RT-PCR genotyping assays to identify SARS-CoV-2 variants in England in 2021: a design and retrospective evaluation study.

BACKGROUND: Whole-genome sequencing (WGS) is the gold standard diagnostic tool to identify and genetically characterise emerging pathogen mutations (variants), but cost, capacity, and timeliness limit its use when large populations need rapidly assessing. We assessed the potential of genotyping assays to provide accurate and timely variant information at scale by retrospectively examining surveillance for SARS-CoV-2 variants in England between March and September, 2021, when genotyping assays were used widely for variant detection. METHODS: We chose a panel of four RT-PCR genotyping assays to detect circulating variants of SARS-COV-2 in England and developed a decision algorithm to assign a probable SARS-CoV-2 variant to samples using the assay results. We extracted surveillance data from the UK Health Security Agency databases for 115 934 SARS-CoV-2-positive samples (March 1-Sept 6, 2021) when variant information was available from both genotyping and WGS. By comparing the genotyping and WGS variant result, we calculated accuracy metrics (ie, sensitivity, specificity, and positive predictive value [PPV]) and the time difference between the sample collection date and the availability of variant information. We assessed the number of samples with a variant assigned from genotyping or WGS, or both, over time. FINDINGS: Genotyping and an initial decision algorithm (April 10-May 11, 2021 data) were accurate for key variant assignment: sensitivities and PPVs were 0·99 (95% CI 0·99-0·99) for the alpha, 1·00 (1·00-1·00) for the beta, and 0·91 (0·80-1·00) for the gamma variants; specificities were 0·97 (0·96-0·98), 1·00 (1·00-1·00), and 1·00 (1·00-1·00), respectively. A subsequent decision algorithm over a longer time period (May 27-Sept 6, 2021 data) remained accurate for key variant assignment: sensitivities were 0·91 (95% CI 0·74-1·00) for the beta, 0·98 (0·98-0·99) for the delta, and 0·93 (0·81-1·00) for the gamma variants; specificities were 1·00 (1·00-1·00), 0·96 (0·96-0·97), and 1·00 (1·00-1·00), respectively; and PPVs were 0·83 (0·62-1·00), 1·00 (1·00-1·00), and 0·78 (0·59-0·97), respectively. Genotyping produced variant information a median of 3 days (IQR 2-4) after the sample collection date, which was faster than with WGS (9 days [8-11]). The flexibility of genotyping enabled a nine-times increase in the quantity of samples tested for variants by this method (from 5000 to 45 000). INTERPRETATION: RT-PCR genotyping assays are suitable for high-throughput variant surveillance and could complement WGS, enabling larger scale testing for known variants and timelier results, with important implications for effective public health responses and disease control globally, especially in settings with low WGS capacity. However, the choice of panels of RT-PCR assays is highly dependent on database information on circulating variants generated by WGS, which could limit the use of genotyping assays when new variants are emerging and spreading rapidly. FUNDING: UK Health Security Agency and National Institute for Health Research Health Protection Research Unit in Emergency Preparedness and Response.

Ovarian Real-World International Consortium (ORWIC): A multicentre, real-world analysis of epithelial ovarian cancer treatment and outcomes.

Introduction: Much drug development and published analysis for epithelial ovarian cancer (EOC) focuses on early-line treatment. Full sequences of treatment from diagnosis to death and the impact of later lines of therapy are rarely studied. We describe the establishment of an international network of cancer centers configured to compare real-world treatment pathways in UK, Portugal, Germany, South Korea, France and Romania (the Ovarian Real-World International Consortium; ORWIC). Methods: 3344 patients diagnosed with EOC (2012-2018) were analysed using a common data model and hub and spoke programming approach applied to existing electronic medical records. Consistent definition of line of therapy between sites and an efficient approach to analysis within the limitations of local information governance was achieved. Results: Median age of participants was 53-67 years old and 5-29% were ECOG >1. Between 62% and 84% of patients were diagnosed with late-stage disease (FIGO III-IV). Sites treating younger and fitter patients had higher rates of debulking surgery for those diagnosed at late stage than sites with older, more frail patients. At least 21% of patients treated with systemic anti-cancer therapy (SACT) had recurrent disease following second-line therapy (2L); up to 11 lines of SACT treatment were recorded for some patients. Platinum-based SACT was consistently used across sites at 1L, but choices at 2L varied, with hormone therapies commonly used in the UK and Portugal. The use (and type) of maintenance therapy following 1L also varied. Beyond 2L, there was little consensus between sites on treatment choice: trial compounds and unspecified combinations of other agents were common. Discussion: Specific treatment sequences are reported up to 4L and the establishment of this network facilitates future analysis of comparative outcomes per line of treatment with the aim of optimizing available options for patients with recurrent EOC. In particular, this real-world network can be used to assess the growing use of PARP inhibitors. The real-world optimization of advanced line treatment will be especially important for patients not usually eligible for involvement with clinical trials. The resources to enable this analysis to be implemented elsewhere are supplied and the network will seek to grow in coverage of further sites.

