Aquaculture 2022

February 28 - March 4, 2022

San Diego, California

THE COMPLETE GENOME OF AN ENDOGENOUS NIMAVIRUS (Nimav-1_LVa) FROM SPECIFIC PATHOGEN-FREE SHRIMP Penaeus vannamei – THE NEED FOR REFERENCE GENOMES OF PENAEIDS AND OTHER CRUSTACEANS

 

Acacia Alcivar-Warren * and Weidong Bao

 

Environmental Genomics Inc., P.O. Box 196, Southborough, MA 01772; and

GIRI (girisnt.org), 20380 Town Center Lane, Suite 240, Cupertino, CA 95014 USA

environmentalgenomics.warren@gmail.com

 



 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.