Dataset Information

Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey.

ABSTRACT: The Office for National Statistics Coronavirus (COVID-19) Infection Survey (ONS-CIS) is the largest surveillance study of SARS-CoV-2 positivity in the community, and collected data on the United Kingdom (UK) epidemic from April 2020 until March 2023 before being paused. Here, we report on the epidemiological and evolutionary dynamics of SARS-CoV-2 determined by analysing the sequenced samples collected by the ONS-CIS during this period. We observed a series of sweeps or partial sweeps, with each sweeping lineage having a distinct growth advantage compared to their predecessors, although this was also accompanied by a gradual fall in average viral burdens from June 2021 to March 2023. The sweeps also generated an alternating pattern in which most samples had either S-gene target failure (SGTF) or non-SGTF over time. Evolution was characterized by steadily increasing divergence and diversity within lineages, but with step increases in divergence associated with each sweeping major lineage. This led to a faster overall rate of evolution when measured at the between-lineage level compared to within lineages, and fluctuating levels of diversity. These observations highlight the value of viral sequencing integrated into community surveillance studies to monitor the viral epidemiology and evolution of SARS-CoV-2, and potentially other pathogens.

SUBMITTER: Lythgoe KA

PROVIDER: S-EPMC10581763 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature

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Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey.

Lythgoe Katrina A KA Golubchik Tanya T Hall Matthew M House Thomas T Cahuantzi Roberto R MacIntyre-Cockett George G Fryer Helen H Thomson Laura L Nurtay Anel A Ghafani Mahan M Buck David D Green Angie A Trebes Amy A Piazza Paolo P Lonie Lorne J LJ Studley Ruth R Rourke Emma E Smith Darren D Bashton Matthew M Nelson Andrew A Crown Matthew M McCann Clare C Young Gregory R GR Andre Nunes Dos Santos Rui R Richards Zack Z Tariq Adnan A Fraser Christophe C Diamond Ian I Barrett Jeff J Walker Ann Sarah AS Bonsall David D

Proceedings. Biological sciences 20231018 2009

The Office for National Statistics Coronavirus (COVID-19) Infection Survey (ONS-CIS) is the largest surveillance study of SARS-CoV-2 positivity in the community, and collected data on the United Kingdom (UK) epidemic from April 2020 until March 2023 before being paused. Here, we report on the epidemiological and evolutionary dynamics of SARS-CoV-2 determined by analysing the sequenced samples collected by the ONS-CIS during this period. We observed a series of sweeps or partial sweeps, with each ...[more]

PMID: 37848057

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Project description:BackgroundComprehensive national assessments of paediatric allergy services are rarely undertaken, and have never been undertaken in the United Kingdom. A 2006 survey estimated national capacity at 30,000 adult or paediatric new allergy appointments per year and identified 58 hospital clinics offering a paediatric allergy service.ObjectiveThe UK Paediatric Allergy Services Survey was the first comprehensive assessment of UK paediatric allergy service provision.MethodsAll 450 UK hospitals responded to a survey. Paediatric allergy services are provided in 154 lead hospitals with 75 further linked hospitals. All 154 lead paediatric allergy services completed a detailed questionnaire between February 2019 and May 2020.ResultsThe 154 paediatric allergy services self-define as secondary (126/154, 82%) or tertiary (28/154, 18%) level services. The annual capacity is 85,600 new and 111,400 follow-up appointments. Fifty-eight percent (85/146) of services offer ≤10 new appointments per week (no data provided from 8 services-2 no response, 6 unknown) and 50% (70/139) of the services undertaking challenges undertake ≤2 food or drug challenges per week (no data from 3 challenge services). Intramuscular adrenaline is rarely used during challenges-median annual frequency 0 in secondary services and 2 in tertiary services. Allergen-specific immunotherapy is offered in 39% (60/154) of services, with 71% (41/58) of these centres treating ≤10 patients per annum (no data from 2 immunotherapy services). The 12 largest services see 31% of all new paediatric allergy appointments, undertake 51% of new immunotherapy patient provision and 33% of food or drug challenges. Seventy percent (97/126) of secondary and all tertiary services are part of a regional paediatric allergy network. Only nine services offer immunotherapy for any food (3 for peanut), 10 drug desensitization and 18 insect venom immunotherapy.ConclusionsThere has been a fourfold increase in paediatric allergy clinics and an approximately sevenfold increase in new patient appointment numbers in the United Kingdom over the past 15 years. Most services are small, with significant regional variation in availability of specific services such as allergen immunotherapy. Our findings emphasize the need for national standards, local networks and simulation training to ensure consistent and safe service provision.

