Publications by authors named "Gael Kurath"

75 Publications

Virus shedding kinetics and unconventional virulence tradeoffs.

PLoS Pathog 2021 May 10;17(5):e1009528. Epub 2021 May 10.

Department of Biology, University of Washington, Seattle, Washington, United States of America.

Tradeoff theory, which postulates that virulence provides both transmission costs and benefits for pathogens, has become widely adopted by the scientific community. Although theoretical literature exploring virulence-tradeoffs is vast, empirical studies validating various assumptions still remain sparse. In particular, truncation of transmission duration as a cost of virulence has been difficult to quantify with robust controlled in vivo studies. We sought to fill this knowledge gap by investigating how transmission rate and duration were associated with virulence for infectious hematopoietic necrosis virus (IHNV) in rainbow trout (Oncorhynchus mykiss). Using host mortality to quantify virulence and viral shedding to quantify transmission, we found that IHNV did not conform to classical tradeoff theory. More virulent genotypes of the virus were found to have longer transmission durations due to lower recovery rates of infected hosts, but the relationship was not saturating as assumed by tradeoff theory. Furthermore, the impact of host mortality on limiting transmission duration was minimal and greatly outweighed by recovery. Transmission rate differences between high and low virulence genotypes were also small and inconsistent. Ultimately, more virulent genotypes were found to have the overall fitness advantage, and there was no apparent constraint on the evolution of increased virulence for IHNV. However, using a mathematical model parameterized with experimental data, it was found that host culling resurrected the virulence tradeoff and provided low virulence genotypes with the advantage. Human-induced or natural culling, as well as host population fragmentation, may be some of the mechanisms by which virulence diversity is maintained in nature. This work highlights the importance of considering non-classical virulence tradeoffs.
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http://dx.doi.org/10.1371/journal.ppat.1009528DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8109835PMC
May 2021

Virulence and Infectivity of UC, MD, and L Strains of Infectious Hematopoietic Necrosis Virus (IHNV) in Four Populations of Columbia River Basin Chinook Salmon.

Viruses 2021 04 18;13(4). Epub 2021 Apr 18.

Western Fisheries Research Center, United States Geological Survey, Seattle, WA 98115, USA.

Infectious Hematopoietic Necrosis Virus (IHNV) infects juvenile salmonid fish in conservation hatcheries and aquaculture facilities, and in some cases, causes lethal disease. This study assesses intra-specific variation in the IHNV susceptibility of Chinook salmon () in the Columbia River Basin (CRB), in the northwestern United States. The virulence and infectivity of IHNV strains from three divergent virus genogroups are measured in four Chinook salmon populations, including spring-run and fall-run fish from the lower or upper regions of the CRB. Following controlled laboratory exposures, our results show that the positive control L strain had significantly higher virulence, and the UC and MD strains that predominate in the CRB had equivalently low virulence, consistent with field observations. By several experimental measures, there was little variation in host susceptibility to infection or disease. However, a small number of exceptions suggested that the lower CRB spring-run Chinook salmon population may be less susceptible than other populations tested. The UC and MD viruses did not differ in infectivity, indicating that the observed asymmetric field prevalence in which IHNV detected in CRB Chinook salmon is 83% UC and 17% MD is not due to the UC virus being more infectious. Overall, we report little intra-species variation in CRB Chinook salmon susceptibility to UC or MD IHNV infection or disease, and suggest that other factors may instead influence the ecology of IHNV in the CRB.
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http://dx.doi.org/10.3390/v13040701DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8072589PMC
April 2021

Infectious hematopoietic necrosis virus specialization in a multihost salmonid system.

Evol Appl 2020 Sep 28;13(8):1841-1853. Epub 2020 Feb 28.

Department of Biological Sciences The University of Alabama Tuscaloosa Alabama.

Many pathogens interact and evolve in communities where more than one host species is present, yet our understanding of host-pathogen specialization is mostly informed by laboratory studies with single species. Managing diseases in the wild, however, requires understanding how host-pathogen specialization affects hosts in diverse communities. Juvenile salmonid mortality in hatcheries caused by infectious hematopoietic necrosis virus (IHNV) has important implications for salmonid conservation programs. Here, we evaluate evidence for IHNV specialization on three salmonid hosts and assess how this influences intra- and interspecific transmission in hatchery-reared salmonids. We expect that while more generalist viral lineages should pose an equal risk of infection across host types, viral specialization will increase intraspecific transmission. We used Bayesian models and data from 24 hatcheries in the Columbia River Basin to reconstruct the exposure history of hatcheries with two IHNV lineages, MD and UC, allowing us to estimate the probability of juvenile infection with these lineages in three salmonid host types. Our results show that lineage MD is specialized on steelhead trout and perhaps rainbow trout (both ), whereas lineage UC displayed a generalist phenotype across steelhead trout, rainbow trout, and Chinook salmon. Furthermore, our results suggest the presence of specialist-generalist trade-offs because, while lineage UC had moderate probabilities of infection across host types, lineage MD had a small probability of infection in its nonadapted host type, Chinook salmon. Thus, in addition to quantifying probabilities of infection of socially and economically important salmonid hosts with different IHNV lineages, our results provide insights into the trade-offs that viral lineages incur in multihost communities. Our results suggest that knowledge of the specialist/generalist strategies of circulating viral lineages could be useful in salmonid conservation programs to control disease.
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http://dx.doi.org/10.1111/eva.12931DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7463311PMC
September 2020

2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.

