{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T04:32:38Z","timestamp":1791433958739,"version":"4.3.3"},"reference-count":162,"publisher":"eLife Sciences Publications, Ltd","license":[{"start":{"date-parts":[[2022,2,28]],"date-time":"2022-02-28T00:00:00Z","timestamp":1646006400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2022,2,28]],"date-time":"2022-02-28T00:00:00Z","timestamp":1646006400000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2022,2,28]],"date-time":"2022-02-28T00:00:00Z","timestamp":1646006400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["203864\/Z\/16\/Z"],"award-info":[{"award-number":["203864\/Z\/16\/Z"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["102163\/Z\/13\/Z"],"award-info":[{"award-number":["102163\/Z\/13\/Z"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["106207\/Z\/14\/Z"],"award-info":[{"award-number":["106207\/Z\/14\/Z"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["202797\/Z\/16\/Z"],"award-info":[{"award-number":["202797\/Z\/16\/Z"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"H2020 European Research Council","doi-asserted-by":"publisher","award":["646891"],"award-info":[{"award-number":["646891"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["2015-67015-22969"],"award-info":[{"award-number":["2015-67015-22969"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elifesciences.org"],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2022,2,26]]},"abstract":"<jats:p>The arterivirus porcine reproductive and respiratory syndrome virus (PRRSV) causes significant economic losses to the swine industry worldwide. Here we apply ribosome profiling (RiboSeq) and parallel RNA sequencing (RNASeq) to characterise the transcriptome and translatome of both species of PRRSV and to analyse the host response to infection. We calculated programmed ribosomal frameshift (PRF) efficiency at both sites on the viral genome. This revealed the nsp2 PRF site as the second known example where temporally regulated frameshifting occurs, with increasing \u22122 PRF efficiency likely facilitated by accumulation of the PRF-stimulatory viral protein, nsp1\u03b2. Surprisingly, we find that PRF efficiency at the canonical ORF1ab frameshift site also increases over time, in contradiction of the common assumption that RNA structure-directed frameshift sites operate at a fixed efficiency. This has potential implications for the numerous other viruses with canonical PRF sites. Furthermore, we discovered several highly translated additional viral ORFs, the translation of which may be facilitated by multiple novel viral transcripts. For example, we found a highly expressed 125-codon ORF overlapping nsp12, which is likely translated from novel subgenomic RNA transcripts that overlap the 3\u2032 end of ORF1b. Similar transcripts were discovered for both PRRSV-1 and PRRSV-2, suggesting a potential conserved mechanism for temporally regulating expression of the 3\u2032-proximal region of ORF1b. We also identified a highly translated, short upstream ORF in the 5\u2032 UTR, the presence of which is highly conserved amongst PRRSV-2 isolates. These findings reveal hidden complexity in the gene expression programmes of these important nidoviruses.<\/jats:p>","DOI":"10.7554\/elife.75668","type":"journal-article","created":{"date-parts":[[2022,2,28]],"date-time":"2022-02-28T10:00:22Z","timestamp":1646042422000},"update-policy":"https:\/\/doi.org\/10.7554\/elife.75668","source":"Crossref","is-referenced-by-count":35,"title":["Ribosome profiling of porcine reproductive and respiratory syndrome virus reveals novel features of viral gene expression"],"prefix":"10.7554","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1577-735X","authenticated-orcid":true,"given":"Georgia M","family":"Cook","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/013meh722","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology, University of Cambridge","place":["Cambridge, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine","family":"Brown","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/013meh722","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology, University of Cambridge","place":["Cambridge, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pengcheng","family":"Shang","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05p1j8758","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Diagnostic Medicine and Pathobiology, Kansas State University","place":["Manhattan, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanhua","family":"Li","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05p1j8758","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Diagnostic Medicine and Pathobiology, Kansas State University","place":["Manhattan, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lior","family":"Soday","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/013meh722","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology, University of Cambridge","place":["Cambridge, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam M","family":"Dinan","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/013meh722","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology, University of Cambridge","place":["Cambridge, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7563-5575","authenticated-orcid":true,"given":"Charlotte","family":"Tumescheit","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/013meh722","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology, University of Cambridge","place":["Cambridge, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"AP Adrian","family":"Mockett","sequence":"additional","affiliation":[{"name":"Cambivac Ltd","place":["Cambridge, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Fang","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05p1j8758","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Diagnostic Medicine and Pathobiology, Kansas State University","place":["Manhattan, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7986-9520","authenticated-orcid":true,"given":"Andrew E","family":"Firth","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/013meh722","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology, University of Cambridge","place":["Cambridge, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3965-4370","authenticated-orcid":true,"given":"Ian","family":"Brierley","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/013meh722","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology, University of Cambridge","place":["Cambridge, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"4374","published-online":{"date-parts":[[2022,2,28]]},"reference":[{"key":"bib1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms22073392","article-title":"Ribosome-Profiling Reveals Restricted Post Transcriptional Expression of Antiviral Cytokines and Transcription Factors during SARS-CoV-2 Infection","volume":"22","author":"Alexander","year":"2021","journal-title":"International