A broadly applicable method to characterize large DNA viruses and adenoviruses based on the DNA polymerase gene

Hanson, Larry A.; Rudis, Mary R.; Vasquez-Lee, Marcia; Montgomery, Roy D.

doi:10.1186/1743-422x-3-28

Cited by 80 publications

(45 citation statements)

References 14 publications

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“…The B-family DNAP gene is a core NCLDV gene traditionally used as a reference phylogenetic marker to establish the taxonomy of large DNA viruses [ 36 , 37 ]. The DNAPs of NCLDVs are phylogenetically related to those of eukaryotes [ 38 ].…”

Section: Resultsmentioning

confidence: 99%

A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window

Gallot-Lavallée

Blanc

2017

Viruses

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The nucleocytoplasmic large DNA viruses (NCLDV) are a group of extremely complex double-stranded DNA viruses, which are major parasites of a variety of eukaryotes. Recent studies showed that certain eukaryotes contain fragments of NCLDV DNA integrated in their genome, when surprisingly many of these organisms were not previously shown to be infected by NCLDVs. We performed an update survey of NCLDV genes hidden in eukaryotic sequences to measure the incidence of this phenomenon in common public sequence databases. A total of 66 eukaryotic genomic or transcriptomic datasets—many of which are from algae and aquatic protists—contained at least one of the five most consistently conserved NCLDV core genes. Phylogenetic study of the eukaryotic NCLDV-like sequences identified putative new members of already recognized viral families, as well as members of as yet unknown viral clades. Genomic evidence suggested that most of these sequences resulted from viral DNA integrations rather than contaminating viruses. Furthermore, the nature of the inserted viral genes helped predicting original functional capacities of the donor viruses. These insights confirm that genomic insertions of NCLDV DNA are common in eukaryotes and can be exploited to delineate the contours of NCLDV biodiversity.

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Section: Resultsmentioning

confidence: 99%

A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window

Gallot-Lavallée

Blanc

2017

Viruses

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“…DNA was extracted from ethanol-preserved skin tissues using the DNeasy Blood and Tissue Kit according to the manufacturer's protocol (QIAGEN). PCR was performed using degenerate primers targeting the DNA polymerase gene of large DNA viruses and adenoviruses (Hanson et al 2006). Briefly, 3 µl of DNA extract was added to 22 µl of master mix containing 0.2 µM degenerate herpesvirus forward (5'-CGG AAT TCT AGA YTT YGC NWS NYT NTA YCC-3') and degenerate reverse (5'-CCC GAA TTC AGA TCT CNG TRT CNC CRT A-3') primers, 1.5 mM MgCl 2 , 0.2 mM dNTPs, 1× PCR buffer and 0.625 U Platinum Taq Polymerase (Invitrogen).…”

Section: Virological Analysis: Pcr and Sequencingmentioning

confidence: 99%

“…As the particles observed through TEM most closely resembled a herpesvirus, a degenerate PCR targeting a conserved region of the polymerase gene of large DNA viruses (Hanson et al 2006) was performed. The PCR generated an amplicon (approximately 520 bp) in 5 of 5 perch skin tissues tested (data not shown).…”

Section: Virology: Cell Culture and Pcr Amplificationmentioning

confidence: 99%

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An alloherpesvirus infection of European perch Perca fluviatilis in Finland

Garver¹,

Leskisenoja²,

MacRae³

et al. 2018

Dis. Aquat. Org.

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The order Herpesvirales includes viruses that infect aquatic and terrestrial vertebrates and several aquatic invertebrates (i.e. mollusks), and share the commonality of possessing a double-stranded DNA core surrounded by an icosahedral capsid. Herpesviruses of the family Alloherpesviridae that infect fish and amphibians, including channel catfish virus and koi herpesvirus, negatively impact aquaculture. Here, we describe a novel herpesvirus infection of wild European perch from lakes in Finland. Infected fish exhibited white nodules on the skin and fins, typically in the spring when prevalence reached nearly 40% in one of the sampled lakes. Transmission electron microscopic examination of affected tissues revealed abundant nuclear and cytoplasmic virus particles displaying herpesvirus morphology. Degenerate PCR targeting a conserved region of the DNA polymerase gene of large DNA viruses amplified a 520 bp product in 5 of 5 affected perch skin samples tested. Phylogenetic analysis of concatenated partial DNA polymerase and terminase (exon 2) gene sequences produced a well-supported tree grouping the European perch herpesvirus with alloherpesviruses infecting acipenserid, esocid, ictalurid, and salmonid fishes. The phenetic analysis of the European perch herpesvirus partial DNA polymerase and terminase nucleotide gene sequences ranged from 34.6 to 63.9% and 39.6 to 59.6% to other alloherpesviruses, respectively. These data support the European perch herpesvirus as a new alloherpesvirus, and we propose the formal species designation of Percid herpesvirus 2 (PeHV2) to be considered for approval by the International Committee on Taxonomy of Viruses.

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“…The DNA was used soon after extraction or stored at −20 °C until use. The extracted DNA was subjected to selected PCR analysis with Taq polymerase (Invitrogen, Carlsbad, CA, USA) in order to detect adenoviruses, herpesviruses, and nucleocytoplasmic large DNA viruses (NCLDVs) that have previously been reported in sturgeons following previously described protocols [ 4 , 5 , 15 , 16 , 17 ].…”

Section: Methodsmentioning

confidence: 99%

Multifactorial Causes of Chronic Mortality in Juvenile Sturgeon (Huso huso)

Ciulli

Volpe

Sirri

et al. 2020

Animals

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This investigation focused on an episode of chronic mortality observed in juvenile Huso huso sturgeons. The examined subjects underwent pathological, microbiological, molecular, and chemical investigations. Grossly severe body shape deformities, epaxial muscle softening, and multifocal ulcerative dermatitis were the main observed findings. The more constant histopathologic findings were moderate to severe rarefaction and disorganization of the lymphohematopoietic lymphoid tissues, myofiber degeneration, atrophy and interstitial edema of skeletal epaxial muscles, and degeneration and atrophy of the gangliar neurons close to the myofibers. Chemical investigations showed a lower selenium concentration in affected animals, suggesting nutritional myopathy. Other manifestations were nephrocalcinosis and splenic vessel wall hyalinosis. Septicemia due to bacteria such as Aeromonas veronii, Shewanella putrefaciens, Citrobacter freundii, Chryseobacterium sp., and pigmented hyphae were found. No major sturgeon viral pathogens were detected by classical methods. Next-generation sequencing (NGS) analysis confirmed the absence of viral pathogens, with the exception of herpesvirus, at the order level; also, the presence of Aeromonas veronii and Shewanella putrefaciens was confirmed at the family level by the metagenomic classification of NGS data. In the absence of a primary yet undetected biological cause, it is supposed that environmental stressors, including nutritional imbalances, may have led to immune system impairment, facilitating the entry of opportunistic bacteria and mycotic hyphae.

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A broadly applicable method to characterize large DNA viruses and adenoviruses based on the DNA polymerase gene

Cited by 80 publications

References 14 publications

A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window

A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window

An alloherpesvirus infection of European perch Perca fluviatilis in Finland

Multifactorial Causes of Chronic Mortality in Juvenile Sturgeon (Huso huso)

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