An B, Lee K, Do HQ, Yoon J, Kim S, Ga E, Lim JW, Y. Genetic and Phylogenetic Characterization of Influenza D Viruses From South Korean Cattle, 2022-2023. Transbound Emerg Dis. 2026;2026(1):e6780142
Influenza D virus (IDV) is an emerging orthomyxovirus with cattle as its principal reservoir, and D/Yama2019-lineage viruses have become dominant in East Asia. Although IDV has been detected in Korean cattle, the genomic identity, phylogenetic placement, and regional evolutionary relationships of circulating Korean strains have not been defined. To address these gaps, nasal swabs were collected from 578 cattle with mild respiratory signs on 157 farms across eight provinces in South Korea during 2022-2023 and screened by RT-qPCR targeting the PB1 gene. Positive samples underwent complete genome sequencing of all seven segments, followed by maximum-likelihood and Bayesian phylogenetic analyses, discrete phylogeographic inference using a Bayesian stochastic search variable selection (BSSVS) model, and positive selection analyses. Six samples from three farms were IDV-positive (sample-level positivity: 1.04%; farm-level positivity: 1.9%), all from 8-to-10-month-old calves. Phylogenetic analysis of all seven genomic segments placed all six Korean strains within the D/Yama2019 lineage with strong bootstrap support (99%-100%), forming a monophyletic cluster more closely related to Chinese than to Japanese D/Yama2019 reference strains. No phylogenetic evidence of reassortment was detected. Bayesian time-scaled analysis estimated the most recent common ancestor of the Korean strains at ~2018.1-2020.1 across all seven segments. HEF-based BSSVS analysis suggested a China-to-South Korea transition within the sampled dataset (posterior probability (PP) = 0.982; Bayes factor (BF) = 163.67), although this result should be interpreted in light of the small number of Korean sequences and the single-segment basis of the phylogeographic analysis. Positive selection analyses revealed limited, method-dependent signals without support from the fixed effects likelihood model, and Korean-associated amino acid substitutions in PB1, P3, NS1, and NS2 were interpreted as lineage-associated molecular signatures rather than evidence of adaptive evolution. These findings provide a whole-genome baseline for IDV surveillance in South Korea and support continued longitudinal monitoring to clarify the persistence and transmission dynamics of D/Yama2019-lineage viruses in the region.
See Also:
Latest articles in those days:
- Avian Influenza Weekly Update # 1062: 18 September 2026 9 hours ago
- Effectiveness of the 2025-2026 seasonal influenza vaccine among U.S. veterans: an observational study 10 hours ago
- Streamlined CRISPR-based assays for detection and subtyping of H5 and H7 avian influenza 2 days ago
- Host-specific effects of a pandemic H1N1 M gene on canine H3N2 influenza virus replication and immune responses 2 days ago
- Rapid Decline of Nesting Peregrine Falcons in the San Francisco Bay Region of California Synchronous with an Outbreak of H5N1 Highly Pathogenic Avian Influenza 2 days ago
[Go Top] [Close Window]