Journal of Molecular Sciences"},{"key":"bib2","doi-asserted-by":"publisher","first-page":"1095","DOI":"10.2174\/1389450118666170130145514","article-title":"TXNIP in Metabolic Regulation: Physiological Role and Therapeutic Outlook","volume":"18","author":"Alhawiti","year":"2017","journal-title":"Current Drug Targets"},{"key":"bib3","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq--A Python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics (Oxford, England)"},{"key":"bib4","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.03971","article-title":"Translation of 5\u2032 leaders is pervasive in genes resistant to eIF2 repression","volume":"4","author":"Andreev","year":"2015","journal-title":"eLife"},{"key":"bib5","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1007\/s11262-005-0030-z","article-title":"The Intraleader AUG Nucleotide Sequence Context is Important for Equine Arteritis Virus Replication","volume":"33","author":"Archambault","year":"2006","journal-title":"Virus Genes"},{"key":"bib6","doi-asserted-by":"publisher","first-page":"2011","DOI":"10.1101\/gr.175893.114","article-title":"Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation","volume":"24","author":"Artieri","year":"2014","journal-title":"Genome Research"},{"key":"bib7","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw530","article-title":"Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use","volume":"44","author":"Atkins","year":"2016","journal-title":"Nucleic Acids Research"},{"key":"bib8","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-14-220","article-title":"Pig immune response to general stimulus and to porcine reproductive and respiratory syndrome virus infection: a meta-analysis approach","volume":"14","author":"Badaoui","year":"2013","journal-title":"BMC Genomics"},{"key":"bib9","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1016\/j.molcel.2004.12.009","article-title":"An extended signal involved in eukaryotic -1 frameshifting operates through modification of the E site tRNA","volume":"17","author":"Bekaert","year":"2005","journal-title":"Molecular Cell"},{"key":"bib10","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1016\/0022-2836(92)90901-U","article-title":"Mutational analysis of the \u201cslippery-sequence\u201d component of a coronavirus ribosomal frameshifting signal","volume":"227","author":"Brierley","year":"1992","journal-title":"Journal of Molecular Biology"},{"key":"bib11","doi-asserted-by":"publisher","first-page":"1619","DOI":"10.1016\/j.cell.2014.04.041","article-title":"Programmed \u20131 Frameshifting by Kinetic Partitioning during Impeded Translocation","volume":"157","author":"Caliskan","year":"2014","journal-title":"Cell"},{"key":"bib12","doi-asserted-by":"publisher","first-page":"558","DOI":"10.1016\/j.molcel.2017.04.023","article-title":"Conditional Switch between Frameshifting Regimes upon Translation of dnaX mRNA","volume":"66","author":"Caliskan","year":"2017","journal-title":"Molecular Cell"},{"key":"bib13","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1016\/j.virol.2016.01.021","article-title":"The non-structural protein Nsp2TF of porcine reproductive and respiratory syndrome virus down-regulates the expression of Swine Leukocyte Antigen class I","volume":"491","author":"Cao","year":"2016","journal-title":"Virology"},{"key":"bib14","first-page":"629","article-title":"Nidovirales: a new order comprising Coronaviridae and Arteriviridae","volume":"142","author":"Cavanagh","year":"1997","journal-title":"Archives of Virology"},{"key":"bib15","doi-asserted-by":"publisher","first-page":"643","DOI":"10.1099\/0022-1317-74-4-643","article-title":"Sequences of 3\u2019 end of genome and of 5\u2019 end of open reading frame 1a of lactate dehydrogenase-elevating virus and common junction motifs between 5\u2019 leader and bodies of seven subgenomic mRNAs","volume":"74 ( Pt 4)","author":"Chen","year":"1993","journal-title":"The Journal of General Virology"},{"key":"bib16","doi-asserted-by":"publisher","first-page":"328","DOI":"10.1038\/nature13428","article-title":"Dynamic pathways of -1 translational frameshifting","volume":"512","author":"Chen","year":"2014","journal-title":"Nature"},{"key":"bib17","doi-asserted-by":"publisher","first-page":"278","DOI":"10.1016\/j.virol.2016.07.008","article-title":"Nuclear export signal of PRRSV NSP1\u03b1 is necessary for type I IFN inhibition","volume":"499","author":"Chen","year":"2016","journal-title":"Virology"},{"key":"bib18","doi-asserted-by":"publisher","first-page":"1560","DOI":"10.1016\/j.cell.2020.07.033","article-title":"Structural Basis for Helicase-Polymerase Coupling in the SARS-CoV-2 Replication-Transcription Complex","volume":"182","author":"Chen","year":"2020","journal-title":"Cell"},{"key":"bib19","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.aax6969","article-title":"The energy landscape of -1 ribosomal frameshifting","volume":"6","author":"Choi","year":"2020","journal-title":"Science Advances"},{"key":"bib20","doi-asserted-by":"publisher","first-page":"1731","DOI":"10.1261\/rna.052548.115","article-title":"The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis","volume":"21","author":"Chung","year":"2015","journal-title":"RNA (New York, N.Y.)"},{"key":"bib21","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1177\/104063879200400201","article-title":"Isolation of swine infertility and respiratory syndrome virus (isolate ATCC VR-2332) in North America and experimental reproduction of the disease in gnotobiotic pigs","volume":"4","author":"Collins","year":"1992","journal-title":"Journal of Veterinary Diagnostic Investigation"},{"key":"bib22","article-title":"RiboSeq-Analysis","volume-title":"GitHub","author":"Cook","year":"2017","unstructured":"Cook GM. 2017. RiboSeq-Analysis. GitHub. swh:1:rev:bd9e04d2d11a4ec27106af57aa8270db2e35b500. https:\/\/archive.softwareheritage.org\/swh:1:dir:c9f35afdeb3845442c77572331b37e2d953da84c;origin=https:\/\/github.com\/firth-lab\/RiboSeq-Analysis;visit=swh:1:snp:16b6d90bf5f8aea7554c79887c52f41846a3afd6;anchor=swh:1:rev:bd9e04d2d11a4ec27106af57aa8270db2e35b500."