Publications by authors named "Kuttichantran Subramaniam"

55 Publications

In-Frame 12-Nucleotide Deletion within Open Reading Frame 3a in a SARS-CoV-2 Strain Isolated from a Patient Hospitalized with COVID-19.

Microbiol Resour Announc 2021 Feb 25;10(8). Epub 2021 Feb 25.

Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain UF-8, with an in-frame 12-nucleotide deletion within open reading frame 3a (ORF3a), was isolated from a 78-year-old COVID-19 patient in March 2020.
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http://dx.doi.org/10.1128/MRA.00137-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7909084PMC
February 2021

Earliest detection to date of SARS-CoV-2 in Florida: Identification together with influenza virus on the main entry door of a university building, February 2020.

PLoS One 2021 13;16(1):e0245352. Epub 2021 Jan 13.

Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America.

In February and March, 2020, environmental surface swab samples were collected from the handle of the main entry door of a major university building in Florida, as part of a pilot surveillance project screening for influenza. Samples were taken at the end of regular classroom hours, between the dates of February 1-5 and February 19-March 4, 2020. Influenza A(H1N1)pdm09 virus was isolated from the door handle on four of the 19 days sampled. Both SARS-CoV-2 and A(H1N1)pdm09 virus were detected in a sample collected on February 21, 2020. Based on sequence analysis, the Florida SARS-CoV-2 strain (designated UF-11) was identical to strains being identified in Washington state during the same time period, while the earliest similar sequences were sampled in China/Hubei between Dec 30th 2019 and Jan 5th 2020. The first human case of COVID-19 was not officially reported in Florida until March 1st. In an analysis of sequences from COVID-19 patients in this region of Florida, there was only limited evidence of subsequent dissemination of the UF-11 strain. Identical or highly similar strains, possibly related through a common transmission chain, were detected with increasing frequency in Washington state between end of February and beginning of March. Our data provide further documentation of the rapid early spread of SARS-CoV-2 and underscore the likelihood that closely related strains were cryptically circulating in multiple U.S. communities before the first "official" cases were recognized.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0245352PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7806172PMC
January 2021

Genome Sequence of a Ranavirus Isolated from a Red-Eared Slider (Trachemys scripta elegans) in Poland.

Microbiol Resour Announc 2020 Nov 19;9(47). Epub 2020 Nov 19.

Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA

The red-eared slider (RES) ranavirus (RESRV) was isolated from a free-ranging RES turtle that died with evidence of respiratory disease. The RESRV genome sequence (106,878 bp) was determined, and phylogenetic analysis revealed that it is a common midwife toad virus (CMTV) strain. This study is the first report of CMTV in RES.
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http://dx.doi.org/10.1128/MRA.00781-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7679084PMC
November 2020

Genomic Characterization of Picornaviruses Isolated From Ribbon () and Harbor () Seals.

Front Vet Sci 2020 30;7:554716. Epub 2020 Oct 30.

Department of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States.

The seal picornavirus 1, species , is currently the only recognized member of the genus within the family . The bear picornavirus 1 was recently proposed as the second species in the genus under the name aquamavirus B. Herein, we determined the complete genomes of two novel pinniped picornaviruses, the harbor seal picornavirus (HsPV) and the ribbon seal picornavirus (RsPV). The HsPV and the RsPV were isolated in Vero.DogSLAMtag cells from samples collected from stranded harbor () and ribbon () seals. RsPV-infected Vero.DogSLAMtag cells displaying extensive cytopathic effects were processed for transmission electron microscopy and revealed non-enveloped viral particles aggregated into paracrystalline arrays in the cytoplasm. A next-generation sequencing approach was used to recover the complete genomes of the HsPV and the RsPV (6,709 and 6,683 bp, respectively). Phylogenetic and genetic analyses supported the HsPV and the RsPV as members of the genus. Based on these results, RsPV represents a novel strain of , while the HsPV is a novel strain of the proposed species aquamavirus B. These discoveries provide information on the evolutionary relationships and ultrastructure of aquamaviruses and expands the known host range of those viruses. Our results underscore the importance of the application of classical virology and pathology techniques coupled with high-throughput sequencing technologies for the discovery and characterization of pathogens in wild marine mammals.
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http://dx.doi.org/10.3389/fvets.2020.554716DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7661754PMC
October 2020

Characterization of an alphavirus isolated from a stranded harbor porpoise (Phocoena phocoena) from Alaska.

Virus Res 2021 01 16;291:198187. Epub 2020 Oct 16.

Department of Infectious Diseases and Immunology, University of Florida, 2187 Mowry Road, 32611, Gainesville, FL, USA.

