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Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: Analysis of data from the COG-UK HOCI study

Colton, Hayley; Parker, Matthew D; Stirrup, Oliver; Blackstone, James; Loose, Matthew; McClure, C Patrick; Roy, Sunando; ... de Silva, Thushan I; + view all (2023) Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: Analysis of data from the COG-UK HOCI study. Journal of Hospital Infection , 131 pp. 34-42. 10.1016/j.jhin.2022.09.022. Green open access

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Abstract

Background: Barriers to rapid return of sequencing results can affect the utility of sequence data for infection prevention and control decisions. Aim: To undertake a mixed-methods analysis to identify challenges sites faced in achieving a rapid turnaround time (TAT) in the COG-UK Hospital-Onset COVID-19 Infection (COG-UK HOCI) study. Methods: For the quantitative analysis, timepoints relating to different stages of the sequencing process were extracted from both the COG-UK HOCI dataset and surveys of study sites. Qualitative data relating to the barriers and facilitators to achieving rapid TAT were included from thematic analysis. Findings: The overall TAT, from sample collection to receipt of sequence report by infection control teams, varied between sites (median 5.1 days, range 3.0 – 29.0 days). Most variation was seen between reporting of a positive COVID-19 PCR result to sequence report generation (median 4.0 days, range 2.3 – 27.0 days). On deeper analysis, most of this variability was accounted for by differences in the delay between the COVID-19 PCR result and arrival of the sample at the sequencing laboratory (median 20.8 hours, 16.0 – 88.7 hours). Qualitative analyses suggest closer proximity of sequencing labs to diagnostic labs, increased staff flexibility and regular transport times facilitated a shorter TAT. Conclusion: Integration of pathogen sequencing into diagnostic laboratories may help improve sequencing TAT to allow sequence data to be of tangible value to infection control practice. Adding a quality control step upstream to increase capacity further down the workflow may also optimise TAT if lower quality samples are removed earlier on.

Type: Article
Title: Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: Analysis of data from the COG-UK HOCI study
Open access status: An open access version is available from UCL Discovery
DOI: 10.1016/j.jhin.2022.09.022
Publisher version: https://doi.org/10.1016/j.jhin.2022.09.022
Language: English
Additional information: Copyright © 2022 The Author(s). This is an open access article under the CC BY 4.0 license Attribution 4.0 International (https://creativecommons.org/licenses/by/4.0/)
Keywords: Infection control, sequencing, SARS-CoV-2, turnaround time
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > Institute for Global Health > Infection and Population Health
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > Institute for Global Health
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
URI: https://discovery.ucl.ac.uk/id/eprint/10157304
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