},{"key":"bib23","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2020.588411","article-title":"Distinctive Cellular and Metabolic Reprogramming in Porcine Lung Mononuclear Phagocytes Infected With Type 1 PRRSV Strains","volume":"11","author":"Crisci","year":"2020","journal-title":"Frontiers in Immunology"},{"key":"bib24","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-020-00763-0","article-title":"Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein","volume":"12","author":"Davidson","year":"2020","journal-title":"Genome Medicine"},{"key":"bib25","doi-asserted-by":"publisher","first-page":"2910","DOI":"10.1128\/JVI.65.6.2910-2920.1991","article-title":"Equine arteritis virus is not a togavirus but belongs to the coronaviruslike superfamily","volume":"65","author":"den Boon","year":"1991","journal-title":"Journal of Virology"},{"key":"bib26","doi-asserted-by":"publisher","first-page":"E8895","DOI":"10.1073\/pnas.1706696114","article-title":"Expanded subgenomic mRNA transcriptome and coding capacity of a nidovirus","volume":"114","author":"Di","year":"2017","journal-title":"PNAS"},{"key":"bib27","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00714-19","article-title":"Comparative Analysis of Gene Expression in Virulent and Attenuated Strains of Infectious Bronchitis Virus at Subcodon Resolution","volume":"93","author":"Dinan","year":"2019","journal-title":"Journal of Virology"},{"key":"bib28","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"bib29","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12917-021-02785-1","article-title":"Gene expression in tonsils in swine following infection with porcine reproductive and respiratory syndrome virus","volume":"17","author":"Dong","year":"2021","journal-title":"BMC Veterinary Research"},{"key":"bib30","doi-asserted-by":"publisher","first-page":"1445","DOI":"10.1161\/ATVBAHA.112.249334","article-title":"Thioredoxin-1 promotes anti-inflammatory macrophages of the M2 phenotype and antagonizes atherosclerosis","volume":"32","author":"El Hadri","year":"2012","journal-title":"Arteriosclerosis, Thrombosis, and Vascular Biology"},{"key":"bib31","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1038\/nmeth.4631","article-title":"Improved Ribo-seq enables identification of cryptic translation events","volume":"15","author":"Erhard","year":"2018","journal-title":"Nature Methods"},{"key":"bib32","doi-asserted-by":"publisher","first-page":"E2920","DOI":"10.1073\/pnas.1211145109","article-title":"Efficient -2 frameshifting by mammalian ribosomes to synthesize an additional arterivirus protein","volume":"109","author":"Fang","year":"2012","journal-title":"PNAS"},{"key":"bib33","doi-asserted-by":"publisher","first-page":"8580","DOI":"10.1128\/JVI.01043-15","article-title":"Characterization of Ribosomal Frameshifting in Theiler\u2019s Murine Encephalomyelitis Virus","volume":"89","author":"Finch","year":"2015","journal-title":"Journal of Virology"},{"key":"bib34","doi-asserted-by":"publisher","first-page":"240","DOI":"10.1038\/s41586-021-03610-3","article-title":"SARS-CoV-2 uses a multipronged strategy to impede host protein synthesis","volume":"594","author":"Finkel","year":"2021","journal-title":"Nature"},{"key":"bib35","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1038\/s41586-020-2739-1","article-title":"The coding capacity of SARS-CoV-2","volume":"589","author":"Finkel","year":"2021","journal-title":"Nature"},{"key":"bib36","doi-asserted-by":"publisher","first-page":"1385","DOI":"10.1099\/vir.0.042499-0","article-title":"Non-canonical translation in RNA viruses","volume":"93","author":"Firth","year":"2012","journal-title":"The Journal of General Virology"},{"key":"bib37","doi-asserted-by":"publisher","first-page":"12425","DOI":"10.1093\/nar\/gku981","article-title":"Mapping overlapping functional elements embedded within the protein-coding regions of RNA viruses","volume":"42","author":"Firth","year":"2014","journal-title":"Nucleic Acids Research"},{"key":"bib38","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1016\/s0098-2997(01)00010-3","article-title":"Redox signaling in macrophages","volume":"22","author":"Forman","year":"2001","journal-title":"Molecular Aspects of Medicine"},{"key":"bib39","doi-asserted-by":"publisher","first-page":"404","DOI":"10.1016\/j.chom.2007.09.014","article-title":"Ovarian tumor domain-containing viral proteases evade ubiquitin- and ISG15-dependent innate immune responses","volume":"2","author":"Frias-Staheli","year":"2007","journal-title":"Cell Host & Microbe"},{"key":"bib40","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku671","article-title":"Translation inhibitors cause abnormalities in ribosome profiling experiments","volume":"42","author":"Gerashchenko","year":"2014","journal-title":"Nucleic Acids Research"},{"key":"bib41","doi-asserted-by":"publisher","first-page":"758","DOI":"10.1139\/bcb-2018-0394","article-title":"SARS coronavirus protein nsp1 disrupts localization of Nup93 from the nuclear pore complex","volume":"97","author":"Gomez","year":"2019","journal-title":"Biochemistry and Cell Biology = Biochimie et Biologie Cellulaire"},{"key":"bib42","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1016\/j.virusres.2006.01.017","article-title":"Nidovirales: evolving the largest RNA virus genome","volume":"117","author":"Gorbalenya","year":"2006","journal-title":"Virus Research"},{"key":"bib43","doi-asserted-by":"publisher","first-page":"1712","DOI":"10.1080\/22221751.2020.1791737","article-title":"Shotgun proteomics analysis of SARS-CoV-2-infected cells and how it can optimize whole viral particle antigen production for vaccines","volume":"9","author":"Grenga","year":"2020","journal-title":"Emerging Microbes & Infections"},{"key":"bib44","doi-asserted-by":"publisher","first-page":"835","DOI":"10.1038\/nature09267","article-title":"Mammalian microRNAs predominantly act to decrease target mRNA levels","volume":"466","author":"Guo","year":"2010","journal-title":"Nature"},{"key":"bib45","doi-asserted-by":"publisher","DOI":"10.1186\/s12985-017-0910-6","article-title":"The prevalent status and genetic diversity of porcine reproductive and respiratory syndrome virus in China: A molecular epidemiological perspective","volume":"15","author":"Guo","year":"2018","journal-title":"Virology Journal"},{"key":"bib46","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1016\/j.virol.2017.12.018","article-title":"Intercellular transfer of mitochondria rescues virus-induced cell death but facilitates cell-to-cell spreading of porcine reproductive and respiratory syndrome virus","volume":"517","author":"Guo","year":"2018","journal-title":"Virology"},{"key":"bib47","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1009403","article-title":"A swine arterivirus deubiquitinase stabilizes two major envelope proteins and promotes production of viral progeny","volume":"17","author":"Guo","year":"2021","journal-title":"PLOS Pathogens"},{"key":"bib48","doi-asserted-by":"publisher","first-page":"9449","DOI":"10.1128\/JVI.00834-09","article-title":"The porcine reproductive and respiratory syndrome virus nsp2 cysteine protease domain possesses both trans- and cis-cleavage activities","volume":"83","author":"Han","year":"2009","journal-title":"Journal of Virology"},{"key":"bib49","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1016\/j.virusres.2012.12.012","article-title":"Degradation of CREB-binding protein and modulation of type I interferon induction by the zinc finger motif of the porcine reproductive and respiratory syndrome virus nsp1\u03b1 subunit","volume":"172","author":"Han","year":"2013","journal-title":"Virus Research"},{"key":"bib50","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1016\/j.virol.2014.04.028","article-title":"Biogenesis of non-structural protein 1 (nsp1) and nsp1-mediated type I interferon modulation in