The family Togaviridae comprises several significant human and veterinary mosquito-borne pathogens. Two togaviruses (genus Alphavirus) have been previously identified in association with marine mammals, the southern elephant seal virus (SESV) and Eastern equine encephalitis virus (EEEV) from a fatal captive harbor seal infection. Herein we report the ultrastructural and phylogenomic characterization of a novel marine togavirus, the first isolated from a cetacean, an Alaskan harbor porpoise (Phocoena phocoena) displaying ulcerative dermatitis. A skin sample was processed for virus isolation on Vero.DogSLAMtag cells and cytopathic effects (CPE) were observed on primary isolation approximately 20 days post-infection. Transmission electron microscopy of the infected Vero.DogSLAMtag cells revealed typical alphavirus particles budding from both plasma and vacuolar membranes of infected cells. A next-generation sequencing approach was used to determine the near complete genome of the Alaskan harbor porpoise alphavirus (AHPV). Phylogenetic analysis supported the AHPV as the sister species to the SESV, forming a marine mammal alphavirus clade separate from the recognized alphavirus antigenic complexes. Genetic comparison of the protein coding sequence of the AHPV to other alphaviruses demonstrated amino acid identities ranging from 42.1-67.1%, with the highest identity to the SESV. Based on its genetic divergence, we propose the AHPV represents a novel alphavirus species, pending formal proposal to and ratification by the International Committee on Taxonomy of Viruses. The ecological and genetic characteristics of the AHPV and the SESV also suggest they represent a novel antigenic complex within the genus Alphavirus, which we propose to be named the Marine Mammal Virus Complex. The role of the AHPV in the associated harbor porpoise cutaneous pathology, if any, remains unclear. Further research is needed to determine AHPV's route(s) of transmission and potential vectors, host range, prevalence, and pathogenicity in cetaceans including harbour porpoises.
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http://dx.doi.org/10.1016/j.virusres.2020.198187DOI Listing
January 2021

Cytochrome oxidase gene sequencing reveals channel catfish ovary cell line is contaminated with brown bullhead cells.

J Fish Dis 2021 Jan 17;44(1):119-122. Epub 2020 Oct 17.

Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS, USA.

The channel catfish (Ictalurus punctatus, Rafinesque) ovary (CCO) cell line is the standard cell line used for channel catfish diagnostics. Next-gen sequencing studies of a virus cultured in the CCO cells revealed mitochondrial sequences matching those of brown bullhead (Ameiurus nebulosus, Lesueur). Therefore, we systematically performed partial cytochrome oxidase 1 gene sequencing of several sources of the CCO cell line and all matched the brown bullhead and not the channel catfish.
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http://dx.doi.org/10.1111/jfd.13278DOI Listing
January 2021

Viable SARS-CoV-2 in the air of a hospital room with COVID-19 patients.

Int J Infect Dis 2020 Nov 16;100:476-482. Epub 2020 Sep 16.

Department of Environmental Engineering Sciences, College of Engineering, University of Florida, USA.

Objectives: Because the detection of SARS-CoV-2 RNA in aerosols but failure to isolate viable (infectious) virus are commonly reported, there is substantial controversy whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be transmitted through aerosols. This conundrum occurs because common air samplers can inactivate virions through their harsh collection processes. We sought to resolve the question whether viable SARS-CoV-2 can occur in aerosols using VIVAS air samplers that operate on a gentle water vapor condensation principle.

Methods: Air samples collected in the hospital room of two coronavirus disease-2019 (COVID-19) patients, one ready for discharge and the other newly admitted, were subjected to RT-qPCR and virus culture. The genomes of the SARS-CoV-2 collected from the air and isolated in cell culture were sequenced.

Results: Viable SARS-CoV-2 was isolated from air samples collected 2 to 4.8 m away from the patients. The genome sequence of the SARS-CoV-2 strain isolated from the material collected by the air samplers was identical to that isolated from the newly admitted patient. Estimates of viable viral concentrations ranged from 6 to 74 TCID units/L of air.

Conclusions: Patients with respiratory manifestations of COVID-19 produce aerosols in the absence of aerosol-generating procedures that contain viable SARS-CoV-2, and these aerosols may serve as a source of transmission of the virus.
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http://dx.doi.org/10.1016/j.ijid.2020.09.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7493737PMC
November 2020

Genome Sequence of a CHeRI Orbivirus 3 Strain Isolated from a Dead White-Tailed Deer (Odocoileus virginianus) in Florida, USA.

Microbiol Resour Announc 2020 Jun 25;9(26). Epub 2020 Jun 25.

Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA

We report the genome sequence of an orbivirus isolated from a dead farmed white-tailed deer in Florida. The deer was coinfected with epizootic hemorrhagic disease virus type 2. Phylogenetic and genetic analyses supported the virus as the fourth strain of the CHeRI orbivirus 3 species.
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http://dx.doi.org/10.1128/MRA.00523-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7317105PMC
June 2020

Characterization of a novel picornavirus isolated from moribund aquacultured clownfish.

