Next-generation T cell–activating vaccination increases influenza virus mutation prevalence

Abstract

To determine the potential for viral adaptation to T cell responses, we probed the full influenza virus genome by next-generation sequencing directly ex vivo from infected mice, in the context of an experimental T cell–based vaccine, an H5N1-based viral vectored vaccinia vaccine Wyeth/IL-15/5Flu, versus the current standard-of-care, seasonal inactivated influenza vaccine (IIV) and unvaccinated conditions. Wyeth/IL-15/5Flu vaccination was coincident with increased mutation incidence and frequency across the influenza genome; however, mutations were not enriched within T cell epitope regions, but high allele frequency mutations within conserved hemagglutinin stem regions and PB2 mammalian adaptive mutations arose. Depletion of CD4 + and CD8 + T cell subsets led to reduced frequency of mutants in vaccinated mice; therefore, vaccine-mediated T cell responses were important drivers of virus diversification. Our findings suggest that Wyeth/IL-15/5Flu does not generate T cell escape mutants but increases stochastic events for virus adaptation by stringent bottlenecks.

Within-host diversity of SARS-CoV-2 lineages and effect of vaccination

“…Only three of the mutations observed in our vaccinated samples overlap with known nAb escape supersites on the Spike NTD or RBD regions and the predicted RBD immune escape potential is only mildly (less than 10% immune escape) affected by these mutations. Evolution of T cell epitopes under selection by the host immune system has been reported for other viruses [43][44][45] , and T cell responses to SARS-CoV-2 have also been reported in most COVID-19 patients 46 . However, we did not detect significant vaccination-specific T cell pressure on within-host diversity, suggesting vaccine-induced pressure may not enhance exploration of immune escape pathways.…”

Early vaccine‐mediated strain‐specific cytokine imbalance induces mild immunopathology during influenza infection

“…Previously we have demonstrated robust protection against lethal (10 times 50% lethal dose [LD 50 ]) challenge with both group 1 (H5N1 and H1N1) and group 2 (H3N2 and H7N7) influenza viruses in Wyeth/IL‐15/5Flu–vaccinated mice 12,14,24 . However, during sublethal infection (0.1LD 50 ) in a related study to characterize the sequence diversity of viruses generated during infection, 13 we observed a group‐specific effect of weight loss and morbidity compared with unvaccinated mice with earlier recovery of H1N1 infection than H3N2 infection in vaccinated mice (Figure 1a, b).…”

“…It has been observed in previous challenge experiments with Wyeth/IL‐15/5Flu‐vaccinated mice that CD4 + and CD8 + T‐cell depletion lead to reduced survival and increased viral loads, 13 with the phenotype of vaccine responses being Th1‐type protection 14 . Although the enhanced T‐cell responses mediated by next‐generation vaccination are essential for heterosubtypic protection, they also are associated with an early cytokine dysregulation and increased morbidity in vaccinated mice.…”

“…However, their rollout and use in an immune population with previous exposure history to seasonal influenza viruses and thus imprinted exposure patterns 26 must generate balanced, protective and robust immunity. In this study, we further assessed an H5N1‐based universal influenza vaccine that elicits broad‐spectrum protective T‐cell responses 13,27,28 . Comparison across multiple experiments showed that early after infection, for H1N1, H3N2 and H7N7 viruses, Wyeth/IL‐15/5Flu significantly lost more weight than PBS‐vaccinated mice despite vaccine responses being protective later against lethal challenge with these viruses.…”

“…We have previously demonstrated substantial heterologous cross reactivity to H1N1, H3N2 and H7N7/9 viruses by our universal vaccinia‐vectored vaccine candidate Wyeth/IL‐15/5flu, which is composed of five proteins from H5N1 viruses: HA, neuraminidase (NA) and nucleoprotein (NP) derived from the A/Vietnam/1203/2004 virus, and M1 and M2 derived from the A/CK/Indonesia/PA/2003 virus 12 . Although homosubtypic H5‐HA–specific antibodies are generated by this vaccine, 13 they do not provide heterosubtypic protection, 12 which is dependent on vaccine‐specific CD4 + T‐cell–mediated protection, 14 and to a lesser extent CD8 + T‐cell responses. Vaccine‐mediated protection, in terms of survival and viral loads, was comparable between H1N1 and H3N2 viruses, and reduced for H7N7 and H7N9 viruses 14 .…”