The 3'-terminal hexamer sequence of classical swine fever virus RNA plays a role in negatively regulating the IRES-mediated translation

A potential long-range RNA-RNA interaction in the HIV-1 RNA

It is well-established that viral and cellular mRNAs alike harbour functional long-range intra-molecular RNA-RNA interactions. Despite the biological importance of such interactions, their identification and characterization remain challenging. Here we present a computational method for the identification of certain kinds of long-range intra-molecular RNA-RNA interactions involving the loop nucleotides of a hairpin loop. Using the computational method, we analysed 4272 HIV-1 genomic mRNAs. A potential long-range intra-molecular RNA-RNA interaction within the HIV-1 genomic RNA was identified. The long-range interaction is mediated by a kissing loop structure between two stem-loops of the previously reported SHAPE-based secondary structure of the entire HIV-1 genome. Structural modelling studies were carried out to show that the kissing loop structure not only is sterically feasible, but also contains a conserved RNA structural motif often found in compact RNA pseudoknots. The computational method should be generally applicable to the identification of potential long-range intra-molecular RNA-RNA interactions in any viral or cellular mRNA sequence.Communicated by Ramaswamy H. Sarma.

Natural selection pressure exerted on "Silent" mutations during the evolution of SARS-CoV-2: Evidence from codon usage and RNA structure

From the first emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) till now, multiple mutations that caused synonymous and nonsynonymous substitutions have accumulated. Among them, synonymous substitutions were regarded as "silent" mutations that received less attention than nonsynonymous substitutions that cause amino acid variations. However, the importance of synonymous substitutions can not be neglected. This research focuses on synonymous substitutions on SARS-CoV-2 and proves that synonymous substitutions were under purifying selection in its evolution. The evidence of purifying selection is provided by comparing the mutation number per site in coding and non-coding regions. We then study the two forces of purifying selection: synonymous codon usage and RNA secondary structure. Results show that the codon usage optimization leads to an adapted codon usage towards humans. Furthermore, our results show that the maintenance of RNA secondary structure causes the purifying of synonymous substitutions in the structural region. These results explain the selection pressure on synonymous substitutions during the evolution of SARS-CoV-2.

Genomic characterization of classical swine fever virus LOM variants with 3'-UTR INDELs from pigs on Jeju Island, South Korea

Classical swine fever virus (CSFV) reemerged in naïve pig herds on Jeju Island, South Korea, due to the accidental introduction of the LOM vaccine strain in 2014. Since this reemergence, the previously CSFV-free region has experienced numerous outbreaks, causing the virus to become endemic in provincial herds. In this study, we determined the complete genome sequences and investigated the molecular characteristics of LOM-derived field CSFV strains with unique insertion-deletion (INDEL) mutations in the 3'-untranslated region (UTR) that were responsible for ongoing sporadic outbreaks on Jeju Island in 2019. The Jeju LOM-derived variants that emerged in 2019 had their own INDEL signatures in the 3'-UTR, resulting in changes to the predicted secondary stem-loop structures. The genomes of these strains were 12,297-12,302 nucleotides in length, one nucleotide (nt) shorter or one, two, or four nt longer than the reference LOM strain. The 3'-UTR INDEL variants shared 98.8-99.0% and 98.3-98.6% identity with the LOM strain at the polyprotein and full-genome level, respectively. The total number of genetic variations between the LOM vaccine strain and the 3'-UTR INDEL isolates ranged from 161 to 202 and 37 to 45 at the nucleotide and amino acid level, respectively. These mutations were broadly dispersed throughout the genome and particularly clustered in NS2 and the 3'-UTR, possibly triggering a reversion to low virulence and allowing the virus to adapt to improve its persistence in the field. This study provides important information about the genetic evolution of LOM-derived CSFV circulating in the free region, and suggests that it arose from continuous non-lethal mutations to ensure viral fitness in host animals.

A Polyuridine Insertion in the 3' Untranslated Region of Classical Swine Fever Virus Activates Immunity and Reduces Viral Virulence in Piglets

Classical swine fever (CSF), a highly contagious viral disease of pigs, is still endemic in some countries of Asia and Central and South America. Considering that the 3′ untranslated region (3′ UTR) plays an important role in flavivirus replication, the present study showed for the first time that a long polyuridine sequence acquired in the 3′ UTR by an endemic CSFV isolate can activate immunity, control viral replication, and modulate disease in piglets. Our findings provide new avenues for the development of novel vaccines against infections with CSF virus and other flaviviruses. Knowledge of molecular virulence determinants is also relevant for future development of rapid and efficient diagnostic tools for the prediction of the virulence of field isolates and for efficient CSF control.

