White spot disease, caused by the white spot syndrome virus (WSSV), has caused major losses in shrimp farming in Egypt since 2009. The genome sequence of the WSSV-Egypt isolate will be valuable in epidemiological studies to delineate the origin and spread of WSSV in Egypt and elsewhere in the world.
ABSTRACT
White spot disease, caused by the white spot syndrome virus (WSSV), has caused major losses in shrimp farming in Egypt since 2009. The genome sequence of the WSSV-Egypt isolate will be valuable in epidemiological studies to delineate the origin and spread of WSSV in Egypt and elsewhere in the world.
ANNOUNCEMENT
In Egypt, Penaeus semisulcatus and Marsupenaeus japonicas are the two native species of shrimp that have been farmed since the early 1980s. In 2009, the Indian white prawn (Fenneropenaeus indicus) was introduced in Egypt as an alternative to the native species. Soon after, shrimp farmers started experiencing large-scale mass mortalities. The clinical signs, histopathology, and PCR detection indicated the presence of white spot disease (WSD).
White spot disease, caused by white spot syndrome virus (WSSV), is the most economically important viral disease of cultured penaeid shrimp worldwide (1–3). WSSV has a large host range, infecting shrimp, crayfish, and lobster, among many other species (3). The virions are enveloped, are elliptical in shape, and measure about 80 to 120 nm wide and 250 to 380 nm long, with a tail like appendage at one end (4). The virus contains a double-stranded DNA genome and belongs to the family Nimaviridae, genus Whispovirus (https://talk.ictvonline.org/ictv-reports/ictv_9th_report/dsdna-viruses-2011/w/dsdna_viruses/119/nimaviridae). The genome sequences of 12 WSSV isolates are available, including those of four isolates from China (GenBank accession no. AF332093, KT995472, KT995470, and KT995471) (5, 6) and one isolate each from Thailand (AF369029) (7), Taiwan (AF440570) (8), Korea (JX515788) (9), India (MG702567) (10), Brazil (MF784752) (11), Mexico (KU216744) (12), Australia (MF768985) (13), and Ecuador (MH090824) (14). The genome size of these isolates varies from 284 to 309 kb, with 147 to 526 predicted open reading frames (ORFs). To determine the genetic identity and origin, we sequenced the genome of the WSSV-Egypt isolate (WSSV-EG3). This is the first WSSV isolate from Egypt that has been completely sequenced.
Shrimp were collected from farms experiencing large-scale mortalities in the Al Dibah Triangle Zone in the Port-Said Governorate during May to November in 2015. Histopathology of moribund animals displayed nuclear hypertrophy, large basophilic intranuclear inclusion bodies in the cuticular epithelial cells, chromatin margination, and variable multifocal necrosis, which are pathognomonic for WSSV infection. The presence of WSSV was further confirmed by PCR using an IQ200 WSSV detection and prevention system (GeneReach, Taiwan). DNA from a WSSV-positive sample was digested with restriction enzymes, and plasmid libraries were made for shotgun sequencing using an ABI 3730XLS sequencer (Macrogen, Inc., South Korea). Contigs were generated and aligned to the WSSV Thailand isolate (AF369029) to separate WSSV contigs from shrimp genome contigs. Sequences were base called by the Phred base caller and assembled with the Phrap assembler (15, 16) using the Gap4 interface. The assembled data were stored in the Gap4 assembly database (17). The Gap4 interface and its features were then used for editing the genome sequence. The complete WSSV-EG3 genome consists of 305,119 bp with 41.0% GC content and 245 open reading frames (ORFs). The average nucleotide identity (ANI) was determined with other WSSV strains with default parameters. The ANI values of WSSV-Egypt compared to those of other WSSV isolates were as follows: 99.81% (Australia), 99.79% (Brazil), 100% (China-CN), 99.94% (China-CN01), 99.82% (China-CN02), 99.84% (China-CN03), 98.33% (India), 99.89% (Korea), 99.8% (Mexico), 98.75% (Taiwan), and 95.22% (Thailand). These genome data are valuable in determining the origin and spread of WSSV in Egypt and elsewhere in the world.
Data availability.
This whole-genome sequence of the WSSV Egypt (WSSV-EG3) isolate has been deposited in GenBank under the accession no. KR083866.
ACKNOWLEDGMENTS
We thank the shrimp farmers at DTZ for providing shrimp samples and information regarding the history of the disease outbreaks.
This work was supported by Science & Technology Development Fund grant no. 5661 and 185840 to Mohamed E. Megahed. Partial funding for this research was provided by The University of Arizona Aquaculture Pathology Laboratory Diagnostic Fund, and Arun K. Dhar received funding from the College of Agriculture & Life Sciences.
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Data Availability Statement
This whole-genome sequence of the WSSV Egypt (WSSV-EG3) isolate has been deposited in GenBank under the accession no. KR083866.
