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White spot syndrome virus (WSSV) is a major pathogen in shrimp culture because of its high infectivity, fast transmission speed, and high fatality rate. White spot disease (WSD), caused by WSSV poses a substantial threat to shrimp production. Therefore, it is crucial to identify effective antiviral agents to mitigate the economic loss caused by WSD. In this study, we prepared 20 ethanol extracts of Chinese herbal medicines (CHMs) and evaluated their anti-WSSV effectiveness using Litopenaeus vannamei larvae as a model. Among the tested extracts, Punica granatum L. exhibited the highest inhibition of WSSV infection at 85%, followed by Gentiana macrophylla at 79% and Isatis tinctoria L. at 63%. Quercetin, an active ingredient found in P. granatum at a concentration of 6.3 μM, increased the survival rate of WSSV-infected larvae by 30% after 72 hpi, and significantly inhibited WSSV infection. Further data from pre-incubation assays indicated that quercetin exhibited a potentially destructive effect on WSSV virions, thereby reducing the virulence and blocking viral horizontal transmission. Moreover, the high stability of the aquacultural water facilitated the continuous exchange of quercetin treatment, which further prolonged the survival time of WSSV-infected shrimp such that the survival rate was still at 13% after 5 days. These results highlight the potential application of quercetin in eliminating WSSV during shrimp larval production. • Pomegranate and quercetin showed anti-WSSV activity in water. • Quercetin blocked horizontal transmission of WSSV virions by reducing its infectivity. • Quercetin was stable in water and had therapeutic effect on WSSV-infected shrimp. [ABSTRACT FROM AUTHOR]