Paediatric acute hepatitis of unknown aetiology: a national investigation and adenoviraemia case-control study in the UK

BACKGROUND

An increase in acute severe hepatitis of unknown aetiology in previously healthy children in the UK in March, 2022, triggered global case-finding. We aimed to describe UK epidemiological investigations of cases and their possible causes.

METHODS

We actively surveilled unexplained paediatric acute hepatitis (transaminase >500 international units per litre) in children younger than 16 years presenting since Jan 1, 2022, through notifications from paediatricians, microbiologists, and paediatric liver units; we collected demographic, clinical, and exposure information. Then, we did a case-control study to investigate the association between adenoviraemia and other viruses and case-status using multivariable Firth penalised logistic regression. Cases aged 1-10 years and tested for adenovirus were included and compared with controls (ie, children admitted to hospital with an acute non-hepatitis illness who had residual blood samples collected between Jan 1 and May 28, 2022, and without known laboratory-confirmed diagnosis or previous adenovirus testing). Controls were frequency-matched on sex, age band, sample months, and nation or supra-region with randomised selection. We explored temporal associations between frequency of circulating viruses identified through routine laboratory pathogen surveillance and occurrence of cases by linear regression. SARS-CoV-2 seropositivity of cases was examined against residual serum from age-matched clinical comparison groups.

FINDINGS

Between Jan 1 and July 4, 2022, 274 cases were identified (median age 3 years [IQR 2-5]). 131 (48%) participants were male, 142 (52%) were female, and one (<1%) participant had sex data unknown. Jaundice (195 [83%] of 235) and gastrointestinal symptoms (202 [91%] of 222) were common. 15 (5%) children required liver transplantation and none died. Adenovirus was detected in 172 (68%) of 252 participants tested, regardless of sample type; 137 (63%) of 218 samples were positive for adenovirus in the blood. For cases that were successfully genotyped, 58 (81%) of 72 had Ad41F, and 57 were identified as positive via blood samples (six of these were among participants who had undergone a transplant). In the case-control analysis, adenoviraemia was associated with hepatitis case-status (adjusted OR 37·4 [95% CI 15·5-90·3]). Increases in the detection of adenovirus from faecal samples, but not other infectious agents, in routine laboratory pathogen surveillance correlated with hepatitis cases 4 weeks later, which independently suggested an association (β 0·06 [95% CI 0·02-0·11]). No association was identified for SARS-CoV-2 antibody seropositivity.

INTERPRETATION

We observed an association between adenovirus 41F viraemia and paediatric acute hepatitis. These results can inform diagnostic testing recommendations, clinical management, and exploratory in vitro or clinical studies of paediatric acute hepatitis of unknown aetiology. The role of potential co-factors, including other viruses and host susceptibility, requires further investigation.

FUNDING

None.

Evaluating the cost implications of integrating SARS-CoV-2 genome sequencing for infection prevention and control investigation of nosocomial transmission within hospitals

BACKGROUND

The COG-UK hospital-onset COVID-19 infection (HOCI) trial evaluated the impact of SARS-CoV-2 whole-genome sequencing (WGS) on acute infection, prevention, and control (IPC) investigation of nosocomial transmission within hospitals.

AIM

To estimate the cost implications of using the information from the sequencing reporting tool (SRT), used to determine likelihood of nosocomial infection in IPC practice.

METHODS

A micro-costing approach for SARS-CoV-2 WGS was conducted. Data on IPC management resource use and costs were collected from interviews with IPC teams from 14 participating sites and used to assign cost estimates for IPC activities as collected in the trial. Activities included IPC-specific actions following a suspicion of healthcare-associated infection (HAI) or outbreak, as well as changes to practice following the return of data via SRT.

FINDINGS

The mean per-sample costs of SARS-CoV-2 sequencing were estimated at £77.10 for rapid and £66.94 for longer turnaround phases. Over the three-month interventional phases, the total management costs of IPC-defined HAIs and outbreak events across the sites were estimated at £225,070 and £416,447, respectively. The main cost drivers were bed-days lost due to ward closures because of outbreaks, followed by outbreak meetings and bed-days lost due to cohorting contacts. Actioning SRTs, the cost of HAIs increased by £5,178 due to unidentified cases and the cost of outbreaks decreased by £11,246 as SRTs excluded hospital outbreaks.

