The discovery is reported of a small molecule drug, GS-5734, which has antiviral activity against Ebola virus and other filoviruses, and is capable of providing post-exposure therapeutic protection against lethal disease in 100% of drug-treated nonhuman primates infected with Ebola virus; the drug targets viral RNA polymerase and can distribute to sanctuary sites (such as testes, eyes and brain), suggesting that it may be able to clear persistent virus infection. These authors report the discovery of a small-molecule drug, GS-5734, which has antiviral activity against Ebola and other filoviruses, and is capable of providing post-exposure protection against Ebola virus in 100% of infected macaques tested. Now in clinical trials ( http://go.nature.com/PEW2Oi ), the drug targets the viral RNA-dependent RNA polymerase and is readily scalable for future outbreaks. GS-5734 is able to distribute to sanctuary sites for viral replication including the testes, eye and brain, offering the hope that this drug may also be able to clear recrudescent and persistent virus infection. The most recent Ebola virus outbreak in West Africa, which was unprecedented in the number of cases and fatalities, geographic distribution, and number of nations affected, highlights the need for safe, effective, and readily available antiviral agents for treatment and prevention of acute Ebola virus (EBOV) disease (EVD) or sequelae1. No antiviral therapeutics have yet received regulatory approval or demonstrated clinical efficacy. Here we report the discovery of a novel small molecule GS-5734, a monophosphoramidate prodrug of an adenosine analogue, with antiviral activity against EBOV. GS-5734 exhibits antiviral activity against multiple variants of EBOV and other filoviruses in cell-based assays. The pharmacologically active nucleoside triphosphate (NTP) is efficiently formed in multiple human cell types incubated with GS-5734 in vitro, and the NTP acts as an alternative substrate and RNA-chain terminator in primer-extension assays using a surrogate respiratory syncytial virus RNA polymerase. Intravenous administration of GS-5734 to nonhuman primates resulted in persistent NTP levels in peripheral blood mononuclear cells (half-life, 14 h) and distribution to sanctuary sites for viral replication including testes, eyes, and brain. In a rhesus monkey model of EVD, once-daily intravenous administration of 10 mg kg−1 GS-5734 for 12 days resulted in profound suppression of EBOV replication and protected 100% of EBOV-infected animals against lethal disease, ameliorating clinical disease signs and pathophysiological markers, even when treatments were initiated three days after virus exposure when systemic viral RNA was detected in two out of six treated animals. These results show the first substantive post-exposure protection by a small-molecule antiviral compound against EBOV in nonhuman primates. The broad-spectrum antiviral activity of GS-5734 in vitro against other pathogenic RNA viruses, including filoviruses, arenaviruses, and coronaviruses, suggests the potential for wider medical use. GS-5734 is amenable to large-scale manufacturing, and clinical studies investigating the drug safety and pharmacokinetics are ongoing.

The large polymerase subunit (L) of non-segmented negative strand RNA viruses transcribes viral mRNAs and replicates the viral genome. Studies with VSV have shown that conserved region V (CRV) of the L protein is part of the capping domain. However, CRV folds over and protrudes into the polymerization domain, suggesting that it might also have a role in RNA synthesis. In this study, the role of respiratory syncytial virus (RSV) CRV was evaluated using single amino acid substitutions and a small molecule inhibitor called BI-D. Effects were analyzed using cell-based minigenome and in vitro biochemical assays. Several amino acid substitutions inhibited production of capped, full-length mRNA and instead resulted in accumulation of short transcripts of approximately 40 nucleotides in length, confirming that RSV CRV has a role in capping. In addition, all six variants tested were either partially or completely defective in RNA replication. This was due to an inability of the polymerase to efficiently elongate the RNA within the promoter region. BI-D also inhibited transcription and replication. In this case, polymerase elongation activity within the promoter region was enhanced, such that the small RNA transcribed from the promoter was not released and instead was elongated past the first gene start signal. This was accompanied by a decrease in mRNA initiation at the first gene start signal and accumulation of aberrant RNAs of varying length. Thus, in addition to its function in mRNA capping, conserved region V modulates the elongation properties of the polymerase to enable productive transcription and replication to occur. Respiratory syncytial virus (RSV) is a leading cause of respiratory illness in infants, elderly, and immunocompromised individuals, yet treatment is limited to supportive medical care. The large polymerase protein (L) of RSV is essential for transcribing viral mRNAs and replicating the genome, and is an attractive target for antiviral intervention. Previous studies from related viruses have shown that a region of the L protein co-transcriptionally adds a cap to nascent mRNAs. In this study, we showed that perturbation of this region of the RSV L protein resulted in capping failure, as expected. In addition, we found that this region altered how efficiently the polymerase could elongate the RNA, impairing recognition of essential signals. Thus, this region of the RSV L protein has more than one function during viral multiplication, making it a particularly appealing target for antiviral development.

