Exploring the viral dynamics of SARS-CoV-2 Omicron variant

Recently, researchers posted the findings of a retrospective study to the medRxiv* preprint server in which they investigated the viral dynamics of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Omicron variant.

Study: Viral dynamics and duration of PCR positivity of the SARS-CoV-2 Omicron variant. Image Credit: Naeblys/Shutterstock

SARS-CoV-2 Omicron variant is responsible for the rapid surge of coronavirus disease 2019 (COVID-19) cases witnessed lately around the globe. Studies have shown increased transmissibility, milder clinical severity of COVID-19, and immune evasive characteristics associated with the Omicron variant. Viral dynamics of SARS-CoV-2 differ by variant and the immune status of infected individuals.

The Omicron variant has been shown to have potentially shorter generation intervals in comparison to other SARS-CoV-2 variants necessitating a rethink of testing and isolation policies. which can only be achieved by understanding the degree and duration of viral shedding during an Omicron infection.

The study

In the present study, researchers evaluated the viral dynamics of the SARS-CoV-2 Omicron variant in infected individuals. A longitudinal set of about 10,324 SARS-CoV-2 samples collected from 537 participants from July 5, 2021, to January 10, 2022, was analyzed. These samples were collected as part of the occupational health program of the National Basketball Association (NBA) where frequent COVID-19 tests are conducted. Combined swabs of the oropharynx and anterior nares were collected for each person by a trained professional.

Viral load in samples was measured using cycle threshold (Ct) values which were converted into viral genome equivalents using standard curves. Samples with positive test results were further subject to a quantitative reverse transcription PCR (RT-qPCR) to identify Delta or Omicron variants based on 69-70 deletion of S-gene seen in the SARS-CoV-2 Omicron lineage BA.1. Samples with an S-gene target failure (SGTF) were marked as suspected Omicron and other specimens were verified by sequencing.

There were 107 and 97 clinical specimens infected with SARS-CoV-2 Delta and Omicron variants, respectively. Of the 97 Omicron samples, 48 were suspected Omicron by SGTF and the remaining samples (49) were confirmed by sequencing. A Ct value < 30 was chosen as the threshold which is assumed to correlate the presence of culturable virus with infectivity. Viral proliferation duration, viral clearance duration, duration of acute infection, and peak viral concentration were quantified by using a Bayesian hierarchical model for each person.

Results

The findings showed considerable heterogeneity in viral trajectories of Omicron samples and found that all individuals had tested negative for COVID-19 by day 15 post-detection as ascertained by RT-PCR. All patients demonstrated a Ct < 30 at some point during infection and were Ct ≥30 by day 11 post detection.

SARS-CoV-2 Omicron-infected individuals had a proliferation phase of 4.52 days and a clearance phase of 5.35 days. Overall, a mean duration of 9.87 days was noted for Omicron infections compared to 10.9 days for those infected with the Delta variant. The clearance phase was 6.23 days for individuals with SARS-CoV-2 Delta infection which is also lower when compared to Omicron-infected individuals. The rate of clearance was similar in both Delta (3.17 Ct per day) and Omicron infections (3.15 Ct per day)

Conclusions

The present study characterized the viral dynamics of SARS-CoV-2 Delta and Omicron variants in infected individuals and noted that the mean duration of infection for both Omicron and Delta variants was approximately 10 ± 1 days. Omicron-infected individuals showed lower peak viral load and shorter clearance phase than Delta-infected persons; however, the clearance rates and proliferation times remained similar in both Omicron- and Delta-driven infections.

All individuals had demonstrated a Ct ≥ 30 by 11 days post detection. The study did not account for prior immunity to SARS-CoV-2 in all subjects which could likely be the reason for the shorter clearance and proliferation phases observed for Omicron infections. The findings of this study could not explain why the SARS-CoV-2 Omicron variant exhibits high infectivity or its potential early onset of infectiousness.

The analyses were conducted based on Ct values, which reveal the number of viral RNA copies which does not necessarily explain infectiousness. The Ct threshold used in this study could not be considered perfect for other investigations and also the Ct values were for the combined nasal and oropharyngeal swabs that may differ for samples obtained from other anatomical sites as well as by PCR platforms.

The subjects of this study are working individuals, younger, and healthier and therefore, are not representative of the general population. Taken together, these results could help design a cautiously approached isolation policy and potentially avoid the unwarranted and pre-mature release of isolated individuals.

*Important notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Written by

Tarun Sai Lomte

Tarun is a writer based in Hyderabad, India. He has a Master’s degree in Biotechnology from the University of Hyderabad and is enthusiastic about scientific research. He enjoys reading research papers and literature reviews and is passionate about writing.