CONCLUSION

Although SARS-CoV-2 WGS adds to the total IPC management cost, additional information provided could balance out the additional cost, depending on identified design improvements and effective deployment.

HTLV seroprevalence in people using HIV pre-exposure prophylaxis in England

OBJECTIVES

HTLV-1 is predominantly a sexually-transmitted infection but testing is not mentioned in HIV-PrEP guidelines. We ascertained HTLV-1/HTLV-2 seroprevalence amongst HIV-PrEP users in England.

METHODS

An unlinked anonymous seroprevalence study.

RESULTS

Amongst 2015 HIV-PrEP users, 95% were men, 76% of white ethnicity and 83% had been born in Europe. There were no HTLV-1/HTLV-2 seropositive cases (95% confidence interval 0% - 0.18%).

CONCLUSIONS

There were no HTLV positive cases, likely reflecting the demographic of mostly white and European-born individuals. Similar studies are needed worldwide to inform public health recommendations for HIV-PrEP using populations, particularly in HTLV-endemic settings.

Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: multicenter, prospective study

Background: Viral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings.

Methods: We conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data-collection period, followed by intervention periods comprising 8 weeks of 'rapid' (<48h) and 4 weeks of 'longer-turnaround' (5-10 day) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital onset COVID-19 infections (HOCIs; detected ≥48h from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on incidence of probable/definite hospital-acquired infections (HAIs) was evaluated.

Results: A total of 2170 HOCI cases were recorded from October 2020-April 2021, corresponding to a period of extreme strain on the health service, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (incidence rate ratio 1.60, 95%CI 0.85-3.01; P=0.14) or rapid (0.85, 0.48-1.50; P=0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8% and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2% and 11.6% of cases where the report was returned. In a 'per-protocol' sensitivity analysis there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days. Capacity to respond effectively to insights from sequencing was breached in most sites by the volume of cases and limited resources.

Conclusion: While we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days.

Funding: COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) [grant code: MC_PC_19027], and Genome Research Limited, operating as the Wellcome Sanger Institute.

Clinical trial number: ClinicalTrials.gov Identifier: NCT04405934.

Evaluation of the artus® Prep&Amp UM RT-PCR for detection of SARS-CoV-2 from nasopharyngeal swabs without prior nucleic acid eluate extraction

Here we describe a retrospective clinical evaluation of the QIAGEN artus® SARS-CoV-2 Prep&Amp UM RT-PCR assay that detects SARS-CoV-2 RNA without the need for a nucleic acid eluate extraction procedure. Using Roche SARS-CoV-2 RT-PCR on the cobas® 8800 platform as a reference standard, a total of 225 confirmed SARS-CoV-2 positive and 320 negative nasopharyngeal swabs in viral transport media, were used to evaluate the artus® assay. Using the RT-PCR cycle threshold as a semi-quantitative marker of viral load, an assessment of over 370,000 SARS-CoV-2 RT-PCR positive results was used in the design of the reference positive specimen cohort. The viral load of all reference positive specimens used in the evaluation was a unique and accurate representation of the range and levels of SARS-CoV-2 positivity observed over a 13-month period of the COVID-19 pandemic. The artus® RT-PCR detects the presence of SARS-CoV-2 RNA, an internal control, and the human RNase P gene to ensure specimen quality. The diagnostic sensitivity of artus® was 92.89% with a specificity of 100%. To assess the analytical sensitivity, a limit of detection was performed using the 1^st WHO NIBSC SARS-CoV-2 international standard, recording a 95% LOD of 1.1 × 10³ IU/ml. The total invalid rate of specimens was 7.34% due to a lack of detectable RNase P (C_t >35). The artus® SARS-CoV-2 Prep&Amp UM RT-PCR assay is a new rapid RT-PCR assay, which may be considered to produce acceptable levels of diagnostic sensitivity and specificity whilst potentially halving the laboratory processing time.

Diagnostic accuracy of loop-mediated isothermal amplification coupled to nanopore sequencing (LamPORE) for the detection of SARS-CoV-2 infection at scale in symptomatic and asymptomatic populations

Objectives

Rapid, high throughput diagnostics are a valuable tool, allowing the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in populations so as to identify and isolate people with asymptomatic and symptomatic infections. Reagent shortages and restricted access to high throughput testing solutions have limited the effectiveness of conventional assays such as quantitative RT-PCR (RT-qPCR), particularly throughout the first months of the coronavirus disease 2019 pandemic. We investigated the use of LamPORE, where loop-mediated isothermal amplification (LAMP) is coupled to nanopore sequencing technology, for the detection of SARS-CoV-2 in symptomatic and asymptomatic populations.