Low-virulence classical swine fever virus (CSFV) strains make CSF eradication particularly difficult. Few data are available on the molecular determinants of CSFV virulence. The aim of the present study was to assess a possible role for CSFV virulence of a unique, uninterrupted 36-uridine (poly-U) sequence found in the 3′ untranslated region (3′ UTR) of the low-virulence CSFV isolate Pinar de Rio (PdR). To this end, a pair of cDNA-derived viruses based on the PdR backbone were generated, one carrying the long poly-U insertion in the 3′ UTR (vPdR-36U) and the other harboring the standard 5 uridines at this position (vPdR-5U). Two groups of 20 5-day-old piglets were infected with vPdR-36U and vPdR-5U. Ten contact piglets were added to each group. Disease progression, virus replication, and immune responses were monitored for 5 weeks. The vPdR-5U virus was significantly more virulent than the vPdR-36U virus, with more severe disease, higher mortality, and significantly higher viral loads in serum and body secretions, despite similar replication characteristics in cell culture. The two viruses were transmitted to all contact piglets. Ninety percent of the piglets infected with vPdR-36U seroconverted, while only one vPdR-5U-infected piglet developed antibodies. The vPdR-5U-infected piglets showed only transient alpha interferon (IFN-α) responses in serum after 1 week of infection, while the vPdR-36U-infected piglets showed sustained IFN-α levels during the first 2 weeks. Taken together, these data show that the 3′ UTR poly-U insertion acquired by the PdR isolate reduces viral virulence and activates the innate and humoral immune responses without affecting viral transmission.

IMPORTANCE Classical swine fever (CSF), a highly contagious viral disease of pigs, is still endemic in some countries of Asia and Central and South America. Considering that the 3′ untranslated region (3′ UTR) plays an important role in flavivirus replication, the present study showed for the first time that a long polyuridine sequence acquired in the 3′ UTR by an endemic CSFV isolate can activate immunity, control viral replication, and modulate disease in piglets. Our findings provide new avenues for the development of novel vaccines against infections with CSF virus and other flaviviruses. Knowledge of molecular virulence determinants is also relevant for future development of rapid and efficient diagnostic tools for the prediction of the virulence of field isolates and for efficient CSF control.

Distinct roles for the IIId2 sub-domain in pestivirus and picornavirus internal ribosome entry sites

Viral internal ribosomes entry site (IRES) elements coordinate the recruitment of the host translation machinery to direct the initiation of viral protein synthesis. Within hepatitis C virus (HCV)-like IRES elements, the sub-domain IIId(1) is crucial for recruiting the 40S ribosomal subunit. However, some HCV-like IRES elements possess an additional sub-domain, termed IIId2, whose function remains unclear. Herein, we show that IIId2 sub-domains from divergent viruses have different functions. The IIId2 sub-domain present in Seneca valley virus (SVV), a picornavirus, is dispensable for IRES activity, while the IIId2 sub-domains of two pestiviruses, classical swine fever virus (CSFV) and border disease virus (BDV), are required for 80S ribosomes assembly and IRES activity. Unlike in SVV, the deletion of IIId2 from the CSFV and BDV IRES elements impairs initiation of translation by inhibiting the assembly of 80S ribosomes. Consequently, this negatively affects the replication of CSFV and BDV. Finally, we show that the SVV IIId2 sub-domain is required for efficient viral RNA synthesis and growth of SVV, but not for IRES function. This study sheds light on the molecular evolution of viruses by clearly demonstrating that conserved RNA structures, within distantly related RNA viruses, have acquired different roles in the virus life cycles.

