Jake Dunning

IFITM3 restricts the morbidity and mortality associated with influenza

The 2009 H1N1 influenza pandemic showed the speed with which a novel respiratory virus can spread and the ability of a generally mild infection to induce severe morbidity and mortality in a subset of the population. Recent in vitro studies show that the interferon-inducible transmembrane (IFITM) protein family members potently restrict the replication of multiple pathogenic viruses. Both the magnitude and breadth of the IFITM proteins’ in vitro effects suggest that they are critical for intrinsic resistance to such viruses, including influenza viruses. Using a knockout mouse model, we now test this hypothesis directly and find that IFITM3 is essential for defending the host against influenza A virus in vivo. Mice lacking Ifitm3 display fulminant viral pneumonia when challenged with a normally low-pathogenicity influenza virus, mirroring the destruction inflicted by the highly pathogenic 1918 ‘Spanish’ influenza. Similar increased viral replication is seen in vitro, with protection rescued by the re-introduction of Ifitm3. To test the role of IFITM3 in human influenza virus infection, we assessed the IFITM3 alleles of individuals hospitalized with seasonal or pandemic influenza H1N1/09 viruses. We find that a statistically significant number of hospitalized subjects show enrichment for a minor IFITM3 allele (SNP rs12252-C) that alters a splice acceptor site, and functional assays show the minor CC genotype IFITM3 has reduced influenza virus restriction in vitro. Together these data reveal that the action of a single intrinsic immune effector, IFITM3, profoundly alters the course of influenza virus infection in mouse and humans.

Experimental Treatment of Ebola Virus Disease with TKM-130803: A Single-Arm Phase 2 Clinical Trial

Background 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. Methods and Findings 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. Conclusions 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. Trial registration Pan African Clinical Trials Registry PACTR201501000997429

Antiviral combinations for severe influenza

Summary Observational data suggest that the treatment of influenza infection with neuraminidase inhibitors decreases progression to more severe illness, especially when treatment is started soon after symptom onset. However, even early treatment might fail to prevent complications in some patients, particularly those infected with novel viruses such as the 2009 pandemic influenza A H1N1, avian influenza A H5N1 virus subtype, or the avian influenza A H7N9 virus subtype. Furthermore, treatment with one antiviral drug might promote the development of antiviral resistance, especially in immunocompromised hosts and critically ill patients. An obvious strategy to optimise antiviral therapy is to combine drugs with different modes of action. Because host immune responses to infection might also contribute to illness pathogenesis, improved outcomes might be gained from the combination of antiviral therapy with drugs that modulate the immune response in an infected individual. We review available data from preclinical and clinical studies of combination antiviral therapy and of combined antiviral-immunomodulator therapy for influenza. Early-stage data draw attention to several promising antiviral combinations with therapeutic potential in severe infections, but there remains a need to substantiate clinical benefit. Combination therapies with favourable experimental data need to be tested in carefully designed aclinical trials to assess their efficacy.

Impaired Antibody-mediated Protection and Defective IgA B-Cell Memory in Experimental Infection of Adults with Respiratory Syncytial Virus

RATIONALE Despite relative antigenic stability, respiratory syncytial virus (RSV) reinfects throughout life. After more than 40 years of research, no effective human vaccine exists and correlates of protection remain poorly defined. Most current vaccine candidates seek to induce high levels of RSV-specific serum neutralizing antibodies, which are associated with reduced RSV-related hospitalization rates in observational studies but may not actually prevent infection. OBJECTIVES To characterize correlates of protection from infection and the generation of RSV-specific humoral memory to promote effective vaccine development. METHODS We inoculated 61 healthy adults with live RSV and studied protection from infection by serum and mucosal antibody. We analyzed RSV-specific peripheral blood plasmablast and memory B-cell frequencies and antibody longevity. MEASUREMENTS AND MAIN RESULTS Despite moderately high levels of preexisting serum antibody, 34 (56%) became infected, of whom 23 (68%) developed symptomatic colds. Prior RSV-specific nasal IgA correlated significantly more strongly with protection from polymerase chain reaction-confirmed infection than serum neutralizing antibody. Increases in virus-specific antibody titers were variable and transient in infected subjects but correlated with plasmablasts that peaked around Day 10. During convalescence, only IgG (and no IgA) RSV-specific memory B cells were detectable in peripheral blood. This contrasted with natural influenza infection, in which virus-specific IgA memory B cells were readily recovered. CONCLUSIONS This observed specific defect in IgA memory may partly explain the ability of RSV to cause recurrent symptomatic infections. If so, vaccines able to induce durable RSV-specific IgA responses may be more protective than those generating systemic antibody alone.

