Molecular evolution of influenza A/H3N2 viruses in the province of Québec (Canada) during the 1997-2000 period

The association between influenza vaccine effectiveness and egg-based manufacturing technology: literature review and US expert consensus

BACKGROUND

Influenza is associated with significant disease burden in the US and is currently best controlled by vaccination programs. Influenza vaccine effectiveness (VE) is low and may be reduced by several factors, including egg adaptations. Although non-egg-based influenza vaccines reportedly have greater VE in egg-adapted seasons, evidence for egg adaptations' reduction of VE is indirect and dissociated, apart from two previous European consensuses.

METHODS

This study replicated the methodology used in a 2020 literature review and European consensus, providing an updated review and consensus opinion of 10 US experts on the evidence for a mechanistic basis for reduction of VE due to egg-based manufacturing methods. A mechanistic basis was assumed if sufficient evidence was found for underlying principles proposed to give rise to such an effect. Evidence for each principle was brought forward from the 2020 review and identified here by structured literature review and expert panel. Experts rated the strength of support for each principle and a mechanistic basis for reduction of VE due to egg-based influenza vaccine manufacture in a consensus method (consensus for strong/very strong evidence = ≥ 3.5 on 5-point Likert scale).

RESULTS

Experts assessed 251 references (from previous study: 185; this study: 66). The majority of references for all underlying principles were rated as strong or very strong supporting evidence (52-86%). Global surveillance, WHO candidate vaccine virus selection, and manufacturing stages involving eggs were identified as most likely to impact influenza VE.

CONCLUSION

After review of extensive evidence for reduction of VE due to egg-based influenza vaccine manufacture, influenza experts in the US joined those in Europe in unanimous agreement for a mechanistic basis for the effect. Vaccine providers and administrators should consider use of non-egg-based influenza vaccine manufacture to reduce the risk of egg adaptations and likely impact on VE.

Genetic and antigenic typing of seasonal influenza virus breakthrough cases from a 2008-2009 vaccine efficacy trial

Estimations of the effectiveness of vaccines against seasonal influenza virus are guided by comparisons of the antigenicities between influenza virus isolates from clinical breakthrough cases with strains included in a vaccine. This study examined whether the prediction of antigenicity using a sequence analysis of the hemagglutinin (HA) gene-encoded HA1 domain is a simpler alternative to using the conventional hemagglutination inhibition (HI) assay, which requires influenza virus culturing. Specimens were taken from breakthrough cases that occurred in a trivalent influenza virus vaccine efficacy trial involving >43,000 participants during the 2008-2009 season. A total of 498 influenza viruses were successfully subtyped as A(H3N2) (380 viruses), A(H1N1) (29 viruses), B(Yamagata) (23 viruses), and B(Victoria) (66 viruses) from 603 PCR- or culture-confirmed specimens. Unlike the B strains, most A(H3N2) (377 viruses) and all A(H1N1) viruses were classified as homologous to the respective vaccine strains based on their HA1 domain nucleic acid sequence. HI titers relative to the respective vaccine strains and PCR subtyping were determined for 48% (182/380) of A(H3N2) and 86% (25/29) of A(H1N1) viruses. Eighty-four percent of the A(H3N2) and A(H1N1) viruses classified as homologous by sequence were matched to the respective vaccine strains by HI testing. However, these homologous A(H3N2) and A(H1N1) viruses displayed a wide range of relative HI titers. Therefore, although PCR is a sensitive diagnostic method for confirming influenza virus cases, HA1 sequence analysis appeared to be of limited value in accurately predicting antigenicity; hence, it may be inappropriate to classify clinical specimens as homologous or heterologous to the vaccine strain for estimating vaccine efficacy in a prospective clinical trial.

Longitudinal analysis of genotype distribution of influenza A virus from 2003 to 2005

Influenza A viruses cause yearly epidemics, in part, due to their ability to overcome immunity from previous infections through acquisition of mutations. Amino acid sequences encoded by genes 4 (HA), 6 (NA), 7 (M), and 8 (NS) from 77 H3N2 influenza A isolates, collected between November 2003 and March 2005, were analyzed to determine the extent to which the viruses mutated within epidemic periods and between the epidemics. Nucleotide and amino acid sequences were stable throughout the epidemics but experienced substantial changes between epidemics. Major changes occurred in the HA gene in 5 to 7 amino acids and the NA gene in 11 to 13 amino acids and changes of 5 amino acids occurred in the M and NS genes. In the HA gene, changes occurred in sites known to be epitopes that determine the hemagglutination inhibition reactivity, and these were shown to be associated with a change of strain from A/Fujian/411/2002-like to A/California/7/2004-like viruses. Our findings indicate that genotype determination promises to be a rapid approach for detecting new strains of influenza A viruses in a population.

Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus

BACKGROUND

The interpandemic evolution of the influenza A virus hemagglutinin (HA) protein is commonly considered a paragon of rapid evolutionary change under positive selection in which amino acid replacements are fixed by virtue of their effect on antigenicity, enabling the virus to evade immune surveillance.

RESULTS

We performed phylogenetic analyses of the recently obtained large and relatively unbiased samples of the HA sequences from 1995-2005 isolates of the H3N2 and H1N1 subtypes of influenza A virus. Unexpectedly, it was found that the evolution of H3N2 HA includes long intervals of generally neutral sequence evolution without apparent substantial antigenic change ("stasis" periods) that are characterized by an excess of synonymous over nonsynonymous substitutions per site, lack of association of amino acid replacements with epitope regions, and slow extinction of coexisting virus lineages. These long periods of stasis are punctuated by shorter intervals of rapid evolution under positive selection during which new dominant lineages quickly displace previously coexisting ones. The preponderance of positive selection during intervals of rapid evolution is supported by the dramatic excess of amino acid replacements in the epitope regions of HA compared to replacements in the rest of the HA molecule. In contrast, the stasis intervals showed a much more uniform distribution of replacements over the HA molecule, with a statistically significant difference in the rate of synonymous over nonsynonymous substitution in the epitope regions between the two modes of evolution. A number of parallel amino acid replacements - the same amino acid substitution occurring independently in different lineages - were also detected in H3N2 HA. These parallel mutations were, largely, associated with periods of rapid fitness change, indicating that there are major limitations on evolutionary pathways during antigenic change. The finding that stasis is the prevailing modality of H3N2 evolution suggests that antigenic changes that lead to an increase in fitness typically result from epistatic interactions between several amino acid substitutions in the HA and, perhaps, other viral proteins. The strains that become dominant due to increased fitness emerge from low frequency strains thanks to the last amino acid replacement that completes the set of replacements required to produce a significant antigenic change; no subset of substitutions results in a biologically significant antigenic change and corresponding fitness increase. In contrast to H3N2, no clear intervals of evolution under positive selection were detected for the H1N1 HA during the same time span. Thus, the ascendancy of H1N1 in some seasons is, most likely, caused by the drop in the relative fitness of the previously prevailing H3N2 lineages as the fraction of susceptible hosts decreases during the stasis intervals.

CONCLUSION

We show that the common view of the evolution of influenza virus as a rapid, positive selection-driven process is, at best, incomplete. Rather, the interpandemic evolution of influenza appears to consist of extended intervals of stasis, which are characterized by neutral sequence evolution, punctuated by shorter intervals of rapid fitness increase when evolutionary change is driven by positive selection. These observations have implications for influenza surveillance and vaccine formulation; in particular, the possibility exists that parallel amino acid replacements could serve as a predictor of new dominant strains.

REVIEWERS

Ron Fouchier (nominated by Andrey Rzhetsky), David Krakauer, Christopher Lee.

Comparison between denaturing gradient gel electrophoresis and phylogenetic analysis for characterization of A/H3N2 influenza samples detected during the 1999-2004 epidemics in Brazil

