Betanodavirus variants circulating in the Mediterranean: a novel, quick and affordable method to identify genotypes and reassortant strains

Viral nervous necrosis (VNN) otherwise known as viral encephalopathy and retinopathy (VER), is the most threatening infectious disease in Mediterranean aquaculture. VNN is caused by the nervous necrosis virus (NNV) a bisegmented ssRNA+ virus included in the genus Betanodavirus, family Nodaviridae. NNV genome consists of two molecules named RNA1 and RNA2, which encodes for the RNA-dependent RNA polymerase and the coat protein, respectively. Four genotypes of NNV have been so far described: RGNNV, SJNNV, BFNNV, TPNNV (Sahul Hameed et al., 2019). Furthermore, reassortant strains have emerged from the reassortment between the RGNNV and the SJNNV genotypes and named RGNNV/SJNNV and SJNNV/RGNNV according to the RNA1 and RNA2 origin. Currently, several NNV strains are co-circulating in the Mediterranean Basin with a high prevalence of the RGNNV genotype and the RGNNV/SJNNV reassortant strain and a more limited diffusion of the SJNNV genotype and the SJNNV/RGNNV reassortant (Bandin and Souto, 2020; Volpe et al., 2020). So far, identification of NNV genotype and reassortant strains is based on amplification, sequencing and phylogenetic analysis of both viral genome RNA molecules requiring time and expertise. As viral identification is an essential information for the management of the disease in the field (Toffan et al., 2021), the development of an easy and affordable method to genotype betanodaviruses was developed in the framework of the H2020 Peformfish Project, an industry-driven project targeting industry defined priorities