Arch Virol 2020 Dec 4;165(12):3023-3072. Epub 2020 Sep 4.

Colorado State University, Fort Collins, CO, USA.

In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
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http://dx.doi.org/10.1007/s00705-020-04731-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7606449PMC
December 2020

ICTV Virus Taxonomy Profile: .

J Gen Virol 2019 12 11;100(12):1593-1594. Epub 2019 Oct 11.

Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Rd, Singapore.

The family consists of large enveloped RNA viruses infecting mammals, birds, reptiles and fish. Many paramyxoviruses are host-specific and several, such as measles virus, mumps virus, Nipah virus, Hendra virus and several parainfluenza viruses, are pathogenic for humans. The transmission of paramyxoviruses is horizontal, mainly through airborne routes; no vectors are known. This is a summary of the current International Committee on Taxonomy of Viruses (ICTV) Report on the family . which is available at ictv.global/report/paramyxoviridae.
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http://dx.doi.org/10.1099/jgv.0.001328DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7273325PMC
December 2019

The Nucleoprotein and Phosphoprotein Are Major Determinants of the Virulence of Viral Hemorrhagic Septicemia Virus in Rainbow Trout.

J Virol 2019 09 28;93(18). Epub 2019 Aug 28.

Western Fisheries Research Center, U.S. Geological Survey, Seattle, Washington, USA

Viral hemorrhagic septicemia virus (VHSV), a fish rhabdovirus, infects several marine and freshwater fish species. There are many strains of VHSV that affect different fish, but some strains of one genetic subgroup have gained high virulence in rainbow trout (). To define the genetic basis of high virulence in trout, we used reverse genetics to create chimeric VHSVs in which viral nucleoprotein (N), P (phosphoprotein), or M (matrix protein) genes, or the N and P genes, were exchanged between a trout-virulent European VHSV strain (DK-3592B) and a trout-avirulent North American VHSV strain (MI03). Testing of the chimeric recombinant VHSV (rVHSV) by intraperitoneal injection in juvenile rainbow trout showed that exchanges of the viral P or M genes had no effect on the trout virulence phenotype of either parental strain. However, reciprocal exchanges of the viral N gene resulted in a partial gain of function in the chimeric trout-avirulent strain (22% mortality) and complete loss of virulence for the chimeric trout-virulent strain (2% mortality). Reciprocal exchanges of both the N and P genes together resulted in complete gain of function in the chimeric avirulent strain (82% mortality), again with complete loss of virulence in the chimeric trout-virulent strain (0% mortality). Thus, the VHSV N gene contains an essential determinant of trout virulence that is strongly enhanced by the viral P gene. We hypothesize that the host-specific virulence mechanism may involve increased efficiency of the viral polymerase complex when the N and P proteins have adapted to more efficient interaction with a host component from rainbow trout. Rainbow trout farming is a major food source industry worldwide that has suffered great economic losses due to host jumps of fish rhabdovirus pathogens, followed by evolution of dramatic increases in trout-specific virulence. However, the genetic determinants of host jumps and increased virulence in rainbow trout are unknown for any fish rhabdovirus. Previous attempts to identify the viral genes containing trout virulence determinants of viral hemorrhagic septicemia virus (VHSV) have not been successful. We show here that, somewhat surprisingly, the viral nucleocapsid (N) and phosphoprotein (P) genes together contain the determinants responsible for trout virulence in VHSV. This suggests a novel host-specific virulence mechanism involving the viral polymerase and a host component. This differs from the known virulence mechanisms of mammalian rhabdoviruses based on the viral P or M (matrix) protein.
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http://dx.doi.org/10.1128/JVI.00382-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714817PMC
September 2019

Taxonomy of the order Mononegavirales: update 2019.

Arch Virol 2019 Jul;164(7):1967-1980

Public Health England, Porton Down, Wiltshire, Salisbury, UK.

In February 2019, following the annual taxon ratification vote, the order Mononegavirales was amended by the addition of four new subfamilies and 12 new genera and the creation of 28 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
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http://dx.doi.org/10.1007/s00705-019-04247-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6641539PMC
July 2019

The glycoprotein, non-virion protein, and polymerase of viral hemorrhagic septicemia virus are not determinants of host-specific virulence in rainbow trout.

Virol J 2019 03 7;16(1):31. Epub 2019 Mar 7.

Institute of Marine & Environmental Technology, University of Maryland Baltimore County, 701 E. Pratt Street, Baltimore, MD, 21202, USA.

Background: Viral hemorrhagic septicemia virus (VHSV), a fish rhabdovirus belonging to the Novirhabdovirus genus, causes severe disease and mortality in many marine and freshwater fish species worldwide. VHSV isolates are classified into four genotypes and each group is endemic to specific geographic regions in the north Atlantic and Pacific Oceans. Most viruses in the European VHSV genotype Ia are highly virulent for rainbow trout (Oncorhynchus mykiss), whereas, VHSV genotype IVb viruses from the Great Lakes region in the United States, which caused high mortality in wild freshwater fish species, are avirulent for trout. This study describes molecular characterization and construction of an infectious clone of the virulent VHSV-Ia strain DK-3592B from Denmark, and application of the clone in reverse genetics to investigate the role of selected VHSV protein(s) in host-specific virulence in rainbow trout (referred to as trout-virulence).