Methods

In an asymptomatic prospective cohort, for 3 weeks in September 2020, health-care workers across four sites (Birmingham, Southampton, Basingstoke and Manchester) self-swabbed with nasopharyngeal swabs weekly and supplied a saliva specimen daily. These samples were tested for SARS-CoV-2 RNA using the Oxford Nanopore LamPORE system and a reference RT-qPCR assay on extracted sample RNA. A second retrospective cohort of 848 patients with influenza-like illness from March 2020 to June 2020 were similarly tested from nasopharyngeal swabs.

Results

In the asymptomatic cohort a total of 1200 participants supplied 23 427 samples (3966 swab, 19 461 saliva) over a 3-week period. The incidence of SARS-CoV-2 detection using LamPORE was 0.95%. Diagnostic sensitivity and specificity of LamPORE was >99.5% (decreasing to approximately 98% when clustered estimation was used) in both swab and saliva asymptomatic samples when compared with the reference RT-qPCR test. In the retrospective symptomatic cohort, the incidence was 13.4% and the sensitivity and specificity were 100%.

Conclusions

LamPORE is a highly accurate methodology for the detection of SARS-CoV-2 in both symptomatic and asymptomatic population settings and can be used as an alternative to RT-qPCR.

Real-world SARS CoV-2 testing in Northern England during the first wave of the COVID-19 pandemic

Objectives

SARS-CoV-2 emerged in South Asia in 2019 and has resulted in a global pandemic. Public Health England (PHE) Manchester rapidly escalated testing for SARS-CoV-2 in the highest COVID-19 incidence location in England. The results of the PHE Manchester SARS-CoV-2 surveillance during the first wave are presented.

Methods

Retrospective data were collected for patients fitting the PHE SARS-CoV-2 case definition from 11th February to 31st August 2020. Respiratory tract, tissue, faecal, fluid and cerebrospinal (CSF) samples were tested for SARS-CoV-2 by a semi-quantitative real-time reverse-transcription PCR.

Results

Of the 204,083 tests for SARS-CoV-2, 18,011 were positive demonstrating a positivity of 8.90%. Highest positivity was in nasal swabs (20.99%) followed by broncheo-alveolar lavage samples (12.50%). None of the faecal, fluid or CSF samples received were positive for SARS-CoV-2.

Conclusions

There was a high incidence of SARS-CoV-2 patients in the North-West of England during the first UK wave of the Covid-19 pandemic. Highest positivity rate was in nasal specimens suggesting this is the optimum sample type within this dataset for detecting SARS-CoV-2. Further studies are warranted to assess the utility of testing faecal, fluid and CSF samples. Rapid escalation of testing via multiple platforms was required to ensure prompt diagnosis and isolate infected cases to reduce transmission of the virus.

Genomic and healthcare dynamics of nosocomial SARS-CoV-2 transmission

Understanding the effectiveness of infection control methods in reducing and preventing SARS-CoV-2 transmission in healthcare settings is of high importance. We sequenced SARS-CoV-2 genomes for patients and healthcare workers (HCWs) across multiple geographically distinct UK hospitals, obtaining 173 high-quality SARS-CoV-2 genomes. We integrated patient movement and staff location data into the analysis of viral genome data to understand spatial and temporal dynamics of SARS-CoV-2 transmission. We identified eight patient contact clusters (PCC) with significantly increased similarity in genomic variants compared to non-clustered samples. Incorporation of HCW location further increased the number of individuals within PCCs and identified additional links in SARS-CoV-2 transmission pathways. Patients within PCCs carried viruses more genetically identical to HCWs in the same ward location. SARS-CoV-2 genome sequencing integrated with patient and HCW movement data increases identification of outbreak clusters. This dynamic approach can support infection control management strategies within the healthcare setting.

