► The Tm of a TaqMan probe employed in a widely used RT-qPCR for HEV was calculated. ► Calculations showed that the melting temperature (Tm) of the probe was suboptimal. ► A Minor Groove Binder ...version of probe was synthesised in order to increase its Tm. ► MGB probe detected HEV in 6 samples that were negative with the unmodified probe. ► False negative results were due to a C→T point mutation in the probe binding region.
Hepatitis E virus (HEV) is a major cause of acute viral hepatitis in many parts of the developing world. It is responsible for both sporadic infections and large scale epidemics and may be associated with significant mortality during pregnancy. Over the past two decades many serological and nucleic acid based diagnostic tests for HEV have been developed, including several reverse transcription real-time polymerase chain reaction assays (RT-qPCR). One of the most widely used of these RT-qPCRs is that developed by Jothikumar and colleagues (Journal of Virological Methods 2006, 131, 65–71). Whilst reviewing this assay we calculated the predicted melting temperature of its TaqMan probe and consequently synthesised a minor groove binder (MGB) version in order to increase its hybridisation stability. In this report the performance of the original unmodified probe is compared with that of the MGB-modified version. We demonstrate that the MGB-modified probe detected HEV RNA in plasma samples from six patients with serologically confirmed hepatitis E in whom the unmodified probe had failed to detect HEV RNA. Sequence analysis of the ORF3 segment targeted by the RT-qPCR was possible in 4 of the 6 patients and revealed an identical C→T single nucleotide mutation in the probe binding region in each case.
We report the molecular investigations of a large influenza A(H3N2) outbreak, in a season characterised by sharp increase in influenza admissions since December 2016. Analysis of haemagglutinin (HA) ...sequences demonstrated co-circulation of multiple clades (3C.3a, 3C.2a and 3C.2a1). Most variants fell into a novel subclade (proposed as 3C.2a2); they possessed four unique amino acid substitutions in the HA protein and loss of a potential glycosylation site. These changes potentially modify the H3N2 strain antigenicity.
Background
The extent of transmission of influenza in hospital settings is poorly understood. Next generation sequencing may improve this by providing information on the genetic relatedness of viral ...strains.
Objectives
We aimed to apply next generation sequencing to describe transmission in hospital and compare with methods based on routinely‐collected data.
Methods
All influenza samples taken through routine care from patients at University College London Hospitals NHS Foundation Trust (September 2012 to March 2014) were included. We conducted Illumina sequencing and identified genetic clusters. We compared nosocomial transmission estimates defined using classical methods (based on time from admission to sample) and genetic clustering. We identified pairs of cases with space‐time links and assessed genetic relatedness.
Results
We sequenced influenza sampled from 214 patients. There were 180 unique genetic strains, 16 (8.8%) of which seeded a new transmission chain. Nosocomial transmission was indicated for 32 (15.0%) cases using the classical definition and 34 (15.8%) based on genetic clustering. Of the 50 patients in a genetic cluster, 11 (22.0%) had known space‐time links with other cases in the same cluster. Genetic distances between pairs of cases with space‐time links were lower than for pairs without spatial links (P < .001).
Conclusions
Genetic data confirmed that nosocomial transmission contributes significantly to the hospital burden of influenza and elucidated transmission chains. Prospective next generation sequencing could support outbreak investigations and monitor the impact of infection and control measures.
This study aimed to assess training of Senior House Officer-grade equivalent doctors in postgraduate surgical training or service (SHO-DIPST) in surgical specialties across the United Kingdom (UK), ...against nationally agreed Joint Committee on Surgical Training Quality Indicators (JCST QIs). Specific recommendations are made, with a view to improving quality of training, workforce retention and recruitment to Higher Surgical Training.
Prospective, observational, multicentre study conducted by the Association of Surgeons in Training, using the UK National Research Collaborative model. Any centres in the UK providing acute surgical services were eligible. SHO-DIPST with a permanent contract, on out-of-hours ‘on-call rota’ were included across four, one-week data capture periods (September to October 2016, February to March 2017). Adherence to five quality indicators was reported using descriptive statistics. P-values were calculated using Student's t-test for continuous data, with a 5% level of significance.
2569 SHO-DIPST were included from all ten surgical specialties in 141 NHS trusts across all 16 Local Education and Training Boards in the UK. 960 SHO-DIPST were in registered ‘training’ posts (37.3%). The median number of SHO-DIPST per rota was 7.0 (IQR 5.0–9.0). Adherence to the five included JCST QIs ranged from 6.0 to 53.1%. Only four SHO-DIPST posts across the study population met all five JCST QIs (0.3%). The total number of training sessions was higher for those in registered training posts (p < 0.001), with significant specialty and regional variation.
Only four early years postgraduate surgical training posts in the UK meet nationally approved minimum quality standards. Specific recommendations are made to improve training in this cohort and to bolster recruitment and retention into Higher Surgical Training.
•Four early years postgraduate surgical training posts met national quality indicators.•There exists significant inter-specialty and regional variation in surgical training.•Half of doctors had no exposure to theatre or clinic during the study week.•This is the first study to assess sessional activities against training quality standards.•Significant efforts are required universally to improve training standards.
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