Methods: Overlapping cDNA fragments of the DK-3592B genome were cloned after RT-PCR amplification, and their DNA sequenced by the di-deoxy chain termination method. A full-length cDNA copy (pVHSVdk) of the DK-3592B strain genome was constructed by assembling six overlapping cDNA fragments by using natural or artificially created unique restriction sites in the overlapping regions of the clones. Using an existing clone of the trout-avirulent VHSV-IVb strain MI03 (pVHSVmi), eight chimeric VHSV clones were constructed in which the coding region(s) of the glycoprotein (G), non-virion protein (NV), G and NV, or G, NV and L (polymerase) genes together, were exchanged between the two clones. Ten recombinant VHSVs (rVHSVs) were generated, including two parental rVHSVs, by transfecting fish cells with ten individual full-length plasmid constructs along with supporting plasmids using the established protocol. Recovered rVHSVs were characterized for viability and growth in vitro and used to challenge groups of juvenile rainbow trout by intraperitoneal injection.

Results: Complete sequence of the VHSV DK-3592B genome was determined from the cloned cDNA and deposited in GenBank under the accession no. KC778774. The trout-virulent DK-3592B genome (genotype Ia) is 11,159 nt in length and differs from the trout-avirulent MI03 genome (pVHSVmi) by 13% at the nucleotide level. When the rVHSVs were assessed for the trout-virulence phenotype in vivo, the parental rVHSVdk and rVHSVmi were virulent and avirulent, respectively, as expected. Four chimeric rVHSVdk viruses with the substitutions of the G, NV, G and NV, or G, NV and L genes from the avirulent pVHSVmi constructs were still highly virulent (100% mortality), while the reciprocal four chimeric rVHSVmi viruses with genes from pVHSVdk remained avirulent (0-10% mortality).

Conclusions: When chimeric rVHSVs, containing all the G, NV, and L gene substitutions, were tested in vivo, they did not exhibit any change in trout-virulence relative to the background clones. These results demonstrate that the G, NV and L genes of VHSV are not, by themselves or in combination, major determinants of host-specific virulence in trout.
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http://dx.doi.org/10.1186/s12985-019-1139-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6407216PMC
March 2019

Taxonomy of the order Mononegavirales: second update 2018.

Arch Virol 2019 Apr;164(4):1233-1244

Public Health England, Porton Down, Salisbury, Wiltshire, UK.

In October 2018, the order Mononegavirales was amended by the establishment of three new families and three new genera, abolishment of two genera, and creation of 28 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
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http://dx.doi.org/10.1007/s00705-018-04126-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6460460PMC
April 2019

Phylogeography and evolution of infectious hematopoietic necrosis virus in China.

Mol Phylogenet Evol 2019 02 25;131:19-28. Epub 2018 Oct 25.

Heilongjiang River Fishery Research Institute Chinese Academy of Fishery Sciences, Harbin 150070, PR China. Electronic address:

Infectious hematopoietic necrosis virus (IHNV) is a well-known rhabdoviral pathogen of salmonid fish. In this study, a comprehensive analysis of 40 IHNV viruses isolated from thirteen fish farms in nine geographically dispersed Chinese provinces during 2012 to 2017 is presented. Identity of nucleotide and amino acid sequences among all the complete glycoprotein (G) genes from Chinese isolates was 98.0-100% and 96.7-100%, respectively. Coalescent phylogenetic analyses revealed that all the Chinese IHN virus characterized in this study were in a monophyletic clade that had a most recent common ancestor with the J Nagano (JN) subgroup within the J genogroup of IHNV. Within the Chinese IHNV clade isolates obtained over successive years from the same salmon fish farm clustered in strongly supported subclades, suggesting maintenance and diversification of virus over time within individual farms. There was also evidence for regional virus transmission within provinces, and some cases of longer distance transmission between distant provinces, such as Gansu and Yunnan. The data demonstrated that IHNV has evolved into a new subgroup in salmon farm environments in China, and IHNV isolates are undergoing molecular evolution within fish farms. We suggest that Chinese IHNV comprises a separate JC subgroup within the J genogroup of IHNV.
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http://dx.doi.org/10.1016/j.ympev.2018.10.030DOI Listing
February 2019

Molecular systematics of sturgeon nucleocytoplasmic large DNA viruses.

Mol Phylogenet Evol 2018 11 27;128:26-37. Epub 2018 Jul 27.

U.S. Geological Survey, Western Fisheries Research Center, 6505 NE 65th Street, Seattle, WA 98115, USA; Department of Microbiology, Oregon State University, 2820 SW Campus Way, Corvallis, OR 97331, USA.