arteriviruses","volume":"458\u2013459","author":"Han","year":"2014","journal-title":"Virology"},{"key":"bib51","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1016\/j.virol.2017.02.004","article-title":"Nuclear imprisonment of host cellular mRNA by nsp1\u03b2 protein of porcine reproductive and respiratory syndrome virus","volume":"505","author":"Han","year":"2017","journal-title":"Virology"},{"key":"bib52","doi-asserted-by":"publisher","DOI":"10.3390\/antiox10020313","article-title":"Functions of ROS in Macrophages and Antimicrobial Immunity","volume":"10","author":"Herb","year":"2021","journal-title":"Antioxidants"},{"key":"bib53","doi-asserted-by":"publisher","first-page":"11938","DOI":"10.1093\/nar\/gkab969","article-title":"Investigating molecular mechanisms of 2A-stimulated ribosomal pausing and frameshifting in Theilovirus","volume":"49","author":"Hill","year":"2021","journal-title":"Nucleic Acids Research"},{"key":"bib54","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-021-27400-7","article-title":"Structural and molecular basis for Cardiovirus 2A protein as a viral gene expression switch","volume":"12","author":"Hill","year":"2021","journal-title":"Nature Communications"},{"key":"bib55","doi-asserted-by":"crossref","first-page":"72","DOI":"10.54846\/jshap\/754","article-title":"Assessment of the economic impact of porcine reproductive and respiratory syndrome virus on United States pork producers","volume":"21","author":"Holtkamp","year":"2013","journal-title":"Journal of Swine Health and Production"},{"key":"bib56","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"Huang","year":"2009","journal-title":"Nature Protocols"},{"key":"bib57","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1016\/j.virol.2013.06.015","article-title":"Involvement of unfolded protein response, p53 and Akt in modulation of porcine reproductive and respiratory syndrome virus-mediated JNK activation","volume":"444","author":"Huo","year":"2013","journal-title":"Virology"},{"key":"bib58","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1126\/science.1168978","article-title":"Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling","volume":"324","author":"Ingolia","year":"2009","journal-title":"Science (New York, N.Y.)"},{"key":"bib59","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1016\/j.cell.2011.10.002","article-title":"Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes","volume":"147","author":"Ingolia","year":"2011","journal-title":"Cell"},{"key":"bib60","doi-asserted-by":"publisher","first-page":"1534","DOI":"10.1038\/nprot.2012.086","article-title":"The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments","volume":"7","author":"Ingolia","year":"2012","journal-title":"Nature Protocols"},{"key":"bib61","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1005473","article-title":"High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling","volume":"12","author":"Irigoyen","year":"2016","journal-title":"PLOS Pathogens"},{"key":"bib62","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1016\/j.virol.2015.02.012","article-title":"PRRSV structure, replication and recombination: Origin of phenotype and genotype diversity","volume":"479\u2013480","author":"Kappes","year":"2015","journal-title":"Virology"},{"key":"bib63","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1016\/j.virol.2015.01.028","article-title":"Porcine reproductive and respiratory syndrome virus nonstructural protein 2 (nsp2) topology and selective isoform integration in artificial membranes","volume":"481","author":"Kappes","year":"2015","journal-title":"Virology"},{"key":"bib64","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1016\/j.virol.2018.01.016","article-title":"Type I interferon suppression-negative and host mRNA nuclear retention-negative mutation in nsp1\u03b2 confers attenuation of porcine reproductive and respiratory syndrome virus in pigs","volume":"517","author":"Ke","year":"2018","journal-title":"Virology"},{"key":"bib65","doi-asserted-by":"publisher","first-page":"469","DOI":"10.1128\/JVI.00469-19","article-title":"Porcine Reproductive and Respiratory Syndrome Virus Nonstructural Protein 1 Beta Interacts with Nucleoporin 62 To Promote Viral Replication and Immune Evasion","volume":"93","author":"Ke","year":"2019","journal-title":"Journal of Virology"},{"key":"bib66","doi-asserted-by":"publisher","first-page":"1717","DOI":"10.1101\/gad.305250.117","article-title":"Non-AUG translation: A new start for protein synthesis in eukaryotes","volume":"31","author":"Kearse","year":"2017","journal-title":"Genes & Development"},{"key":"bib67","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1007\/BF00284650","article-title":"Sequence determination of the extreme 5\u2032 end of equine arteritis virus leader region","volume":"12","author":"Kheyar","year":"1996","journal-title":"Virus Genes"},{"key":"bib68","first-page":"345","article-title":"Diverse functions of VDUP1 in cell proliferation, differentiation, and diseases","volume":"4","author":"Kim","year":"2007","journal-title":"Cellular & Molecular Immunology"},{"key":"bib69","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1016\/j.virol.2010.03.039","article-title":"Modulation of type I interferon induction by porcine reproductive and respiratory syndrome virus and degradation of CREB-binding protein by non-structural protein 1 in MARC-145 and HeLa cells","volume":"402","author":"Kim","year":"2010","journal-title":"Virology"},{"key":"bib70","doi-asserted-by":"publisher","first-page":"914","DOI":"10.1016\/j.cell.2020.04.011","article-title":"The Architecture of SARS-CoV-2 Transcriptome","volume":"181","author":"Kim","year":"2020","journal-title":"Cell"},{"key":"bib71","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-021-25361-5","article-title":"A high-resolution temporal atlas of the SARS-CoV-2 translatome and transcriptome","volume":"12","author":"Kim","year":"2021","journal-title":"Nature Communications"},{"key":"bib72","doi-asserted-by":"publisher","first-page":"2474","DOI":"10.1128\/JVI.06677-11","article-title":"Ultrastructural Characterization of Arterivirus Replication Structures: Reshaping the Endoplasmic Reticulum To Accommodate Viral RNA Synthesis","volume":"86","author":"Knoops","year":"2012","journal-title":"Journal of Virology"},{"key":"bib73","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1016\/0168-1702(96)01313-5","article-title":"Porcine reproductive and respiratory syndrome virus enters cells through a low pH-dependent endocytic pathway","volume":"42","author":"Kreutz","year":"1996","journal-title":"Virus Research"},{"key":"bib74","doi-asserted-by":"publisher","first-page":"119140","DOI":"10.1016\/j.bbamcr.2021.119140","article-title":"Regulation of gene expression via translational buffering","volume":"1869","author":"Kusnadi","year":"2022","journal-title":"Biochimica et Biophysica Acta. Molecular Cell