key: cord-0996373-41r16txz
authors: Mellis, A. M.; Meece, J. K.; Halasa, N. B.; Chappell, J. D.; McLean, H. Q.; Grijalva, C. G. Q.; Hanson, K. E.; Zhu, Y.; Kim, A.; Deyoe, J.; Ivacic, L. C.; Reed, C.; Talbot, H. K.; Rolfes, M. A.
title: SARS-CoV-2 virus dynamics in recently infected people - data from a household transmission study
date: 2022-03-18
journal: nan
DOI: 10.1101/2022.03.17.22272516
sha: dc7609ec3cb6d36f38efc00f81fa218710d07c80
doc_id: 996373
cord_uid: 41r16txz

We used daily real-time reverse-transcription polymerase chain reaction (rRT-PCR) results from 67 cases of SARS-CoV-2 infection in a household transmission study to examine the trajectory of cycle threshold (Ct) values, an inverse correlate of viral RNA concentration, from nasal specimens collected between April 2020 and May 2021. Ct values varied over the course of infection, across RT-PCR platforms, and by participant age. Specimens collected from children and adolescents showed higher Ct values and adults aged [≥]50 years showed lower Ct values than adults aged 18-49 years. Ct values were lower on days when participants reported experiencing symptoms.

for use under a CC0 license. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. Cycle threshold (Ct) values are generated from real-time reverse-transcription 2 polymerase chain reaction (RT-PCR) assays and represent the minimum number of amplification 3 cycles needed to generate a signal for a specific target. Ct values are sometimes used as a 4 surrogate signal for SARS-CoV-2 viral loads [1] , as they are inversely related to the amount of 5 virus present in the tested specimen, but are best interpreted as viral RNA template 6 concentration. Widespread availability has led to comparisons of Ct values at the patient [2] and 7 community[3] levels to infer associations with illness severity and patient characteristics. 8

However, Ct values can vary by assay, specimen type and quality, and time during the infection 9 course, especially complicating cross-sectional comparisons. Use of serial specimens collected 10 from one individual over the course of infection on the same assay can partially mitigate these 11

concerns, yet few investigations have used serial sampling to describe the natural history of 12 SARS-Co-V2 infection [4, 5] and even fewer have been conducted among the general 13 population[6, 7]. 14 We described SARS-CoV-2 RT-PCR Ct values in newly infected individuals who 15 underwent daily specimen collection as part of a multi-site prospective household transmission 16 study. We examined the impact of age and symptoms on Ct value trajectories to understand the 17 natural history of infection. 18

We conducted a household transmission study of SARS-CoV-2 in Tennessee and 20

Wisconsin[8] between April 2020 and May 2021. Index participants were first identified as non-21 hospitalized individuals who had tested positive for SARS-CoV-2 by a provider-ordered nucleic 22 acid amplification test, and resided with at least one other individual. Index participants and 23 for use under a CC0 license. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. participants also completed demographic surveys and self-reported pre-existing conditions 4 (asthma, chronic liver disease, premature birth, cardiac conditions, diabetes, cancer, 5 immunocompromising conditions, extreme obesity, kidney disease, or pregnancy) and, after 6 COVID-19 vaccines became available, vaccination status (which was also verified against health 7 records and immunization information systems). 8

Anterior nasal swabs were self-/parent-collected by study participants. Swabs were either 9 placed in viral transport media (Remel MicroTest M4RT ®, Lenexa, KS USA) and refrigerated 10 by participants for 7-10 days before transport, or placed in inactivating viral transport media 11 As an additional quality control measure for this analysis, we excluded Ct values from any test 20 where the control (RNase P or MS2) result was interpreted as negative or where the RNase P 21 control target had a Ct value greater than 35 (though this exclusion did not change results). 22

for use under a CC0 license. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. Viral culture was conducted on positive specimens from a subset of participants tested 1 using the CDC assay. Wells were seeded with Vero E6-TMPRSS2 cells, to which 100μl of 2 participant specimen was added. Wells were monitored daily for culture positivity for five days 3 after inoculation. If >20% of cells were detached in wells exhibiting viral cytopathic effect, the 4 specimen was interpreted as culture positive. Additional detail of culture methods and results are 5 included in another report [9] . 6