Namao virus (NV) is a sturgeon nucleocytoplasmic large DNA virus (sNCLDV) that can cause a lethal disease of the integumentary system in lake sturgeon Acipenser fulvescens. As a group, the sNCLDV have not been assigned to any currently recognized taxonomic family of viruses. In this study, a data set of NV DNA sequences was generated and assembled as two non-overlapping contigs of 306,448 bp and then used to conduct a comprehensive systematics analysis using Bayesian inference of phylogeny for NV, other sNCLDV and representative members of six families of the NCLDV superfamily. The phylogeny of NV was reconstructed using protein homologues encoded by nine nucleocytoplasmic virus orthologous genes (NCVOGs): NCVOG0022 - mcp, NCVOG0038 - DNA polymerase B elongation subunit, NCVOG0076 - VV A18-type helicase, NCVOG0249 - VV A32-type ATPase, NCVOG0262 - AL2 VLTF3-like transcription factor, NCVOG0271 - RNA polymerase II subunit II, NCVOG0274 - RNA polymerase II subunit I, NCVOG0276 - ribonucleotide reductase small subunit and NCVOG1117 - mRNA capping enzyme. The accuracy of our phylogenetic method was evaluated using a combination of Bayesian statistical analysis and congruence analysis. Stable tree topologies were obtained with data sets differing in target molecule(s), sequence length and taxa. Congruent topologies were obtained in phylogenies constructed using individual protein data sets. The major capsid protein phylogeny inferred that ten representative sNCLDV form a monophyletic group comprised of four lineages within a polyphyletic Mimi-Phycodnaviridae group of taxa. Overall, the analyses revealed that Namao virus is a member of the Mimiviridae family with strong and consistent support for a clade containing NV and CroV as sister taxa.
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http://dx.doi.org/10.1016/j.ympev.2018.07.019DOI Listing
November 2018

Taxonomy of the order Mononegavirales: update 2018.

Arch Virol 2018 Aug 11;163(8):2283-2294. Epub 2018 Apr 11.

Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institute, WHO Collaborating Centre for Rabies Surveillance and Research, Greifswald-Insel Riems, Germany.

In 2018, the order Mononegavirales was expanded by inclusion of 1 new genus and 12 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future.
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http://dx.doi.org/10.1007/s00705-018-3814-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6076851PMC
August 2018

ICTV Virus Taxonomy Profile: Rhabdoviridae.

J Gen Virol 2018 04 19;99(4):447-448. Epub 2018 Feb 19.

Department of Plant Pathology, Kansas State University, Manhattan KS 66506, USA.

The family Rhabdoviridae comprises viruses with negative-sense (-) single-stranded RNA genomes of 10.8-16.1 kb. Virions are typically enveloped with bullet-shaped or bacilliform morphology but can also be non-enveloped filaments. Rhabdoviruses infect plants and animals including mammals, birds, reptiles and fish, as well as arthropods which serve as single hosts or act as biological vectors for transmission to animals or plants. Rhabdoviruses include important pathogens of humans, livestock, fish and agricultural crops. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of Rhabdoviridae, which is available at www.ictv.global/report/rhabdoviridae.
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http://dx.doi.org/10.1099/jgv.0.001020DOI Listing
April 2018

Problems of classification in the family Paramyxoviridae.

Arch Virol 2018 May 25;163(5):1395-1404. Epub 2018 Jan 25.

Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.

A number of unassigned viruses in the family Paramyxoviridae need to be classified either as a new genus or placed into one of the seven genera currently recognized in this family. Furthermore, numerous new paramyxoviruses continue to be discovered. However, attempts at classification have highlighted the difficulties that arise by applying historic criteria or criteria based on sequence alone to the classification of the viruses in this family. While the recent taxonomic change that elevated the previous subfamily Pneumovirinae into a separate family Pneumoviridae is readily justified on the basis of RNA dependent -RNA polymerase (RdRp or L protein) sequence motifs, using RdRp sequence comparisons for assignment to lower level taxa raises problems that would require an overhaul of the current criteria for assignment into genera in the family Paramyxoviridae. Arbitrary cut off points to delineate genera and species would have to be set if classification was based on the amino acid sequence of the RdRp alone or on pairwise analysis of sequence complementarity (PASC) of all open reading frames (ORFs). While these cut-offs cannot be made consistent with the current classification in this family, resorting to genus-level demarcation criteria with additional input from the biological context may afford a way forward. Such criteria would reflect the increasingly dynamic nature of virus taxonomy even if it would require a complete revision of the current classification.
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http://dx.doi.org/10.1007/s00705-018-3720-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6309968PMC
May 2018

Vaccine Effects on Heterogeneity in Susceptibility and Implications for Population Health Management.

mBio 2017 11 21;8(6). Epub 2017 Nov 21.

Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA.

Heterogeneity in host susceptibility is a key determinant of infectious disease dynamics but is rarely accounted for in assessment of disease control measures. Understanding how susceptibility is distributed in populations, and how control measures change this distribution, is integral to predicting the course of epidemics with and without interventions. Using multiple experimental and modeling approaches, we show that rainbow trout have relatively homogeneous susceptibility to infection with infectious hematopoietic necrosis virus and that vaccination increases heterogeneity in susceptibility in a nearly all-or-nothing fashion. In a simple transmission model with an of 2, the highly heterogeneous vaccine protection would cause a 35 percentage-point reduction in outbreak size over an intervention inducing homogenous protection at the same mean level. More broadly, these findings provide validation of methodology that can help to reduce biases in predictions of vaccine impact in natural settings and provide insight into how vaccination shapes population susceptibility. Differences among individuals influence transmission and spread of infectious diseases as well as the effectiveness of control measures. Control measures, such as vaccines, may provide leaky protection, protecting all hosts to an identical degree, or all-or-nothing protection, protecting some hosts completely while leaving others completely unprotected. This distinction can have a dramatic influence on disease dynamics, yet this distribution of protection is frequently unaccounted for in epidemiological models and estimates of vaccine efficacy. Here, we apply new methodology to experimentally examine host heterogeneity in susceptibility and mode of vaccine action as distinct components influencing disease outcome. Through multiple experiments and new modeling approaches, we show that the distribution of vaccine effects can be robustly estimated. These results offer new experimental and inferential methodology that can improve predictions of vaccine effectiveness and have broad applicability to human, wildlife, and ecosystem health.
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http://dx.doi.org/10.1128/mBio.00796-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5698548PMC
November 2017

Complete sequences of 4 viral hemorrhagic septicemia virus IVb isolates and their virulence in northern pike fry.

