Characterising the persistence of RT-PCR positivity and incidence in a community survey of SARS-CoV-2
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Abstract
Background
Community surveys of SARS-CoV-2 RT-PCR swab-positivity provide prevalence estimates largely unaffected by biases from who presents for routine case testing. The REal-time Assessment of Community Transmission-1 (REACT-1) has estimated swab-positivity approximately monthly since May 2020 in England from RT-PCR testing of self-administered throat and nose swabs in random non-overlapping cross-sectional community samples. Estimating infection incidence from swab-positivity requires an understanding of the persistence of RT-PCR swab positivity in the community.
Methods
During round 8 of REACT-1 from 6 January to 22 January 2021, of the 2,282 participants who tested RT-PCR positive, we recruited 896 (39%) from whom we collected up to two additional swabs for RT-PCR approximately 6 and 9 days after the initial swab. We estimated sensitivity and duration of positivity using an exponential model of positivity decay, for all participants and for subsets by initial N-gene cycle threshold (Ct) value, symptom status, lineage and age. Estimates of infection incidence were obtained for the entire duration of the REACT-1 study using P-splines.
Results
We estimated the overall sensitivity of REACT-1 to detect virus on a single swab as 0.79 (0.77, 0.81) and median duration of positivity following a positive test as 9.7 (8.9, 10.6) days. We found greater median duration of positivity where there was a low N-gene Ct value, in those exhibiting symptoms, or for infection with the Alpha variant. The estimated proportion of positive individuals detected on first swab, P 0 , was found to be higher for those with an initially low N-gene Ct value and those who were pre-symptomatic. When compared to swab-positivity, estimates of infection incidence over the duration of REACT-1 included sharper features with evident transient increases around the time of key changes in social distancing measures.
Discussion
Home self-swabbing for RT-PCR based on a single swab, as implemented in REACT-1, has high overall sensitivity. However, participants’ time-since-infection, symptom status and viral lineage affect the probability of detection and the duration of positivity. These results validate previous efforts to estimate incidence of SARS-CoV-2 from swab-positivity data, and provide a reliable means to obtain community infection estimates to inform policy response.
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SciScore for 10.1101/2021.08.12.21261987: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:The model used in calculating daily incidence has a number of limitations. Firstly we assumed an exponential decay to describe the probability of a participant testing positive in our study, which would not capture non-exponential longer-term trends in the waning of positivity. This limitation is unavoidable because our maximum follow-up …
SciScore for 10.1101/2021.08.12.21261987: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:The model used in calculating daily incidence has a number of limitations. Firstly we assumed an exponential decay to describe the probability of a participant testing positive in our study, which would not capture non-exponential longer-term trends in the waning of positivity. This limitation is unavoidable because our maximum follow-up was17 days after the initial positive infection, while it is known that people may remain positive for much longer periods [12]. Secondly, in estimating incidence we have assumed that the parameter estimates obtained for the decay of positivity from our round 8 substudy are representative of the entire study duration. Subgroup analysis showed there were differences in sensitivity and duration of positivity in individuals based on initial N-gene Ct value, symptomatology and viral lineage. With N-gene Ct value highly dependent on the contemporaneous growth rate of the pandemic [13], the distribution of Ct values may vary between rounds. Furthermore, lineages responsible for infections changed over the study period with the emergence of the Alpha variant in late 2020 [14], and the Delta variant in April 2021 [15]. We were unable to use lineage specific parameter estimates in estimates of infection incidence as lineage was only determined (via viral sequencing) in samples with lower Ct values (<34). The median and mean durations of positivity we report do not directly inform isolation and quarantine policy. For example, the shorter duration of po...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
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- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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