A Prospective Study to Identify Rates of SARS-CoV-2 Virus in the Peritoneum and Lower Genital Tract of Patients Having Surgery: An Observational Study

Study Objective

The risks to surgeons of carrying out aerosol-generating procedures during the coronavirus disease 2019 (COVID-19) pandemic are unknown. To start to define these risks, in a systematic manner, we investigated the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus in the abdominal fluid and lower genital tract of patients undergoing surgery.

Design

Prospective cross-sectional observational study.

Setting

Single, large United Kingdom hospital.

Patients

Total of 113 patients undergoing abdominal surgery or instrumentation of the lower genital tract.

Interventions

We took COVID-19 swabs from the peritoneal cavity and from the vagina from all eligible patients. Results were stratified by preoperative COVID-19 status.

Measurements and Main Results

In patients who were presumed COVID-19 negative at the time of surgery, SARS-CoV-2 virus RNA was detected in 0 of 102 peritoneal samples and 0 of 98 vaginal samples. Both cohorts included 4 patients who were antibody positive but nasopharyngeal swab test negative at the time of surgery. Peritoneal and vaginal swabs were also negative in 1 patient who had a positive nasopharyngeal swab immediately before surgery.

Conclusion

The presence of SARS-CoV-2 RNA in the abdominal fluid or lower genital tract of presumed negative patients is nil or extremely low. These data will inform surgeons of the risks of restarting laparoscopic surgery at a time when COVID-19 is endemic in the population.

Six-year experience of detection and investigation of possible Middle East Respiratory Syndrome coronavirus cases, England, 2012-2018

OBJECTIVES

Surveillance for Middle East Respiratory Syndrome (MERS) has been undertaken in the UK since September 2012. This study describes the surveillance outcomes in England from 2012 to 2018.

STUDY DESIGN

This was a descriptive study using surveillance data.

METHODS

Local health protection teams in England report possible MERS cases to the National Infection Service with clinical and laboratory data.

RESULTS

A total of 1301 possible MERS cases were identified in the study period. Five cases were laboratory-confirmed MERS. The majority of cases had travelled to Saudi Arabia (56.7%) and United Arab Emirates (25.9%). Fifty-four percent of cases were men and 43.7% were women. The majority of cases (65.1%) were aged 45 years or older. The number of tests increased in the period after Hajj each year. Laboratory-confirmed alternative diagnoses were available for 513 (39.4%) cases; influenza was the most common virus detected (n = 255, 52.4%).

CONCLUSIONS

Our study highlights the importance of differential diagnosis of influenza and other respiratory pathogens and early influenza antiviral treatment.

Middle East respiratory syndrome coronavirus (MERS-CoV) - Surveillance and testing in North England from 2012 to 2019

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MERS is an emerging infectious disease with high consequences.

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PHE Manchester receives a high number of MERS surveillance samples.

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Sputum samples are the optimum samples for diagnosing respiratory viruses.

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Multiple samples per patient result in a 100% diagnostic yield and a confirmed end-diagnosis.

Background

Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in Saudi Arabia in 2012 and caused an epidemic in the Middle East. Public Health England (PHE) Manchester is one of the two PHE centres in the UK that perform testing for MERS-CoV. The results of the PHE Manchester MERS surveillance from 2012 to 2019 are presented in this report.

Methods

Retrospective data were collected for returning travellers from the Middle East fitting the PHE MERS case definition. Respiratory samples were tested for respiratory viruses and MERS-CoV using an in-house RT-PCR assay.

Results

Four hundred and twenty-six (426) samples from 264 patients were tested for MERS Co-V and respiratory viruses. No MERS-CoV infections were identified by PCR. Fifty-six percent of samples were PCR positive for viral or bacterial pathogen with Influenza A as the predominant virus (44%). Sixty-two percent of all patients had a pathogen identified with the highest positivity from sputum samples. Patients with multiple samples demonstrated a 100% diagnostic yield.

Conclusions

Although no cases of MERS were identified, the majority of patients had Influenza infection for which oseltamivir treatment was indicated and isolation warranted. Sputum samples were the most useful in diagnosing respiratory viruses with a 100% diagnostic yield from patients with multiple samples.

Barr humbug: acute cerebellar ataxia due to Epstein-Barr virus

Epstein-Barr virus (EBV) infection is associated with neurological sequellae, but rarely there is acute cerebellar ataxia (ACA) in an adult. We present a novel case of a 26-year-old man, who presented with ACA. He had normal MRI and CSF analysis. Serum testing confirmed active EBV. A course of oral prednisolone 1 mg/kg for 4 weeks, with a subsequent taper was started. He made a full recovery within 3 weeks of presentation.