Dis Aquat Organ 2017 11;126(3):211-227

Aquatic Animal Health Program, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.

Four viral hemorrhagic septicemia virus (VHSV) genotype IVb isolates were sequenced, their genetic variation explored, and comparative virulence assayed with experimental infections of northern pike Esox lucius fry. In addition to the type strain MI03, the complete 11183 bp genome of the first round goby Neogobius melanostomus isolate from the St. Lawrence River, and the 2013 and 2014 isolates from gizzard shad Dorosoma cepedianum die-offs in Irondequoit Bay, Lake Ontario and Dunkirk Harbor, Lake Erie were all deep sequenced on an Illumina platform. Mutations documented in the 11 yr since the MI03 index case from Lake St. Clair muskellunge Esox masquinongy showed 87 polymorphisms among the 4 isolates. Twenty-six mutations were non-synonymous and located at 18 different positions within the matrix protein, glycoprotein, non-virion protein, and RNA polymerase genes. The same 4 isolates were used to infect northern pike fry by a single 1 h bath exposure. Cumulative percent mortality varied from 42.5 to 62.5%. VHSV was detected in 57% (41/72) of the survivors at the end of the 21-d trial, suggesting that the virus was not rapidly cleared. Lesions were observed in many of the moribund and dead northern pike, such as hemorrhaging in the skin and fins, as well as hydrocephalus. Mean viral load measured from the trunk and visceral tissues of MI03-infected pike was significantly higher than the quantities detected in fish infected with the most recent isolates of genotype IVb, but there were no differences in cumulative mortality observed.
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http://dx.doi.org/10.3354/dao03171DOI Listing
November 2017

ICTV Virus Taxonomy Profile: Pneumoviridae.

J Gen Virol 2017 Dec 31;98(12):2912-2913. Epub 2017 Oct 31.

Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, Singapore.

The family Pneumoviridae comprises large enveloped negative-sense RNA viruses. This taxon was formerly a subfamily within the Paramyxoviridae, but was reclassified in 2016 as a family with two genera, Orthopneumovirus and Metapneumovirus. Pneumoviruses infect a range of mammalian species, while some members of the Metapneumovirus genus may also infect birds. Some viruses are specific and pathogenic for humans, such as human respiratory syncytial virus and human metapneumovirus. There are no known vectors for pneumoviruses and transmission is thought to be primarily by aerosol droplets and contact. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Pneumoviridae, which is available at www.ictv.global/report/pneumoviridae.
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http://dx.doi.org/10.1099/jgv.0.000959DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5775899PMC
December 2017

Transmission routes maintaining a viral pathogen of steelhead trout within a complex multi-host assemblage.

Ecol Evol 2017 10 6;7(20):8187-8200. Epub 2017 Sep 6.

Cary Institute for Ecosystems Studies Millbrook NY USA.

This is the first comprehensive region wide, spatially explicit epidemiologic analysis of surveillance data of the aquatic viral pathogen infectious hematopoietic necrosis virus (IHNV) infecting native salmonid fish. The pathogen has been documented in the freshwater ecosystem of the Pacific Northwest of North America since the 1950s, and the current report describes the disease ecology of IHNV during 2000-2012. Prevalence of IHNV infection in monitored salmonid host cohorts ranged from 8% to 30%, with the highest levels observed in juvenile steelhead trout. The spatial distribution of all IHNV-infected cohorts was concentrated in two sub-regions of the study area, where historic burden of the viral disease has been high. During the study period, prevalence levels fluctuated with a temporal peak in 2002. Virologic and genetic surveillance data were analyzed for evidence of three separate but not mutually exclusive transmission routes hypothesized to be maintaining IHNV in the freshwater ecosystem. Transmission between year classes of juvenile fish at individual sites (route 1) was supported at varying levels of certainty in 10%-55% of candidate cases, transmission between neighboring juvenile cohorts (route 2) was supported in 31%-78% of candidate cases, and transmission from adult fish returning to the same site as an infected juvenile cohort was supported in 26%-74% of candidate cases. The results of this study indicate that multiple specific transmission routes are acting to maintain IHNV in juvenile fish, providing concrete evidence that can be used to improve resource management. Furthermore, these results demonstrate that more sophisticated analysis of available spatio-temporal and genetic data is likely to yield greater insight in future studies.
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http://dx.doi.org/10.1002/ece3.3276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5648648PMC
October 2017

Taxonomy of the order Mononegavirales: update 2017.

Arch Virol 2017 Aug 7;162(8):2493-2504. Epub 2017 Apr 7.

State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology of Húběi Province, College of Plant Science and Technology, Huázhōng Agricultural University, Wǔhàn, China.

In 2017, the order Mononegavirales was expanded by the inclusion of a total of 69 novel species. Five new rhabdovirus genera and one new nyamivirus genus were established to harbor 41 of these species, whereas the remaining new species were assigned to already established genera. Furthermore, non-Latinized binomial species names replaced all paramyxovirus and pneumovirus species names, thereby accomplishing application of binomial species names throughout the entire order. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
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http://dx.doi.org/10.1007/s00705-017-3311-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5831667PMC
August 2017

A effective DNA vaccine against diverse genotype J infectious hematopoietic necrosis virus strains prevalent in China.

