Colton, H, Parker, MD, Stirrup, O 
ORCID: 0000-0002-8705-3281, Blackstone, J, Loose, M, McClure, CP, Roy, S, Williams, C, McLeod, J, Smith, D ORCID: 0000-0003-4925-467X et al (show 12 more authors)
(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.
The Journal of hospital infection, 131.
pp. 34-42.
Abstract
<h4>Background</h4>Barriers to rapid return of sequencing results can affect the utility of sequence data for infection prevention and control decisions.<h4>Aim</h4>To undertake a mixed-methods analysis to identify challenges that sites faced in achieving a rapid turnaround time (TAT) in the COVID-19 Genomics UK Hospital-Onset COVID-19 Infection (COG-UK HOCI) study.<h4>Methods</h4>For the quantitative analysis, timepoints relating to different stages of the sequencing process were extracted from both the COG-UK HOCI study dataset and surveys of study sites. Qualitative data relating to the barriers and facilitators to achieving rapid TATs were included from thematic analysis.<h4>Findings</h4>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 polymerase chain reaction (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 h, range 16.0-88.7 h). Qualitative analyses suggest that closer proximity of sequencing laboratories to diagnostic laboratories, increased staff flexibility and regular transport times facilitated a shorter TAT.<h4>Conclusion</h4>Integration of pathogen sequencing into diagnostic laboratories may help to 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 optimize TAT if lower quality samples are removed at an earlier stage.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | COG-UK HOCI Investigators, COVID-19 Genomics UK (COG-UK) Consortium, Humans, Decision Making, Inpatients, United Kingdom, COVID-19, SARS-CoV-2 |
| Divisions: | Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 31 Jan 2024 10:19 |
| Last Modified: | 31 Jan 2024 10:20 |
| DOI: | 10.1016/j.jhin.2022.09.022 |
| Open Access URL: | https://doi.org/10.1016/j.jhin.2022.09.022 |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3178167 |
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