White spot syndrome virus (WSSV), the lone virus of the genus Whispovirus under the family Nimaviridae, is one of the most devastating viruses affecting the shrimp farming industry (https://pubmed.ncbi.nlm.nih.gov/31947590/). Knowledge about this virus, in particular its evolution history, has been limited, partly due to its large genome and the lack of other closely related free-living viruses for comparative studies.
A reconstructed full-length endogenous nimavirus consensus genome, Nimav-1_LVa (279,905 bp) was found in the genome sequence of the Kehai isolate of Penaeus vannamei from China ( GCA_003789085.1; breed Kehai No. 1 , cultured shrimp imported from USA; 1.6 Gb) in which ~12 copies of Nimav-1_LVa exist. This endogenous virus seems to insert exclusively into the telomeric pentanucleotide microsatellite (TAACC/GGTTA)n. 117 putative genes are predicted. Sequence analysis of these genes indicates that there are four more recognizable nimaviruses core/ancestor genes, wsv112 (dUTPase ), wsv206, wsv226 and wsv308 (nucleocapsid protein), making the total number to be 43. Some Nimav-1_LVa contain introns, such as g012 (IAP), g046 (CHH), g155 (innexin), g158 (BI-1-like). More than a dozen Nimav-1_LVa genes are involved in the pathogen-host interactions. We hypothesize that g046, g155, g158 and g227 (semaphorin 1A like) are recruited host genes for their roles in immune regulation.
Availability of Nimav-1_LVa sequence will help understand the genetic diversity, epidemiology, evolution, pathogenicity, and virulence of WSSV. Future studies will focus on the possibility that Nimav-1-LVa represents a free-living virus, yet unidentified but infecting crustacean s, because almost identical Nimav-1_LVa sequences were also found in genome sequences from black tiger shrimp P. monodon isolate Shenzhen from China (GCA_002291185.1 , wild shrimp; 1.4 Gb ) and P. japonicus Guanxi isolate from Japan (GCA_002291165.1; wild shrimp; 1.6 Gb). In addition, three relatives of Nimav-1_Lva are detected in P. monodon: Nimav-1_PMo, Nimav-2_PMo and Nimav-3_PMo . So far, Nimav-1_LVa sequences have not been found in the genomes of P. monodon isolate 26D (GCA_007890405.1; cultured shrimp from Vietnam, originally from Australia ; ~ 1.6 Gb), P. monodon isolate SGIC_2016 from Thailand (GCA_015228065.1; cultured shrimp from Surat Thani, Thailand ; ~2.4 Gb), and P. chinensis isolate QD-2010 from China (GCA_016920825.1; wild shrimp; ~1.6 Gb).
Future r esearch should focus on (a) sequencing fully assembled reference genomes for all Penaeid shrimp, (b) determine, by FISH, the chromosome location of the integrated Nimav-1_LVa or its relatives in crustacean genomes, and (c) s urvey the existence of Nimavirus in more Crustacean species. Search and isolate the free-living Nimav-1_LVa virus, if possible.