Baseline innate and T cell populations are correlates of protection against symptomatic influenza virus infection independent of serology
Authors: Thomas Paul , Mettelman Robert , Souquette Aisha , De Velde Lee-Ann Van , Vegesana Kasi , Allen Emma , Wilson Taylor , Kackos Christina , DeBeauchamp Jennifer , Trifkovic Sanja , Wood Timothy , Jelley Lauren , Webby Richard , Huang Q. Sue , Bocacao Judy , Ralston Jacqui , Danielewicz Jessica , Gunn Wendy , Aminisani Nayyereh , Waite Ben , Kawakami Pam , Nesdale Annette , Balm Michelle , Turner Nikki , Dowell Tony 
Published: January 2023

Abstract
Influenza viruses remain a leading cause of global respiratory illness in humans. The suboptimal effectiveness of seasonal influenza vaccination underscores the need for a more comprehensive understanding of immune mediators of protection, especially in populations with diverse baseline immune profiles and exposure histories. While anti-influenza antibody titers are typically used to define correlates of protection, mounting evidence suggests a substantive role for innate and cellular immunity in determining tolerance and resistance during influenza virus infection. However, distinct cell subsets that correlate with protection against symptomatic influenza remain to be identified in humans. Here, we measured baseline cellular and serologic profiles in peripheral blood from 206 vaccinated or unvaccinated adult subjects enrolled in the 2018 SHIVERS-II cohort to determine how baseline variations in the cellular and humoral immune compartments contribute independently or synergistically to the risk of developing symptomatic influenza infection. Protection from symptomatic influenza correlated with increased individual frequencies of diverse and polyfunctional CD4 and CD8 T cells, cells associated with engagement of humoral responses including cTfh and mDCs, Th17 cells, and innate effector CD16-expressing cytotoxic and cytokine-producing NK cells. In contrast, increased susceptibility was predominantly attributed to nonspecific inflammatory populations including γδ T cells and activated CD16neg NK cells, as well as TNFα+ single-producing CD8 T cells. A trained random forest model categorizing symptomatic influenza cases identified that cellular covariates substantially improved model accuracy up to 86% over demographic and serologic factors alone (61%). A corresponding variable importance analysis showed cellular populations comprise 28 of the top 30 covariates (from 48 total), with the single most important factor being ICOS+ cTfh cells. Lastly, using a multivariate logistic regression model considering participant demographics, anti-influenza antibody titers, vaccination status, and cell population covariates, we quantified how these factors contribute to risk of symptomatic influenza infection. Protection was associated with a combination of lymphocyte populations including naïve, CD107a+, and Th17 CD4 T cells, and serologic factors including antibodies targeting neuraminidase. Increased risk of symptomatic influenza (95% subtype A) was associated with elevated anti-hemagglutinin antibodies against influenza B (Yamagata), along with γδ T cells and TNFα+ CD8 T cell single-cytokine producers. Together, these results demonstrate that the composition of pre-infection peripheral cell profiles is a stronger predictor of symptomatic influenza susceptibility than vaccination, demographics, or serology.