Research"},{"key":"bib75","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biology"},{"key":"bib76","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.01257","article-title":"Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments","volume":"3","author":"Lareau","year":"2014","journal-title":"eLife"},{"key":"bib77","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/j.immuni.2004.12.012","article-title":"VDUP1 is required for the development of natural killer cells","volume":"22","author":"Lee","year":"2005","journal-title":"Immunity"},{"key":"bib78","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1016\/j.virol.2007.04.001","article-title":"Porcine reproductive and respiratory syndrome virus induces apoptosis through a mitochondria-mediated pathway","volume":"365","author":"Lee","year":"2007","journal-title":"Virology"},{"key":"bib79","doi-asserted-by":"publisher","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","article-title":"Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences","volume":"22","author":"Li","year":"2006","journal-title":"Bioinformatics (Oxford, England)"},{"key":"bib80","doi-asserted-by":"publisher","first-page":"829","DOI":"10.1099\/vir.0.039289-0","article-title":"Identification of porcine reproductive and respiratory syndrome virus ORF1a-encoded non-structural proteins in virus-infected cells","volume":"93","author":"Li","year":"2012","journal-title":"The Journal of General Virology"},{"key":"bib81","doi-asserted-by":"publisher","first-page":"E2172","DOI":"10.1073\/pnas.1321930111","article-title":"Transactivation of programmed ribosomal frameshifting by a viral protein","volume":"111","author":"Li","year":"2014","journal-title":"PNAS"},{"key":"bib82","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1016\/j.virol.2017.12.017","article-title":"Nonstructural proteins nsp2TF and nsp2N of porcine reproductive and respiratory syndrome virus (PRRSV) play important roles in suppressing host innate immune responses","volume":"517","author":"Li","year":"2018","journal-title":"Virology"},{"key":"bib83","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00370-19","article-title":"Programmed -2\/-1 Ribosomal Frameshifting in Simarteriviruses: an Evolutionarily Conserved Mechanism","volume":"93","author":"Li","year":"2019","journal-title":"Journal of Virology"},{"key":"bib84","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13567-020-00850-5","article-title":"Integrated time-serial transcriptome networks reveal common innate and tissue-specific adaptive immune responses to PRRSV infection","volume":"51","author":"Lim","year":"2020","journal-title":"Veterinary Research"},{"key":"bib85","doi-asserted-by":"publisher","first-page":"961","DOI":"10.1292\/jvms.64.961","article-title":"Leader-Body Junction Sequence of the Viral Subgenomic mRNAs of Porcine Reproductive and Respiratory Syndrome Virus Isolated in Taiwan","volume":"64","author":"Lin","year":"2002","journal-title":"Journal of Veterinary Medical Science"},{"key":"bib86","doi-asserted-by":"publisher","first-page":"1095","DOI":"10.1128\/MCB.20.4.1095-1103.2000","article-title":"Kinetics of ribosomal pausing during programmed -1 translational frameshifting","volume":"20","author":"Lopinski","year":"2000","journal-title":"Molecular and Cellular Biology"},{"key":"bib87","doi-asserted-by":"publisher","first-page":"E1111","DOI":"10.1073\/pnas.1102932108","article-title":"Ribosomal frameshifting into an overlapping gene in the 2B-encoding region of the cardiovirus genome","volume":"108","author":"Loughran","year":"2011","journal-title":"PNAS"},{"key":"bib88","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biology"},{"key":"bib89","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1016\/j.freeradbiomed.2013.07.036","article-title":"The thioredoxin antioxidant system","volume":"66","author":"Lu","year":"2014","journal-title":"Free Radical Biology & Medicine"},{"key":"bib90","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1016\/j.abb.2016.09.011","article-title":"Thioredoxin and redox signaling: Roles of the thioredoxin system in control of cell fate","volume":"617","author":"Matsuzawa","year":"2017","journal-title":"Archives of Biochemistry and Biophysics"},{"key":"bib91","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1006\/viro.1993.1008","article-title":"Lelystad virus, the causative agent of porcine epidemic abortion and respiratory syndrome (PEARS), is related to LDV and EAV","volume":"192","author":"Meulenberg","year":"1993","journal-title":"Virology"},{"key":"bib92","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1007\/978-3-7091-9326-6_43","article-title":"Lelystad virus belongs to a new virus family, comprising lactate dehydrogenase-elevating virus, equine arteritis virus, and simian hemorrhagic fever virus","volume":"9","author":"Meulenberg","year":"1994","journal-title":"Archives of Virology. Supplementum"},{"key":"bib93","doi-asserted-by":"publisher","first-page":"2491","DOI":"10.1099\/0022-1317-81-10-2491","article-title":"The arterivirus replicase is the only viral protein required for genome replication and subgenomic mRNA transcription","volume":"81","author":"Molenkamp","year":"2000","journal-title":"The Journal of General Virology"},{"key":"bib94","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1111\/tbed.12272","article-title":"Pathology and Virus Distribution in the Lung and Lymphoid Tissues of Pigs Experimentally Inoculated with Three Distinct Type 1 PRRS Virus Isolates of Varying Pathogenicity","volume":"63","author":"Morgan","year":"2016","journal-title":"Transboundary and Emerging Diseases"},{"key":"bib95","doi-asserted-by":"publisher","first-page":"244","DOI":"10.1038\/nature04735","article-title":"A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting","volume":"441","author":"Namy","year":"2006","journal-title":"Nature"},{"key":"bib96","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.01635","article-title":"Improved Vaccine against PRRSV: Current Progress and Future Perspective","volume":"8","author":"Nan","year":"2017","journal-title":"Frontiers in Microbiology"},{"key":"bib97","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.00970","article-title":"The Network of Interactions Among Porcine Reproductive and Respiratory Syndrome Virus Non-structural Proteins","volume":"9","author":"Nan","year":"2018","journal-title":"Frontiers in Microbiology"},{"key":"bib98","doi-asserted-by":"publisher","first-page":"5491","DOI":"10.1093\/nar\/gkw480","article-title":"A novel role for poly(C) binding proteins in programmed ribosomal frameshifting","volume":"44","author":"Napthine","year":"2016","journal-title":"Nucleic Acids Research"},{"key":"bib99","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms15582","article-title":"Protein-directed ribosomal frameshifting temporally regulates gene expression","volume":"8","author":"Napthine","year":"2017","journal-title":"Nature Communications"},{"key":"bib100","doi-asserted-by":"publisher","first-page":"8207","DOI":"10.1093\/nar\/gkz503","article-title":"Characterization of the stimulators of protein-directed ribosomal frameshifting in Theiler\u2019s murine