Genomic analysis of a decapod Penstylidensovirus 1 isolated from Penaeus semisulcatus

Abstract

The purpose of this study was to identify the genomic characteristics of Penaeus stylirostris densovirus (PstDNV 1) affected farming of the green tiger shrimp Penaeus semisulcatus. Shrimp samples tested positive for PstDNV 1 by PCR and showing pathognomonic lesions were taken for cloning. Genomic DNA from infected shrimp was digested with restriction enzymes and plasmid libraries made before taking recombinant clones for shotgun sequencing. Altogether, 11 PstDNV1 contigs 3,530 to 3,912 nucleotides (nt) long were generated from P. semisulcatus. Each sequence contained ORFs encoding nonstructural (NS) proteins NS1 and NS2 and coat protein. The genome length of the isolates ranged from 3,598 to 3,912 bases. The GC content of the isolates varied from 42.5 % to 43.2%. These eleven PstDNV 1 isolates shared a pairwise identity of 96.4%. The phylogenetic analysis of the eleven PstDNV 1 isolates and the previously reported sequences showed the formation of 5 groups. Group 1 contains isolates from China, Brazil, California, Hawaii and 4 sequences from Egypt (KT316255.1, KT316260.1, KT316256.1 and KT316256.1). The second group contains sequences from Australia and 4 sequences from Egypt (KT316253.1, KT316252.1, KT316251.1 and KT316250.1). The third group clusters sequences from Thailand, Vietnam, Taiwan and two sequences from Egypt (KT316257.1 and KT316259.1). The appearance of PstDNV 1 in Egypt occurred after the introduction of Litopenaeus vannamei and Fenneropenaeus indicus. The complete genomes characterized in this study suggest that PstDNV was introduced to Egypt via movement of infected animals from distinct parts of the world. These finding serve as evidence that stricter monitoring protocols for the movement of shrimp species are fundamental as biosecurity measures to avoid the spread of pathogens that could potentially compromise the growth of the shrimp industry in Egypt.