin (HA) protein. However, IBV strains maintain a seasonal presence in the human population and changes in IBV genomes in response to immune pressure are not well characterized. There are two lineages of IBV that have circulated in the human population since the 1980s, B-Victoria and B-Yamagata. It is hypothesized that early exposure to one influenza subtype leads to immunodominance. Subsequent seasonal vaccination or exposure to new subtypes may modify subsequent immune responses, which, in turn, results in selection of escape mutations in the viral genome. Here we show that while some mutations do occur in known epitopes suggesting antibody escape, many mutations occur in other parts of the HA protein. Analysis of mutations outside of the known epitopes revealed that these mutations occurred at the same amino acid position in viruses from each of the two IBV lineages. Interestingly, where the amino acid sequence differed between viruses from each lineage, reciprocal amino acid changes were observed. That is, the virus from the Yamagata lineage become more like the Victoria lineage virus and vice versa. Our results suggest that some IBV HA sequences are constrained to specific amino acid codons when viruses are cultured in the presence of antibodies. Some changes to the known antigenic regions may also be restricted in a lineage-dependent manner. Questions remain regarding the mechanisms underlying these results. The presence of amino acid residues that are constrained within the HA may provide a new target for universal vaccines for IBV.

Insights from the comparison of genomic variants from two influenza B viruses grown in the presence of human antibodies in cell culture

“…One IBV virus from each lineage was propagated in the presence of human sera in MDCK cells. RNA was extracted, amplified and sequenced using NGS as previously described [ 41 ]. Each parental virus was passaged in MDCK cells in parallel once without sera and the genomes sequenced using NGS.…”

“…A qualitative analysis of the HA segment indicated that variants were present at the same loci in viruses from both lineages [ 41 ]. We analyzed the variants in the remainder of the genomic segments and observed a similar pattern.…”

“…More in depth analyses of influenza A viruses passaged in mice demonstrated that single nucleotide variants associated with adaptation were present in all genomic segments [ 22 , 54 ]. Our prior analysis of the HA gene demonstrated parallel evolution in IBV [ 41 ]. Here we interrogate the quasispecies population for each of these viruses and document parallel evolution in all the genomic segments.…”

“…The methods for virus growth, library preparation and Illumina sequencing have been described elsewhere [ 41 ]. Briefly, one Yamagata-lineage (B/Phuket/3073/2013) and one Victoria-lineage (B/Colorado/06/2017) IBV were propagated in tissue culture in the presence of sera from vaccine recipients.…”

“…The sera were from subjects vaccinated with IBV strains that are antigenically distinct from the passaged viruses. Prior analyses revealed some sera-specific changes in which identical mutations arose in escape viruses from both lineages that altered antigenicity [ 41 ]. In addition the analyses also revealed that some changes in the HA segment made the virus from one lineage appear more like the other lineage [ 41 ].…”