Complete Genome Sequences of Four Major Viruses Infecting Marine Shrimp in Egypt

The genome sequences of four economically important shrimp viruses, Penaeus stylirostris densovirus 1, hepatopancreatic parvovirus, yellow head virus, and gill-associated virus, are reported here. Genome data are fundamental for epidemiological studies in determining the origins of these viruses detected for the first time in Egypt and in developing disease management strategies.

P enaeus semisulcatus and Marsupenaeus japonicas are the two native shrimp species in Egypt cultured since the 1980s. With the introduction of Fenneropenaeus indicus, a nonnative species, shrimp farmers started experiencing disease outbreaks. Laboratory diagnosis revealed the presence of Penaeus stylirostris densovirus 1 (PstDNV1), hepatopancreatic parvovirus (HPV), yellow head virus (YHV), and gill-associated virus (GAV). The genome sequences of these viruses are presented here.
Total DNA and RNA were extracted from pleopods and hepatopancreas of shrimp using DNeasy and RNeasy minikits (Qiagen). Samples that tested positive by PCR (PstDNV1 and HPV) and reverse transcription-PCR (RT-PCR) (YHV and GAV) were taken for cloning. DNA and cDNA were digested with restriction enzymes, and plasmid libraries were made before taking recombinant clones for shotgun sequencing using an ABI 3730XLS sequencer (Macrogen, Inc.). Contigs were generated and aligned to the viral reference genomes to separate viral contigs from shrimp genome contigs. Sequences were examined using Chromas version 1.45 (1) and BioEdit 7.0.9, open reading frames (ORFs) were annotated using BLASTn, and Geneious R11 and multiple alignments were performed using CLUSTALW.
The genome sizes of 10 HPV-Egypt isolates varied from 5,685 to 6,336 nt. All but one isolate (GenBank accession number KT316245) contained three ORFs in the order of NS2, NS1, and VP, similar to the reference strain (6). HPV-Egypt isolates showed 80.62% to 100% identity to the reference sequence (RefSeq accession number NC_007218) (6). The KT316245 isolate presented left (partial), middle, and right ORFs and showed 100% identity to an isolate from Madagascar (7).
Data availability.

ACKNOWLEDGMENTS
We thank the shrimp farmers at DTZ, Egypt, for providing shrimp samples and information regarding the history of the disease outbreaks. Special thanks are due to the fishermen who cooperated and supplied wild shrimp samples from different sites. This work was supported by Science & Technology Development Fund grants 5661 and 185840. Partial funding for this research was provided by The University of Arizona Aquaculture Pathology Laboratory Diagnostic Fund and by the College of Agriculture & Life Sciences to Arun K. Dhar.