9 Distribution of sequence reads mapping to the EBOV genome before and after randomised sub sampling. key questions remained including establishing if monoclonal antibody therapy was effective in humans with severe EVD, whether virus escape mutants were selected during treatment, and what is the potential mechanism(s) of persistence. This was made possible through longitudinal samples taken from a UK patient with EVD. Methods Several different sample types, plasma and cerebrospinal fluid, were collected and sequenced using Illumina-based RNAseq. Sequence reads were mapped both to EBOV and the human genome and differential gene expression analysis used to identify changes in the abundance of gene transcripts as infection progressed. Digital Cell Quantitation analysis was used to predict the immune phenotype in samples derived from blood. Results The findings were compared to equivalent data from West African patients. The study found that both virus and host markers were predictive of a fatal outcome. This suggested HERPUD1 that the extensive supportive care, and most likely the application of the medical countermeasure ZMab (a monoclonal antibody cocktail), contributed to survival of the UK patient. The switch from progression to a fatal outcome to a survival outcome could be seen in both the viral and host markers. The UK patient also suffered a recrudescence infection 10?months after the initial infection. Analysis of the sequencing data indicated that the virus entered a period of reduced or minimal replication, rather than other potential mechanisms of persistencesuch as defective interfering genomes. Conclusions The data showed that comprehensive supportive care and the application of medical countermeasures are worth pursuing despite an initial unfavourable prognosis. Background Ebola virus disease (EVD) has a high case fatality rate and is caused by infection of humans with Ebola virus (EBOV) [1]. Once confined to isolated outbreaks, West Africa witnessed the largest ever EBOV outbreak between 2013 and 2016 [2] and a large outbreak then occurred in the Democratic Republic of Congo [3]. The outcome of infection (death/survival) in EVD may be influenced by several factors including viral load [4, 5], the host BNC105 response [6, 7] and the presence of other infections at the time of acute symptoms [8]. Generally, at the time of diagnosis, for the West African outbreak, patients with higher viral loads (as measured by RT-qPCR) had a BNC105 poorer prognosis than patients with lower viral loads [5]. RNA sequencing of blood samples taken by the European Mobile Laboratory (EMLab) from acute patients at the time of presentation to a treatment centre during the West African outbreak indicated that the blood transcriptome was different between individuals in the acute phase who went on to have a fatal infection or survived [6, 7]. This included stronger upregulation of interferon signalling and acute phase responses in patients progressing to a fatal infection and increased NK-cell populations in patients who went BNC105 on to survive infection. During the West African outbreak, several medical countermeasures were used and evaluated both in Africa and on repatriated health care works including favipiravir, convalescent plasma and monoclonal antibodies targeted against the EBOV glycoprotein (GP) [9C11]. Whilst the presence of EBOV in seminal fluid was described in 1977 [12] and shown to persist after non-detectable amounts were found in the blood [12], the West African outbreak illustrated that a number of patients had recrudescent infections. This often correlated with persistence of the virus in what can be described as immune-privileged sites including the testes [13] and the eye [14]. Analysis of EBOV evolution rates in semen suggested a mechanism of persistence rather than latency and indicated that EBOV replication continued during convalescence [15]. Thus, several key questions remained including establishing if monoclonal antibody therapy was effective in humans with severe EVD, whether virus escape mutants were selected during treatment, and what is the potential mechanism(s) of persistence. Such a study was made possible in a healthcare worker in the UK with EVD (referred to as UK2), who had recently returned from Sierra Leone and who developed relapse of EVD in association with meningoencephalitis 10?months after initial presentation [16]. Longitudinal and recrudescence blood, plasma, and cerebral spinal fluid samples were taken from UK2; RNA was extracted and sequenced. This provided a unique opportunity to study both EBOV population genetics and BNC105 the host response over the course of EVD and to probe the effectiveness of antibody-based interventions given as part of extensive supportive care. The peak viral load in UK2 during the early course of infection and together with host markers was predictive of a fatal outcome when compared to equivalent Guinean patients. Our study found little change.