encephalomyelitis virus","volume":"47","author":"Napthine","year":"2019","journal-title":"Nucleic Acids Research"},{"key":"bib101","doi-asserted-by":"publisher","first-page":"5671","DOI":"10.1128\/JVI.00261-09","article-title":"Biochemical characterization of arterivirus nonstructural protein 11 reveals the nidovirus-wide conservation of a replicative endoribonuclease","volume":"83","author":"Nedialkova","year":"2009","journal-title":"Journal of Virology"},{"key":"bib102","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1128\/JVI.73.1.270-280.1999","article-title":"Porcine reproductive and respiratory syndrome virus comparison: divergent evolution on two continents","volume":"73","author":"Nelsen","year":"1999","journal-title":"Journal of Virology"},{"key":"bib103","doi-asserted-by":"publisher","first-page":"21645","DOI":"10.1074\/jbc.274.31.21645","article-title":"Identification of thioredoxin-binding protein-2\/vitamin D(3) up-regulated protein 1 as a negative regulator of thioredoxin function and expression","volume":"274","author":"Nishiyama","year":"1999","journal-title":"The Journal of Biological Chemistry"},{"key":"bib104","doi-asserted-by":"publisher","first-page":"17904","DOI":"10.1074\/jbc.RA120.016105","article-title":"Molecular characterization of the RNA-protein complex directing -2\/-1 programmed ribosomal frameshifting during arterivirus replicase expression","volume":"295","author":"Patel","year":"2020","journal-title":"The Journal of Biological Chemistry"},{"key":"bib105","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1073\/pnas.0809211106","article-title":"Slow peptide bond formation by proline and other N-alkylamino acids in translation","volume":"106","author":"Pavlov","year":"2008","journal-title":"PNAS"},{"key":"bib106","doi-asserted-by":"publisher","first-page":"1825","DOI":"10.1093\/nar\/gki329","article-title":"Torsional restraint: A new twist on frameshifting pseudoknots","volume":"33","author":"Plant","year":"2005","journal-title":"Nucleic Acids Research"},{"key":"bib107","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1016\/j.virusres.2017.01.023","article-title":"Nidovirus RNA polymerases: Complex enzymes handling exceptional RNA genomes","volume":"234","author":"Posthuma","year":"2017","journal-title":"Virus Research"},{"key":"bib108","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0187735","article-title":"Transcriptome profile of lung dendritic cells after in vitro porcine reproductive and respiratory syndrome virus (PRRSV) infection","volume":"12","author":"Pr\u00f6ll","year":"2017","journal-title":"PLOS ONE"},{"key":"bib109","doi-asserted-by":"publisher","DOI":"10.1101\/2020.11.03.367516","article-title":"The Translational Landscape of SARS-CoV-2 and Infected Cells","volume-title":"bioRxiv","author":"Puray-Chavez","year":"2021"},{"key":"bib110","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1002\/embr.201337762","article-title":"Structured mRNA induces the ribosome into a hyper-rotated state","volume":"15","author":"Qin","year":"2014","journal-title":"EMBO Reports"},{"key":"bib111","doi-asserted-by":"publisher","first-page":"2977","DOI":"10.1016\/j.bbamcr.2016.09.012","article-title":"Activation of apoptosis signalling pathways by reactive oxygen species","volume":"1863","author":"Redza-Dutordoir","year":"2016","journal-title":"Biochimica et Biophysica Acta (BBA) - Molecular Cell Research"},{"key":"bib112","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku699","article-title":"leeHom: adaptor trimming and merging for Illumina sequencing reads","volume":"42","author":"Renaud","year":"2014","journal-title":"Nucleic Acids Research"},{"key":"bib113","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1016\/j.imbio.2018.11.010","article-title":"Reactive oxygen species (ROS) in macrophage activation and function in diabetes","volume":"224","author":"Rendra","year":"2019","journal-title":"Immunobiology"},{"key":"bib114","doi-asserted-by":"publisher","first-page":"1056","DOI":"10.1093\/nar\/gkz783","article-title":"Translational recoding: canonical translation mechanisms reinterpreted","volume":"48","author":"Rodnina","year":"2020","journal-title":"Nucleic Acids Research"},{"key":"bib115","doi-asserted-by":"publisher","first-page":"1211","DOI":"10.1210\/me.2014-1095","article-title":"Minireview: Thioredoxin-interacting protein: regulation and function in the pancreatic \u03b2-cell","volume":"28","author":"Shalev","year":"2014","journal-title":"Molecular Endocrinology (Baltimore, Md.)"},{"key":"bib116","doi-asserted-by":"publisher","DOI":"10.1186\/s12917-016-0717-5","article-title":"Nonstructural protein 11 (nsp11) of porcine reproductive and respiratory syndrome virus (PRRSV) promotes PRRSV infection in MARC-145 cells","volume":"12","author":"Shi","year":"2016","journal-title":"BMC Veterinary Research"},{"key":"bib117","doi-asserted-by":"publisher","first-page":"21769","DOI":"10.1073\/pnas.1910613116","article-title":"Ribosome collisions alter frameshifting at translational reprogramming motifs in bacterial mRNAs","volume":"116","author":"Smith","year":"2019","journal-title":"PNAS"},{"key":"bib118","doi-asserted-by":"publisher","first-page":"5755","DOI":"10.1128\/JVI.68.9.5755-5764.1994","article-title":"Proteolytic processing of the replicase ORF1a protein of equine arteritis virus","volume":"68","author":"Snijder","year":"1994","journal-title":"Journal of Virology"},{"key":"bib119","doi-asserted-by":"publisher","first-page":"961","DOI":"10.1099\/0022-1317-79-5-961","article-title":"The molecular biology of arteriviruses","volume":"79","author":"Snijder","year":"1998","journal-title":"Journal of General Virology"},{"key":"bib120","doi-asserted-by":"publisher","first-page":"985","DOI":"10.1099\/0022-1317-82-5-985","article-title":"Non-structural proteins 2 and 3 interact to modify host cell membranes during the formation of the arterivirus replication complex","volume":"82","author":"Snijder","year":"2001","journal-title":"Journal of General Virology"},{"key":"bib121","doi-asserted-by":"publisher","first-page":"2141","DOI":"10.1099\/vir.0.056341-0","article-title":"Arterivirus molecular biology and pathogenesis","volume":"94","author":"Snijder","year":"2013","journal-title":"The Journal of General Virology"},{"key":"bib122","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1016\/s0165-2478(03)00024-5","article-title":"Vitamin D(3) up-regulating protein 1 (VDUP1) antisense DNA regulates tumorigenicity and melanogenesis of murine melanoma cells via regulating the expression of fas ligand and reactive oxygen species","volume":"86","author":"Song","year":"2003","journal-title":"Immunology Letters"},{"key":"bib123","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1016\/j.virol.2010.08.025","article-title":"Nonstructural protein 1\u03b1 subunit-based inhibition of NF-\u03baB activation and suppression of interferon-\u03b2 production by porcine reproductive and respiratory syndrome