Assessing the treatment pattern, health care resource utilisation, and economic burden of multiple myeloma in France using the Système National des Données de Santé (SNDS) database: a retrospective cohort study.

BACKGROUND: Real-world data on health care resource utilisation (HCRU) and costs for French patients with multiple myeloma (MM) are limited due to the quickly evolving MM treatment landscape. This retrospective, national-level study quantified the MM economic burden in France. METHODS: The study included patients with newly diagnosed MM from the Système National des Données de Santé coverage claims database between 2013 and 2018 who received active treatment within 30 days of diagnosis. HCRU included hospitalisations, drugs, consultations, procedures, tests, devices, transport, and sick leave. Costs were annualized to 2019 prices. Drug treatments, reported by line of therapy (LOT), were algorithmically defined using drug regimen, duration of therapy, and gaps between treatments. Analyses were stratified by stem cell transplantation status and LOT. RESULTS: Among 6413 eligible patients, 6229 (97.1%) received ≥ 1 identifiable LOT; most received 1 (39.8%) or 2 LOT (27.5%) during follow-up. Average annual hospitalisation was 6.3 episodes/patient/year (median duration: 11.6 days). The average annual cost/patient was €58.3 K. Key cost drivers were treatment (€28.2 K; 39.5% of total HCRU within one year of MM diagnosis) and hospitalisations (€22.2 K; 48.6% of total HCRU costs in first year). Monthly treatment-related costs increased from LOT1 (€2.447 K) and LOT5 + (€7.026 K); only 9% of patients received LOT5 + . At LOT4 + , 37 distinct regimens were identified. Hospitalisation costs were higher in patients with stem cell transplantation than total population, particularly in the first year. CONCLUSIONS: This study showed a high economic burden of MM in France (€72.37 K/patient/year in the first year) and the diversity of regimens used in late-line treatments.

Treatment patterns and survival outcomes for patients with non-small cell lung cancer in the UK in the preimmunology era: a REAL-Oncology database analysis from the I-O Optimise initiative.

OBJECTIVES: To report characteristics, treatment and overall survival (OS) trends, by stage and pathology, of patients diagnosed with non-small cell lung cancer (NSCLC) at Leeds Teaching Hospital NHS Trust in 2007-2018. DESIGN: Retrospective cohort study based on electronic medical records. SETTING: Large NHS university hospital in Leeds. PARTICIPANTS: 3739 adult patients diagnosed with incident NSCLC from January 2007 to August 2017, followed up until March 2018. MAIN OUTCOME MEASURES: Patient characteristics at diagnosis, treatment patterns and OS. RESULTS: 34.3% of patients with NSCLC were clinically diagnosed (without pathological confirmation). Among patients with known pathology, 45.2% had non-squamous cell carcinoma (NSQ) and 33.3% had squamous cell carcinoma (SQ). The proportion of patients diagnosed at stage I increased (16.4%-27.7% in 2010-2017); those diagnosed at stage IV decreased (57.0%-39.1%). Surgery was the most common initial treatment for patients with pathologically confirmed stage I NSCLC. Use of radiotherapy alone increased over time in patients with clinically diagnosed stage I NSCLC (39.1%-60.3%); chemoradiation increased in patients with stage IIIA NSQ (21.6%-33.3%) and SQ (24.2%-31.9%). Initial treatment with systemic anticancer therapy (SACT) increased in patients with stages IIIB-IV NSQ (49.0%-67.5%); the proportion of untreated patients decreased (30.6%-15.0%). Median OS improved for patients diagnosed with stage I NSQ and SQ and stage IIIA NSQ over time. Median OS for patients with stages IIIB-IV NSQ and SQ remained stable, <10% patients were alive 3 years after diagnosis. Median OS for clinically diagnosed stages IIIB-IV patients was 1.2 months in both periods. CONCLUSIONS: OS for stage I and IIIA patients improved over time, likely due to increased use of stereotactic ablative radiation, surgery (stage I) and chemoradiation (stage IIIA). Conversely, OS outcomes remained poor for stage IIIB-IV patients despite increasing use of SACT for NSQ. Many patients with advanced-stage disease remained untreated.

