Mortalities of cultured shrimp induced by white spot syndrome virus (Viruses; Naldaviricetes; Nimaviridae; Whispovirus; WSSV) have occurred in Ecuador since 1996. Endogenous WSSV-like sequences (WSSV-EVE, Utari et al. 2017) have been reported in Penaeus vannamei farmed in Thailand and in expressed sequence tags (EST) libraries prepared from the first specific pathogen-free (SPF) P. vannamei domesticated by the breeding program of the U.S. Marine Shrimp Farming Program (USMSFP) maintained at the Oceanic Institute in Hawaii.
The WSSV genome sequence form China (AF332093.3, 305119bp), Ecuador (MH090824, 288,997bp), two isolates from Mexico, and 13 complete WSSV genome sequences available in GenBank database were used in this study. Twelve whole genome shotgun (WGS) assemblies and 35 transcriptome shotgun assembly (TSA) databases available for Penaeoidea were used to determine if the WSSV genome, and its nimaviridae family gene Nimav-1_LVa (279905bp; Bao et al. 2020; https://pubmed.ncbi.nlm.nih.gov/31947590/), are integrated in the shrimp genome.
WGS searches revealed that none of the WSSV genomes are integrated in the draft genome assembly of P. vannamei farmed in China (ASM378908v1; ~1.8-Gb) and in other draft genome assemblies for P. japonicus, P. chinensis and P. indicus, P. japonicus, and P. monodon. However, large fragments of Nimav-1_LVa are integrated in the genome of P. vannamei farmed in China (Penaeus vannamei breed Kehai No.1 LVANscaffold_3666 (QCYY01003664, 990704-bp, 428 fragment matches). TSA analyses revealed that many cDNAs and ESTs isolated from SPF P. vannamei from USMSFP and other Penaeids are similar to portions of WSSV and Nimav-1_LVa sequences, representing putative WSSV-EVE sequences.
To better understand the molecular regulation and evolution of WSSV-EVE sequences, a new, continuous, whole reference genome sequence for P. vannamei is needed, particularly considering the variability of current draft genome assemblies for P. vannamei, while the expected genome size of SPF P. vannamei from an American company is 2.89-Gb (Jeffery & Gregory, 2014).