Temporal Dynamics and (Para)Clinical Factors Associated With (Long) Viral RNA Shedding in COVID-19 Nonhospitalized Individuals - The COVID-HOME Study

Abstract

Understanding temporal patterns and determinants of RNA shedding is important to comprehend SARS-CoV-2 transmission and improve biosafety/isolation guidelines. Nonhospitalized SARS-CoV-2-infected individuals and household members were enrolled between March 2020 and June 2021 and followed prospectively ≥ 3 weeks during acute disease and at 3-, 6-, 12-, and 18-months to obtain (para)clinical data and biospecimens. Flow cytometry-based surrogate assay (FlowSA) detected viable SARS-CoV-2. Determinants of long RNA shedding ( ≥ 21 days) were investigated. RNA shedding median duration was 14 days (IQR 8.0-21.0) for nasopharyngeal/throat (NPT) and 7 days (IQR 1.0-27.0) for feces- but 20 days (IQR 7.0-27.8) when excluding individuals positive at a single timepoint (25.2%). Among 17 NPT long shedders with FlowSA results, 12 (70.6%) demonstrated viable virus. NPT long shedding was independently positively associated with endocrine disease and chills. Fecal long shedding was independently inversely associated with age, female sex, and fatigue, but positively with vomiting. No associations with long-term COVID-19-related complaints were observed. Finally, fecal long shedders demonstrated higher anti-spike(S1) IgG levels over 18-month follow-up than non-long shedders (p = 0.006). (Long) SARS-CoV-2 RNA shedding in NPT and feces associates with age and acute-but not prolonged-symptoms. The roles of prolonged infectious shedding and fecal shedding in transmission and immunity remain unclear.

Keywords: COVID‐19; SARS‐CoV‐2; post‐COVID‐19 syndrome; viral shedding.

Figure 1

Temporal dynamics in Ct values in NPT and fecal samples by age and sex. (A) Viral RNA shedding by specimen type. (B) NPT viral RNA shedding by sex. (C) NPT viral RNA shedding by age. (D) Fecal viral RNA shedding by sex. (E) Fecal viral RNA shedding by age. Data are presented as estimated marginal means (EMM) of Ct values. The error bars represent the 95% confidence intervals. Abbreviation: NPT, nasopharyngeal/throat.

Figure 2

Duration of viral RNA shedding (in days) by age group. (A) NPT viral RNA shedding increases with age, with a significant difference between age groups ≤ 15 and > 50 years (p = 0.004). (B) Fecal viral RNA shedding decreases with age, with significant differences between age groups ≤ 15 and 16–50 years (p = 0.005), and between age groups ≤ 15 and > 50 years (p = 0.024). Each point denotes the maximum duration of viral RNA shedding per individual.

Figure 3

Univariable analysis of association between clinical parameters and the odds of viral long shedding. (A) The likelihood of NPT long shedding (≥ 21 days) increases with age (chi‐square test for trend p = 0.006) and positively associates with diarrhea and chills as presenting symptom, and with chills, fever, and anorexia at any time during the 21‐day follow‐up. (B) The likelihood of long shedding in feces (≥ 21 days) decreases with age (chi‐square test for trend p = 0.030) and inversely associates with myalgia and fatigue at any time during the 21‐day follow‐up. Abbreviations: NPT, nasopharyngeal/throat; CI, confidence intervals.

Figure 4

Comparison of anti‐S1 SARS‐CoV‐2 IgG levels in individuals with and without long viral RNA shedding. (A) NPT. (B) Feces. Data are presented as estimated marginal means (EMM) of log‐transformed anti‐S1 SARS‐CoV‐2 IgG levels in BAU/mL. The error bars represent 95% confidence intervals. Abbreviations: D, days; M, months; NPT, nasopharyngeal/throat.

Figure 5

Detection of viable virus in selected samples by sampling day and Ct value. (A) Detection levels of N protein in NPT samples by FlowSA methodology, stratified by day of sampling. Error bars represent mean ± standard error of the mean (SEM). Dotted line indicates threshold below which NPT samples are considered negative for FlowSA. (B) Correlation between FlowSA results and Ct values for SARS‐CoV‐2 E gene of respective Association of percentage of SARS‐CoV‐2 N⁺ cells with SARS‐CoV‐2 qRT‐PCR Ct values were determined using Spearman's correlation method.