Trends in the prescription of systemic anticancer therapy and mortality among patients with advanced non-small cell lung cancer: a real-world retrospective observational cohort study from the I-O optimise initiative.

OBJECTIVES: To assess how a decade of developments in systematic anticancer therapy (SACT) for advanced non-small cell lung cancer (NSCLC) affected overall survival (OS) in a large UK University Hospital. DESIGN: Real-world retrospective observational cohort study using existing data recorded in electronic medical records. SETTING: A large National Health Service (NHS) university teaching hospital serving 800 000 people living in a diverse metropolitan area of the UK. PARTICIPANTS: 2119 adults diagnosed with advanced NSCLC (tumour, node, metastasis stage IIIB or IV) between 2007 and 2017 at Leeds Teaching Hospitals NHS Trust. MAIN OUTCOMES AND MEASURES: OS following diagnosis and the analysis of factors associated with receiving SACT. RESULTS: Median OS for all participants was 2.9 months, increasing for the SACT-treated subcohort from 8.4 months (2007-2012) to 9.1 months (2013-2017) (p=0.02); 1-year OS increased from 33% to 39% over the same period for the SACT-treated group. Median OS for the untreated subcohort was 1.6 months in both time periods. Overall, 30.6% (648/2119) patients received SACT; treatment rates increased from 28.6% (338/1181) in 2007-2012 to 33.0% (310/938) in 2013-2017 (p=0.03). Age and performance status were independent predictors for SACT treatment; advanced age and higher performance status were associated with lower SACT treatment rates. CONCLUSION: Although developments in SACT during 2007-2017 correspond to some changes in survival for treated patients with advanced NSCLC, treatment rates remain low and the prognosis for all patients remains poor.

Current Treatment and Outcomes Benchmark for Locally Advanced or Metastatic Urothelial Cancer From a Large UK-Based Single Centre.

Objectives: To characterize treatment patterns and survival outcomes for patients with locally advanced or metastatic malignancy of the urothelial tract during a period immediately preceding the widespread use of immune checkpoint inhibitors in the UK. Patients and Methods: We retrospectively examined the electronic case notes of patients attending the Leeds Cancer Center, UK with locally advanced or metastatic urothelial carcinoma, receiving chemotherapy between January 2003 and March 2017. Patient characteristics, treatment patterns, and outcomes were collected. Summary and descriptive statistics were calculated for categorical and continuous variables as appropriate. The Kaplan-Meier method was used to estimate median survival and Cox regression proportional hazards model was used to explore relationships between clinical variables and outcome. Results: Two hundred and sixteen patients made up the study cohort, with a median age of 66 years (range: 35-83) and 72.7% being male. First-line treatment consisted of either a cisplatin- (44%) or carboplatin-based regimen (48%) in the majority of patients. Twenty seven percent of patients received a second-line of treatment (most commonly single-agent paclitaxel) following a first-line platinum containing regimen. Grade 4 neutropenia was observed in 19 and 27% of those treated with a first-line cisplatin- and carboplatin-based regimen, respectively. The median overall survival (mOS) of the study cohort was estimated to be 16.2 months (IQR: 10.6-28.3 months). Receipt by patients of cisplatin-based chemotherapy was associated with a longer mOS and this association persisted when survival analysis was adjusted for age, sex, performance status and presence of distant metastases. Conclusions: This study provides a useful benchmark for outcomes achieved in a real-world setting for patients with locally advanced or metastatic UC treated with chemotherapy in the immediate pre-immunotherapy era.

