Sequence determination of a mildly virulent strain (CU-2) of Gallid herpesvirus type 2 using 454 pyrosequencing

Abstract

The complete DNA sequence of the mildly virulent Gallid herpesvirus type 2 strain CU-2 was determined and consists of 176,922 bp with an overall gene organization typical of class E herpesviruses. Phylogenetically, this strain partitions in its own branch between the virulent strains RB-1B, Md11, and Md5, and the vaccine strain CVI988. Overall, the genome of CU-2 is more similar to that of CVI988, with identically sized unique short regions of 11,651 bp. As in CVI988, an insertion of 177 bp was identified in the overlapping genes encoding the Meq, RLORF6, and 23 kDa proteins within the repeat long region of the genome. A total of 15 single nucleotide polymorphisms (SNPs) common to both CU-2 and CVI988, and not occurring in virulent strains, were identified in the genes encoding UL29, UL45, UL50, UL52, LORF10, RLORF14a, RLORF12, Meq(RLORF7), 23kDa, ICP4, US3, and two hypothetical proteins MDV071.4 and MDV076.4. Each gene encoding UL29 and Meq contained two SNPs. Only one major open reading frame (ORF) encoding UL41, the virus host shutoff (VHS) ribonuclease, was disrupted in the CU-2 genome. An additional cytosine after the 25 codon is predicted to produce a truncated protein of 97 aa. Since GaHV-2 mutants lacking UL41 have been reported to retain their virulence, other factors are likely responsible for the low virulence of CU-2. It is largely suspected that SNPs in common with CVI988 along with the insertions in the Meq loci are responsible for its phenotype. Conversely, we identified 43 nonsynonymous mutations (within 23 genes) that may contribute to the virulence of CU-2. These SNPs are shared exclusively with all sequenced virulent strains (Md5, Md11, and RB-1B) and not present within the CVI988 genome. Although most occur in proteins of unknown function, a significant percentage is in proteins involved in virion assembly.

High levels of genetic variation within core Helicoverpa armigera nucleopolyhedrovirus genes

“…The overall coverage of 339 is similar to the coverage obtained in studies where the entire genome has been sequenced [50,51].…”

Pathogenicity and genomic characterization of a pseudorabies virus variant isolated from Bartha-K61-vaccinated swine population in China

“…Accordingly, we will try to characterize the molecular basis associated with the enhanced pathogenicity and virulence of the TJ strain. For the larger size of herpesvirus genomes, conventional sequencing methods usually work less efficiently to rapidly get sequence data of novel virus strains (Spatz and Rue, 2008), and also the high G + C content of the genome, averaging 74%, makes reliable sequencing extremely difficult. For a long time, sequence determinations remained limited to fragments encompassing one or a few Single AA residues changes are written in standard format, including AA of the earlier isolates, its position, and the AA residue found in protein sequence of the TJ strain and/or recent isolates, e.g., S100P.…”

Complete Genome Sequence of a Recombinant Marek's Disease Virus Field Strain with One Reticuloendotheliosis Virus Long Terminal Repeat Insert

“…MDV causes Marek's disease in chickens with lymphomas (14). So far, the genome sequences of a total of 10 MDV strains have been analyzed (4,6,7,8,9,10,13,16). The GX0101 strain in this report was the first recombinant MDV field strain containing the reticuloendotheliosis virus (REV) long terminal repeat (LTR) insert (17), and it is a very virulent MDV with higher horizontal transmission ability (1,12).…”