Comparison of viral levels in individuals with or without symptoms at time of COVID-19 testing among 32,480 residents and staff of nursing homes and assisted living facilities in Massachusetts
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Abstract
Background
Transmission of COVID-19 from people without symptoms poses considerable challenges to public health containment measures. The distribution of viral loads in individuals with and without symptoms remains uncertain. Comprehensive cross-sectional screening of all individuals in a given setting provides an unbiased way to assess viral loads independent of symptoms, which informs transmission risks. COVID-19 cases initially peaked in Massachusetts in mid-April 2020 before declining through June, and congregate living facilities were particularly affected during this early surge. We performed a retrospective analysis of data from a large public health-directed outbreak response initiative that involved comprehensive screening within nursing homes and assisted living facilities in Massachusetts to compare nasopharyngeal (NP) viral loads (as measured by RT-PCR cycle threshold (Ct) levels) in residents and staff to inform our ability to detect SARS-CoV-2 in individuals with or without symptoms in the population.
Methods
Between April 9 and June 9, 2020, we tested NP swabs from 32,480 unique individuals comprising staff and residents of the majority of nursing homes and assisted living facilities in Massachusetts. Under the direction of the MA Department of Public Health (MDPH), symptomatology at the time of sampling and demographic information was provided by each facility for each individual to facilitate reporting to health officials. NP swabs were collected, RNA extracted, and SARS-CoV-2 testing performed using quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR).
Results
The nursing home and assisted living facilities resident cohort (N =16,966) was 65% female with a mean age of 82 years (SD 13 yrs). The staff cohort (N = 15,514) was 76% female with a median age of 45 (SD 15 yrs). A total 2654 residents (15.5%) and 624 staff (4.1%) tested positive for SARS-CoV-2. 12.7% of residents and 3.7% of staff without symptoms tested positive for SARS-CoV-2, compared to 53.1% of residents and 18.2% of staff with symptoms. Of the individuals who tested positive, 70.8% of residents and 92.4% of staff lacked symptoms at the time of testing. In aggregate, the distributions of Cts for viral probes used in the qRT-PCR assay were very similar, with a statistically but not meaningfully different mean (ΔCt 0.71 cycles, p = 0.006) and a similar range (12-38 cycles), between populations with and without symptoms over the entire time period, across all sub-categories examined (age, race, ethnicity, sex, resident/staff). Importantly, the Ct mean values and range were indistinguishable between the populations by symptom class during the peak of the outbreak in Massachusetts, with a Ct gap appearing only later in the survey period, reaching >3 cycles (p ≤ 0.001) for facilities sampled during the last two weeks of the study.
Conclusions
In a large cohort of individuals screened for SARS-CoV-2 by qRT-PCR, we found strikingly similar distributions of viral load in patients with or without symptoms at the time of testing during the local peak of the epidemic; as the epidemic waned, individuals without symptoms at the time of testing had lower viral loads. The size of the study population, including both staff and residents spanning a wide range of ages, provides a comprehensive cross-sectional point prevalence measurement of viral burden in a study spanning 2 months. Because the distributions of viral loads in infected individuals irrespective of symptomatology are very similar, existing testing modalities that have been validated for detection of SARS-CoV-2 RNA in symptomatic patients should perform similarly in individuals without symptoms at the time of testing.
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SciScore for 10.1101/2020.07.20.20157792: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Internal Ct data were collected as part of the diagnostic efforts as part of this public health response and were deemed exempt human subjects research by the Broad Institute Office of Research Subject Protection and approved with waiver of informed consent by the MA Department of Public Health’s Institutional Review Board.
IRB: Internal Ct data were collected as part of the diagnostic efforts as part of this public health response and were deemed exempt human subjects research by the Broad Institute Office of Research Subject Protection and approved with waiver of informed consent by the MA Department of Public Health’s Institutional Review Board.Rando… SciScore for 10.1101/2020.07.20.20157792: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Internal Ct data were collected as part of the diagnostic efforts as part of this public health response and were deemed exempt human subjects research by the Broad Institute Office of Research Subject Protection and approved with waiver of informed consent by the MA Department of Public Health’s Institutional Review Board.
IRB: Internal Ct data were collected as part of the diagnostic efforts as part of this public health response and were deemed exempt human subjects research by the Broad Institute Office of Research Subject Protection and approved with waiver of informed consent by the MA Department of Public Health’s Institutional Review Board.Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources All analyses were completed with SAS JMP software, version 13 (SAS Institute). SAS JMPsuggested: NoneSAS Institutesuggested: (Statistical Analysis System, RRID:SCR_008567)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:This study should be interpreted with certain caveats. First, without longitudinal follow-up, we cannot distinguish infected individuals who are permanently asymptomatic from those who are pre-symptomatic. However, both classes likely carry risk for transmitting the virus in the absence of symptoms 8,14,42 even while differing in their implications for contact tracing and for understanding the natural history of COVID-191. Quantifying the viral burden in individuals without symptoms at the time of testing is thus an important step towards better understanding their transmission risk relative to symptomatic individuals. Second, with only a binary point-prevalence assessment of symptoms at the time of testing, we cannot draw any conclusions about the relationship between viral load and concurrent or future symptom severity in this population; however, the similarity in viral load distributions between individuals with and without symptoms suggests that viral load may not be the sole determinant of symptoms. These are important avenues for future study in longitudinal studies. Third, nursing home residents and staff may differ with respect to stages or disease severity from other populations, such as severely symptomatic individuals presenting to an acute setting for testing or requiring hospitalization12, or asymptomatic individuals in different settings. Nonetheless, these data represent Ct values for non-hospitalized individuals who did not seek acute testing, which represent...
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.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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SciScore for 10.1101/2020.07.20.20157792: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Internal Ct data were collected as part of the diagnostic efforts as part of this public health response and were deemed exempt human subjects research by the Broad Institute Office of Research Subject Protection and approved with waiver of informed consent by the MA Department of Public Health’s Institutional Review Board. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable Results The nursing home and assisted living facilities resident cohort (N =16,966) was 65% female with a mean age of 82 years (SD 13 yrs). Table 2: Resources
Software and Algorithms Sentences Resources All analyses were … SciScore for 10.1101/2020.07.20.20157792: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Internal Ct data were collected as part of the diagnostic efforts as part of this public health response and were deemed exempt human subjects research by the Broad Institute Office of Research Subject Protection and approved with waiver of informed consent by the MA Department of Public Health’s Institutional Review Board. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable Results The nursing home and assisted living facilities resident cohort (N =16,966) was 65% female with a mean age of 82 years (SD 13 yrs). Table 2: Resources
Software and Algorithms Sentences Resources All analyses were completed with SAS JMP software, version 13 (SAS Institute). SAS JMPsuggested: None<div style="margin-bottom:8px"> <div><b>SAS Institute</b></div> <div>suggested: (Statistical Analysis System, <a href="https://scicrunch.org/resources/Any/search?q=SCR_008567">SCR_008567</a>)</div> </div> </td></tr></table>Data from additional tools added to each annotation on a weekly basis.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.
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