Systemic treatment of hormone receptor positive, human epidermal growth factor 2 negative metastatic breast cancer: retrospective analysis from Leeds Cancer Centre.

BACKGROUND: Study aimed to characterise treatment and outcomes for patients with hormone receptor positive (HR+), human epidermal growth factor 2 negative (HER2-) metastatic breast cancer (MBC) within a large regional cancer centre, as a benchmark for evaluating real-world impact of novel therapies. METHODS: Retrospective longitudinal cohort, using electronic patient records of adult females with a first diagnosis of HR+/HER2- MBC January 2012-March 2018. RESULTS: One hundred ninety-six women were identified with HR+/HER2- MBC. Median age was 67 years, 85.2% were post-menopausal and median time between primary diagnosis and metastasis was 5.4 years. Most (75.1%) patients received endocrine therapy as first line systemic treatment (1st LoT); use of 1st LoT chemotherapy halved between 2012 and 2017. Patients receiving 1st LoT chemotherapy were younger and more likely to have visceral metastasis (p < 0.01). Median OS was 29.5 months and significantly greater for patients with exclusively non-visceral metastasis (p < 0.01). The adjusted hazard ratio for death of patients with visceral (or CNS) metastasis was 1.91 relative to those with exclusively non-visceral metastasis. CONCLUSIONS: Diverse endocrine therapies predominate as 1st LoT for patients with HR+/HER2- MBC, chemotherapy being associated with more aggressive disease in younger patients, emphasising the importance of using effective and tolerable therapies early.

Norovirus outbreak in a cruise ship sailing around the British Isles: investigation and multi-agency management of an international outbreak.

OBJECTIVE: Managing an outbreak of gastroenteritis (GI) on board a cruise ship while minimising disruption to passengers' on board and shore visit activities is difficult. For this reason it is important to understand the complex patterns of transmission in a closed community. We describe the epidemiological investigation of an outbreak of norovirus during an international cruise. METHODS: A retrospective cohort study was conducted using information from lists routinely maintained by the travel company, including the passenger manifest, and organised coach tour lists. Information on air-conditioning (AC) systems was used to assess the possible sources of exposures. FINDINGS: Of the 1194 passengers 191 (16%) and 5 crew (<1%) became ill with GI symptoms. The attack rate was higher amongst passengers whose cabin was on the main deck (RR 3.41, 95% CI 1.47-7.94) that houses both passengers' cabins and leisure facilities including shops. Passengers who went on one of the organised coach tours where there were symptomatic passengers were at an increased risk of infection (RR 2.14, CI 1.51-3.03). Analysis of the 56 AC sections on the ship and did not detect an association with infection. CONCLUSIONS: Patterns of transmission of norovirus on a cruise ship are complex. Our study suggests infections are more likely among those passengers staying in areas of the ship that are highly transited or used for communal activities and more difficult to clean. Emphasis on the importance of early reporting of symptoms can help minimise transmission. Internationally agreed guidelines on the management of outbreaks on cruise ships are needed.

Investigation of food and environmental exposures relating to the epidemiology of Campylobacter coli in humans in Northwest England.

This study uses multilocus sequence typing (MLST) to investigate the epidemiology of Campylobacter coli in a continuous study of a population in Northwest England. All cases of Campylobacter identified in four Local Authorities (government administrative boundaries) between 2003 and 2006 were identified to species level and then typed, using MLST. Epidemiological information was collected for each of these cases, including food and recreational exposure variables, and the epidemiologies of C. jejuni and C. coli were compared using case-case methodology. Samples of surface water thought to represent possible points of exposure to the populations under study were also sampled, and campylobacters were typed with multilocus sequence typing. Patients with C. coli were more likely to be older and female than patients with C. jejuni. In logistic regression, C. coli infection was positively associated with patients eating undercooked eggs, eating out, and reporting problems with their water supply prior to illness. C. coli was less associated with consuming pork products. Most of the cases of C. coli yielded sequence types described elsewhere in both livestock and poultry, but several new sequence types were also identified in human cases and water samples. There was no overlap between types identified in humans and surface waters, and genetic analysis suggested three distinct clades but with several "intermediate" types from water that were convergent with the human clade. There is little evidence to suggest that epidemiological differences between human cases of C. coli and C. jejuni are a result of different food or behavioral exposures alone.