virus","volume":"407","author":"Song","year":"2010","journal-title":"Virology"},{"key":"bib124","doi-asserted-by":"publisher","first-page":"1112","DOI":"10.1128\/JVI.01112-18","article-title":"Mapping the Nonstructural Protein Interaction Network of Porcine Reproductive and Respiratory Syndrome Virus","volume":"92","author":"Song","year":"2018","journal-title":"Journal of Virology"},{"key":"bib125","doi-asserted-by":"publisher","DOI":"10.1101\/2020.08.28.269175","article-title":"A SARS-CoV-2 BioID-Based Virus-Host Membrane Protein Interactome and Virus Peptide Compendium: New Proteomics Resources for COVID-19 Research","volume-title":"bioRxiv","author":"St-Germain","year":"2020"},{"key":"bib126","doi-asserted-by":"publisher","first-page":"957","DOI":"10.1038\/224957a0","article-title":"Polypeptide chain initiation: nucleotide sequences of the three ribosomal binding sites in bacteriophage R17 RNA","volume":"224","author":"Steitz","year":"1969","journal-title":"Nature"},{"key":"bib127","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1128\/JVI.00589-18","article-title":"Transcriptional and Translational Landscape of Equine Torovirus","volume":"92","author":"Stewart","year":"2018","journal-title":"Journal of Virology"},{"key":"bib128","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00175-18","article-title":"The Superimposed Deubiquitination Effect of OTULIN and Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Nsp11 Promotes Multiplication of PRRSV","volume":"92","author":"Su","year":"2018","journal-title":"Journal of Virology"},{"key":"bib129","doi-asserted-by":"publisher","first-page":"7832","DOI":"10.1128\/JVI.00217-10","article-title":"The cysteine protease domain of porcine reproductive and respiratory syndrome virus nonstructural protein 2 possesses deubiquitinating and interferon antagonism functions","volume":"84","author":"Sun","year":"2010","journal-title":"Journal of Virology"},{"key":"bib130","doi-asserted-by":"publisher","first-page":"3839","DOI":"10.1128\/JVI.06466-11","article-title":"Nonstructural Protein 2 of Porcine Reproductive and Respiratory Syndrome Virus Inhibits the Antiviral Function of Interferon-Stimulated Gene 15","volume":"86","author":"Sun","year":"2012","journal-title":"Journal of Virology"},{"key":"bib131","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0168314","article-title":"Nonstructural Protein 11 of Porcine Reproductive and Respiratory Syndrome Virus Suppresses Both MAVS and RIG-I Expression as One of the Mechanisms to Antagonize Type I Interferon Production","volume":"11","author":"Sun","year":"2016","journal-title":"PLOS ONE"},{"key":"bib132","doi-asserted-by":"publisher","DOI":"10.1101\/2020.03.05.976167","article-title":"Direct RNA Sequencing and Early Evolution of SARS-CoV-2","volume-title":"bioRxiv","author":"Taiaroa","year":"2020"},{"key":"bib133","doi-asserted-by":"publisher","DOI":"10.1155\/2016\/2795090","article-title":"The Reactive Oxygen Species in Macrophage Polarization: Reflecting Its Dual Role in Progression and Treatment of Human Diseases","volume":"2016","author":"Tan","year":"2016","journal-title":"Oxidative Medicine and Cellular Longevity"},{"key":"bib134","doi-asserted-by":"publisher","DOI":"10.3390\/v12020215","article-title":"Helicase of Type 2 Porcine Reproductive and Respiratory Syndrome Virus Strain HV Reveals a Unique Structure","volume":"12","author":"Tang","year":"2020","journal-title":"Viruses"},{"key":"bib135","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.12983","article-title":"CIAlign: A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments","volume":"10","author":"Tumescheit","year":"2022","journal-title":"PeerJ"},{"key":"bib136","doi-asserted-by":"publisher","first-page":"991","DOI":"10.1073\/pnas.94.3.991","article-title":"An infectious arterivirus cDNA clone: identification of a replicase point mutation that abolishes discontinuous mRNA transcription","volume":"94","author":"van Dinten","year":"1997","journal-title":"PNAS"},{"key":"bib137","doi-asserted-by":"publisher","first-page":"773","DOI":"10.1128\/JVI.06277-11","article-title":"Arterivirus and nairovirus ovarian tumor domain-containing Deubiquitinases target activated RIG-I to control innate immune signaling","volume":"86","author":"van Kasteren","year":"2012","journal-title":"Journal of Virology"},{"key":"bib138","doi-asserted-by":"publisher","first-page":"1545","DOI":"10.1101\/gr.247064.118","article-title":"Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis","volume":"29","author":"Viehweger","year":"2019","journal-title":"Genome Research"},{"key":"bib139","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1016\/j.molimm.2015.08.011","article-title":"The nonstructural protein 11 of porcine reproductive and respiratory syndrome virus inhibits NF-\u03baB signaling by means of its deubiquitinating activity","volume":"68","author":"Wang","year":"2015","journal-title":"Molecular Immunology"},{"key":"bib140","doi-asserted-by":"publisher","first-page":"1906","DOI":"10.1292\/jvms.17-0258","article-title":"Porcine alveolar macrophage polarization is involved in inhibition of porcine reproductive and respiratory syndrome virus (PRRSV) replication","volume":"79","author":"Wang","year":"2017","journal-title":"The Journal of Veterinary Medical Science"},{"key":"bib141","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00623-19","article-title":"Porcine Reproductive and Respiratory Syndrome Virus nsp11 Antagonizes Type I Interferon Signaling by Targeting IRF9","volume":"93","author":"Wang","year":"2019","journal-title":"Journal of Virology"},{"key":"bib142","doi-asserted-by":"publisher","first-page":"1501","DOI":"10.1080\/22221751.2019.1679010","article-title":"The Nsp12-coding region of type 2 PRRSV is required for viral subgenomic mRNA synthesis","volume":"8","author":"Wang","year":"2019","journal-title":"Emerging Microbes & Infections"},{"key":"bib143","doi-asserted-by":"publisher","first-page":"2135","DOI":"10.1016\/j.molcel.2021.02.036","article-title":"The SARS-CoV-2 subgenome landscape and its novel regulatory features","volume":"81","author":"Wang","year":"2021","journal-title":"Molecular Cell"},{"key":"bib144","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1080\/01652176.1991.9694296","article-title":"Mystery swine disease in The Netherlands: the isolation of Lelystad virus","volume":"13","author":"Wensvoort","year":"1991","journal-title":"The Veterinary Quarterly"},{"key":"bib145","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12864-016-2720-4","article-title":"Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal\/fetal interface and in the fetus","volume":"17","author":"Wilkinson","year":"2016","journal-title":"BMC Genomics"},{"key":"bib146","doi-asserted-by":"publisher","first-page":"12495","DOI":"10.1128\/JVI.79.19.12495-12506.2005","article-title":"Envelope protein requirements for the assembly of infectious virions of porcine reproductive and respiratory syndrome virus","volume":"79","author":"Wissink","year":"2005","journal-title":"Journal of