Experimental Treatment of Ebola Virus Disease with Brincidofovir

Background The nucleotide analogue brincidofovir was developed to prevent and treat infections caused by double-stranded DNA viruses. Based on in vitro data suggesting an antiviral effect against Ebola virus, brincidofovir was included in the World Health Organisation list of agents that should be prioritised for clinical evaluation in patients with Ebola virus disease (EVD) during the West African epidemic. Methods and Findings In this single-arm phase 2 trial conducted in Liberia, patients with laboratory-confirmed EVD (two months of age or older, enrolment bodyweight ≥50 kg) received oral brincidofovir 200 mg as a loading dose on day 0, followed by 100 mg brincidofovir on days 3, 7, 10, and 14. Bodyweight-adjusted dosing was used for patients weighing <50 kg at enrolment. The primary outcome was survival at Day 14 after the first dose of brincidofovir. Four patients were enrolled between 01 January 2015 and 31 January 2015. The trial was stopped following the decision by the manufacturer to terminate their program of development of brincidofovir for EVD. No Serious Adverse Reactions or Suspected Unexpected Serious Adverse Reactions were identified. All enrolled subjects died of an illness consistent with EVD. Conclusions Due to the small sample size it was not possible to determine the efficacy of brincidofovir for the treatment of EVD. The premature termination of the trial highlights the need to establish better practices for preclinical in-vitro and animal screening of therapeutics for potentially emerging epidemic infectious diseases prior to their use in patients. Trial Registration Pan African Clinical Trials Registry PACTR201411000939962

Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases

Abstract To end the largest known outbreak of Ebola virus disease (EVD) in West Africa and to prevent new transmissions, rapid epidemiological tracing of cases and contacts was required. The ability to quickly identify unknown sources and chains of transmission is key to ending the EVD epidemic and of even greater importance in the context of recent reports of Ebola virus (EBOV) persistence in survivors. Phylogenetic analysis of complete EBOV genomes can provide important information on the source of any new infection. A local deep sequencing facility was established at the Mateneh Ebola Treatment Centre in central Sierra Leone. The facility included all wetlab and computational resources to rapidly process EBOV diagnostic samples into full genome sequences. We produced 554 EBOV genomes from EVD cases across Sierra Leone. These genomes provided a detailed description of EBOV evolution and facilitated phylogenetic tracking of new EVD cases. Importantly, we show that linked genomic and epidemiological data can not only support contact tracing but also identify unconventional transmission chains involving body fluids, including semen. Rapid EBOV genome sequencing, when linked to epidemiological information and a comprehensive database of virus sequences across the outbreak, provided a powerful tool for public health epidemic control efforts.

Accumulation of Human-Adapting Mutations during Circulation of A(H1N1)pdm09 Influenza Virus in Humans in the United Kingdom

ABSTRACT The influenza pandemic that emerged in 2009 provided an unprecedented opportunity to study adaptation of a virus recently acquired from an animal source during human transmission. In the United Kingdom, the novel virus spread in three temporally distinct waves between 2009 and 2011. Phylogenetic analysis of complete viral genomes showed that mutations accumulated over time. Second- and third-wave viruses replicated more rapidly in human airway epithelial (HAE) cells than did the first-wave virus. In infected mice, weight loss varied between viral isolates from the same wave but showed no distinct pattern with wave and did not correlate with viral load in the mouse lungs or severity of disease in the human donor. However, second- and third-wave viruses induced less alpha interferon in the infected mouse lungs. NS1 protein, an interferon antagonist, had accumulated several mutations in second- and third-wave viruses. Recombinant viruses with the third-wave NS gene induced less interferon in human cells, but this alone did not account for increased virus fitness in HAE cells. Mutations in HA and NA genes in third-wave viruses caused increased binding to α-2,6-sialic acid and enhanced infectivity in human mucus. A recombinant virus with these two segments replicated more efficiently in HAE cells. A mutation in PA (N321K) enhanced polymerase activity of third-wave viruses and also provided a replicative advantage in HAE cells. Therefore, multiple mutations allowed incremental changes in viral fitness, which together may have contributed to the apparent increase in severity of A(H1N1)pdm09 influenza virus during successive waves. IMPORTANCE Although most people infected with the 2009 pandemic influenza virus had mild or unapparent symptoms, some suffered severe and devastating disease. The reasons for this variability were unknown, but the numbers of severe cases increased during successive waves of human infection in the United Kingdom. To determine the causes of this variation, we studied genetic changes in virus isolates from individual hospitalized patients. There were no consistent differences between these viruses and those circulating in the community, but we found multiple evolutionary changes that in combination over time increased the viruss ability to infect human cells. These adaptations may explain the remarkable ability of A(H1N1)pdm09 virus to continue to circulate despite widespread immunity and the apparent increase in severity of influenza over successive waves of infection.

