Identification of Various InDel-II Variants of the White Spot Syndrome Virus Isolated from Frozen Shrimp and Bivalves Obtained in the Korean Commercial Market

SIMPLE SUMMARY: The white spot syndrome virus (WSSV) is a harmful pathogen with significant economic implications for the shrimp industry. This study investigated the presence of WSSV in frozen shrimp and bivalves in the Korean commercial market, with a specific focus on WSSV genetic variants. The research revealed that WSSV was detected in both domestic and imported shrimp, with higher viral loads in domestic samples. Various genetic variants of WSSV have been identified that exhibit differences in pathogenicity associated with longer deletion lengths in specific genetic regions linked to initial viral replication. Additionally, the presence of WSSV variants in bivalve mollusks suggested their potential utility as biomarkers for viral tracking. This study offers valuable insights into the prevalence and genetic diversity of WSSV in aquatic animal products that are essential for disease control and management in the aquaculture industry. ABSTRACT: White spot syndrome virus (WSSV) poses a significant threat to the global shrimp industry. We investigated the presence of WSSV in frozen shrimp (n = 86) and shellfish (n = 185) from the Korean market (2010–2018). The detection rate of first-step polymerase chain reaction (PCR) in domestic shrimp was 36.8% (7/19), whereas that in imported shrimp was 0.01% (1/67). Furthermore, the WSSV genome was amplified from domestic bivalve mollusks by first- and second-step PCR with accuracies of 3.4% (5/147) and 15.6% (23/147), respectively. The genetic relatedness of InDel-II regions among WSSVs detected in domestic shrimp groups revealed four variants (777, 5649, 11,070 and 13,046 bp insertion or deletion), and imported shrimp groups had four variants (10,778, 11,086, 11,500 and 13,210 bp) compared with the putative ancestor WSSV strain. The 5649 bp variant was the dominant type among the WSSV variants detected in domestic shrimp (54.5%, 6/11). Notably, bivalve mollusks exhibited six variants (777, 5649, 5783, 5876, 11,070 and 13,046 bp), including four variants detected in shrimp, indicating that bivalve mollusks could facilitate WSSV tracking. In a challenge test, whiteleg shrimp (Litopenaeus vannamei) exhibited varying mortality rates, indicating a link between InDel-II deletion and viral replication. These findings highlight the complexity of WSSV transmission.