Aquaculture 2022

February 28 - March 4, 2022

San Diego, California

ENDOGENOUS VIRAL ELEMENTS (EVE) OF Decapod penstylhamaparvovirus 1 (INFECTIOUS HYPODERMAL AND HEMATOPOIETIC NECROSIS VIRUS, IHHNV) – IMPLICATIONS FOR SHRIMP DIAGNOSIS

Acacia Alcivar-Warren* , Weidong Bao  and  Kathy  F. Tang

 

ONE HEALTH Epigenomics Educational Initiative,

Environmental Genomics Inc.

P.O. Box 196, Southborough, MA 01772, USA

environmentalgenomics.warren@gmail.com

 



Shrimp e ndogenous viral elements (EVE)  have been reported in  White Spot Syndrome Virus (WSSV) and  Infectious H ypodermal and H ematopoietic N ecrosis V irus (IHHNV) , now renamed  Decapod penstylhamaparvovirus 1 . IHHNV is a ssDNA  virus in the family Parvoviridae , one of the smallest penaeid shrimp viruses encoding three ORFs and  listed by the World Organisation for Animal Health (OIE). It was first reported in the 1980s in Hawaii , USA  (reference genome

, 3909 bp) .  This virus was found  integrated in the P. monodon genome collected from Australia, Thailand, Africa (Tang et al. 2003; Tang & Lightner. 2006). In some African isolates, IHHNV (DQ228358 ) was found inserted into RTE-2_PMo non-LTR retrotransposon in Repbase (www.girinst.org) ,  and these DQ228358-like insertions  are  absent in other P. monodon isolates. We suspect IHHNV have also endogenized P. vannamei  and some IHHNV-EVEs  remain  in some P. vannamei genomes , introduced to the American continent in the 1970s. IHHNV causes high mortality in  Penaeus stylirostris ; but no mortality has been reported in P. vannamei and P. monodon where is known to cause slow growth and deformities in the exoskeleton (called Runt d eformity syndrome) , causing  serious economic losses.

H omology searches using the 10 whole genome sequence (wgs )  databases  for five penaeid species in GenBank  revealed that the  sequences of  infectious IHHNV isolates Hawaii (AF218266.2 ), P. vannamei of Ecuador (AY362548 , 3775bp and OL598344 , 3203bp) and Australia (EU675312, 3832bp) are integrated in chromosome_ 35 of P. monodon  genome from Thailand (NSTDA _Pmon_1, GCF_015228065.1, 2.39 Gb).  These IHHNV-EVE-related sequences  are also present in P. vannamei breed Kehai No.1 LVANscaffold_759 of  P. vannamei  genome farmed in China  (assembly ASM378908v1 , ~1.86 Gb). Non-infectious IHHNV-EVEs  have  also  been  found  within the shrimp genome in populations of P. monodon from Africa (Type A  from Madagascar:  DQ228358, 4655bp) and Australia , and they are also integrated in  both chromosome_35  of P. monodon  genome from Thailand and  the genome of P. vannamei breed Kehai No.1 LVANscaffold_759 , to be confirmed  once a  new,  continuous, fully assembled reference genome for SPF P. vannamei from the USA is available (expected size: 2.87 Gb) . A new reference genome for  P. vannamei is urgently needed to help improve accuracy in diagnosis of IHHNV/ Decapod penstylhamaparvovirus 1 (OIE PCR, multiplex PCR, IQ 2000 LAMP).