At what times during infection is SARS-CoV-2 detectable and no longer detectable using RT-PCR based tests?: A systematic review of individual participant data
Authors: Mallett Sue , Allen A. Joy , Graziadio Sara , Taylor Stuart , Sakai Naomi S , Green Kile , Suklan Jana , Hyde Chris , Shinkins Bethany , Zhelev Zhivko , Peters Jaime , Turner Philip , Roberts Nia W. , di Ruffano Lavinia Ferrante , Wolff Robert , Whiting Penny , Winter Amanda , Bhatnagar Gauraang , Nicholson Brian D. , Halligan Steve 
Published: July 2020

STRUCTURED SUMMARYBackgroundTests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral ribonucleic acid (RNA), using reverse transcription polymerase chain reaction (RT-PCR) are pivotal to detecting current coronavirus disease (COVID-19) and duration of detectable virus indicating potential for infectivity.MethodsWe conducted an individual participant data (IPD) systematic review of longitudinal studies of RT-PCR test results in symptomatic SARS-CoV-2. We searched PubMed, LitCOVID, medRxiv and COVID-19 Living Evidence databases. We assessed risk of bias using a QUADAS- 2 adaptation. Outcomes were the percentage of positive test results by time and the duration of detectable virus, by anatomical sampling sites.FindingsOf 5078 studies screened, we included 32 studies with 1023 SARS-CoV-2 infected participants and 1619 test results, from -6 to 66 days post-symptom onset and hospitalisation. The highest percentage virus detection was from nasopharyngeal sampling between 0 to 4 days post-symptom onset at 89% (95% confidence interval (CI) 83 to 93) dropping to 54% (95% CI 47 to 61) after 10 to 14 days. On average, duration of detectable virus was longer with lower respiratory tract (LRT) sampling than upper respiratory tract (URT). Duration of faecal and respiratory tract virus detection varied greatly within individual participants. In some participants, virus was still detectable at 46 days post- symptom onset.InterpretationRT-PCR misses detection of people with SARS-CoV-2 infection; early sampling minimises false negative diagnoses. Beyond ten days post-symptom onset, lower RT or faecal testing may be preferred sampling sites. The included studies are open to substantial risk of bias so the positivity rates are probably overestimated.PANEL: RESEARCH IN CONTEXTEvidence before this studyThere are numerous reports of negative severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse transcription polymerase chain reaction (RT-PCR) test results in participants with known SARS-CoV-2 infection, and increasing awareness that the ability of RT-PCR tests to detect virus depends on the timing of sample retrieval and anatomical sampling site.Individual studies suggest that positive test results from RT-PCR with nasopharyngeal sampling declines within a week of symptoms and that a positive test later in the disease course is more likely from sputum, bronchoalveolar lavage (BAL) or stool, but data are inconsistent.Added value of this studyWe searched 5078 titles and abstracts for longitudinal studies reporting individual participant data (IPD) for RT-PCR for participants with COVID-19 linked to either time since symptom onset or time since hospitalisation. Search included SARS-CoV-2 and RT-PCR keywords and MeSH terms. Each included study was subject to careful assessment of risk of bias. This IPD systematic review (SR) addresses RT-PCR test detection rates at different times since symptom onset and hospitalisation for different sampling sites, and summarises the duration of detectable virus. To our knowledge, this is the first rapid SR addressing this topic. We identified 32 studies available as published articles or pre-prints between January 1stand April 24th2020, including participants sampled at 11 different sampling sites and some participants sampled at more than one site. At earlier time points, nasopharyngeal sampling had the highest virus detection, but the duration of shedding was shorter compared to lower respiratory tract sampling. At 10 to 14 days post-symptom onset, the percentage of positive nasopharyngeal test results was 54% compared to 89% at day 0 to 4. Presence and duration of faecal detection varied by participant, and in nearly half duration was shorter than respiratory sample detection. Virus detection varies for participants and can continue to be detected up to 46 days post-symptom onset or hospitalisation. The included studies were open to substantial risk of bias, so the detection rates are probably overestimates. There was also poor reporting of sampling methods and sparse data on sampling methods that are becoming more widely implemented, such as self-sampling and short nasal swab sampling (anterior nares/mid turbinate).Implications of all the available evidenceResults from this IPD SR of SARS-CoV-2 testing at different time points and using different anatomical sample sites are important to inform strategies of testing. For prevention of ongoing transmission of SARS-CoV-2, samples for RT-PCR testing need to be taken as soon as possible post-symptom onset, as we confirm that RT-PCR misses more people with infection if sampling is delayed. The percentage of positive RT-PCR tests is also highly dependent on the anatomical site sampled in infected people. Sampling at more than one anatomical site may be advisable as there is variation between individuals in the sites that are infected, as well as the timing of SARS-CoV-2 virus detection at an anatomical site. Testing ten days after symptom onset will lead to a higher frequency of negative tests, particularly if using only upper respiratory tract sampling. However, our estimates may considerably understate the frequency of negative RT-PCR results in people with SARS-CoV- 2 infection. Further investment in this IPD approach is recommended as the amount data available was small given the scale of the pandemic and the importance of the question. More studies, learning from our observations about risk of bias and strengths of example studies (Box 1, Box 2) are urgently needed to inform the optimal sampling strategy by including self-collected samples such as saliva and short nasal swabs. Better reporting of anatomical sampling sites with a detailed methodology on sample collection is also urgently needed.