---
title: "Host type shapes influenza H3Nx evolution: reassortment in birds, adaptation in mammals"
id: "biorxiv-10-host-type-governs-influenza-evolutionary-strategy-across-reservoir-and"
canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-10-host-type-governs-influenza-evolutionary-strategy-across-reservoir-and"
content_type: "clinical_feed_article"
specialty: "Infectious Disease"
source_name: "bioRxiv (Biomedical Preprints)"
source_url: "https://www.biorxiv.org/content/10.64898/2026.09.15.751820v1?rss=1"
published_at: "2026-09-17T12:00:00.000Z"
evidence_level: "Verified Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Host type shapes influenza H3Nx evolution: reassortment in birds, adaptation in mammals
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-10-host-type-governs-influenza-evolutionary-strategy-across-reservoir-and
- **Specialty:** [Infectious Disease](https://medichelpline.com/clinical-feed/infectious-disease.md)
- **Primary Source:** bioRxiv (Biomedical Preprints)
- **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.09.15.751820v1?rss=1)
- **Published At:** 2026-09-17T12:00:00.000Z
- **Evidence Rating:** Verified Feed
## Executive GIST (TL;DR)
- The study analyzed 13,295 **H3Nx** influenza virus sequences to compare evolutionary processes across reservoir (avian) and spillover (mammalian) hosts. - The authors developed a pipeline to map **reassortment** events onto phylogenetic trees and to quantify host-specific adaptive evolution, with measures of statistical uncertainty. - In mammalian hosts (humans, swine, equine, canine), H3Nx viruses show measurable **adaptive evolution** in surface glycoprotein genes **HA** and **NA**. - Avian H3Nx lineages exhibit very little evidence of directional selection; instead, evolution in birds is dominated by frequent **reassortment**, producing many transient novel lineages. - Between 29.8% and 47.4% of avian reassortant lineages are lost within the first year of circulation, indicating rapid turnover and no detectable fitness benefit of reassortment in birds. - In contrast, reassortant lineages in **swine** are more likely to persist long-term, suggesting reassortment may confer broad advantages in swine populations. - Segment-specific reassortment differences were observed: **NA** reassorts more frequently than expected in birds but less frequently than expected in swine. - Reassortment is enriched around mammalian-to-mammalian host switches but not enriched for avian host switches, implying reassortment may facilitate mammalian host transitions. - The overall interpretation is a host-dependent shift in evolutionary strategy: **reassortment-dominant evolution** in the avian reservoir transitions to varying degrees of **adaptive evolution** upon establishment in mammals. - Data and code supporting the analysis are available at the authors’ GitHub repository; funding sources and a competing interest statement were reported in the source.
## Clinical Analysis & Structured Key Points
Host type governs influenza evolutionary strategy across reservoir and spillover hosts | bioRxiv Skip to main content New Results Host type governs influenza evolutionary strategy across reservoir and spillover hosts View ORCID Profile Maria A Maltepes , View ORCID Profile Alexey Markin , View ORCID Profile Tavis K Anderson , View ORCID Profile Kathryn Kistler , Grant Park , View ORCID Profile Lambodhar Damodaran , View ORCID Profile Jordan Ort , Jared Sabre , View ORCID Profile Stephen Shank , View ORCID Profile Louise H Moncla doi: https://doi.org/10.64898/2026.09.15.751820 Maria A Maltepes 1 University of Pennsylvania; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Maria A Maltepes Alexey Markin 2 National Animal Disease Center, USDA-ARS; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Alexey Markin Tavis K Anderson 2 National Animal Disease Center, USDA-ARS; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Tavis K Anderson Kathryn Kistler 3 Fred Hutchinson Cancer Research Center; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Kathryn Kistler Grant Park 1 University of Pennsylvania; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Lambodhar Damodaran 4 Emory University Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Lambodhar Damodaran Jordan Ort 1 University of Pennsylvania; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Jordan Ort Jared Sabre 1 