Studies on infectious myonecrosis virus (IMNV) and infectious hypodermal and hematopoietic necrosis virus (IHHNV) in cultured penaeid shrimp in Egypt

The present study aimed to diagnose infectious myonecrosis virus (IMNV) and infectious hypodermal and hematopoietic necrosis virus (IHHNV) among cultured penaeid shrimp (Penaeus semisulcatus, n = 120) collected from private farms in 2 Egyptian provinces (Damietta and North Sinai) along the Mediterranean coast. The collected shrimp were subjected to clinical examination, histopathology, molecular characterization, and phylogenetic analysis. Most of the shrimp infected with IMNV showed a distinctive appearance resembling cooked shrimp and white necrosis on distal abdominal segments and tail fans. Simultaneously, IHHNV-infected cases displayed opaque abdominal muscles, white milky to buff mottling on the shell, and a pathognomonic runt-deformity syndrome. Histopathological examination of infected specimens revealed muscular edema, hemocyte infiltration, deformities, Zenker's necrosis, and eosinophilic intra-nuclear inclusion bodies (Cowdry type A). PCR results gave predictable amplicon sizes of 139 and 81 bp and confirmed the presence of IMNV and IHHNV with a total prevalence of 37.5 and 25%, respectively. A homology search by BLAST analysis showed that the retrieved isolates putatively belonged to IMNV and IHHNV based on 96.3 to 97% nucleotide identity to the corresponding open reading frame gene of each virus. The phylogenetic analysis clearly showed genetic similarity and cross-lineage between our isolates and other isolates from Egypt, the USA, Brazil, Indonesia, China, Korea, Taiwan, and Ecuador. In conclusion, gross inspection and histopathology may aid in the diagnosis of viral diseases; however, molecular tools are indispensable for confirming a possible infection. The current study recommends strict regulations during live shrimp transportation and implementing health control certificates over all imports and exports, especially in developing countries, including Egypt.

Novel infectious myonecrosis virus (IMNV) genotypes associated with disease outbreaks on Penaeus vannamei shrimp farms in Indonesia

Infectious myonecrosis virus (IMNV) is one of the most pathogenic viruses that affect Penaeus vannamei shrimp. In 2018, IMNV was reported in grow-out ponds of P. vannamei in Situbondo, Indonesia. Diseased animals displayed clinical signs of infectious myonecrosis (IMN) characterized by white discoloration of skeletal muscle. Histopathology of affected shrimp revealed lesions that are pathognomonic of IMNV infection. The major capsid protein (MCP) gene was amplified and sequenced from representative samples showing IMN pathology. Multiple alignment of predicted amino acid sequences of the MCP gene with known IMNV genotypes in the GenBank database revealed three unique genotypes, SB-A, SB-B and SB-C,in Situbondo samples. The number of amino acid changes in SB-A, SB-B and SB-C compared to known IMNV genotypes ranged from 7-710, including the isolate SB-B, which contains deletion of 622 aa. A phylogenetic analysis using homologous sequences from Brazil and Indonesia showed that these three isolates represent new IMNV genotypes.

Advances in the application of high-throughput sequencing in invertebrate virology

Over the last decade, advances in high-throughput sequencing technologies have revolutionised biological research, making it possible for DNA/RNA sequencing of any organism of interest to be undertaken. Sequencing approaches are now routinely used in the detection and characterisation of (novel) viruses, investigation of host-pathogen interactions, and effective development of disease treatment strategies. For the sequencing and identification of viruses of interest, metagenomics approaches using infected host tissue are frequently used, as it is not always possible to culture and isolate these pathogens. High-throughput sequencing can also be used to investigate host-pathogen interactions by investigating (temporal) transcriptomic responses of both the host and virus, potentially leading to the discovery of novel opportunities for treatment and drug targets. In addition, viruses in environmental samples (e.g. water or soil samples) can be identified using eDNA/metagenomics approaches. The promise that recent developments in sequencing brings to the field of invertebrate virology are not devoid of technical challenges, including the need for better laboratory and bioinformatics strategies to sequence and assemble virus genomes within complex tissue or environmental samples, and the difficulties associated with the annotation of the large number of novel viruses being discovered.