Project description:Key epidemiological parameters, including the effective reproduction number, R(t), and the instantaneous growth rate, r(t), generated from an ensemble of models, have been informing public health policy throughout the COVID-19 pandemic in the four nations of the United Kingdom of Great Britain and Northern Ireland (UK). However, estimation of these quantities became challenging with the scaling down of surveillance systems as part of the transition from the "emergency" to "endemic" phase of the pandemic. The Office for National Statistics (ONS) COVID-19 Infection Survey (CIS) provided an opportunity to continue estimating these parameters in the absence of other data streams. We used a penalised spline model fitted to the publicly-available ONS CIS test positivity estimates to produce a smoothed estimate of the prevalence of SARS-CoV-2 positivity over time. The resulting fitted curve was used to estimate the "ONS-based" R(t) and r(t) across the four nations of the UK. Estimates produced under this model are compared to government-published estimates with particular consideration given to the contribution that this single data stream can offer in the estimation of these parameters. Depending on the nation and parameter, we found that up to 77% of the variance in the government-published estimates can be explained by the ONS-based estimates, demonstrating the value of this singular data stream to track the epidemic in each of the four nations. We additionally find that the ONS-based estimates uncover epidemic trends earlier than the corresponding government-published estimates. Our work shows that the ONS CIS can be used to generate key COVID-19 epidemiological parameters across the four UK nations, further underlining the enormous value of such population-level studies of infection. This is not intended as an alternative to ensemble modelling, rather it is intended as a potential solution to the aforementioned challenge faced by public health officials in the UK in early 2022.

Project description:BackgroundTinnitus service provision in the United Kingdom has been investigated from the healthcare provider's perspective demonstrating considerable regional variation particularly regarding availability of psychological treatments. An audiological-based tinnitus service, however, was reportedly available for all tinnitus patients in the UK. The aim of the current study was to define and evaluate nationwide tinnitus healthcare services from the patients' viewpoint.MethodsSecondary analyses were performed on data from a 33-item questionnaire provided by the British Tinnitus Association. The questionnaire had been distributed via email and social media.ResultsResponses from 937 participants who had or had previously experienced tinnitus were analysed. All but one person had at some time consulted their GP. About one in five received medication in primary care. The majority were referred to secondary care, generally an ENT surgeon or audiovestibular physician; some were referred directly to audiological services. In secondary care the majority underwent audiometric testing and over half underwent MRI scanning. Drugs were prescribed less frequently in secondary care. About one third of patients were referred onwards from diagnostic services in secondary care to receive therapeutic interventions for tinnitus. Therapy was generally delivered by an audiologist or hearing therapist. Just under two fifths of people discharged from secondary care returned to their GP, with most returning within one year. Over a third of this group were re-referred to secondary care. Few patients saw a psychologist (2.6%) though some psychological treatments were delivered by appropriately trained audiologists. Negative counselling from healthcare professionals in both primary and secondary care settings was reported.ConclusionsAlthough the UK has developed a national service for patients with tinnitus many people find it difficult to access, being blocked at the primary care level or after secondary care diagnostic services. Many of those discharged from secondary care return to their GP within a short space of time and are re-referred to secondary care creating an unsatisfactory and expensive revolving-door pattern of healthcare. Despite psychological treatment modalities having the best evidence base for successful tinnitus management, only a minority of tinnitus patients ever get to meet a psychologist.

Dataset Information

Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey.

Publications

Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey.

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