The ribonucleocapsid complex of respiratory syncytial virus (RSV) is responsible for both viral mRNA transcription and viral replication during infection, though little is known about how this dual function is achieved. Here, we report the use of a recombinant RSV virus with a FLAG-tagged large polymerase protein, L, to characterize and localize RSV ribonucleocapsid structures during the early and late stages of viral infection. Through proximity ligation assays and super-resolution microscopy, viral RNA and proteins in the ribonucleocapsid complex were revealed to dynamically rearrange over time, particularly between 6 and 8 hours post infection, suggesting a connection between the ribonucleocapsid structure and its function. The timing of ribonucleocapsid rearrangement corresponded with an increase in RSV genome RNA accumulation, indicating that this rearrangement is likely involved with the onset of RNA replication and secondary transcription. Additionally, early overexpression of RSV M2-2 from in vitro transcribed mRNA was shown to inhibit virus infection by rearranging the ribonucleocapsid complex. Collectively, these results detail a critical understanding into the localization and activity of RSV L and the ribonucleocapsid complex during RSV infection. Respiratory syncytial virus is a common respiratory disease among children under the age of five. Yearly, approximately three million children infected require hospitalization for treatment. However, no vaccine or effective antiviral treatment for respiratory syncytial virus yet exists. Understanding how respiratory syncytial virus replicates in cells will provide key knowledge for the development of more effective countermeasures. Here, we investigated the interactions between the large protein subunit of the respiratory syncytial virus polymerase, which is responsible for viral mRNA synthesis and replication, and other viral proteins during infection, as well as the localization of the large protein subunit over time in key viral structures. Our study provides new insights into the localization and activity of the respiratory syncytial virus polymerase, and suggests ribonucleocapsid complex rearrangement plays a key role in the function of the respiratory syncytial virus polymerase in replication of the virus, leading to a better understanding of respiratory syncytial virus biology.

The respiratory syncytial virus (RSV) RNA dependent RNA polymerase (RdRp) initiates two RNA synthesis processes from the viral promoter: genome replication from position 1U and mRNA transcription from position 3C. Here, we examined the mechanism by which a single promoter can direct initiation from two sites. We show that initiation at 1U and 3C occurred independently of each other, and that the same RdRp was capable of precisely selecting the two sites. The RdRp preferred to initiate at 3C, but initiation site selection could be modulated by the relative concentrations of ATP versus GTP. Analysis of template mutations indicated that the RdRp could bind ATP and CTP, or GTP, independently of template nucleotides. The data suggest a model in which innate affinity of the RdRp for particular NTPs, coupled with a repeating element within the promoter, allows precise initiation of replication at 1U or transcription at 3C.

Respiratory syncytial virus (RSV) is a major cause of respiratory disease in infants and the elderly. RSV is a non-segmented negative strand RNA virus. The viral M2-1 protein plays a key role in viral transcription, serving as an elongation factor to enable synthesis of full-length mRNAs. M2-1 contains an unusual CCCH zinc-finger motif that is conserved in the related human metapneumovirus M2-1 protein and filovirus VP30 proteins. Previous biochemical studies have suggested that RSV M2-1 might bind to specific virus RNA sequences, such as the transcription gene end signals or poly A tails, but there was no clear consensus on what RSV sequences it binds. To determine if M2-1 binds to specific RSV RNA sequences during infection, we mapped points of M2-1:RNA interactions in RSV-infected cells at 8 and 18 hours post infection using crosslinking immunoprecipitation with RNA sequencing (CLIP-Seq). This analysis revealed that M2-1 interacts specifically with positive sense RSV RNA, but not negative sense genome RNA. It also showed that M2-1 makes contacts along the length of each viral mRNA, indicating that M2-1 functions as a component of the transcriptase complex, transiently associating with nascent mRNA being extruded from the polymerase. In addition, we found that M2-1 binds specific cellular mRNAs. In contrast to the situation with RSV mRNA, M2-1 binds discrete sites within cellular mRNAs, with a preference for A/U rich sequences. These results suggest that in addition to its previously described role in transcription elongation, M2-1 might have an additional role involving cellular RNA interactions.

Norovirus is a leading cause of acute gastroenteritis globally, with infections in older adults associated with heightened severity and increased risk of mortality. Currently, no licensed vaccines are available to prevent norovirus infection. We developed an orally administered vaccine tablet (VXA-G1.1-NN) that delivers a nonreplicating adenoviral vector expressing norovirus GI.1 major capsid protein VP1 to the small intestine. Here, we report safety and immunogenicity results of a randomized, double-blind, placebo-controlled clinical trial (NCT04854746) that investigated the oral administration of VXA-G1.1-NN in two groups of healthy older adults aged 55 to 65 and 66 to 80 years. VXA-G1.1-NN was administered orally at three dose levels by prime and boost, 28 days apart. Immunization was well tolerated regardless of dose, with mild to moderate reported solicited symptoms and no related serious or grade 3 adverse events. Oral delivery of VXA-G1.1-NN elicited VP1-specific serum immunoglobulin G (IgG) and IgA and functional antibodies in a dose-dependent manner 28 days postvaccination and remained above baseline for 210 days. Moreover, robust circulating VP1-specific IgA antibody-secreting cells were detected 1 week postvaccination along with IgA ⁺ plasmablasts expressing the mucosal-homing marker α4β7. VP1-specific IgA increased in saliva and nasal lining fluid 28 days postvaccination in both age groups and remained above baseline concentrations through 210 days, demonstrating durable mucosal responses. This clinical trial established that oral administration of VXA-G1.1-NN is safe, well tolerated, and induces robust systemic and mucosal immune responses in adults up to 80 years old.