Genome replication in picornaviruses is catalyzed by a virally encoded RNA-dependent RNA polymerase, termed 3D. The enzyme performs this operation, together with other viral and probably host proteins, in the cytoplasm of their host cells. The crystal structure of the 3D polymerase of foot-and-mouth disease virus, one of the most important animal pathogens, has been determined unliganded and bound to a template-primer RNA decanucleotide. The enzyme folds in the characteristic fingers, palm and thumb subdomains, with the presence of an NH₂-terminal segment that encircles the active site. In the complex, several conserved amino acid side chains bind to the template-primer, likely mediating the initiation of RNA synthesis. The structure provides essential information for studies on RNA replication and the design of antiviral compounds.

Biological adaptive systems share some common features: variation among their constituent elements and continuity of core information. Some of them, such as the immune system, are endowed with memory of past events. In this study we provide direct evidence that evolving viral quasispecies possess a molecular memory in the form of minority components that populate their mutant spectra. The experiments have involved foot-and-mouth disease virus populations with known evolutionary histories. The composition and behavior of the viral population in response to a selective constraint were influenced by past evolutionary history in a way that could not be predicted from examination of consensus nucleotide sequences of the viral populations. The molecular memory of the viral quasispecies influenced both the nature and the intensity of the response of the virus to a selective constraint.

TKM-130803, a small interfering RNA lipid nanoparticle product, has been developed for the treatment of Ebola virus disease (EVD), but its efficacy and safety in humans has not been evaluated. In this single-arm phase 2 trial, adults with laboratory-confirmed EVD received 0.3 mg/kg of TKM-130803 by intravenous infusion once daily for up to 7 d. On days when trial enrolment capacity was reached, patients were enrolled into a concurrent observational cohort. The primary outcome was survival to day 14 after admission, excluding patients who died within 48 h of admission. After 14 adults with EVD had received TKM-130803, the pre-specified futility boundary was reached, indicating a probability of survival to day 14 of ≤0.55, and enrolment was stopped. Pre-treatment geometric mean Ebola virus load in the 14 TKM-130803 recipients was 2.24 × 10⁹ RNA copies/ml plasma (95% CI 7.52 × 10⁸, 6.66 × 10⁹). Two of the TKM-130803 recipients died within 48 h of admission and were therefore excluded from the primary outcome analysis. Of the remaining 12 TKM-130803 recipients, nine died and three survived. The probability that a TKM-130803 recipient who survived for 48 h will subsequently survive to day 14 was estimated to be 0.27 (95% CI 0.06, 0.58). TKM-130803 infusions were well tolerated, with 56 doses administered and only one possible infusion-related reaction observed. Three patients were enrolled in the observational cohort, of whom two died. Administration of TKM-130803 at a dose of 0.3 mg/kg/d by intravenous infusion to adult patients with severe EVD was not shown to improve survival when compared to historic controls. Pan African Clinical Trials Registry PACTR201501000997429 Ebola virus disease (EVD) is a frequently fatal disease that first appeared in human populations in 1976 in central Africa and that recently caused thousands of deaths in West Africa. Ebola virus is transmitted to people from wild animals and spreads in human populations through contact with the bodily fluids (including blood, saliva, and urine) and organs of infected people and through contact with bedding and other materials contaminated with bodily fluids. The symptoms of EVD, which start 2–21 days after infection, include fever, headache, vomiting, diarrhea, and internal and external bleeding. Infected individuals are not infectious until they develop symptoms, but they remain infectious as long as their bodily fluids contain virus, which can be several weeks. Infectious virus can persist in the semen of male survivors and suspected male-to-female sexual transmission was reported to have occurred five months after resolution of EVD. In West Africa supportive care—given under strict isolation conditions to prevent the spread of the virus—may improve survival, but there is no proven, specific treatment for EVD. Several potential treatments for EVD have looked promising in animal studies, including TKM-130803, a drug that prevents the production of two essential viral proteins. In rhesus monkeys, the active component of TKM-130803 provided 100% protection against Makona Ebola virus, the virus variant responsible for the West African EVD outbreak. Here, the researchers evaluate the effectiveness of TKM-130803 in a single-arm phase 2 clinical trial. During the West African EVD outbreak, experts designed the RAPIDE (Rapid Assessment of Potential Interventions and Drugs for Ebola) clinical trial platform to speed up the development of treatments for EVD. Using this platform, prioritised drugs go straight into a single-arm phase 2 trial in which people with EVD are administered a selected drug to generate early evidence of the drug’s effectiveness or ineffectiveness. For the assessment of the TKM-130803, a modified RAPIDE approach identifies evidence of lack of effectiveness in the phase 2 trial, by assessing whether a “futility” boundary—a pre-specified survival probability threshold at 14 days after admission—is reached. Adults with laboratory-confirmed EVD volunteered to participate in the trial, which was undertaken in Sierra Leone. Trial participants were given TKM-130803 once daily by intravenous infusion for up to seven days, in addition to supportive care. The primary outcome was survival to 14 days after admission, excluding patients who died within 48 hours of admission. Using historical data on survival rates for 1,820 people with EVD, the researchers designed their trial so that if the survival probability of the trial participants was greater than 0.55 (that is, if the chance of a patient being alive after 14 days was greater than 55%), TKM-130803 would be regarded as promising and worthy of further evaluation; if the survival probability of the participants was less than or equal to 0.55, then the futility boundary would be reached and enrollment stopped. After 14 adults had received TKM-130803, the pre-specified futility boundary was reached, and enrollment was stopped. Two patients who received TKM-130803 died within 48 hours of admission and were excluded from the primary outcome analysis. Of the remaining patients who received TKM-130803, nine died and three survived. The researchers estimated that TKM-130803 recipients who survived for 48 hours after being admitted had a probability of surviving to 14 days of 0.27. These findings show that TKM-130803 given once daily at the dose used in this trial did not improve survival in patients with EVD compared to historic controls. This result contrasts with the protective effect of TKM-130803 and related formulations in non-human primates “challenged” (infected) with Ebola virus. One reason for this difference may be that, whereas in the animal studies, experimental drugs were given soon after viral challenge, in the phase 2 trial, the drug was given when the patients had advanced disease. That is, the failure of TKM-130803 to achieve a survival probability exceeding 0.55 in this study may be because the experimental drug had an insufficient antiviral effect in the face of the high viral loads and existing organ damage in these patients. In patients with advanced disease, it could be that the target survival rate was set too high to detect a small or even moderate beneficial effect of TKM-130803. Thus, further work is needed to assess whether the lack of effectiveness seen in this trial is generalizable to other patient subgroups (for example, patients with less advanced disease and lower viral loads) in other treatment settings. This list of resources contains links that can be accessed when viewing the PDF on a device or via the online version of the article at http://dx.doi.org/10.1371/journal.pmed.1001997.