Viral dynamics of the SARS-CoV-2 Omicron Variant among household contacts with 2 or 3 COVID-19 vaccine doses

Abstract

Objectives: SARS-CoV-2 shedding has changed as new variants have emerged. It is important to understand the trajectory of PCR positivity due to Omicron in vaccinated populations.

Methods: Double- or triple-vaccinated adult household contacts of individuals with COVID-19 self-collected oral-nasal swabs for 14 days. A hierarchical linear model estimated viral load trajectories and an exploratory logistic regression model assessed for factors associated with viral detection before symptom onset.

Results: Forty-one participants developed COVID-19 with 37 (90%) symptomatic. Viral load peaked 3 days after symptom onset at a median concentration of 8.83 log₁₀ copies/milliliter (range 5.95-10.32) and the mean difference between participants with two or three COVID-19 vaccine doses was 0.02 log₁₀ copies/milliliter (95% CI -0.13 to 0.16). PCR positivity began with a range of 4 days prior to 3 days after symptom onset and was positive on the day of symptom onset in 76% (28/37). SARS-CoV-2 detection on the day of symptom onset was less likely among those with 2 vaccine doses (OR 0.13, 95%CI 0.02-0.79). 68% (25/37) of infected participants had detectable SARS-CoV-2 with Ct<30 at 7 days after symptom onset.

Conclusions: Peak viral load and duration of PCR positivity were similar in participants with COVID-19 after two versus three COVID-19 vaccine doses. Onset of viral detection relative to symptom onset was variable.

Keywords: COVID-19; Omicron; Viral trajectory.

Fig. 1

SARS-CoV-2 viral load trajectories from self-collected oral-nasal swabs standardized to the date of symptom onset for the 37 participants with symptoms (A, B) and from the first positive swab in the 26 participants with at least one preceding negative swab (C, D). Each participant's viral load trajectory is represented along with the modeled trajectory using a generalized additive model with a smoothing spline placed on the time for the overall cohort (A, C). The viral load trajectories of participants with 2 or 3 COVID-19 vaccine doses are also depicted (B, D).

Fig. 2

Daily SARS-CoV-2 viral load with their trajectory modeled using a hierarchical generalized additive model with a smoothing spline placed on the day from symptom onset (day 0) for each individual with symptoms. Rows are grouped by timing of SARS-CoV-2 detection in relation to symptom onset; yellow lines/dots represent participants who had received 3 doses of a COVID-9 vaccine, and gray lines/dots those who had received 2 doses.

Fig. 3

The proportion of participants with an E-gene cycle threshold above 30 and a negative swab standardized to the day of symptom onset (A) and day of first positive test (B).