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Spatz S.J.,Southeast Poultry Research Laboratory | Volkening J.D.,BASE2BIO | Keeler C.L.,University of Delaware | Kutish G.F.,University of Connecticut | And 8 more authors.
Virus Genes | Year: 2012

Gallid herpesvirus-1 (GaHV-1), commonly named infectious laryngotracheitis (ILT) virus, causes the respiratory disease in chickens known as ILT. The molecular determinants associated with differences in pathogenicity of GaHV-1 strains are not completely understood, and a comparison of genomic sequences of isolates that belong to different genotypes could help identify genes involved in virulence. Dideoxy sequencing, 454 pyrosequencing and Illumina sequencing-by-synthesis were used to determine the nucleotide sequences of four genotypes of virulent strains from GaHV-1 groups I-VI. Three hundred and twenty-five open reading frames (ORFs) were compared with those of the recently sequenced genome of the Serva vaccine strain. Only four ORFs, ORF C, U L37, ICP4 and U S2 differed in amino acid (aa) lengths among the newly sequenced genomes. Genome sequence alignments were used to identify two regions (5′ terminus and the unique short/repeat short junction) that contained deletions. Seventy-eight synonymous and 118 non-synonymous amino acid substitutions were identified with the examined ORFs. Exclusive to the genome of the Serva vaccine strain, seven non-synonymous mutations were identified in the predicted translation products of the genes encoding glycoproteins gB, gE, gL and gM and three non-structural proteins U L28 (DNA packaging protein), U L5 (helicase-primase) and the immediate early protein ICP4. Furthermore, our comparative sequence analysis of published and newly sequenced GaHV-1 isolates has provided evidence placing the cleavage/packaging site (a-like sequence) within the inverted repeats instead of its placement at the 3′ end of the U L region as annotated in the GenBank's entries NC006623 and HQ630064. © Springer Science+Business Media, LLC (Outside the USA) 2011.

PubMed | BASE2BIO, National Veterinary Research Institute and U.S. Department of Agriculture
Type: Journal Article | Journal: Genome announcements | Year: 2016

The first complete genome sequence of a strain of Newcastle disease virus (NDV) from genotype XIV is reported here. Strain duck/Nigeria/NG-695/KG.LOM.11-16/2009 was isolated from an apparently healthy domestic duck from a live bird market in Kogi State, Nigeria, in 2009. This strain is classified as a member of subgenotype XIVb of class II.

PubMed | University of Ibadan, BASE2BIO, National Veterinary Research Institute, U.S. Department of Agriculture and University of Pretoria
Type: Journal Article | Journal: Genome announcements | Year: 2016

The first complete genome sequence of a strain of Newcastle disease virus (NDV) of genotype XVII is described here. A velogenic strain (duck/Nigeria/903/KUDU-113/1992) was isolated from an apparently healthy free-roaming domestic duck sampled in Kuru, Nigeria, in 1992. Phylogenetic analysis of the fusion protein gene and complete genome classified the isolate as a member of NDV class II, genotype XVII.

Volkening J.D.,BASE2BIO | Spatz S.J.,U.S. Department of Agriculture
Avian Diseases | Year: 2013

Herpesvirus replication within host cells results in concatemeric genomic DNA, which is cleaved into unit-length genomes and packaged into the capsid by a complex of proteins. The sites of cleavage have been identified for many herpesviruses, and conserved signaling sequences involved in cleavage and packaging have been characterized. The cleavage/packaging motifs pac-1, pac-2, and DR1 and two distinct groups of telomeric repeat sequences (static TRS and variable TRS) have been identified. By sequencing the termini of the gallid herpesvirus type 2 (GaHV-2) strain CU-2, two different cleavage sites (classical and aberrant) have been identified. Unlike classical cleavage of human herpesvirus type 1, which occurs within the DR1 site, classical cleavage of the GaHV-2 concatemers occurs 8.5 bp upstream of the DR1 site and results in an S-terminus containing telomeric repeats. Aberrant cleavage occurs the same distance from the DR1 site and generates a telomeric S-terminus but an L-terminus lacking an a sequence. These results are consistent with previous findings in other herpesviruses and should prove useful in the future study and manipulation of the GaHV-2 genome. © American Association of Avian Pathologists.