Medical oaths and declarations

The newly qualified doctors of Imperial College School of Medicine recently adopted a ceremony in which they declare their commitment to assume the responsibilities and obligations of the medical profession. The decision to create a declaration ceremony was widely supported by the final year students and it reflects a recent resurgence in interest in medical oaths in the United Kingdom. 1 2 Some 98% of American 1 3 and nearly 50% of British medical students 1 4 swear some kind of oath, either on entry to medical school5 or at graduation.4 One reason why oaths are more common in America may be that American children are brought up to swear their allegiance to the flag, so the concept of affirming their beliefs is less alien than to British students. Oaths are neither a universal endeavour 3 4 nor a legal obligation, and they cannot guarantee morality. So why should doctors take an oath at all? In 1992 a BMA working party found that affirmation may strengthen a doctors resolve to behave with integrity in extreme circumstances. This group recommended that …

Open source clinical science for emerging infections

8 www.thelancet.com/infection Vol 14 January 2014 Emerging infections cause justifi able global concern. Current outbreaks of avian infl uenza A H7N9 and the Middle East respiratory syndrome (MERS) raise troubling memories of pandemic infl uenza and severe acute respiratory syndrome (SARS). With few mutations, these or other pathogens could evolve to cause widespread outbreaks. When new threats emerge, well established public health systems rapidly identify cases and evaluate sources, clinicians provide early descriptive case reports, and laboratories develop diagnostics and characterise pathogens. Clinical science is markedly less agile. We lack the tools to answer key questions rapidly. Who is susceptible, and why? What are the mechanisms of disease? What are the sites and dynamics of pathogen replication? How can early cases be identifi ed and stratifi ed? What is the clinical utility of new diagnostics? What treatments might work? Each emerging infection presents these fundamental questions. The method of answering them need not be reinvented from one infection to the next. If clinical scientists across the world were able to agree on methods and cooperate, the results of separate studies from diverse locations and conditions could be collated, allowing clinically useful conclusions to be reached from shared data. The International Severe Acute Respiratory and Emerging Infection Consortium (ISARIC) grew from the recognition that we have to do things diff erently, in the light of our experience during the epidemics of SARS, H5N1, and the 2009–10 infl uenza pandemic, but also regional epidemics of enterovirus 71, dengue, viral haemorrhagic fevers, and even during the rapid emergence of drug resistant malaria. We must motivate and equip individual investigators and networks around the world to work together to rapidly answer basic questions when new threats emerge. Academic credit and access to data and samples must be given to clinical investigators, who often recruit patients in extremely challenging circumstances. Unlike the existing model that prioritises independence, eff ective collaboration should be rewarded. The core materials needed to enrol patients must be freely available, making it as easy as possible for investigators at the front line. The core materials of clinical research—protocols, information sheets, consent forms, and case report forms—are analogous to the source code of computer software. In open-source software projects contributors receive recognition that builds their reputation within the software community. We propose a similar approach to clinical research, in parallel with the drive towards open access in academic publishing. Although community projects have a long history in other fi elds, individual recognition is required for scientists to obtain funding and promotion; to succeed, academic institutions, funders, journals, the clinical science and public health communities, and the public need to be in full support. To develop a consensus set of documentation, we engaged with investigators across countries and disciplines, in collaboration with WHO, in a systematic three-stage process: fi rst, to agree criteria by which to prioritise and stratify studies; second, to identify important unanswered questions relating to pathogenesis, susceptibility, and pharmacology in severe infection; and to allocate studies within a globally scalable framework. In the resulting protocol, research intensity is stratifi ed according to the local costs incurred. The lowest tiers have a minimum requirement for staff and resources to recruit a case (fi gure), enabling adaptation for use in places with diff ering resource levels, and also in diff erent phases of an outbreak. For example, early in an outbreak there are urgent questions that require Open source clinical science for emerging infections

Impact of the 2009 influenza pandemic

One year on from the start of the 21st centurys first influenza pandemic, it is a good time to take stock of how the outbreak evolved and what has been learned. Although we now know that many infections were mild or inapparent, it is important not to forget the severe disease that it sometimes caused, and may still cause, in future winters. During April 2009, reports from Mexico provided a worrying picture of unusually severe influenza in large numbers of healthy people including healthcare workers.1 The impact on hospitals was particularly marked with up to one in four specialist beds being occupied by patients with influenza, often needing highly specialised care and mechanical ventilation. Medical resources were exceeded by demand, and elective admissions and surgery halted; transmission to staff and to other patients was common, placing specialised nursing care, consumables, ventilators, drugs and containment facilities under great pressure. Once cases began to appear in UK schools in May 2009, an intensive cooperative campaign of quarantine and antiviral prophylaxis was mounted by the Heath Protection Agency, the Department of Health and the NHS. Antiviral drugs have not been used in this way in previous pandemics; although it was unlikely that the spread of influenza could be halted, it was important to gather information about the pattern and severity of disease and to slow the spread, buying time for vaccine development and capacity building. Despite the public health campaign, the numbers of cases increased in London and the West Midlands, putting considerable strain on primary care. By 2 July, case numbers were rising sharply in most parts of the UK and containment measures no longer seemed appropriate. Routine antiviral prophylaxis was discontinued and a telephone helpline was launched on 23 July.2 Call centres took a history according to defined algorithms …