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• DHAV-3 infection results in glucose metabolism abnormalities in susceptible ducklings. • Hypoglycemia is the noticeable sign of fatal cases caused by DHAV-3 infection. • Cytokines regulates negatively glucose metabolism-related pathways by JAK2. • JAK2 results in down-regulated expression of HPGDS directly. Earlier works identified the second generation (Z8R2) of a resistant Pekin duck line to duck hepatitis A virus genotype 3 (DHAV-3), which displays significantly strong resistance than that of the second generation (Z8S2) of a susceptible Pekin duck line. To understand the genetic mechanisms that determine the different resistance/susceptibility of Z8R2 and Z8S2 to DHAV-3, transcriptome analysis on livers of infected Pekin ducklings was performed to screen differentially expressed genes (DEGs). We found that DHAV-3 infection has a great effect on metabolism of Z8S2 at the transcription level. Using a newly created fourth generation of the resistant Pekin duck line (Z8R4) and an unselected Pekin duck flock (Z7) as models, hypoglycemia and dramatically increased aspartate aminotransferase and alanine aminotransferase were shown to be noticeable signs of fatal cases caused by DHAV-3 infection. These findings, together with expression analysis and verification of DEGs, support the view that DHAV-3 infection results in glucose metabolic abnormalities in susceptible individuals and that there are significant differences in expression patterns of glucose metabolism-related DEGs between susceptible and resistant individuals. Notably, cytokines displayed a negative correlation with glucose synthesis in terms of expression in susceptible individuals following DHAV-3 infection. Mechanism analyses suggests that cytokines will activate PI3K-AKT pathway and/or JAK-STAT pathway by up-regulated expression of JAK2, and thereby causes down-regulated expression of G6PC and/or ACAT1. Cytokines can also cause down-regulated expression of HPGDS by JAK2. The present work contributes to the understanding of pathogenesis of DHAV-3 infection and the resistance breeding project against DHAV-3. [ABSTRACT FROM AUTHOR]