Nuclear Magnetic Resonance Study of RNA Structures at the 3'-End of the Hepatitis C Virus Genome

The 3'-end of the genomic RNA of the hepatitis C virus (HCV) embeds conserved elements that regulate viral RNA synthesis and protein translation by mechanisms that have yet to be elucidated. Previous studies with oligo-RNA fragments have led to multiple, mutually exclusive secondary structure predictions, indicating that HCV RNA structure may be context-dependent. Here we employed a nuclear magnetic resonance (NMR) approach that involves long-range adenosine interaction detection, coupled with site-specific ²H labeling, to probe the structure of the intact 3'-end of the HCV genome (385 nucleotides). Our data reveal that the 3'-end exists as an equilibrium mixture of two conformations: an open conformation in which the 98 nucleotides of the 3'-tail (3'X) form a two-stem-loop structure with the kissing-loop residues sequestered and a closed conformation in which the 3'X rearranges its structure and forms a long-range kissing-loop interaction with an upstream cis-acting element 5BSL3.2. The long-range kissing species is favored under high-Mg²⁺ conditions, and the intervening sequences do not affect the equilibrium as their secondary structures remain unchanged. The open and closed conformations are consistent with the reported function regulation of viral RNA synthesis and protein translation, respectively. Our NMR detection of these RNA conformations and the structural equilibrium in the 3'-end of the HCV genome support its roles in coordinating various steps of HCV replication.

Novel poly-uridine insertion in the 3'UTR and E2 amino acid substitutions in a low virulent classical swine fever virus

In this study, we compared the virulence in weaner pigs of the Pinar del Rio isolate and the virulent Margarita strain. The latter caused the Cuban classical swine fever (CSF) outbreak of 1993. Our results showed that the Pinar del Rio virus isolated during an endemic phase is clearly of low virulence. We analysed the complete nucleotide sequence of the Pinar del Rio virus isolated after persistence in newborn piglets, as well as the genome sequence of the inoculum. The consensus genome sequence of the Pinar del Rio virus remained completely unchanged after 28days of persistent infection in swine. More importantly, a unique poly-uridine tract was discovered in the 3'UTR of the Pinar del Rio virus, which was not found in the Margarita virus or any other known CSFV sequences. Based on RNA secondary structure prediction, the poly-uridine tract results in a long single-stranded intervening sequence (SS) between the stem-loops I and II of the 3'UTR, without major changes in the stem- loop structures when compared to the Margarita virus. The possible implications of this novel insertion on persistence and attenuation remain to be investigated. In addition, comparison of the amino acid sequence of the viral proteins E^rns, E1, E2 and p7 of the Margarita and Pinar del Rio viruses showed that all non-conservative amino acid substitutions acquired by the Pinar del Rio isolate clustered in E2, with two of them being located within the B/C domain. Immunisation and cross-neutralisation experiments in pigs and rabbits suggest differences between these two viruses, which may be attributable to the amino acid differences observed in E2. Altogether, these data provide fresh insights into viral molecular features which might be associated with the attenuation and adaptation of CSFV for persistence in the field.

Live Cell Reporter Systems for Positive-Sense Single Strand RNA Viruses

Cell-based reporter systems have facilitated studies of viral replication and pathogenesis, virus detection, and drug susceptibility testing. There are three types of cell-based reporter systems that express certain reporter protein for positive-sense single strand RNA virus infections. The first type is classical reporter system, which relies on recombinant virus, reporter virus particle, or subgenomic replicon. During infection with the recombinant virus or reporter virus particle, the reporter protein is expressed and can be detected in real time in a dose-dependent manner. Using subgenomic replicon, which are genetically engineered viral RNA molecules that are capable of replication but incapable of producing virions, the translation and replication of the replicon could be tracked by the accumulation of reporter protein. The second type of reporter system involves genetically engineered cells bearing virus-specific protease cleavage sequences, which can sense the incoming viral protease. The third type is based on viral replicase, which can report the specific virus infection via detection of the incoming viral replicase. This review specifically focuses on the major technical breakthroughs in the design of cell-based reporter systems and the application of these systems to the further understanding and control of viruses over the past few decades.

Roles of nucleic acid substrates and cofactors in the vhs protein activity of pseudorabies virus

Pseudorabies virus (PrV) belongs to the α-herpesvirinae of which human simplex virus (HSV) is the prototype virus. One of the hallmarks of HSV infection is shutoff of protein synthesis that is mediated by various viral proteins including vhs (virion host shutoff), which is encoded by the UL41 gene. However, the function of PrV vhs is poorly understood. Due to the low sequence similarity (39.3%) between the HSV and PrV UL41 proteins, vhs might not share the same biochemistry characteristics. The purpose of this study was to characterize the nuclease activity of the PrV vhs protein with respect to substrate specificity, its requirements in terms of cofactors, and the protein regions, as well as key amino acids, which contribute to vhs activity. Our results indicated that, similar to HSV vhs, PrV vhs is able to degrade ssRNA and mRNA. However, PrV vhs also targeted rRNA for degradation, which is novel compared to the HSV-1 vhs. Activity assays indicated that Mg²⁺ alone enhances RNA degradation mediated by PrV vhs, while K⁺ and ATP are not sufficient to induce activity. Finally, we demonstrated that each of the four highly conserved functional boxes of PrV vhs contributes to RNA degradation and that, in particular, residues 152, 169, 171, 172, 173 343, 345, 352 and 356, which are conserved among α-herpesviruses, are key amino acids needed for PrV vhs ribonuclease activity.

