Genome Sequences of Two Pseudorabies Virus Strains Isolated in Greece

Παπαγεωργιου, Κωνσταντινοσ; Suárez, Nicolás M.; Wilkie, Gavin S.; Filioussis, George; Papaioannou, Nikolaos; Nauwynck, Hans; Davison, Andrew J.; Kritas, S. K.

doi:10.1128/genomea.01624-15

Cited by 10 publications

(8 citation statements)

References 9 publications

(9 reference statements)

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“…The original genome sequence of the PRV was a composite generated from six viral strains [ 25 ] and determined using the traditional Sanger method. The complete genome of PRV strain Ka and other strains have been sequenced both by Sanger capillary sequencing [ 26 ] and by Illumina deep sequencing [ 27 – 29 ]. We earlier used the Pacific Biosciences (PacBio) platform to sequence the wild-type Kaplan (Ka) strain of the PRV genome [ 30 ].…”

Section: Introductionmentioning

confidence: 99%

Full-Length Isoform Sequencing Reveals Novel Transcripts and Substantial Transcriptional Overlaps in a Herpesvirus

et al. 2016

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Whole transcriptome studies have become essential for understanding the complexity of genetic regulation. However, the conventionally applied short-read sequencing platforms cannot be used to reliably distinguish between many transcript isoforms. The Pacific Biosciences (PacBio) RS II platform is capable of reading long nucleic acid stretches in a single sequencing run. The pseudorabies virus (PRV) is an excellent system to study herpesvirus gene expression and potential interactions between the transcriptional units. In this work, non-amplified and amplified isoform sequencing protocols were used to characterize the poly(A+) fraction of the lytic transcriptome of PRV, with the aim of a complete transcriptional annotation of the viral genes. The analyses revealed a previously unrecognized complexity of the PRV transcriptome including the discovery of novel protein-coding and non-coding genes, novel mono- and polycistronic transcription units, as well as extensive transcriptional overlaps between neighboring and distal genes. This study identified non-coding transcripts overlapping all three replication origins of the PRV, which might play a role in the control of DNA synthesis. We additionally established the relative expression levels of gene products. Our investigations revealed that the whole PRV genome is utilized for transcription, including both DNA strands in all coding and intergenic regions. The genome-wide occurrence of transcript overlaps suggests a crosstalk between genes through a network formed by interacting transcriptional machineries with a potential function in the control of gene expression.

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Section: Introductionmentioning

confidence: 99%

Full-Length Isoform Sequencing Reveals Novel Transcripts and Substantial Transcriptional Overlaps in a Herpesvirus

et al. 2016

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“…215 partial Ul44 nucleotide sequences of SuHV-1 were collected from GenBank with the largest possible amount of information available on host, year, and country of isolation [4,5,6,8,17,18,19,20,21,22,23]. The sequences were identified using the name of the isolate in GenBank followed by a three-letter code to identify the country of origin: Germany (GER), Argentina (ARG), Austria (AUS), Brazil (BRA), China (CHI), Croatia (CRO), Greece (GRE), South Korea (SKO), Slovakia (SLK), Spain (ESP), United States (USA), Japan (JAP), Hungary (HUN), Italy (ITA), Northern Ireland (NIR), Malaysia (MAL), or Sweden (SWE).…”

Section: Methodsmentioning

confidence: 99%

Evolutionary Diversity of Suid Herpesvirus 1 Based on Ul44 Partial Sequences

Fonseca¹,

Camargos²,

Barbosa³

et al. 2016

Intervirology

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Objective: The aim of this study was to use partial Ul44 sequences (glycoprotein C) of Suid herpesvirus 1 to examine the evolution and dynamics of the virus in different periods and hosts. Methods: Phylogenetic trees were constructed using the software MrBayes after analysis in the software jModelTest to evaluate the best phylogenetic models. The software SplitsTree 4.0 was used to create phylogenetic networks, and the BEAST program was used to generate data on phylogeography. Replication kinetics and serum neutralization tests were applied to tree strains from different phylogenetic groups. Results:Ul44 sequences derived from domestic swine and wild swine clustered in different clades and had different selective pressures depending on the host. We found no differences in replication kinetics and serum neutralization tests in the strains tested. Data show that the evolution of herpesviruses is complex, and different genetic groups may be evolving at different rates. Ul44 is an important marker for molecular evolution and epidemiology studies, but it is not useful for biological information.

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“…The virus was seeded in porcine kidney (PK-15) cells for virus isolation. Virus DNA was extracted from the 2nd passage of the virus and subjected to sequencing using Illumina MiSeq technology as described previously ( 4 ). The genome was analyzed and spliced using DNAStar Lasergene v7.1 (DNASTAR Inc, Madison, WI, USA).…”

Section: Genome Announcementmentioning

confidence: 99%