University of Pennsylvania; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Stephen Shank 1 University of Pennsylvania; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Stephen Shank Louise H Moncla 1 University of Pennsylvania; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Louise H Moncla For correspondence: lhmoncla{at}upenn.edu Abstract Info/History Metrics Supplementary material Data/Code Preview PDF Abstract Despite its high propensity for host switching, the evolutionary mechanisms underlying influenza host adaptation remain unclear. H3Nx influenza viruses are uniquely generalist, with long-term lineages that circulate in avian, human, swine, equine, and canine hosts. Using 13,295 H3Nx sequences, we quantified host-specific adaptive evolution and developed a pipeline to map reassortment events onto trees with measures of statistical uncertainty. We find that while H3Nx viruses in mammals undergo adaptive evolution in HA and NA, viruses in birds experience very little directional selection. Instead, avian lineages exhibit high rates of reassortment, frequently generating novel reassortant lineages that persist transiently and turn over rapidly. 29.8-47.4% of all avian reassortant lineages are purged within the first year of circulation, and reassortment shows no fitness benefit in birds. In contrast, reassorted lineages in swine are more likely to persist long-term, suggesting that reassortment in swine may be broadly beneficial. Segment-specific reassortment patterns were also distinct between avian and mammalian viruses, with NA reassorting more frequently than expected in birds, but less frequently than expected in swine. Reassortment events are enriched between mammalian, but not avian, host switches, suggesting that reassortment may be most beneficial for mediating host switches among mammalian species. Together, our data suggest that host differences drive fundamentally different evolutionary outcomes for influenza viruses, transitioning from reassortment-dominant evolution in their avian reservoir, to varying degrees of adaptation upon establishment in mammals. Competing Interest Statement The authors have declared no competing interest. Footnotes https://github.com/moncla-lab/h3nx-paper Funder Information Declared Pew Charitable Trusts Margaret Q. Landenberger Research Foundation National Institute of Allergy and Infectious Diseases National Institutes of Health Department of Health and Human Services United States Department of Agriculture Agricultural Research Service Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license . Back to top Previous Next Posted September 17, 2026. Download PDF Supplementary Material Data/Code Email Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. 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Share Host type governs influenza evolutionary strategy across reservoir and spillover hosts Maria A Maltepes , Alexey Markin , Tavis K Anderson , Kathryn Kistler , Grant Park , Lambodhar Damodaran , Jordan Ort , Jared Sabre , Stephen Shank , Louise H Moncla bioRxiv 2026.09.15.751820; doi: https://doi.org/10.64898/2026.09.15.751820 Share This Article: Copy Citation Tools Host type governs influenza evolutionary strategy across reservoir and spillover hosts Maria A Maltepes , Alexey Markin , Tavis K Anderson , Kathryn Kistler , Grant Park , Lambodhar Damodaran , Jordan Ort , Jared Sabre , Stephen Shank , Louise H Moncla bioRxiv 2026.09.15.751820; doi: https://doi.org/10.64898/2026.09.15.751820 Citation Manager Formats BibTeX Bookends EasyBib EndNote (tagged) EndNote 8 (xml) Medlars Mendeley Papers RefWorks Tagged Ref Manager RIS Zotero Tweet Widget Facebook Like Google Plus One Subject Areas All Articles Animal Behavior and Cognition (8006) Biochemistry (18718) Bioengineering (14854) Bioinformatics (44374) Biophysics (22569) Cancer Biology (19698) Cell Biology (26873) Clinical Trials (138) Developmental Biology (13951) Ecology (20984) Epidemiology (2067) Evolutionary Biology (25420) Genetics (16155) Genomics (23490) Immunology (18687) Microbiology (42428) Molecular Biology (18040) Neuroscience (93379) Paleontology (700) Pathology (2977) Pharmacology and Toxicology (5087) Physiology (8109) Plant Biology (15985) Scientific Communication and Education (2095) Synthetic Biology (4556) Systems Biology (10225) Zoology (2386)
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