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).