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

COG-UK HOCI Investigators, The COVID-19 Genomics UK (COG-UK) Consortium, Hayley Colton, Matthew D. Parker, Oliver Stirrup, James Blackstone, Matthew Loose, C Patrick McClure, Sunando Roy, Charlotte Williams, Julie McLeod, Darren Smith, Yusri Taha, Peijun Zhang, Sharon Nienyun Hsu, Beatrix Kele, Kathryn Harris, Fiona Mapp, Rachel Williams, Paul Flowers, Judith BreuerDavid G. Partridge, Thushan I. de Silva

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Abstract

BackgroundBarriers to rapid return of sequencing results can affect the utility of sequence data for infection prevention and control decisions.AimTo 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.MethodsFor 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.FindingsThe 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.ConclusionIntegration 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.
Original languageEnglish
Pages (from-to)34-42
Number of pages9
JournalThe Journal of Hospital Infection
Volume131
Early online date10 Oct 2022
DOIs
Publication statusPublished - 1 Jan 2023

Keywords

  • turnaround time
  • sequencing
  • infection control
  • SARS-CoV-2

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