In a preliminary study, a denaturing gradient gel electrophoresis method (DGGE) was described for influenza virus variants screening [Motta, F.C., Rosado, A.S., Couceiro, J.N.S.S., 2002. Standardization of denaturing gradient gel electrophoresis for mutant screening of influenza A (H3N2) virus samples. J. Virol. Meth. 105, 105-115]. Such a protocol has confirmed its usefulness, discriminating closely related samples by the evaluation of the HA1 portion of haemagglutinin coding RNA segment. In this study, the HA1 sequence/phylogenetic analysis was compared with DGGE results to evaluate the degree of agreement between these methods. Forty-one influenza clinical samples characterized as the A/H3 subtype by a multiplex-PCR throughout 1999-2004 epidemics were chosen at random. The 569 bp DGGE amplicons were generated by nested-PCR using the first round multiplex-PCR product as template. The amplicons were analyzed on a 6% polyacrylamide gel with a urea-formamide gradient (25-35%) at 60 degrees C/150 V/5 h, being differentiated by their melting profiles. Even with the multiple melting domains characteristic of the region used in this study, the 41 samples could be grouped in 7 distinct clusters by DGGE. Five of the clusters reproduced exactly the phylogenetic tree topology, including the most external branches. Although the other two clusters demonstrated a poorer match, the internal genetic correlations were conserved, and just four samples were grouped incorrectly in comparison with the phylogenetic results. The results demonstrated the usefulness of this method for screening of variant samples throughout or in subsequent epidemics, thus improving the detection of influenza variants.

Evolution of surface and nonstructural-1 genes of influenza B viruses isolated in the Province of Québec, Canada, during the 1998-2001 period

After 2 minor winter seasons, influenza B viruses were predominantly isolated in the Province of Quebec, Canada, during the 2000-2001 season representing 74% of laboratory-confirmed influenza viruses. We performed an antigenic study of the hemagglutinin (HA) protein and a molecular characterization of the HA1 region, nonstructural-1 (NS1) and neuraminidase (NA)/NB genes of 20 influenza B strains isolated in the Province of Quebec during the 1998-2001 period. Our isolates were compared to recent vaccine strains (B/Harbin/7/94 in 1998-1999, B/Yamanashi/166/98 in 1999-2000 and 2000-2001, and B/Sichuan/379/99 in 2001-2002). The hemagglutination inhibition (HI) test revealed that all isolates were different from B/Harbin/7/94 and were more related to the 2 other vaccine strains although precise identification was often impossible. Molecular analysis of the HA1 gene revealed that both B/Yamanashi/166/98-like and B/Sichuan/379/99-like isolates co-circulated during the 1998-1999 season whereas isolates from the 2 subsequent years were more related to B/Sichuan/379/99. Most isolates (8/9) of the 2000-2001 season contained a N126D substitution recently associated with altered antigenicity in recent influenza B/Yamagata/16/88-related viruses. Although the HA1 and NS1 protein sequences of viruses isolated during the 1998-1999 season were clearly different from those of the respective vaccine strain (B/Harbin/7/94), the NA protein sequence of those isolates was slightly more related to B/Harbin/7/94 than B/Yamanashi/166/98 suggesting distinct patterns of evolution for these genes. This study confirms the importance of a detailed molecular analysis for understanding the evolution of influenza B viruses.

Divergent evolution of hemagglutinin and neuraminidase genes in recent influenza A:H3N2 viruses isolated in Canada

Limited information is available concerning the molecular drift of the influenza neuraminidase (NA) genes. We report on the genetic variability of the NA gene from 31 influenza A:H3N2 viruses isolated in the Province of Québec (Canada) during the last three flu seasons (1997-2000). Amino acid substitutions within the NA protein were observed at rates of 1.01% and 0.45% between strains of the 1997-1998 and 1998-1999 seasons and between those of the 1998-1999 and 1999-2000 seasons, respectively. In most strains (28/31), amino acid changes occurred within at least one of four codons (197, 339, 370, and 401) previously implicated as antigenic sites. The 8 functional and 10 framework residues that compose the catalytic site of the NA enzyme were completely conserved over the study period. All isolates contained the seven conserved asparagine-linked glycosylation sites found in the NA of the progenitor A/Hong Kong/8/68 strain. In addition, most strains (30/31) had an eighth potential glycosylation site at position 329, whereas a ninth one was found at position 93 in 16 strains. The NA of all strains in this study was related to that of the vaccine strain A/Beijing/353/89, whereas the HA genes of these strains were related to the A/Beijing/32/92 vaccine strain. Thus, it appears that recent influenza strains continue to evolve from a reassortant produced during the cocirculation of the two above variants. Interestingly, some strains whose HA genes were closely related showed significant differences in their NA genes and conversely. This study confirms the importance of analyzing both the NA and the HA genes to assess the evolution of recent influenza epidemic strains.