Spatz S.J.,U.S. Department of Agriculture | Volkening J.D.,BASE2BIO | Ross T.A.,U.S. Department of Agriculture
Virus Research | Year: 2014

Falconid herpesvirus type 1 (FaHV-1) is the causative agent of falcon inclusion body disease, an acute, highly contagious disease of raptors. The complete nucleotide sequence of the genome of FaHV-1 has been determined using Illumina MiSeq sequencing. The genome is 204,054 nucleotides in length and has a class E organization. The genome encodes approximately 130 putative protein-coding genes, of which 70 are orthologs of conserved alphaherpesvirus and Mardivirus proteins. Three FaHV-1 genes (UL3.5, UL44.5 and CIRC) were identified that encode protein homologues unique to Mardivirus and Varicellovirus. The genome also encodes homologues to the Mardivirus genes LORF2, LORF3, LORF4, LORF5, SORF3 and SORF4. An opal mutation resulting in premature termination was identified in the FaHV-1 UL43 gene. Phylogenetically, FaHV-1 resides in a monophyletic group with the other Mardiviruses but, along with anatid herpesvirus 1, represents a more distant divergence from the rest of the Mardivirus genus. © 2014.

Spatz S.J.,U.S. Department of Agriculture | Volkening J.D.,BASE2BIO | Mullis R.,U.S. Department of Agriculture | Li F.,U.S. Department of Agriculture | And 2 more authors.
Virus Genes | Year: 2013

Meleagrid herpesvirus type 1 (MeHV-1) is an ideal vector for the expression of antigens from pathogenic avian organisms in order to generate vaccines. Chicken parvovirus (ChPV) is a widespread infectious virus that causes serious disease in chickens. It is one of the etiological agents largely suspected in causing Runting Stunting Syndrome (RSS) in chickens. Initial attempts to express the wild-type gene encoding the capsid protein VP2 of ChPV by insertion into the thymidine kinase gene of MeHV-1 were unsuccessful. However, transient expression of a codon-optimized synthetic VP2 gene cloned into the bicistronic vector pIRES2-Ds-Red2, could be demonstrated by immunocytochemical staining of transfected chicken embryo fibroblasts (CEFs). Red fluorescence could also be detected in these transfected cells since the red fluorescent protein gene is downstream from the internal ribosome entry site (IRES). Strikingly, fluorescence could not be demonstrated in cells transiently transfected with the bicistronic vector containing the wild-type or non-codon-optimized VP2 gene. Immunocytochemical staining of these cells also failed to demonstrate expression of wild-type VP2, indicating that the lack of expression was at the RNA level and the VP2 protein was not toxic to CEFs. Chickens vaccinated with a DNA vaccine consisting of the bicistronic vector containing the codon-optimized VP2 elicited a humoral immune response as measured by a VP2-specific ELISA. This VP2 codon-optimized bicistronic cassette was rescued into the MeHV-1 genome generating a vectored vaccine against ChPV disease. © 2013 Springer Science+Business Media New York (Outside the USA).

Spatz S.J.,U.S. Department of Agriculture | Volkening J.D.,BASE2BIO | Gimeno I.M.,North Carolina State University | Heidari M.,U.S. Department of Agriculture | Witter R.L.,U.S. Department of Agriculture
Virus Genes | Year: 2012

Attenuation of Gallid herpesvirus-2 (GaHV-2), the causative agent of Marek's disease, can occur through serial passage of a virulent field isolate in avian embryo fibroblasts. In order to gain a better understanding of the genes involved in attenuation and associate observed changes in phenotype with specific genetic variations, the genomic DNA sequence of a single GaHV-2 virulent strain (648A) was determined at defined passage intervals. Biological characterization of these "interval-isolates" in chickens previously indicated that the ability to induce transient paralysis was lost by passages 40 and the ability to induce persistent neurological disease was lost after passage 80, coincident with the loss of neoplastic lesion formation. Deep sequencing of the interval-isolates allowed for a detailed cataloguing of the mutations that exist within a single passage population and the frequency with which a given mutation occurs across passages. Gross genetic alterations were identified in both novel and well-characterized genes and cis-acting regions involved in replication and cleavage/packaging. Deletions in genes encoding the virulence factors vLipase, vIL8, and RLORF4, as well as a deletion in the promoter of ICP4, appeared between passages 61 and 101. Three mutations in the virus-encoded telomerase which predominated in late passages were also identified. Overall, the frequency of mutations fluctuated greatly during serial passage and few genetic changes were absolute. This indicates that serial passage of GaHV-2 results in the generation of a collection of genomes with limited sequence heterogeneity. © 2012 Springer Science+Business Media, LLC (Outside the USA).

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