A prospective study of enterovirus D68 in a regional UK center

Aim: A prospective study was undertaken to establish the prevalence of enterovirus D68 (EV-D68) in the northwest of England. Patients & samples: In the period 24 October through 31 December 2014, respiratory samples were screened by a specific real-time PCR and EV-D68 was identified by nucleotide sequence-based typing. Results: Enterovirus was detected in 7.4% of samples and EV-D68 was confirmed in 32 cases. Phylogenetic analysis showed that EV-D68 strains corresponded to clades A and B. Clinical presentation of cases ranged from mild to severe respiratory infection. The majority of cases had comorbidities that might predispose to severe infection. Conclusion: EV-D68 was circulating in our region during late 2014 and has the potential to cause severe disease.

The use of a European telemedicine system to examine the effects of pollutants and allergens on asthmatic respiratory health

The experience of using a telemedicine feasibility study to integrate respiratory health response and environmental stimuli information is presented. The effects of ambient air quality, pollen and local environment conditions on asthmatic patients' lung function were investigated through the use of a novel European health telematic system. The Medical Diagnosis, Communication and Analysis Throughout Europe (MEDICATE) project developed and tested the feasibility of using a telemedicine system for chronic asthmatics in London, UK, and Barcelona, Spain. The key to this was the determination of the real time health (lung function) response to the ambient environment and allergens. Air quality, pollen and environmental lifestyle information were related to respiratory measurements for recruited asthmatic patients in the study through the design of a dedicated environmental management system (EMS) database. In total, 28 patients completed the study trial, subject to ambulatory monitoring of spirometric lung function (PEF, FEV(1) and FVC) up to four times a day over a 2-week period recorded during the year 2000. Alongside this, ambient air quality and pollen counts were used to represent local exposure to potential environmental stimuli. Personal questionnaire interviewing collected additional data about patient lifestyles, social-economic conditions and quality of life perceptions. The methods and indicative results of integrating environmental and health data in this respect are examined. Assessment tools such as GIS and object-orientated databases were designed to locate and compile environmental information about the patients' locations and lifestyles in the study areas (London and Barcelona). Socioeconomic and lifestyle factors, such as exposure to smoking, pets, personal journey lengths and modes, income, household occupancy and domestic fuel use, were found to have limited detectable effects on the patients' basic lung function levels. Patients' gender, age and predicted PEFR were significantly associated with the 2-week mean and minimum respiratory measurements. Lung function data were compared with air quality and pollen indicators to examine relationships on a daily or lagged-day basis controlling for confounding factors. The paper discusses the new methodology and the practicalities of using the telemedical system as a tool for assessing the impacts of environmental stimuli on respiratory health.

Social awareness of air quality information

In the UK, air quality information is made available through a range of media. However, limited attention has been paid to ensuring that the information is provided to the public in a format that is understandable and relevant to their needs. This research has begun the task of determining the nature and extent of public air quality requirements by performing a social survey (using a postal questionnaire) to provide a basic snapshot of the public's views and by determining the views of information providers and interested professionals. The paper identifies the main shortcomings in current public air quality information provision. The social survey and workshop results demonstrate that current information provision and dissemination does not match public requirements; the depth and breadth of local information needs to be enhanced. Local authorities need to improve their co-ordination and collaboration, the role of the mass-media needs to be considered carefully, air quality needs to be better described and its implications for individuals spelled out and certain public groups need special consideration. In addition, local authorities need more guidance on communicating air quality, possibly through a best practice guide. Further research is required to identify the best descriptors for air quality, to improve the effectiveness of public advice during episodes of poor air quality and to use public air quality information to effect behavioral changes.

A DNA double chain break stimulates triparental recombination in Saccharomyces cerevisiae

Mitotic recombination between his3 heteroalleles on heterologous chromosomes is stimulated by a DNA double chain break delivered in vivo at a site 8.6 kilobase pairs distant from one his3 allele and unlinked to the other. The induced recombination at his3 is accompanied by gap repair at the break site using the uncut homolog as a template. The DNA between the break site and his3 is not deleted in most of the His+ recombinants.