Sturgeon nucleo-cytoplasmic large DNA virus phylogeny and PCR tests

Abstract

Sturgeon epitheliotropic nucleo-cytoplasmic large DNA viruses (NCLDVs) can cause a lethal disease of the integumentary system. These viruses have not been assigned to any currently recognized family or genus. In this study, phylogenetic analyses using the major capsid protein (MCP) showed that the sturgeon NCLDVs formed a cohesive taxonomic group, could be identified to the species or possibly sub-species level and formed a distinct evolutionary lineage within the Megavirales. The genetic relatedness of the sturgeon virus MCP allowed design of 3 PCR diagnostic tests with analytical specificity (ASp) inclusive of this group of viruses. The conventional PCR test, C1, had broader ASp than the 2 quantitative PCR tests, Q1 and Q2, and was inclusive of the sturgeon viruses as well as some viruses belonging to the families Mimi-, Phycodna-, or Iridoviridae. Q2 had broader specificity than Q1 but both tests recognized the sturgeon NCLDVs and did not cross-react with co-localizing sturgeon herpesviruses. Analytical test performance characteristics evaluated for Q1 and Q2 revealed sensitive assays with observed 50% limits of detection between 3 and 6.25 plasmid copies and high intra- and inter-assay repeatability. Q1 was used to test for sturgeon viruses in endangered populations of lake sturgeon Acipenser fulvescens within the Winnipeg River or Nelson River drainage systems of Manitoba, Canada. Test results indicated that namao virus is endemic in the Nelson River water basin. These tests meet the analytical requirements for diagnostic testing in Canada and are useful tools for disease management in sturgeon conservation stocking programs in North America.

Molecular identification of iridoviruses infecting various sturgeon species in Europe

“…Two real‐time PCR assays were recently developed, targeting viruses from North America (Clouthier et al . ). These tools are not adapted to detecting AcIV‐E because there are differences in the sequences.…”

“…The partial sequence of the MCP gene of this virus, provisionally named the shortnose sturgeon virus (SNSV), shows strong similarity with the group containing NV, MRSIV and another American virus (British Colombia white sturgeon virus, BCWSV) (Clouthier et al . ).…”

“…). A recent comparison of the partial sequences of the major capsid protein (MCP) in MRSIV and WSIV (Clouthier, Vanwalleghem & Anderson ) shows that, although they are highly related, there are nine differences among the 183 nucleotides of the sequence. This moderate level of substitution may explain why the molecular diagnostic tools set up for MRSIV do not detect WSIV, and vice versa (Kwak et al .…”

Outbreak of Mortality Associated with Acipenser Iridovirus European (AcIV-E) Detection in Siberian Sturgeon (Acipenser baerii) Farmed in Sweden

“…The taxonomical classification of these viruses is yet to be elucidated. They were recently moved from Iridoviridae to Mimiviridae [4,5], a viral family characterized by extreme genomic complexity and plasticity. In fact, the genomes of these viruses are still largely unknown.…”

Giant mimiviruses escape many canonical criteria of the virus definition

“…Three groups, A, B and C, of mimiviruses replicating in Acanthamoeba species were delineated based on phylogenomic analyses [8]. These giant viruses are common in water and soil worldwide, and in a few cases were detected and isolated from animals and humans [2,9,10].…”