An Integrated Sequencing Approach for Updating the Pseudorabies Virus Transcriptome

Torma, Gábor; Tombácz, Dóra; Csabai, Zsolt; Göbhardter, Dániel; Deim, Zoltán; Snyder, M; Boldogkői, Zsolt

doi:10.3390/pathogens10020242

Cited by 12 publications

(14 citation statements)

References 60 publications

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“…We describe several 5'-truncated RNA molecules containing nested in-frame ORFs. This phenomenon has been described in other viruses 51,62 . It has to be determined whether these transcripts carry the information of N-terminally-truncated polypeptides.…”

Section: Discussionsupporting

confidence: 73%

Dual Isoform Sequencing Reveals a Multifaceted Transcriptional Architecture of a Prototype Baculovirus

Torma

Tombácz

Moldován

et al. 2021

Preprint

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In this study, we used two long-read sequencing (LRS) techniques, Sequel from the Pacific Biosciences and MinION from Oxford Nanopore Technologies, for the transcriptional characterization of a prototype baculovirus, Autographacalifornica multiple nucleopolyhedrovirus. LRS is able to read full-length RNA molecules, and thereby to distinguish between transcript isoforms, mono- and polycistronic RNAs, and overlapping transcripts. Altogether, we detected 875 transcripts, of which 759 are novel and 116 have been annotated previously. These RNA molecules include 41 novel putative protein coding transcript (each containing 5’-truncated in-frame ORFs), 14 monocistronic transcripts, 99 multicistronic RNAs, 101 non-coding RNA, and 504 length isoforms. We also detected RNA methylation in 12 viral genes and RNA hyper-editing in the longer 5’-UTR transcript isoform of ORF 19 gene.

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Section: Discussionsupporting

confidence: 73%

Dual Isoform Sequencing Reveals a Multifaceted Transcriptional Architecture of a Prototype Baculovirus

Torma

Tombácz

Moldován

et al. 2021

Preprint

Self Cite

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“…In comparison, PRV could highly efficiently utilize TISs and integrate the genes of hosts or other viruses, providing more additional possibilities for PRV genetic variation. Indeed, PRV variants delineated a more complex transcriptome and identified an unexpectedly large number of potential novel genes [28]. Additionally, mounting research suggests that overlapping transcription may be the novel strategies of the PRV to regulate its gene expression, escape host innate antiviral immunity, and fulfill genetic evolution at different infection stages [27,29].…”

Section: Discussionmentioning

confidence: 99%

Isolation and Characterization of Two Pseudorabies Virus and Evaluation of Their Effects on Host Natural Immune Responses and Pathogenicity

Zhou

Zhang

et al. 2022

Viruses

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Pseudorabies, caused by the pseudorabies virus (PRV), is an acute fatal disease, which can infect rodents, mammals, and other livestock and wild animals across species. Recently, the emergence of PRV virulent isolates indicates a high risk of a variant PRV epidemic and the need for continuous surveillance. In this study, PRV-GD and PRV-JM, two fatal PRV variants, were isolated and their pathogenicity as well as their effects on host natural immune responses were assessed. PRV-GD and PRV-JM were genetically closest to PRV variants currently circulating in Heilongjiang (HLJ8) and Jiangxi (JX/CH/2016), which belong to genotype 2.2. Consistently, antisera from sows immunized with PRV-Ea classical vaccination showed much lower neutralization ability to PRV-GD and PRV-JM. However, the antisera from the pigs infected with PRV-JM had an extremely higher neutralization ability to PRV-TJ (as a positive control), PRV-GD and PRV-JM. In vivo, PRV-GD and PRV-JM infections caused 100% death in mice and piglets and induced extensive tissue damage, cell death, and inflammatory cytokine release. Our analysis of the emergence of PRV variants indicate that pigs immunized with the classical PRV vaccine are incapable of providing sufficient protection against these PRV isolates, and there is a risk of continuous evolution and virulence enhancement. Efforts are still needed to conduct epidemiological monitoring for the PRV and to develop novel vaccines against this emerging and reemerging infectious disease.

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“…We note that the long 3′ UTR isoforms with unique TES are extremely rare in αHV mRNAs. The list of this family has been updated later 58 and a more detailed update is published in this current report. CTO transcripts were also detected in EHV-1 ( Figure 3 ; Supplementary Figures 3 and 5, and Supplementary Table 2 ), but not in other herpesviruses with annotated transcriptome.…”

Section: Resultsmentioning

confidence: 99%

“…However, since no precise function has been linked to these transcripts until now, we cannot term them as ‘replication RNAs’ that would refer to a still undisclosed role in DNA replication. Furthermore, the genes around the Oris have been shown to produce TIs with long 5′-untranslated regions (5′ UTRs – TSS isoforms), or 3′ UTRs (TES isoforms) that overlap the replication origin 57, 58 . Many or all of the mRNAs with very long 5′ UTR are probably also lncRNAs because their translation initiation sites are too far from their TSSs.…”

Section: Introductionmentioning

confidence: 99%

Novel Herpesvirus Transcripts with Putative Regulatory Roles in DNA Replication and Global Transcription

Torma

Tombácz

Almsarrhad

et al. 2023

Preprint

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In the last couple of years, the rapid advances and decreasing costs of sequencing technologies have revolutionized transcriptomic research. Long-read sequencing (LRS) techniques are able to detect full-length RNA molecules in a single run without the need for additional assembly steps. LRS studies have revealed an unexpected transcriptomic complexity in a variety of organisms, including viruses. A number of transcripts with proven or putative regulatory role, mapping close to or overlapping the replication origins (Oris) and the nearby transcription activator genes, have been described in herpesviruses. In this study, we applied both newly generated and previously published LRS and short-read sequencing datasets to discover additional Ori-proximal transcripts in nine herpesviruses belonging to all of the three subfamilies (alpha, beta and gamma). We identified novel long non-coding RNAs (lncRNAs), as well as splice and length isoforms of mRNAs and lncRNAs. Furthermore, our analysis disclosed an intricate meshwork of transcriptional overlaps at the examined genomic regions. Our results suggest the existence of a super regulatory center, which controls both the replication and the global transcription through multilevel interactions between the molecular machineries.

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An Integrated Sequencing Approach for Updating the Pseudorabies Virus Transcriptome

Cited by 12 publications

References 60 publications

Dual Isoform Sequencing Reveals a Multifaceted Transcriptional Architecture of a Prototype Baculovirus

Dual Isoform Sequencing Reveals a Multifaceted Transcriptional Architecture of a Prototype Baculovirus

Isolation and Characterization of Two Pseudorabies Virus and Evaluation of Their Effects on Host Natural Immune Responses and Pathogenicity

Novel Herpesvirus Transcripts with Putative Regulatory Roles in DNA Replication and Global Transcription

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