Vaccine 2017 04 23;35(18):2420-2426. Epub 2017 Mar 23.

Heilongjiang River Fishery Research Institute Chinese Academy of Fishery Sciences, Harbin 150070, PR China. Electronic address:

Infectious hematopoietic necrosis virus (IHNV) is the most important pathogen threatening the aquaculture of salmonid fish in China. In this study, a DNA vaccine, designated pIHNch-G, was constructed with the glycoprotein (G) gene of a Chinese IHNV isolate SD-12 (also called Sn1203) of genotype J. The minimal dose of vaccine required, the expression of the Mx-1 gene in the muscle (vaccine delivery site) and anterior kidney, and the titers of the neutralizing antibodies produced were used to evaluate the vaccine efficacy. To assess the potential utility of the vaccine in controlling IHNV throughout China, the cross protective efficacy of the vaccine was determined by challenging fish with a broad range of IHNV strains from different geographic locations in China. A single 100ng dose of the vaccine conferred almost full protection to rainbow trout fry (3g) against waterborne or intraperitoneal injection challenge with IHNV strain SD-12 as early as 4days post-vaccination (d.p.v.), and significant protection was still observed at 180d.p.v. Intragenogroup challenges showed that the DNA vaccine provided similar protection to the fish against all the Chinese IHNV isolates tested, suggesting that the vaccine can be widely used in China. Mx-1 gene expression was significantly upregulated in the muscle tissue (vaccine delivery site) and anterior kidney in the vaccinated rainbow trout at both 4 and 7d.p.v. Similar levels of neutralizing antibodies were determined with each of the Chinese IHNV strains at 60 and 180d.p.v. This DNA vaccine should play an important role in the control of IHN in China.
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http://dx.doi.org/10.1016/j.vaccine.2017.03.047DOI Listing
April 2017

Infectious hematopoietic necrosis virus virological and genetic surveillance 2000-2012.

Ecology 2017 Jan;98(1):283

Cary Institute for Ecosystems Studies, Millbrook, New York, 12545, USA.

Surveillance records of the acute RNA pathogen of Pacific salmonid fish infectious hematopoietic necrosis virus are combined for the first time to enable landscape-level ecological analyses and modeling. The study area is the freshwater ecosystems of the large Columbia River watershed in the U.S. states of Washington, Oregon, and Idaho, as well as coastal rivers in Washington and Oregon. The study period is 2000-2012, and records were contributed by all five resource management agencies that operate conservation hatcheries in the study area. Additional records from wild fish were collected from the National Wild Fish Health Survey, operated by the U.S. Fish and Wildlife Survey. After curation and normalization, the data set consists of 6766 records, representing 1146 sample sites and 15 different fish hosts. The virus was found in an average of 12.4% of records, and of these 66.2% also have viral genetic analysis available. This data set is used to conduct univariate ecological and epidemiological analyses and develop a novel hierarchical landscape transmission model for an aquatic pathogen.
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http://dx.doi.org/10.1002/ecy.1634DOI Listing
January 2017

Geography and host species shape the evolutionary dynamics of U genogroup infectious hematopoietic necrosis virus.

Virus Evol 2016 Jul 26;2(2):vew034. Epub 2016 Dec 26.

U.S. Geological Survey, Western Fisheries Research Center, 6505 NE 65th St, Seattle, WA 98115.

Infectious hematopoietic necrosis virus (IHNV) is a negative-sense RNA virus that infects wild and cultured salmonids throughout the Pacific Coastal United States and Canada, from California to Alaska. Although infection of adult fish is usually asymptomatic, juvenile infections can result in high mortality events that impact salmon hatchery programs and commercial aquaculture. We used epidemiological case data and genetic sequence data from a 303 nt portion of the viral glycoprotein gene to study the evolutionary dynamics of U genogroup IHNV in the Pacific Northwestern United States from 1971 to 2013. We identified 114 unique genotypes among 1,219 U genogroup IHNV isolates representing 619 virus detection events. We found evidence for two previously unidentified, broad subgroups within the U genogroup, which we designated 'UC' and 'UP'. Epidemiologic records indicated that UP viruses were detected more frequently in sockeye salmon () and in coastal waters of Washington and Oregon, whereas UC viruses were detected primarily in Chinook salmon () and steelhead trout () in the Columbia River Basin, which is a large, complex watershed extending throughout much of interior Washington, Oregon, and Idaho. These findings were supported by phylogenetic analysis and by . Ancestral state reconstruction indicated that early UC viruses in the Columbia River Basin initially infected sockeye salmon but then emerged via host shifts into Chinook salmon and steelhead trout sometime during the 1980s. We postulate that the development of these subgroups within U genogroup was driven by selection pressure for viral adaptation to Chinook salmon and steelhead trout within the Columbia River Basin.
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http://dx.doi.org/10.1093/ve/vew034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5822886PMC
July 2016

The family Rhabdoviridae: mono- and bipartite negative-sense RNA viruses with diverse genome organization and common evolutionary origins.

Virus Res 2017 01 20;227:158-170. Epub 2016 Oct 20.

Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, 77555, USA.

