TY - JOUR
AU - Williams, Thomas C.
AU - Wastnedge, Elizabeth
AU - McAllister, Gina E.M.
AU - Bhatia, Ramya
AU - Cuschieri, Kate
AU - Kefala, Kallirroi
AU - Hamilton, Fiona
AU - Johannessen, Ingólfur
AU - Laurenson, Ian F.
AU - Shepherd, Jill
AU - Stewart, Alistair
AU - Waters, Donald
AU - Wise, Helen
AU - Templeton, Kate E.
PY - 2020
DA - October
TI - Sensitivity of RT-PCR testing of upper respiratory tract samples for SARS-CoV-2 in hospitalised patients: a retrospective cohort study
JO - Wellcome Open Research
VL - 5
DO - https://doi.org/10.12688/wellcomeopenres.16342.1
AB - Background:This study aimed to determine the sensitivity and specificity of reverse transcription PCR (RT-PCR) testing of upper respiratory tract (URT) samples from hospitalised patients with coronavirus disease 2019 (COVID-19), compared to the gold standard of a clinical diagnosis. Methods:All URT RT-PCR testing for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in NHS Lothian, Scotland, United Kingdom between the 7thof February and 19thApril 2020 (inclusive) was reviewed, and hospitalised patients were identified. All URT RT-PCR tests were analysed for each patient to determine the sequence of negative and positive results. For those who were tested twice or more but never received a positive result, case records were reviewed, and a clinical diagnosis of COVID-19 allocated based on clinical features, discharge diagnosis, and radiology and haematology results. For those who had a negative RT-PCR test but a clinical diagnosis of COVID-19, respiratory samples were retested using a multiplex respiratory panel, a second SARS-CoV-2 RT-PCR assay, and a human RNase P control. Results:Compared to the gold standard of a clinical diagnosis of COVID-19, the sensitivity of a single upper respiratory tract RT-PCR for COVID-19 was 82.2% (95% confidence interval 79.0-85.1%).   The sensitivity of two upper respiratory tract RT-PCR tests increased sensitivity to 90.6% (CI 88.0-92.7%). A further 2.2% and 0.9% of patients who received a clinical diagnosis of COVID-19 were positive on a third and fourth test; this may be an underestimate of the value of further testing as the majority of patients 93.0% (2999/3226) only had one or two URT RT-PCR tests. Conclusions:The sensitivity of a single RT-PCR test of URT samples in hospitalised patients is 82.2%. Sensitivity increases to 90.6% when patients are tested twice.  A proportion of cases with clinically defined COVID-19 never test positive on URT RT-PCR despite repeat testing.
PB - F1000 Research
UR - https://www.research.ed.ac.uk/portal/en/publications/sensitivity-of-rtpcr-testing-of-upper-respiratory-tract-samples-for-sarscov2-in-hospitalised-patients-a-retrospective-cohort-study(211f8c37-5bd7-4d1a-b6e3-b826e17b5948).html
KW - Coronavirus (COVID-19)
KW - Hospital care
ER