Limited clinical utility of early repeat RT-PCR testing for SARS-CoV-2

The gold standard diagnostic assay for severe acute respiratory syndrome coronavirus (SARS-CoV-2) is reverse-transcription polymerase chain reaction (RT-PCR).  The analytical performance of SARS-CoV-2 RT-PCR tests has been well described (1), however there are limited data regarding the clinical (cf. analytical) performance of RT-PCR (2). Pre-analytical factors such as timing of illness, anatomical sample site and sample collection may impact on clinical performance.

To further understand the clinical performance of SARS-CoV-2 RT-PCR, we assessed the frequency and characteristics of discordant SARS-CoV-2 RT-PCR results in Melbourne, Victoria, Australia.  Between 1^st June and 21^st July 2020 Melbourne was experiencing a “second wave” of COVID-19.  A total of 15,358 SARS-CoV-2 RT-PCR tests were performed in our laboratory at the Royal Melbourne Hospital, Melbourne, Australia on 12,569 unique patients (Table 1 - available in PDF), using previously described methods [3]. Of these 15,358 SARS-CoV-2 RT-PCR tests, 12,215 (79.5%) were performed on patients attending health services for SARS-CoV-2 testing, with the remainder performed on symptomatic or asymptomatic healthcare workers. A risk-based approach to screening was undertaken; all patients requiring hospital admission who met the Victorian Department of Health and Human Services case definition for suspected COVID-19 [4] required two consecutive negative combined deep nasal and oropharyngeal swabs, or one negative combined deep nasal and oropharyngeal swab and one negative sputum or tracheal aspirate prior to standing down transmission-based infection control precautions (Supplementary Table 1 - available in PDF). 

Of the 12,569 patients tested during the study period, 2,218 (17.6%) underwent repeat testing.  Repeat testing was performed within 7 days in 1,391 patients (Supplementary Figure 1 - available in PDF).  Of these, 25/1,391 (1.8%) had initial negative results followed by a subsequent positive result within 7 days. All 25 patients had at least one epidemiological risk factor for COVID-19 (known contact with a confirmed COVID-19 case; contact with a confirmed outbreak within the healthcare or residential setting; or occupational healthcare exposure) (Table 1 - available in PDF).  Although a detailed assessment of epidemiological risk factors could not be performed for all individuals tested during the study period for comparison, this finding is notable given the relatively low prevalence of COVID-19 in Victoria during this period (peak rate of infection 54.2 per 100,000 population [5]).  Importantly, 12/25 (48%) patients were asymptomatic at the time of their initial sample, which was collected in the setting of contact with a confirmed COVID-19 case, outbreak or asymptomatic healthcare worker surveillance; suggesting the initial swab may have represented the patients’ incubation period after a known exposure, rather than a false negative result. Of 1,105 patients with a repeat SARS-CoV-2 RT-PCR within 24 hours of their initial test, only one patient returned a subsequent positive result.  This patient had a sputum collected as their subsequent sample after a negative nasopharyngeal swab, which has been demonstrated to be a more sensitive sample type for SARS-CoV-2 [6].

Our observations in a low-prevalence setting suggest that progression from a negative to a positive SARS-Co-2 RT-PCR result within 7 days was uncommon and was not observed outside of well-defined epidemiological risk groups. These findings suggest that a risk-based approach to repeat testing for SARS-CoV-2 based on epidemiological risk factors may safely reduce the need for repeat sampling.   These data informed a change in hospital policy such that repeat swabs were not routinely required for hospitalized patients except in defined epidemiological risk groups. We suggest that in low-prevalence settings, a risk-based approach to screening may result in improved patient flow in healthcare settings, reduced use of personal protective equipment, reduced patient discomfort and conservation of limited testing reagents.

Acknowledgements: We thank Kirsty Buising, Louis Irving, Mark Putland, Douglas F. Johnson, Caroline Marshall, Benjamin C. Cowie and Stephen Muhi for their tireless service in the COVID-19 response and for their review of this work. We thank the staff in the Department of Microbiology at the Royal Melbourne Hospital for their technical support.

Conflicts of interest: The authors declare no conflicts of interest.

Ethics approval: This study was undertaken as part of routine validation and quality assurance activities related to the introduction of new in-vitro diagnostic devices, approved by the Melbourne Health HREC (QA2019134).

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