The family Rhabdoviridae consists of mostly enveloped, bullet-shaped or bacilliform viruses with a negative-sense, single-stranded RNA genome that infect vertebrates, invertebrates or plants. This ecological diversity is reflected by the diversity and complexity of their genomes. Five canonical structural protein genes are conserved in all rhabdoviruses, but may be overprinted, overlapped or interspersed with several novel and diverse accessory genes. This review gives an overview of the characteristics and diversity of rhabdoviruses, their taxonomic classification, replication mechanism, properties of classical rhabdoviruses such as rabies virus and rhabdoviruses with complex genomes, rhabdoviruses infecting aquatic species, and plant rhabdoviruses with both mono- and bipartite genomes.
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http://dx.doi.org/10.1016/j.virusres.2016.10.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5124403PMC
January 2017

Replication and shedding kinetics of infectious hematopoietic necrosis virus in juvenile rainbow trout.

Virus Res 2017 01 19;227:200-211. Epub 2016 Oct 19.

USGS Western Fisheries Research Center, 6505 NE 65th St., Seattle, WA 98115, United States.

Viral replication and shedding are key components of transmission and fitness, the kinetics of which are heavily dependent on virus, host, and environmental factors. To date, no studies have quantified the shedding kinetics of infectious hematopoietic necrosis virus (IHNV) in rainbow trout (Oncorhynchus mykiss), or how they are associated with replication, making it difficult to ascertain the transmission dynamics of this pathogen of high agricultural and conservation importance. Here, the replication and shedding kinetics of two M genogroup IHNV genotypes were examined in their naturally co-evolved rainbow trout host. Within host virus replication began rapidly, approaching maximum values by day 3 post-infection, after which viral load was maintained or gradually dropped through day 7. Host innate immune response measured as stimulation of Mx-1 gene expression generally followed within host viral loads. Shedding also began very quickly and peaked within 2days, defining a generally uniform early peak period of shedding from 1 to 4days after exposure to virus. This was followed by a post-peak period where shedding declined, such that the majority of fish were no longer shedding by day 12 post-infection. Despite similar kinetics, the average shedding rate over the course of infection was significantly lower in mixed compared to single genotype infections, suggesting a competition effect, however, this did not significantly impact the total amount of virus shed. The data also indicated that the duration of shedding, rather than peak amount of virus shed, was correlated with fish mortality. Generally, the majority of virus produced during infection appeared to be shed into the environment rather than maintained in the host, although there was more retention of within host virus during the post-peak period. Viral virulence was correlated with shedding, such that the more virulent of the two genotypes shed more total virus. This fundamental understanding of IHNV shedding kinetics and variation at the individual fish level could assist with management decisions about how to respond to disease outbreaks when they occur.
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http://dx.doi.org/10.1016/j.virusres.2016.10.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5206995PMC
January 2017

Possibility and Challenges of Conversion of Current Virus Species Names to Linnaean Binomials.

Syst Biol 2017 05;66(3):463-473

Transboundary Animal Diseases Research Center, Joint Faculty of Veterinary Medicine, Kagoshima University, 890-0065 Japan Korimoto Kagoshima, Japan.

Botanical, mycological, zoological, and prokaryotic species names follow the Linnaean format, consisting of an italicized Latinized binomen with a capitalized genus name and a lower case species epithet (e.g., Homo sapiens). Virus species names, however, do not follow a uniform format, and, even when binomial, are not Linnaean in style. In this thought exercise, we attempted to convert all currently official names of species included in the virus family Arenaviridae and the virus order Mononegavirales to Linnaean binomials, and to identify and address associated challenges and concerns. Surprisingly, this endeavor was not as complicated or time-consuming as even the authors of this article expected when conceiving the experiment. [Arenaviridae; binomials; ICTV; International Committee on Taxonomy of Viruses; Mononegavirales; virus nomenclature; virus taxonomy.].
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http://dx.doi.org/10.1093/sysbio/syw096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5837305PMC
May 2017

Increasing virulence, but not infectivity, associated with serially emergent virus strains of a fish rhabdovirus.

Virus Evol 2016 Jan 20;2(1):vev018. Epub 2016 Jan 20.

US Geological Survey, Western Fisheries Research Center, 6505 NE 65th St., Seattle, WA 98115 and.

Surveillance and genetic typing of field isolates of a fish rhabdovirus, infectious hematopoietic necrosis virus (IHNV), has identified four dominant viral genotypes that were involved in serial viral emergence and displacement events in steelhead trout () in western North America. To investigate drivers of these landscape-scale events, IHNV isolates designated 007, 111, 110, and 139, representing the four relevant genotypes, were compared for virulence and infectivity in controlled laboratory challenge studies in five relevant steelhead trout populations. Viral virulence was assessed as mortality using lethal dose estimates (LD50), survival kinetics, and proportional hazards analysis. A pattern of increasing virulence for isolates 007, 111, and 110 was consistent in all five host populations tested, and correlated with serial emergence and displacements in the virus-endemic lower Columbia River source region during 1980-2013. The fourth isolate, 139, did not have higher virulence than the previous isolate 110. However, the mG139M genotype displayed a conditional displacement phenotype in that it displaced type mG110M in coastal Washington, but not in the lower Columbia River region, indicating that factors other than evolution of higher viral virulence were involved in some displacement events. Viral infectivity, measured as infectious dose (ID50), did not correlate consistently with virulence or with viral emergence, and showed a narrow range of variation relative to the variation observed in virulence. Comparison among the five steelhead trout populations confirmed variation in resistance to IHNV, but correlations with previous history of virus exposure or with sites of viral emergence varied between IHNV source and sink regions. Overall, this study indicated increasing viral virulence over time as a potential driver for emergence and displacement events in the endemic Lower Columbia River source region where these IHNV genotypes originated, but not in adjacent sink regions.
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http://dx.doi.org/10.1093/ve/vev018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4989874PMC
January 2016

Spatial and temporal heterogeneity of infectious hematopoietic necrosis virus in Pacific Northwest salmonids.

