Beatrix Kele | PubMed Health

PubMed2025

Analysis of Variants' Dynamic Using the CLIMB Database in COVID-19 Patients Admitted to Hospitals of Barts Health NHS Trust.

The COVID-19 pandemic, caused by SARS-CoV-2, has led to significant global health challenges. This study analyzes the dynamics of SARS-CoV-2 variants among patients admitted to Barts Health National Health Service (NHS) Trust hospitals using data from the CLIMB-COVID decentralized digital infrastructure allowing precise identification of SARS-CoV-2 variants. A total of 423 patients admitted between October 2020 and March 2021 were included in the study and divided into two groups: the alpha lineage group, which comprised the B.1.1.7 variant, and the other lineages group, which included all other variants. Whole-genome sequencing of SARS-CoV-2 genomes was conducted using the COVID-CLIMB pipelines. Clinical outcomes, such as mortality rates and deterioration within 28 days, were analyzed. To ensure robust findings, analyzes were adjusted for confounding factors, including age and comorbidities. Our findings revealed a significant increase in mortality with age for the alpha lineage and other lineages. The study underscores the importance of age adjustment in clinical studies to accurately assess the impact of different variants. Consistent genomic sequencing and data completeness are crucial for obtaining reliable results and guiding public health responses. These insights are vital for improving patient outcomes and providing a truthful picture of the pandemic, informing both current and future healthcare strategies.

Humans↗

PubMed2022

Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, 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' (<48 hr) and 4 weeks of 'longer-turnaround' (5-10 days) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital-onset COVID-19 infections (HOCIs; detected ≥48 hr from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on the incidence of probable/definite hospital-acquired infections (HAIs), was evaluated. RESULTS: A total of 2170 HOCI cases were recorded from October 2020 to 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. CONCLUSIONS: 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: NCT04405934.

Humans↗