Complete genome sequencing and evolutionary analyses of duck hepatitis a viruses in Egyptian duck farms.

BACKGROUND

Duck hepatitis virus (DHV) continues to pose a substantial threat to duck production worldwide, causing acute hepatitis, neurological manifestations, and elevated mortality rates, even in vaccinated flocks. During 2022-2023, a significant outbreak involving DHV-1 and DHV-3 was reported in duck farms across five governorates in North Egypt. The outbreaks primarily affected Pekin ducklings aged 4-15 days, with mortality rates ranging from 50% to 70%. Affected ducklings exhibited characteristic pathological lesions, including hepatomegaly with haemorrhages, splenomegaly, and renal enlargement.

RESULTS

A total of 30 liver and spleen samples collected from affected farms were analysed using reverse transcription PCR (RT-PCR) targeting the 3' untranslated region (3'UTR) and the VP1 gene. DHV was detected in 56.7% (17/30) of the samples. Among the positive cases (n = 17), DHV-1 was identified in 29.4% (5/17), whereas DHV-3 accounted for 70.6% (12/17). Phylogenetic analysis based on whole-genome sequencing revealed that DHV-1 strains clustered within sub-clade 1a, demonstrating high genetic similarity (99.2-99.8%) with previously reported Egyptian isolates and Chinese reference strains (e.g., DHAV-1-CH-2012). In contrast, DHV-3 strains grouped within sub-clade 3a and showed close genetic relatedness to Chinese strains (97.1-98.7%), while showing marked divergence (75.9-76.3% nucleotide identity) from currently used vaccine strains. Genetic analysis identified multiple mutations in both viral types. DHV-1 exhibited amino acid substitutions within VP0, VP3, and non-structural protein regions, alongside five mutations in hypervariable region 1 (HVR1) and one mutation in HVR2 of the VP1. DHV-3 demonstrated distinct mutations within the VP1, including a unique E681K substitution identified in the Egyptian strain ND3.

CONCLUSION

The findings demonstrate ongoing genetic evolution of DHV circulating in Egyptian duck farms, characterized by the predominance of genetically distinct DHAV-3 strains, with significant divergence from currently used vaccine strains. This genetic divergence may contribute to altered vaccine performance and continued disease outbreaks; however, its impact on vaccine-induced protection requires further experimental validation. Continuous genomic surveillance and the development of updated, strain-matched or multivalent vaccines are therefore essential to control DHV infections and minimise economic losses in Egypt's duck industry.