Complete genome sequence and phylogenetic analysis of megalocytivirus RSIV-Ku: A natural recombination infectious spleen and kidney necrosis virus

Abstract

Megalocytiviruses are classified into three genotypes, infectious spleen and kidney necrosis virus (ISKNV), red seabream virus (RSIV), and turbo reddish body iridovirus (TRBIV), based on the major capsid protein and ATPase genes. However, only a few complete genome sequences have been obtained. This paper reports the complete genome sequence and phylogenetic analysis of an RSIV-Ku strain megalocytivirus. The genome sequence comprises 111,154 bp, has 132 putative open reading frames, and is homologous mostly to ISKNV, except for the sequence in the region 58981-66830, which is more closely related to that of the RSIV genotype. The results imply that RSIV-Ku is actually a natural recombinant virus.

Draft genome sequence of scale drop disease virus (SDDV) retrieved from metagenomic investigation of infected barramundi, Lates calcarifer (Bloch, 1790)

“…However, the possible recombination likely occurred among other megalocytivirus species (GSIV, OSGIV, RSIV, RBIV, SACIV, TBIV, TRBIV, TSGIV and ISKNV) rather than between ECIV and SDDV strains since the reticulation pattern of the network, an indication of recombination, can be found exclusively among the former species (Figure 3b). In fact, the evidence of interspecies recombination between isolate RSIV‐Ku and GSIV‐K1 has been reported previously, which is consistent with the network analysis result obtained in this study (Shiu, Hong, Ku, & Wen, 2018). Regarding the genetic components, a unique 7.6‐kb‐long genomic region was found in TH2019 but not in the reference genome (Figure 4), giving more understanding about genomic structure and diversity of SDDV.…”

Molecular evidence for homologous strains of infectious spleen and kidney necrosis virus (ISKNV) genotype I infecting inland freshwater cultured Asian sea bass (Lates calcarifer) in Thailand

“…3C) showed the reticulation pattern within ISKNV and RSIV groups which implied the possible genetic recombination between the members of these groups. In fact, one of the ISKNV group members, RSIV-Ku, harbored 7% of genome contents similar to the GSIV-K1 (belonging to RSIV group) which indicated that this strain was ISKNV/RSIV recombinant [42]. Herein, possible recombination between ISKNV KU1/KU2 and other megalocytiviruses was screened using the RDP4 program [35] but no evidence of recombination was found in their genomes (data not shown).…”

“…Orthology analysis showed a surprisingly high number of unassigned orthogroups (unique genes) among the genomes of ISKNN KU1/KU2, RSIV-Ku, and reference strain. It is predictable that the strain RSIV-Ku, a natural recombinant virus, may possess numerous unique genes since its genome carried a 7.8-kb-long region similar to RSIV genotype II rather than ISKNV [42]. In the case of the ISKNV reference strain, 18 genes were unassigned to any orthologous groups, though the core genome similarity comparing to the ISKNV KU1/KU2 was as high as 99.98%.…”

Complete Genome Sequences and Pathogenicity Analysis of Two Red Sea Bream Iridoviruses Isolated from Cultured Fish in Korea

“…Of note, RSIV subtype II has been identified as the major causative pathogen of endemic RSIVD in cultured marine fish in Korea [5]. Recently, an ISKNV/RSIV recombinant type was isolated from red sea bream (Pagrus major) in Taiwan, known as RSIV-Ku [13]. Its genome shares a high degree of homology with ISKNV-type viruses, except for specific nucleotide sequences that are closely related to RSIV-type viruses, implying that RSIV-Ku is a natural recombinant of ISKNV-and RSIVtype viruses [13].…”

“…Recently, an ISKNV/RSIV recombinant type was isolated from red sea bream (Pagrus major) in Taiwan, known as RSIV-Ku [13]. Its genome shares a high degree of homology with ISKNV-type viruses, except for specific nucleotide sequences that are closely related to RSIV-type viruses, implying that RSIV-Ku is a natural recombinant of ISKNV-and RSIVtype viruses [13]. Moreover, RSIV SB5-TY from a diseased Japanese seabass (Lateolabrax japonicus) in Korea is believed to be a genetic variant of RSIV-type viruses based on sequence difference in MCP and ankyrin repeat domains [5].…”