Infect Genet Evol 2016 11 28;45:347-358. Epub 2016 Sep 28.

Cary Institute for Ecosystems Studies, 2801 Sharon Turnpike (Route 44), 12545-0129 Millbrook, N.Y., United States; US Geological Survey Western Fisheries Research Center, Seattle WA.

The aquatic rhaboviral pathogen infectious hematopoietic necrosis virus (IHNV) causes acute disease in juvenile fish of a number of populations of Pacific salmonid species. Heavily managed in both marine and freshwater environments, these fish species are cultured during the juvenile stage in freshwater conservation hatcheries, where IHNV is one of the top three infectious diseases that cause serious morbidity and mortality. Therefore, a comprehensive study of viral genetic surveillance data representing 2590 field isolates collected between 1958 and 2014 was conducted to determine the spatial and temporal patterns of IHNV in the Pacific Northwest of the contiguous United States. Prevalence of infection varied over time, fluctuating over a rough 5-7yearcycle. The genetic analysis revealed numerous subgroups of IHNV, each of which exhibited spatial heterogeneity. Within all subgroups, dominant genetic types were apparent, though the temporal patterns of emergence of these types varied among subgroups. Finally, the affinity or fidelity of subgroups to specific host species also varied, where UC subgroup viruses exhibited a more generalist profile and all other subgroups exhibited a specialist profile. These complex patterns are likely synergistically driven by numerous ecological, pathobiological, and anthropogenic factors. Since only a few anthropogenic factors are candidates for managed intervention aimed at improving the health of threatened or endangered salmonid fish populations, determining the relative impact of these factors is a high priority for future studies.
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http://dx.doi.org/10.1016/j.meegid.2016.09.022DOI Listing
November 2016

Susceptibility of ocean- and stream-type Chinook salmon to isolates of the L, U, and M genogroups of infectious hematopoietic necrosis virus (IHNV).

Dis Aquat Organ 2016 08;121(1):15-28

University of Washington, School of Aquatic and Fishery Sciences, Box 355020, Seattle, WA 98195, USA.

This study examined the susceptibility of Chinook salmon Oncorhynchus tshawytscha to viral strains from the L, U, and M genogroups of infectious hematopoietic necrosis virus (IHNV) present in western North America. The goal of this investigation was to establish a baseline understanding of the susceptibility of ocean- and stream-type Chinook salmon to infection and mortality caused by exposure to commonly detected strains of L, U, and M IHNV. The L IHNV strain tested here was highly infectious and virulent in both Chinook salmon populations, following patterns previously reported for Chinook salmon. Furthermore, ocean- and stream-type Chinook salmon fry at 1 g can also become subclinically infected with U and M strains of IHNV without experiencing significant mortality. The stream-type life history phenotype was generally more susceptible to infection and suffered greater mortality than the ocean-type phenotype. Between the U and M genogroup strains tested, the U group strains were generally more infectious than the M group strains in both Chinook salmon types. Substantial viral clearance occurred by 30 d post exposure, but persistent viral infection was observed with L, U, and M strains in both host populations. While mortality decreased with increased host size in stream-type Chinook salmon, infection prevalence was not lower for all strains at a greater size. These results suggest that Chinook salmon may serve as reservoirs and/or vectors of U and M genogroup IHNV.
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http://dx.doi.org/10.3354/dao03030DOI Listing
August 2016

Taxonomy of the order Mononegavirales: update 2016.

Arch Virol 2016 Aug 23;161(8):2351-60. Epub 2016 May 23.

Plant Pathology, University of Kentucky, Lexington, KY, USA.

In 2016, the order Mononegavirales was emended through the addition of two new families (Mymonaviridae and Sunviridae), the elevation of the paramyxoviral subfamily Pneumovirinae to family status (Pneumoviridae), the addition of five free-floating genera (Anphevirus, Arlivirus, Chengtivirus, Crustavirus, and Wastrivirus), and several other changes at the genus and species levels. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
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http://dx.doi.org/10.1007/s00705-016-2880-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4947412PMC
August 2016

Potential drivers of virulence evolution in aquaculture.

Evol Appl 2016 02 11;9(2):344-54. Epub 2016 Jan 11.

Virginia Institute of Marine Science College of William and Mary Gloucester Point VA USA.

Infectious diseases are economically detrimental to aquaculture, and with continued expansion and intensification of aquaculture, the importance of managing infectious diseases will likely increase in the future. Here, we use evolution of virulence theory, along with examples, to identify aquaculture practices that might lead to the evolution of increased pathogen virulence. We identify eight practices common in aquaculture that theory predicts may favor evolution toward higher pathogen virulence. Four are related to intensive aquaculture operations, and four others are related specifically to infectious disease control. Our intention is to make aquaculture managers aware of these risks, such that with increased vigilance, they might be able to detect and prevent the emergence and spread of increasingly troublesome pathogen strains in the future.
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http://dx.doi.org/10.1111/eva.12342DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4721074PMC
February 2016