Comparison of secondary attack rate and viable virus shedding between patients with SARS-CoV-2 Delta and Omicron variants: A prospective cohort study

Abstract

There are limited data comparing the transmission rates and kinetics of viable virus shedding of the Omicron variant to those of the Delta variant. We compared these rates in hospitalized patients infected with Delta and Omicron variants. We prospectively enrolled adult patients with COVID-19 admitted to a tertiary care hospital in South Korea between September 2021 and May 2022. Secondary attack rates were calculated by epidemiologic investigation, and daily saliva samples were collected to evaluate viral shedding kinetics. Genomic and subgenomic SARS-CoV-2 RNA was measured by PCR, and virus culture was performed from daily saliva samples. A total of 88 patients with COVID-19 who agreed to daily sampling and were interviewed, were included. Of the 88 patients, 48 (59%) were infected with Delta, and 34 (41%) with Omicron; a further 5 patients gave undetectable or inconclusive RNA PCR results and 1 was suspected of being coinfected with both variants. Omicron group had a higher secondary attack rate (31% [38/124] vs. 7% [34/456], p < 0.001). Survival analysis revealed that shorter viable virus shedding period was observed in Omicron variant compared with Delta variant (median 4, IQR [1-7], vs. 8.5 days, IQR [5-12 days], p < 0.001). Multivariable analysis revealed that moderate-to-critical disease severity (HR: 1.96), and immunocompromised status (HR: 2.17) were independent predictors of prolonged viral shedding, whereas completion of initial vaccine series or first booster-vaccinated status (HR: 0.49), and Omicron infection (HR: 0.44) were independently associated with shorter viable virus shedding. Patients with Omicron infections had higher transmission rates but shorter periods of transmissible virus shedding than those with Delta infections.

Keywords: COVID-19; infection dynamics; virus shedding.

Figure 1

Genomic and subgenomic viral copy numbers with timing of presence or absence of viable SARS‐CoV‐2 on viral vulture from the symptom onset and daily culture positivity between Delta and Omicron infections. Viral loads were determined with the viral copy numbers for N gene of SARS‐CoV‐2. Each dot represents a sample obtained on the specified day. (A) Genomic RNA PCR viral copy number and viral copy results of Delta variants. (B) Subgenomic RNA PCR and culture results of Delta variants. (C) Daily culture positivity of samples of Delta variants. (D) Genomic RNA PCR viral copy number and viral copy results of Omicron variants. (E) Subgenomic RNA PCR and culture results of Omicron variants. (F) Daily culture positivity of samples of Omicron variants. Fraction above bar graph indicates number of positive sample/number of collected sample of day.

Figure 2

Comparison of viral shedding period between Delta and Omicron infections. (A) Genomic RNA PCR for N gene of SARS‐CoV‐2. (B) Subgenomic RNA PCR for N gene of SARS‐CoV‐2. (C) Culture‐based virus isolation. Red line indicates Delta group, whereas blue line indicates Omicron group. p Value in figures were calculated from log‐rank test.