Virology"},{"key":"bib147","doi-asserted-by":"publisher","first-page":"3559","DOI":"10.1002\/j.1460-2075.1988.tb03233.x","article-title":"Ribosome pausing and stacking during translation of a eukaryotic mRNA","volume":"7","author":"Wolin","year":"1988","journal-title":"The EMBO Journal"},{"key":"bib148","doi-asserted-by":"publisher","first-page":"959","DOI":"10.1016\/j.molcel.2018.12.009","article-title":"High-Resolution Ribosome Profiling Defines Discrete Ribosome Elongation States and Translational Regulation during Cellular Stress","volume":"73","author":"Wu","year":"2019","journal-title":"Molecular Cell"},{"key":"bib149","doi-asserted-by":"publisher","first-page":"39394","DOI":"10.1074\/jbc.M502966200","article-title":"Catalytic degradation of vitamin D up-regulated protein 1 mRNA enhances cardiomyocyte survival and prevents left ventricular remodeling after myocardial ischemia","volume":"280","author":"Xiang","year":"2005","journal-title":"The Journal of Biological Chemistry"},{"key":"bib150","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/j.virusres.2011.03.001","article-title":"Identification of new defective interfering RNA species associated with porcine reproductive and respiratory syndrome virus infection","volume":"158","author":"Xiao","year":"2011","journal-title":"Virus Research"},{"key":"bib151","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/ncomms11194","article-title":"Genome-wide assessment of differential translations with ribosome profiling data","volume":"7","author":"Xiao","year":"2016","journal-title":"Nature Communications"},{"key":"bib152","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01352-19","article-title":"Nonstructural Protein 11 of Porcine Reproductive and Respiratory Syndrome Virus Induces STAT2 Degradation To Inhibit Interferon Signaling","volume":"93","author":"Yang","year":"2019","journal-title":"Journal of Virology"},{"key":"bib153","doi-asserted-by":"publisher","DOI":"10.5808\/GI.2018.16.4.e28","article-title":"STADIUM: Species-Specific tRNA Adaptive Index Compendium","volume":"16","author":"Yoon","year":"2018","journal-title":"Genomics & Informatics"},{"key":"bib154","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1006\/viro.2000.0639","article-title":"Heteroclite subgenomic RNAs are produced in porcine reproductive and respiratory syndrome virus infection","volume":"275","author":"Yuan","year":"2000","journal-title":"Virology"},{"key":"bib155","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1016\/j.virusres.2004.04.015","article-title":"Characterization of heteroclite subgenomic RNAs associated with PRRSV infection","volume":"105","author":"Yuan","year":"2004","journal-title":"Virus Research"},{"key":"bib156","doi-asserted-by":"publisher","DOI":"10.1155\/2018\/1538127","article-title":"Transcriptome Analysis Reveals Dynamic Gene Expression Profiles in Porcine Alveolar Macrophages in Response to the Chinese Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus","volume":"2018","author":"Zeng","year":"2018","journal-title":"BioMed Research International"},{"key":"bib157","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-05279-z","article-title":"Genome-wide analysis of long noncoding RNA profiling in PRRSV-infected PAM cells by RNA sequencing","volume":"7","author":"Zhang","year":"2017","journal-title":"Scientific Reports"},{"key":"bib158","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2019.01221","article-title":"Global miRNA, lncRNA, and mRNA Transcriptome Profiling of Endometrial Epithelial Cells Reveals Genes Related to Porcine Reproductive Failure Caused by Porcine Reproductive and Respiratory Syndrome Virus","volume":"10","author":"Zhang","year":"2019","journal-title":"Frontiers in Immunology"},{"key":"bib159","doi-asserted-by":"publisher","first-page":"782","DOI":"10.1016\/j.tibs.2019.03.002","article-title":"Function and Evolution of Upstream ORFs in Eukaryotes","volume":"44","author":"Zhang","year":"2019","journal-title":"Trends in Biochemical Sciences"},{"key":"bib160","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abe7386","article-title":"Nsp1 protein of SARS-CoV-2 disrupts the mRNA export machinery to inhibit host gene expression","volume":"7","author":"Zhang","year":"2021","journal-title":"Science Advances"},{"key":"bib161","doi-asserted-by":"publisher","DOI":"10.3390\/v13122531","article-title":"Nanopore-Based Direct RNA-Sequencing Reveals a High-Resolution Transcriptional Landscape of Porcine Reproductive and Respiratory Syndrome Virus","volume":"13","author":"Zhang","year":"2021","journal-title":"Viruses"},{"key":"bib162","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1038\/ni.1831","article-title":"Thioredoxin-interacting protein links oxidative stress to inflammasome activation","volume":"11","author":"Zhou","year":"2010","journal-title":"Nature Immunology"}],"container-title":["eLife"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/cdn.elifesciences.org\/articles\/75668\/elife-75668-v2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/cdn.elifesciences.org\/articles\/75668\/elife-75668-v2.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/elifesciences.org\/articles\/75668","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,19]],"date-time":"2024-09-19T09:17:48Z","timestamp":1726737468000},"score":1,"resource":{"primary":{"URL":"https:\/\/elifesciences.org\/articles\/75668"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,2,28]]},"references-count":162,"alternative-id":["10.7554\/eLife.75668"],"URL":"https:\/\/doi.org\/10.7554\/elife.75668","archive":["CLOCKSS"],"relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.11.17.468997","asserted-by":"subject"},{"id-type":"doi","id":"10.1101\/2021.11.17.468997","asserted-by":"object"}],"is-supplemented-by":[{"id-type":"accession","id":"E-MTAB-10621","asserted-by":"subject"},{"id-type":"accession","id":"E-MTAB-10622","asserted-by":"subject"},{"id-type":"accession","id":"E-MTAB-10623","asserted-by":"subject"}],"has-review":[{"id-type":"doi","id":"10.7554\/eLife.75668.sa0","asserted-by":"object"},{"id-type":"doi","id":"10.7554\/eLife.75668.sa1","asserted-by":"object"},{"id-type":"doi","id":"10.7554\/eLife.75668.sa2","asserted-by":"object"}]},"ISSN":["2050-084X"],"issn-type":[{"value":"2050-084X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,2,28]]},"assertion":[{"value":"single anonymised","name":"peer_review_transparency","label":"Peer review transparency","group":{"name":"peer_review_taxonomy"}},{"value":"other reviewer(s), editor","name":"peer_review_interaction","label":"Peer review interaction","group":{"name":"peer_review_taxonomy"}},{"value":"review summaries, review reports, author\/editor communication, reviewer identities reviewer opt in, editor identities","name":"peer_review_published","label":"Peer review published","group":{"name":"peer_review_taxonomy"}},{"value":"open (sign in with ORCID iD required)","name":"post_publication_commenting","label":"Post publication commenting","group":{"name":"post_publication_commenting"}}],"article-number":"e75668"}}