J Gen Virol 2020 07;101(7):735-745

Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA.

Over the last decade, a number of USA aquaculture facilities have experienced periodic mortality events of unknown aetiology in their clownfish (). Clinical signs of affected individuals included lethargy, altered body coloration, reduced body condition, tachypnea, and abnormal positioning in the water column. Samples from outbreaks were processed for routine parasitological, bacteriological, and virological diagnostic testing, but no consistent parasitic or bacterial infections were observed. Histopathological evaluation revealed individual cell necrosis and mononuclear cell inflammation in the branchial cavity, pharynx, oesophagus and/or stomach of four examined clownfish, and large basophilic inclusions within the pharyngeal mucosal epithelium of one fish. Homogenates from pooled external and internal tissues from these outbreaks were inoculated onto striped snakehead (SSN-1) cells for virus isolation and cytopathic effects were observed, resulting in monolayer lysis in the initial inoculation and upon repassage. Transmission electron microscopy of infected SSN-1 cells revealed small round particles (mean diameter=20.0-21.7 nm) within the cytoplasm, consistent with the ultrastructure of a picornavirus. Full-genome sequencing of the purified virus revealed a novel picornavirus most closely related to the bluegill picornavirus and other members of the genus . Additionally, pairwise protein alignments between the clownfish picornavirus (CFPV) and other known members of the genus yielded results in accordance with the current International Committee on Taxonomy of Viruses criteria for members of the same genus. Thus, CFPV represents a proposed new limnipivirus species. Future experimental challenge studies are needed to determine the role of CFPV in disease.
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http://dx.doi.org/10.1099/jgv.0.001421DOI Listing
July 2020

Genomic Characterization of Tilapia Lake Virus Isolates Recovered from Moribund Nile Tilapia () on a Farm in the United States.

Microbiol Resour Announc 2020 Jan 23;9(4). Epub 2020 Jan 23.

Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA

Here, we present the complete coding sequences of two tilapia lake virus (TiLV) isolates recovered during an investigation of a mortality event in farmed Nile tilapia in the United States. Phylogenetic analysis supported the isolates as each other's closest relatives and members of a clade of Thai TiLV strains.
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http://dx.doi.org/10.1128/MRA.01368-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6979302PMC
January 2020

A New Family of DNA Viruses Causing Disease in Crustaceans from Diverse Aquatic Biomes.

mBio 2020 01 14;11(1). Epub 2020 Jan 14.

Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA

Panulirus argus virus 1 (PaV1) is the only known virus infecting the Caribbean spiny lobster () from the Caribbean Sea. Recently, related viruses, Dikerogammarus haemobaphes virus 1 (DhV1) and Carcinus maenas virus 1 (CmV1), have been detected in the demon shrimp () and the European shore crab (), respectively, from sites in the United Kingdom. The virion morphology of these crustacean viruses is similar to that of iridoviruses. However, unlike iridoviruses and other nucleocytoplasmic large DNA viruses (NCLDVs), these viruses complete their morphogenesis in the host cell nucleus rather than in the cytoplasm. To date, these crustacean viruses have remained unclassified due to a lack of genomic data. Using an Illumina MiSeq sequencer, we sequenced the complete genomes of PaV1, CmV1, and DhV1. Comparative genome analysis shows that these crustacean virus genomes encode the 10 hallmark proteins previously described for the NCLDVs of eukaryotes, strongly suggesting that they are members of this group. With a size range of 70 to 74 kb, these are the smallest NCLDV genomes identified to date. Extensive gene loss, divergence of gene sequences, and the accumulation of low-complexity sequences reflect the extreme degradation of the genomes of these "minimal" NCLDVs rather than any direct relationship with the NCLDV ancestor. Phylogenomic analysis supports the classification of these crustacean viruses as a distinct family, "Mininucleoviridae," within the pitho-irido-Marseille branch of the NCLDVs. Recent genomic and metagenomic studies have led to a dramatic expansion of the known diversity of nucleocytoplasmic large DNA viruses (NCLDVs) of eukaryotes, which include giant viruses of protists and important pathogens of vertebrates, such as poxviruses. However, the characterization of viruses from nonmodel hosts still lags behind. We sequenced the complete genomes of three viruses infecting crustaceans, the Caribbean spiny lobster, demon shrimp, and European shore crab. These viruses have the smallest genomes among the known NCLDVs, with losses of many core genes, some of which are shared with iridoviruses. The deterioration of the transcription apparatus is compatible with microscopic and ultrastructural observations indicating that these viruses replicate in the nucleus of infected cells rather than in the cytoplasm. Phylogenomic analysis indicates that these viruses are sufficiently distinct from all other NCLDVs to justify the creation of a separate family, for which we propose the name "Mininucleoviridae" (i.e., small viruses reproducing in the cell nucleus).
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http://dx.doi.org/10.1128/mBio.02938-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6960288PMC
January 2020

Genome characterization of cetaceanpox virus from a managed Indo-Pacific bottlenose dolphin (Tursiops aduncus).

