First detection and molecular characterization of influenza D virus in livestock from Kazakhstan reveals circulation of the D/Yama2019 lineage

Abstract

Influenza D virus (IDV) is an emerging Orthomyxovirus primarily associated with cattle and increasingly recognized as a pathogen of veterinary and zoonotic relevance. Despite growing evidence of its circulation across Asia, Europe, and North America, no data have previously been available from Kazakhstan or Central Asia. This study investigated the presence of IDV in domestic livestock samples collected during active surveillance between 2023 and 2026. A total of 867 biological samples were obtained from cattle (n = 611), camels (n = 175), Maral Deer (n = 51), and pigs (n = 30) across multiple regions of Kazakhstan. Viral RNA was screened by reverse transcription polymerase chain reaction (RT-PCR) targeting the HEF, PB1, PB2, and P3 genes using a newly designed primer panel. Positive amplicons were subjected to Sanger sequencing and phylogenetic analysis. IDV RNA was detected in 11 animals, corresponding to an overall prevalence of 1.27%. Positive samples were identified in several geographically distinct regions, indicating wider circulation than previously recognized. Complete HEF gene sequences were successfully obtained from two representative cattle strains, designated D/bovine/Zhetysu/KAZ/678/2025 and D/bovine/Zhetysu/KAZ/680/2025. Phylogenetic analysis demonstrated that both strains clustered within the D/Yama2019 lineage and shared >98.83% nucleotide identity with contemporary Asian strains. To our knowledge, this is the first report of IDV detection in Kazakhstan. These findings expand the known geographic range of IDV and suggest possible transboundary transmission routes across Central Asia. Continued molecular surveillance is warranted to clarify epidemiology, host range, and potential economic impact.