
==== Front
bioRxiv
BIORXIV
bioRxiv
2692-8205
Cold Spring Harbor Laboratory

10.1101/2024.08.15.608152
preprint
1
Article
Influenza A virus within-host evolution and positive selection in a densely sampled household cohort over three seasons
Bendall Emily E.
Zhu Yuwei
Fitzsimmons William J.
Rolfes Melissa http://orcid.org/0000-0002-0483-9941

Mellis Alexandra http://orcid.org/0000-0001-6756-1425

Halasa Natasha
Martin Emily T. http://orcid.org/0000-0002-5771-8895

Grijalva Carlos G. http://orcid.org/0000-0002-2329-7797

Talbot H. Keipp
Lauring Adam S. http://orcid.org/0000-0003-2906-8335

19 8 2024
2024.08.15.608152https://creativecommons.org/licenses/by-nc-nd/4.0/ This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator.
http://biorxiv.org/lookup/doi/10.1101/2024.08.15.608152
nihpp-2024.08.15.608152.pdf
Abstract

While influenza A virus (IAV) antigenic drift has been documented globally, in experimental animal infections, and in immunocompromised hosts, positive selection has generally not been detected in acute infections. This is likely due to challenges in distinguishing selected rare mutations from sequencing error, a reliance on cross-sectional sampling, and/or the lack of formal tests of selection for individual sites. Here, we sequenced IAV populations from 346 serial, daily nasal swabs from 143 individuals collected over three influenza seasons in a household cohort. Viruses were sequenced in duplicate, and intrahost single nucleotide variants (iSNV) were identified at a 0.5% frequency threshold. Within-host populations were subject to purifying selection with >75% mutations present at <2% frequency. Children (0-5 years) had marginally higher within-host evolutionary rates than adolescents (6-18 years) and adults (>18 years, 4.4x10 -6 vs. 9.42x10 -7 and 3.45x10 -6 , p <0.001). Forty-five iSNV had evidence of parallel evolution, but were not overrepresented in HA and NA. Several increased from minority to consensus level, with strong linkage among iSNV across segments. A Wright Fisher Approximate Bayesian Computational model identified positive selection at 23/256 loci (9%) in A(H3N2) specimens and 19/176 loci (11%) in A(H1N1)pdm09 specimens, and these were infrequently found in circulation. Overall, we found that within-host IAV populations were subject to purifying selection and genetic drift, with only subtle differences across seasons, subtypes, and age strata. Positive selection was rare and inconsistently detected.
==== Body
pmc