Virus Res 2020 03 7;278:197861. Epub 2020 Jan 7.

Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, 2187 Mowry Road, 32611 Gainesville, Florida, USA. Electronic address:

Cetaceanpox viruses (CePVs) are associated with a cutaneous disease in cetaceans often referred to as "tattoo" lesions. To date, only partial genomic data are available for CePVs, and thus, they remain unclassified members of the subfamily Chordopoxvirinae within the family Poxviridae. Herein, we describe the first complete CePV genome sequenced from the tattoo lesion of a managed Indo-Pacific bottlenose dolphin (Tursiops aduncus), using next-generation sequencing. The T. aduncus CePV genome (CePV-TA) was determined to encode 120 proteins, including eight genes unique to the CePV-TA and five genes predicted to function as immune-evasion genes. The results of CePV-TA genetic analyses supported the creation of a new chordopoxvirus genus for CePVs. The complete sequencing of a CePV represents an important first step in unraveling the evolutionary relationship and taxonomy of CePVs, and significantly increases our understanding of the genomic characteristics of these chordopoxviruses.
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http://dx.doi.org/10.1016/j.virusres.2020.197861DOI Listing
March 2020

Detection and Preliminary Characterization of Phocine Distemper Virus in a Stranded Harp Seal () from the Gulf of St. Lawrence, Canada.

J Wildl Dis 2020 07 9;56(3):646-650. Epub 2020 Jan 9.

Department of Fisheries and Oceans Canada, 501 University Crescent, Winnipeg, Manitoba R3T 2N6, Canada.

A lethargic juvenile male harp seal () in poor nutritional condition was found on the beach on the north shore of Prince Edward Island, Canada, in June 2017. Microscopic examination revealed a severe nonsuppurative encephalitis positive for morbillivirus antigen on immunohistochemistry. Virus isolation attempts were negative. However, phocine distemper virus (PDV) was detected in brain tissue RNA extracts by a seminested reverse transcription PCR that targeted the paramyxovirus RNA-dependent RNA polymerase () gene. Comparison of the resulting partial PDV nucleotide sequence revealed it was nearly identical to PDV strains isolated from eastern Atlantic harbor seals () during a 1988 epizootic in the Wadden and Irish seas, and a western Atlantic harbor seal () that stranded in Maine, US, in 2006. Our study confirmed that closely related PDV strains are circulating in multiple seal species along the coastlines of North America and Europe.
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http://dx.doi.org/10.7589/2019-10-267DOI Listing
July 2020

Characterization of ranaviruses isolated from lumpfish L. in the North Atlantic area: proposal for a new ranavirus species (European North Atlantic Ranavirus).

J Gen Virol 2020 02 20;101(2):198-207. Epub 2019 Dec 20.

Technical University of Denmark, National Institute of Aquatic Resources, Aquatic Animal Health Unit, Kgs. Lyngby, Denmark.

The commercial production of lumpfish L. is expanding with the increased demand for their use as cleaner fish, to control sea-lice numbers, at marine Atlantic salmon L. aquaculture sites throughout Northern Europe. A new ranavirus has been isolated from lumpfish at multiple locations in the North Atlantic area. First isolated in 2014 in the Faroe Islands, the virus has subsequently been found in lumpfish from Iceland in 2015 and from Scotland and Ireland in 2016. The Icelandic lumpfish ranavirus has been characterized by immunofluorescent antibody test, optimal growth conditions and transmission electron microscopy. Partial sequences of the major capsid protein gene from 12 isolates showed 99.79-100% nt identity between the lumpfish ranaviruses. Complete genome sequencing from three of the isolates and phylogenetic analysis based on the concatenated 26 iridovirus core genes suggest these lumpfish ranavirus isolates form a distinct clade with ranaviruses from cod L. and turbot L. isolated in Denmark in 1979 and 1999, respectively. These data suggest that these viruses should be grouped together as a new ranavirus species, European North Atlantic Ranavirus, which encompasses ranaviruses isolated from marine fishes in European North Atlantic waters.
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http://dx.doi.org/10.1099/jgv.0.001377DOI Listing
February 2020

Three New Species Isolated from Farmed White-Tailed Deer () in the United States.

Viruses 2019 12 20;12(1). Epub 2019 Dec 20.

Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA.