In Vitro Coinfection and Replication of Classical Swine Fever Virus and Porcine Circovirus Type 2 in PK15 Cells

Increasing clinical lines of evidence have shown the coinfection/superinfection of porcine circovirus type 2 (PCV2) and classical swine fever virus (CSFV). Here, we investigated whether PCV2 and CSFV could infect the same cell productively by constructing an in vitro coinfection model. Our results indicated that PCV2-free PK15 cells but not ST cells were more sensitive to PCV2, and the PK15 cell line could stably harbor replicating CSFV (PK15-CSFV cells) with a high infection rate. Confocal and super-resolution microscopic analysis showed that PCV2 and CSFV colocalized in the same PK15-CSFV cell, and the CSFV E2 protein translocated from the cytoplasm to the nucleus in PK15-CSFV cells infected with PCV2. Moreover, PCV2-CSFV dual-positive cells increased gradually in PK15-CSFV cells in a PCV2 dose-dependent manner. In PK15-CSFV cells, PCV2 replicated well, and the production of PCV2 progeny was not influenced by CSFV infection. However, CSFV reproduction decreased in a PCV2 dose-dependent manner. In addition, cellular apoptosis was not strengthened in PK15-CSFV cells infected with PCV2 in comparison with PCV2-infected PK15 cells. Moreover, using this coinfection model we further demonstrated PCV2-induced apoptosis might contribute to the impairment of CSFV HCLV strain replication in coinfected cells. Taken together, our results demonstrate for the first time the coinfection/superinfection of PCV2 and CSFV within the same cell, providing an in vitro model to facilitate further investigation of the underlying mechanism of CSFV and PCV2 coinfection.

Functional long-range RNA-RNA interactions in positive-strand RNA viruses

Long-range RNA–RNA interactions, many of which span several thousands of nucleotides, have been discovered within the genomes of positive-strand RNA viruses. These interactions mediate fundamental viral processes, including translation, replication and transcription.

In certain plant viruses that have uncapped, non-polyadenylated RNA genomes, translation initiation is facilitated by 3′ cap-independent translational enhancers (3′ CITEs) that are located in or near to their 3′ UTRs. These RNA elements function by binding to either the ribosome-recruiting eukaryotic translation initiation factor 4F (eIF4F) complex or ribosomal subunits, and they enhance translation initiation by engaging the 5′ end of the genome via a 5′-to-3′ RNA-based bridge.

The activities of the internal ribosome entry sites (IRESs) in the 5′ UTRs of various viruses are modulated by RNA-based interactions between the IRESs and elements near to the 3′ ends of their genomes.

In several plant viruses, translational recoding events, including ribosomal frameshifting and stop codon readthrough, have been found to rely on long-range RNA–RNA interactions.

Multiple 5′-to-3′ base-pairing interactions facilitate genome circularization in flaviviruses, which has been proposed to reposition the 5′-bound RNA-dependent RNA polymerase (RdRp) to the initiation site of negative-strand synthesis at the 3′ terminus.

The long-distance interaction between two cis-acting replication elements in tombusviruses generates a bipartite RNA platform for the assembly of the replicase complex and repositions the internally bound RdRp to the 3′ terminus.

Tombusviruses also rely on several long-range interactions that mediate the premature termination of the RdRp during negative-strand synthesis that leads to transcription of subgenomic mRNAs (sgmRNAs).

In a coronavirus, an exceptionally long-range interaction, which spans ∼26,000 nucleotides, promotes polymerase repriming during the discontinuous template synthesis step of sgmRNA-N transcription.

A challenge for the future will be to determine how these long-range interactions are integrated and regulated in the complex context of viral RNA genomes.

Long-range intragenomic RNA–RNA interactions in the genomes of positive-strand RNA viruses involve direct nucleotide base pairing and can span distances of thousands of nucleotides. In this Review, Nicholson and White discuss recent insights into the structure and function of these genomic features and highlight their diverse roles in the gene expression and genome replication of positive-strand RNA viruses.