Healthcare-associated viral gastroenteritis among children in a large pediatric hospital, United Kingdom.

Viruses are the major pathogens of community-acquired (CA) acute gastroenteritis (AGE) in children, but their role in healthcare-associated (HA) AGE is poorly understood. Children with AGE hospitalized at Alder Hey Children's Hospital, Liverpool, UK, were enrolled over a 2-year period. AGE was classified as HA if diarrhea developed > or =48 hours after admission. Rotavirus, norovirus, adenovirus 40/41, astrovirus, and sapovirus were detected by PCR. A total of 225 children with HA-AGE and 351 with CA-AGE were enrolled in the study. HA viral gastroenteritis constituted one fifth of the diarrheal diseases among hospitalized children and commonly occurred in critical care areas. We detected > or =1 virus in 120 (53%) of HA-AGE cases; rotavirus (31%), norovirus (16%), and adenovirus 40/41 (15%) were the predominant viruses identified. Molecular evidence indicated rotaviruses and noroviruses were frequently introduced into the hospital from the community. Rotavirus vaccines could substantially reduce the incidence of HA-AGE in children.

Identification of potential environmentally adapted Campylobacter jejuni strain, United Kingdom.

In a study of Campylobacter infection in northwestern England, 2003-2006, C. jejuni multilocus sequence type (ST)-45 was associated with early summer onset and was the most prevalent C. jejuni type in surface waters. ST-45 is likely more adapted to survival outside a host, making it a key driver of transmission between livestock, environmental, and human settings.

Campylobacter jejuni multilocus sequence types in humans, northwest England, 2003-2004.

Detailed understanding of the epidemiology of Campylobacter is increasingly facilitated through use of universal and reproducible techniques for accurate strain differentiation and subtyping. Multilocus sequence typing (MLST) enables discriminatory subtyping and grouping of isolate types into genetically related clonal complexes; it also has the advantage of ease of application and repeatability. Recent studies suggest that a measure of host association may be distinguishable with this system. We describe the first continuous population-based survey to investigate the potential of MLST to resolve questions of campylobacteriosis epidemiology. We demonstrate the ability of MLST to identify variations in the epidemiology of campylobacteriosis between distinct populations and describe the distribution of key subtypes of interest.

Preventing infection from reusable medical equipment: a systematic review.

BACKGROUND: In 2000, the World Health Organization (WHO) had eight sets of conflicting recommendations for decontaminating medical equipment. We conducted a systematic review of observational studies to assist WHO in reconciling the various guidelines. This paper summarises the methods developed and illustrates the results for three procedures--alcohol, bleach and povidone iodine. METHODS: We developed a Medline search strategy and applied inclusion criteria specifying the decontamination procedures of interest and an outcome of microbial destruction for a set of marker organisms. We developed protocols to assess the quality of studies and categorised them according to the reliability of the methods used. Through an iterative process we identified best practice for the decontamination methods and key additional factors required to ensure their effectiveness. We identified 88 published papers for inclusion, describing 135 separate studies of decontamination. RESULTS: For disinfection with alcohol, best practice was identified from 23 studies as an exposure to 70-80% ethanol or isopropanol for at least 5 minutes. Bleach was effective for sterilization at a concentration of 5000 ppm for 5 minutes and for disinfection at 1000 ppm for 10 minutes (33 studies). Povidone iodine was only partially effective for disinfection at a concentration of 1% for 15 minutes (15 studies). CONCLUSIONS: Our findings provide an evidence base for WHO guidelines on decontaminating medical equipment. The results support the recommended use of bleach and show that alcohol could be used more widely than current guidelines suggest, provided best practice is followed. The effectiveness of povidone iodine is uncertain.