We report the detection and gene coding sequences of three novel species found in six dead farmed white-tailed deer in the United States. Phylogenetic analyses indicate that the new orbiviruses are genetically closely related to the Guangxi, Mobuck, Peruvian horse sickness, and Yunnan orbiviruses, which are thought to be solely borne by mosquitos. However, four of the six viruses analyzed in this work were found as co-infecting agents along with a known cervid pathogen, epizootic hemorrhagic disease virus-2 (EHDV-2), raising questions as to whether the new viruses are primary pathogens or secondary pathogens that exacerbate EHDV-2 infections. Moreover, EHDV-2 is known to be a -borne virus, raising additional questions as to whether species can also serve as vectors for the novel orbiviruses, if mosquitoes can vector EHDV-2, or whether the deer were infected through separate bites by the insects. Our findings expand knowledge of the possible viral pathogens of deer in the United States. Moreover, due to the close genetic relatedness of the three new orbiviruses to viruses that are primary pathogens of cattle and horses, our findings also underscore a crucial need for additional research on the potential role of the three new orbiviruses as pathogens of other animals.
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http://dx.doi.org/10.3390/v12010013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7019857PMC
December 2019

Genomic characterization of a novel circovirus from a stranded Longman's beaked whale (Indopacetus pacificus).

Virus Res 2020 02 29;277:197826. Epub 2019 Nov 29.

Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States. Electronic address:

Tissues from a juvenile Longman's beaked whale that stranded in Hawaii in 2010 were screened for viruses using a Next-Generation Sequencing (NGS) approach. From the NGS data, the full genome (1,849 bp) of a novel beaked whale circovirus (BWCV) was determined. Two open reading frames (ORF) were annotated, including ORF1 that encodes the capsid gene, ORF2 that encodes the replication-associated gene, and a 9-bp conserved nonamer on the apex of the open loop found in all circoviruses. Independent phylogenetic analyses based on amino acid sequence alignments of the two CV proteins supported the BWCV as a member of the genus Circovirus, branching as the sister species to the recently discovered canine circovirus. A sequence identity matrix generated from complete genome alignments revealed the BWCV displays between from 51.1 to 56.7% nucleotide identity to other circoviruses, which is lower than the 80% threshold proposed for species demarcation. Considering the genetic and phylogenetic analyses, we propose the formal species designation of beaked whale circovirus. An endpoint PCR assay targeting the BWCV genome confirmed the presence of the BWCV DNA in every tissue from which DNA was extracted, including spleen, muscle, left ventricle, left adrenal gland, liver, lung, cerebrum, cerebellum, and lymph node. An automated in situ hybridization assay utilizing RNAscope® technology and targeting the replication-associated gene resulted in labeling of individual cells morphologically resembling mononuclear leukocytes and cells of blood vessels in diaphragm, liver, lymph nodes, lung, pericardium, oral mucosa and tongue, adrenal gland, testis, aorta, intestine, stomach and heart. The clinical or pathologic significance of BWCV is undetermined, as are its host range, prevalence, and pathogenicity in cetaceans of Hawaiian waters and elsewhere.
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http://dx.doi.org/10.1016/j.virusres.2019.197826DOI Listing
February 2020

Characterization of a peribunyavirus isolated from largemouth bass (Micropterus salmoides).

Virus Res 2019 11 17;273:197761. Epub 2019 Sep 17.

University of Wisconsin-La Crosse, 54601, La Crosse, WI, USA.

We report the complete genome sequencing of the first fish peribunyavirus determined using a next-generation sequencing approach. The virus was isolated during a routine health assessment of wild largemouth bass (Micropterus salmoides) in Wisconsin in April of 2009. Further research is needed to determine the epidemiology and pathogenicity of the largemouth bass bunyavirus.
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http://dx.doi.org/10.1016/j.virusres.2019.197761DOI Listing
November 2019

Genomic and developmental characterisation of a novel bunyavirus infecting the crustacean Carcinus maenas.

Sci Rep 2019 09 10;9(1):12957. Epub 2019 Sep 10.

Fisheries and Aquatic Science, University of Florida, Gainesville, Florida, 32653, USA.

Carcinus maenas is in the top 100 globally invasive species and harbours a wide diversity of pathogens, including viruses. We provide a detailed description for a novel bunyavirus (Carcinus maenas Portunibunyavirus 1) infecting C. maenas from its native range in the Faroe Islands. The virus genome is tripartite, including large (L) (6766 bp), medium (M) (3244 bp) and small (S) (1608 bp) negative sense, single-stranded RNA segments. Individual genomic segments are flanked by 4 bp regions of similarity (CCUG). The segments encode an RNA-dependent RNA-polymerase, glycoprotein, non-structural protein with a Zinc-Finger domain and a nucleoprotein. Most show highest identity to the 'Wenling Crustacean Virus 9' from an unidentified crustacean host. Phylogenomics of crustacean-infecting bunyaviruses place them across multiple bunyavirus families. We discuss the diversity of crustacean bunyaviruses and provide an overview of how these viruses may affect the health and survival of crustacean hosts, including those inhabiting niches outside of their native range.
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http://dx.doi.org/10.1038/s41598-019-49260-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736955PMC
September 2019

Characterization of a novel rhabdovirus isolated from a stranded harbour porpoise (Phocoena phocoena).