Positive-strand RNA viruses are important human, animal and plant pathogens that are defined by their single-stranded positive-sense RNA genomes. In recent years, it has become increasingly evident that interactions that occur between distantly positioned RNA sequences within these genomes can mediate important viral activities. These long-range intragenomic RNA–RNA interactions involve direct nucleotide base pairing and can span distances of thousands of nucleotides. In this Review, we discuss recent insights into the structure and function of these intriguing genomic features and highlight their diverse roles in the gene expression and genome replication of positive-strand RNA viruses.

The untranslated regions of classic swine fever virus RNA trigger apoptosis

Classical swine fever virus (CSFV) causes a broad range of disease in pigs, from acute symptoms including high fever and hemorrhages, to chronic disease or unapparent infection, depending on the virus strain. CSFV belongs to the genus Pestivirus of the family Flaviviridae. It carries a single-stranded positive-sense RNA genome. An internal ribosomal entry site (IRES) in the 5′ untranslated region (UTR) drives the translation of a single open reading frame encoding a 3898 amino acid long polypeptide chain. The open reading frame is followed by a 3′ UTR comprising four highly structured stem-loops. In the present study, a synthetic RNA composed of the 5′ and 3′ UTRs of the CSFV genome devoid of any viral coding sequence and separated by a luciferase gene cassette (designated 5′UTR-Luc-3′UTR) triggered apoptotic cell death as early as 4 h post-transfection. The apoptosis was measured by DNA laddering analysis, TUNEL assay, annexin-V binding determined by flow cytometry, and by analysis of caspase activation. Contrasting with this, only trace DNA laddering was observed in cells transfected with the individual 5′ or 3′ UTR RNA; even when the 5′ UTR and 3′ UTR were co-transfected as separate RNA molecules, DNA laddering did not reach the level induced by the chimeric 5′UTR-Luc-3′UTR RNA. Interestingly, RNA composed of the 5′UTR and of stem-loop I of the 3′UTR triggered much stronger apoptosis than the 5′ or 3′UTR alone. These results indicate that the 5′ and 3′ UTRs act together in cis induce apoptosis. We furthered obtained evidence that the UTR-mediated apoptosis required double-stranded RNA and involved translation shutoff possibly through activation of PKR.

Hepatitis C virus 3'UTR regulates viral translation through direct interactions with the host translation machinery

The 3′ untranslated region (3′UTR) of hepatitis C virus (HCV) messenger RNA stimulates viral translation by an undetermined mechanism. We identified a high affinity interaction, conserved among different HCV genotypes, between the HCV 3′UTR and the host ribosome. The 3′UTR interacts with 40S ribosomal subunit proteins residing primarily in a localized region on the 40S solvent-accessible surface near the messenger RNA entry and exit sites. This region partially overlaps with the site where the HCV internal ribosome entry site was found to bind, with the internal ribosome entry site-40S subunit interaction being dominant. Despite its ability to bind to 40S subunits independently, the HCV 3′UTR only stimulates translation in cis, without affecting the first round translation rate. These observations support a model in which the HCV 3′UTR retains ribosome complexes during translation termination to facilitate efficient initiation of subsequent rounds of translation.

Translational enhancing activity in 5' UTR of peste des petits ruminants virus fusion gene

The fusion gene of peste des petits ruminants virus (PPRV-F), a paramyxovirus, contains an unusual long 5' untranslated region (5' UTR) with a high GC content that is capable of folding into secondary structure proximally to the 5' cap. Sequence analysis further suggested that the proximal end of this UTR contains a nine-nucleotide sequence which could perfectly complement the 18S rRNA and might affect translation through mRNA-rRNA interaction. Based on these features, we examined the functional role of the proximal PPRV-F 5' UTR on translational efficiency compared with two other morbilliviruses. From reporter gene assays, PPRV-F 5' UTR functioned as a strong enhancer of translational efficiency independent of cell and gene specificity. Northern blot analysis of the accumulative RNA levels and mRNA stability suggested that elevated gene expression driven by PPRV-F 5' UTR was accompanied by an increased mRNA level and enhanced mRNA stability. Deletion analysis identified the complementary sequence and distal nucleotides necessary for the enhancing activity, and results suggest RNA structural conformation is important. Taken together, we conclude that the proximal PPRV-F 5' UTR functions as a translational enhancer by promoting translation efficiency and mRNA stability.