To examine trajectories of Ct values over the course of infection, we selected data from 7 household contacts who met the following criteria: individuals' first specimen must have been 8

negative, they must have tested positive in 3 or more tests, and all tests must have been 9 conducted on the same assay (Supplemental Figure 1 ). Days of lowest Ct values were defined 10 per target ( N1, N2, N, S, or ORF1ab). We described Ct values over time using generalized 11 additive models controlling for the target of each assay (which also differed by assay type), with 12 a random effect spline for repeated measurements. We compared three models for age: 1) a null 13 model with no age effect and a single smoothing spline for the effect of each day since first 14 testing positive, representing a null hypothesis; 2) a model with categorical age (0-11, 12-17, 18-15 49, or ≥50 years) and a single spline for time since first positive specimen, representing an 16 impact of age on Ct values but not necessarily on how those Ct values change over time; 3) a 17 model with both age and different splines for time since first positive in each age category, 18

representing an impact of age both on Ct values overall and on how trajectories change over 19 time. Model 2 had the lowest Akaike Information Criterion (AIC), and accounted for the greatest 20 deviance (50.4%). We also explored the effects of symptoms on each day of infection, 21

controlling for age as in Model 2; symptoms were considered as binary (whether the participant 22

reported any symptom on that day, yes/no) and categorical indicators (whether a participant was 23 for use under a CC0 license.

This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. post-symptomatic that day); the binary model was chosen by smaller AIC and used for both the 2 primary results (on impact of any symptom) and post-hoc analysis of individual symptoms 3 (Supplemental Table 1 ). Similar models were used for analysis by other demographic factors. 4

A total of 577 household contacts from 302 households were enrolled in the parent study 6

April 2020 -May 2021. Sixty-seven contacts from 50 households met our criteria for "incident 7 10.4% having received only one dose of an mRNA COVID-19 vaccine before enrollment; Table  10 1 for demographics and Supplemental This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted March 18, 2022. ; https://doi.org/10.1101/2022.03.17.22272516 doi: medRxiv preprint especially in our ability to assess the impact of vaccination status or dissociate vaccination or 1 other demographics from age. Ct values also cannot be converted to a quantitative representation 2 of viral load, and cannot be used to directly infer differences in infectiousness. However, despite 3 these limitations, clinical interpretation of Ct values (or their trajectories) may be "tempting" 4 (IDSA and AMP joint statement on the use of SARS-CoV-2 PCR cycle threshold (Ct) values for 5 clinical decision-making, page 3) [14] . The present data are directly relevant to these 6 interpretations. Specifically, specimens that were collected within 4 days of symptom onset may 7 represent periods when Ct values are still declining. 8

These findings contribute to our understanding of RT-PCR Ct values during SARS-CoV-9 2 infections over a broad range of ages, in a community setting with mostly mildly symptomatic 10 illness, and among individuals with a known date of first shedding. While these data were 11 collected prior to Delta and Omicron circulation, and prior to widespread vaccination, they may 12 provide context for interpreting trajectories in Ct values in similar populations during later 13 SARS-CoV-2 outbreaks. 14 for use under a CC0 license.

This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. ComboKit).

To Interpret the SARS-CoV-2 Test, Consider the Cycle Threshold Value

Coronavirus 2 Viral Load on Risk of Intubation and Mortality Among Hospitalized Patients With 5

Correlation of Population SARS-CoV

Cycle Threshold Values to Local Disease Dynamics: Exploratory Observational Study. JMIR 8 public health and surveillance

Viral dynamics of acute SARS-CoV-2 infection and 10 applications to diagnostic and public health strategies

Longitudinal analysis of SARS-CoV-2 vaccine 12 breakthrough infections reveal limited infectious virus shedding and restricted tissue distribution

Community transmission and viral load kinetics 15 of the SARS-CoV-2 delta (B.1.617.2) variant in vaccinated and unvaccinated individuals in the 16 UK: a prospective, longitudinal, cohort study

Trajectory of Viral RNA Load Among 18

Persons With Incident SARS-CoV-2 G614 Infection (Wuhan Strain) in Association With 19 COVID-19 Symptom Onset and Severity

Transmission of SARS-COV-2 infections in 21 households-Tennessee and Wisconsin

Surveillance and correlation of SARS-CoV-2 viral RNA

antigen, virus isolation, and self-reported symptoms in a longitudinal study with daily sampling

Committee Perspective: Caution Must Be Used in Interpreting the Cycle Threshold

Reaction Cycle Threshold Values in the Detection of Severe Acute Respiratory Syndrome 8

Coronavirus 2 (SARS-CoV-2)

Differences in Nasopharyngeal Severe Acute Respiratory Syndrome Coronavirus

Levels in Patients With Mild to Moderate Coronavirus Disease 2019 (COVID-19)

Comparison of Reverse-Transcription Polymerase 14

Chain Reaction Cycle Threshold Values From Respiratory Specimens in Symptomatic and 15

Asymptomatic Children With Severe Acute Respiratory Syndrome Coronavirus 2 Infection

Infectious Diseases Society of America AfMP. IDSA and AMP joint statement on the use of 18

SARS-CoV-2 PCR cycle threshold (Ct) values for clinical decision-making

Household Transmission and Clinical Features 20 of SARS-CoV-2 Infections by Age in 2 US Communities. medRxiv : the preprint server for 21