Virus Res 2019 11 6;273:197742. Epub 2019 Sep 6.

University of Florida, 2187 Mowry Road, 32611, Gainesville, Florida, USA. Electronic address:

An adult male harbour porpoise (Phocoena phocoena) stranded off the coast of Alaska displaying poor body condition, scattered mild ulcerative dermatitis, and necrotizing balanoposthitis. Necropsy findings included severe verminous panniculitis, pneumonia, hepatitis, and enteritis. Histopathological examination of skin lesions revealed a pustular epidermitis and dermatitis, with ballooning degeneration of keratinocytes and occasional amphophilic intracytoplasmic inclusion bodies. A swab sample collected from the ulcerative penile lesions was processed for virus isolation resulting in cytopathic effects observed in primary beluga whale kidney (BWK) cells. Transmission electron microscopy revealed bullet-shaped virions budding from the cell surface of infected BWK cells consistent with a rhabdovirus. A cDNA library was prepared using RNA extracted from infected cell culture supernatant and sequenced on an Illumina MiSeq sequencer. The near-complete genome of a novel rhabdovirus was recovered. Genetic and phylogenetic analyses based on the complete L gene supported the harbour porpoise rhabdovirus (HPRV) as a new species. HPRV clustered phylogenetically with dolphin rhabdovirus (DRV) and this cetacean rhabdovirus clade was found to be the sister group to members of the genus Perhabdovirus that infect fish. A specific nested RT-PCR assay detected HPRV RNA in the epaxial musculature of the harbour porpoise. Our results are consistent with a previous hypothesis that cetacean rhabdoviruses may have arisen following a host jump from fish and suggest that DRV and HPRV represent separate species belonging in a new genus within the family Rhabdoviridae. Further research is needed to determine the health impact of HPRV in harbour porpoise populations, its prevalence, and route of transmission.
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http://dx.doi.org/10.1016/j.virusres.2019.197742DOI Listing
November 2019

FATAL RANAVIRUS INFECTION IN A GROUP OF ZOO-HOUSED MELLER'S CHAMELEONS ().

J Zoo Wildl Med 2019 Sep;50(3):696-705

Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA,

A group of five juvenile Meller's chameleons () experienced 100% mortality over a period of 1 mo due to ranavirus infection. The index case was found dead without premonitory signs. The three subsequent cases presented with nonspecific clinical signs (lethargy, decreased appetite, ocular discharge) and were ultimately euthanatized. The final case died after initially presenting with skin lesions. Postmortem examination revealed thin body condition in all five animals and mild coelomic effusion and petechiae affecting the tongue and kidneys of one animal. Microscopically, all animals had multifocal necrosis of the spleen, liver, and kidney; four of five animals had necrosis of the nasal cavity; and two of five had necrosis of adrenal tissue, bone marrow, and skin. Numerous basophilic intracytoplasmic inclusions were present in the liver of all animals and nasal mucosa of three of the five animals. Consensus polymerase chain reaction for herpesvirus and adenovirus were negative, whereas ranavirus quantitative polymerase chain reaction was positive. Virus isolation followed by whole genome sequencing and Bayesian phylogenetic analysis classified the isolates as a strain of frog virus 3 (FV3) most closely related to an FV3 isolate responsible for a previous outbreak in the zoo's eastern box turtle () group. This case series documents the first known occurrence of ranavirus-associated disease in chameleons and demonstrates the potential for interspecies transmission between chelonian and squamate reptiles.
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http://dx.doi.org/10.1638/2018-0044DOI Listing
September 2019

Molecular characterization of a novel reassortment Mammalian orthoreovirus type 2 isolated from a Florida white-tailed deer fawn.

Virus Res 2019 09 19;270:197642. Epub 2019 Jun 19.

Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA. Electronic address:

Mammalian orthoreovirus (MRV) is the type species of the genus Orthoreovirus and causes a range of significant respiratory, nervous or enteric diseases in humans and animals. In 2016 a farmed white-tailed deer (Odocoileus virginianus) fawn became ill, displaying clinical signs of lethargy, dehydration, and profuse foul-smelling diarrhea. A necropsy was performed after the three-week-old fawn died and various tissue samples were submitted to the University of Florida's Cervidae Health Research Initiative for diagnostic evaluation. Aliquots of homogenized heart, liver, and spleen tissues were inoculated onto Vero E6 cells. After virus-specific cytopathic effects (CPE) were detected in Vero cells inoculated with spleen homogenate, infected cells were fixed in glutaraldehyde and analyzed by transmission electron microscopy (TEM), which revealed icosahedral virus particles approximately 75 nm in diameter with morphologies consistent with those of reoviruses within the cytoplasm of the infected cells. RNA extracted from virions in the spent media of infected cells with advanced CPE was used to prepare a cDNA library, which was sequenced using an Illumina MiSeq sequencer. Complete coding sequences for ten separate reovirus segments were attained, and these indicated the isolated agent was a MRV. Genetic and phylogenetic analyses based on the outer capsid sigma-1 (σ1) protein gene sequences supported the Florida white-tailed fawn isolate as a type 2 MRV that branched as the sister group to a MRV-2 strain previously characterized from the urine of a moribund lion (Panthera leo) in Japan. However, analyses based on 7/10 genes (L1-L2, M2-M3, S2-S4) supported the white-tailed deer MRV as the closest relative to a type 3 MRV strain isolated from a dead mink in China. These data suggest the white-tailed deer MRV may have resulted from the natural reassortment of MRVs originating from multiple wildlife species. To our knowledge, this is the first detection of MRV-2 infection in a white-tailed deer. Continued surveillance efforts are needed to determine whether this MRV-2 strain poses a health threat to farmed white-tailed deer populations.
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http://dx.doi.org/10.1016/j.virusres.2019.197642DOI Listing
September 2019

Characterization of a Novel Megalocytivirus Isolated from European Chub ().

Viruses 2019 05 15;11(5). Epub 2019 May 15.

Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA.

A novel virus from moribund European chub () was isolated on (EPC) cells. Transmission electron microscopic examination revealed abundant non-enveloped, hexagonal virus particles in the cytoplasm of infected EPC cells consistent with an iridovirus. Illumina MiSeq sequence data enabled the assembly and annotation of the full genome (128,216 bp encoding 108 open reading frames) of the suspected iridovirus. Maximum Likelihood phylogenetic analyses based on 25 iridovirus core genes supported the European chub iridovirus (ECIV) as being the sister species to the recently-discovered scale drop disease virus (SDDV), which together form the most basal megalocytivirus clade. Genetic analyses of the ECIV major capsid protein and ATPase genes revealed the greatest nucleotide identity to members of the genus including SDDV. These data support ECIV as a novel member within the genus . Experimental challenge studies are needed to fulfill River's postulates and determine whether ECIV induces the pathognomonic microscopic lesions (i.e., megalocytes with basophilic cytoplasmic inclusions) observed in megalocytivirus infections.
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http://dx.doi.org/10.3390/v11050440DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6563503PMC
May 2019

Genome Sequence of Tilapia Lake Virus Associated with Syncytial Hepatitis of Tilapia in an Ecuadorian Aquaculture Facility.

Microbiol Resour Announc 2019 May 2;8(18). Epub 2019 May 2.

Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA

Here, we report the complete coding sequences of tilapia lake virus (TiLV) associated with syncytial hepatitis of tilapia (SHT). The TiLV strain was sequenced from the liver RNA extract of a moribund Nile tilapia () fingerling from an Ecuadorian aquaculture facility in 2012.
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http://dx.doi.org/10.1128/MRA.00084-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6498224PMC
May 2019

Genomic sequence of a Bohle iridovirus strain isolated from a diseased boreal toad (Anaxyrus boreas boreas) in a North American aquarium.

Arch Virol 2019 Jul 16;164(7):1923-1926. Epub 2019 Apr 16.

Department of Microbiology and Immunology, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS, 39216, USA.

Genomic sequence analysis of zoo ranavirus (ZRV) suggests it is a strain of Bohle iridovirus (BIV), a virus that was first detected in, and thought to be confined to, Australia. Furthermore, marked sequence similarity and genomic co-linearity among ZRV, BIV, and German gecko ranavirus (GGRV) are consistent with the view that all three are strains  of Frog virus 3, the type species of the genus Ranavirus, family Iridoviridae.
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http://dx.doi.org/10.1007/s00705-019-04244-7DOI Listing
July 2019

Complete Genome Sequence of an Ictalurid Herpesvirus 1 Strain Isolated from Blue Catfish (Ictalurus furcatus).

Microbiol Resour Announc 2019 Apr 11;8(15). Epub 2019 Apr 11.

Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, Mississippi, USA

The complete genome sequence of an alloherpesvirus isolated from blue catfish () is reported. Genomic analyses revealed that this virus is a distinct strain of ictalurid herpesvirus 1, the first strain of which was isolated previously from a channel catfish ().
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http://dx.doi.org/10.1128/MRA.00082-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6460021PMC
April 2019

Genome Sequences of a Novel Strain of Big Cypress Orbivirus Isolated from a Dead Florida White-Tailed Deer (Odocoileus virginianus).

Microbiol Resour Announc 2019 Mar 14;8(11). Epub 2019 Mar 14.

Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA

Here, we report the coding sequences of Big Cypress orbivirus isolated from a dead white-tailed deer () from Florida in 2017. To our knowledge, this is the first detection of Big Cypress orbivirus in a vertebrate host.
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http://dx.doi.org/10.1128/MRA.01717-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6424215PMC
March 2019

Phylogenomic characterization of red seabream iridovirus from Florida pompano Trachinotus carolinus maricultured in the Caribbean Sea.

Arch Virol 2019 Apr 11;164(4):1209-1212. Epub 2019 Feb 11.

Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Bldg. 1379, Mowry Road, Gainesville, FL, 32611, USA.

Between 2010 and 2016, six mortality events were observed in Florida pompano (Trachinotus carolinus) maricultured in the Dominican Republic. Histopathological examination and conventional PCR confirmed a megalocytivirus (MCV) infection in each case. Subsequently, next-generation sequencing and phylogenomic analyses confirmed that MCV DNA was present in the infected pompano tissue samples from 2010, 2014, and 2016, and each was determined to be red seabream iridovirus (RSIV). Annotation of the RSIV genome sequences identified 121 open reading frames, and BLASTN analysis revealed the highest nucleotide sequence identity (> 99%) to a RSIV clade 1 MCV isolated from a moribund red seabream (Pagrus major) maricultured in Japan. These cases represent the first fully sequenced RSIV genomes detected outside of Asia and are the earliest reports of MCV infections in Florida pompano. This recent geographical expansion of RSIV warrants further attention to determine its potential economic and ecological impact.
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http://dx.doi.org/10.1007/s00705-019-04155-7DOI Listing
April 2019

Complete Genome Sequence of Mobuck Virus Isolated from a Florida White-Tailed Deer (Odocoileus virginianus).

Microbiol Resour Announc 2019 Jan 17;8(3). Epub 2019 Jan 17.

Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA.

Here, we report the complete genome sequence of mobuck virus isolated from a Florida white-tailed deer (Odocoileus virginianus) in 2017. This is the second report of mobuck virus in the United States and expands the known geographic range of this novel orbivirus into Florida.
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http://dx.doi.org/10.1128/MRA.01324-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6346154PMC
January 2019

Genomic sequencing of a virus representing a novel type within the species Dyopipapillomavirus 1 in an Indian River Lagoon bottlenose dolphin.

Arch Virol 2019 Mar 20;164(3):767-774. Epub 2019 Jan 20.

Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Bldg 1379, Mowry Road, Gainesville, FL, 32611, USA.

Fecal samples collected from free-ranging Atlantic bottlenose dolphins (BDs) in the Indian River Lagoon of Florida were processed for viral discovery using a next-generation sequencing (NGS) approach. A 693-bp contig identified in the NGS data was nearly identical to the partial L1 gene sequence of a papillomavirus (PV) previously found in a penile papilloma in a killer whale (Orcinus orca). Based on this partial bottlenose dolphin papillomavirus (BDPV) sequence, a nested inverse PCR and primer-walking strategy was employed to generate the complete genome sequence. The full BDPV genome consisted of 7299 bp and displayed a typical PV genome organization. The BDPV E6 protein contained a PDZ-binding motif, which has been shown to be involved in carcinogenic transformation involving high-risk genital human PVs. Screening of 12 individual fecal samples using a specific endpoint PCR assay revealed that the feces from a single female BD displaying a genital papilloma was positive for the BDPV. Genetic analysis indicated that this BDPV (Tursiops truncatus papillomavirus 8; TtPV8) is a new type of Dyopipapillomavirus 1, previously sequenced from an isolate obtained from a penile papilloma in a harbor porpoise (Phocoena phocoena). Although only a partial L1 sequence has been determined for a PV detected in a killer whale genital papilloma, our finding of a nearly identical sequence in an Atlantic BD may indicate that members of this viral species are capable of host jumping. Future work is needed to determine if this virus is a high-risk PV that is capable of inducing carcinogenic transformation and whether it poses a significant health risk to wild delphinid populations.
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http://dx.doi.org/10.1007/s00705-018-04117-5DOI Listing
March 2019

Genomic characterization of a novel pegivirus species from free-ranging bottlenose dolphins (Tursiops truncatus) in the Indian River Lagoon, Florida.

Virus Res 2019 04 8;263:98-101. Epub 2019 Jan 8.

University of Florida, 2187 Mowry Road, 32611, Gainesville, FL, USA. Electronic address:

We report the discovery of the first cetacean pegivirus (family Flaviviridae) using a next-generation sequencing approach. One of two infected bottlenose dolphins had elevated activities of liver enzymes, which may suggest hepatocellular injury. Further research is needed to determine the epidemiology and pathogenicity of dolphin pegivirus.
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http://dx.doi.org/10.1016/j.virusres.2019.01.002DOI Listing
April 2019