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This study aimed to understand the interaction of virus and host factors in LPAIV reproductive tract infection. Oviduct organ cultures (OOCs) were prepared from two chicken lines, brown layers (BL) and white layers (WL), to compare virus replication, microscopical lesions, and host-immune responses between two atypical virulent LPAIV strains H3N1 (A\/chicken\/Belgium\/460\/2019) and H6N1 (A\/chicken\/Netherlands\/917\/2010), and an avirulent H9N2 strain (A\/chicken\/Saudi Arabia\/2525\/2000). mRNA levels of interferon \u03bb (IFN \u03bb), inducible nitric oxide synthase (iNOS), host factors such as importin (Imp) \u03b13, \u03b18, and chemerin were measured by quantitative reverse transcription polymerase chain reaction (qRT\u2013PCR). High-throughput transcriptomic profiling of innate immune genes using a quantitative polymerase chain reaction (qPCR) array focused on H3N1- and H9N2-infected BL-OOCs. H3N1- and H6N1-infected BL-OOCs showed significantly higher viral loads compared with H9N2-inoculated OOCs (\n                    <jats:italic>p<\/jats:italic>\n                    \u2009&lt;\u20090.05). This was associated with higher mRNA levels of innate-immunity related genes, including Pentraxin (\n                    <jats:italic>PTX3<\/jats:italic>\n                    ) at 48\u00a0hours post-infection (hpi) after H9N2 inoculation. Compared with H9N2, H3N1 triggered a stronger yet delayed innate immune response at 48 hpi with an 8- and 256-fold increase in IFN \u03bb and C\u2013C motif chemokine ligand 4 (\n                    <jats:italic>CCL4<\/jats:italic>\n                    ) expression, respectively, along with upregulation of Imp \u03b13 in BL-OOCs. WL\u2013OOCs were less susceptible to H6N1 with lower viral loads compared with BL-OOCs, which coincided with lower IFN \u03bb expression levels after virus infection (\n                    <jats:italic>p<\/jats:italic>\n                    \u2009&lt;\u20090.05). Overall, the OOCs model was a suitable model to demonstrate variable pathogenicity of LPAIV strains across chicken genotypes. Variations in host responses were detected impacting virus replication in a strain-dependent manner.\n                  <\/jats:p>","DOI":"10.1186\/s13567-026-01799-7","type":"journal-article","created":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T16:03:08Z","timestamp":1782403388000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Virus and host-associated variations in the interaction of low-pathogenic avian influenza viruses with the epithelial target tissue of the chicken reproductive tract"],"prefix":"10.1186","volume":"57","author":[{"given":"Basel A.","family":"Abukhadra","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frederik","family":"Bexter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sana I.","family":"Mohamed","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lonneke","family":"Vervelde","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kate","family":"Sutton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sjaak","family":"de Wit","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silke","family":"Rautenschlein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,6,25]]},"reference":[{"key":"1799_CR1","doi-asserted-by":"publisher","DOI":"10.3390\/v15040980","volume":"15","author":"EM Abdelwhab","year":"2023","unstructured":"Abdelwhab EM, Mettenleiter TC (2023) Zoonotic animal influenza virus and potential mixing vessel hosts. 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