Characterization of SARS-CoV-2 Omicron persistence and infectivity among children

In a recent study posted to the medRxiv* preprint server, researchers characterized the persistence and infectivity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron among children.

Study: Persistence of SARS-CoV-2 omicron variant in children and utility of rapid antigen testing as an indicator of culturable virus. Image Credit: L Julia/Shutterstock


Since the first reports of coronavirus disease 2019 (COVID-19), our understanding of SARS-CoV-2 transmission has evolved with the emergence of newer variants. In July 2020, the United States (US) Centers for Disease Control and Prevention (CDC) recommended a 10-day isolation period for SARS-CoV-2-infected individuals without the need for an associated negative result.

The Florida Department of Health (FDOH) in September 2021 ruled that infected children could return to schools earlier than ten days, provided that they test negative for SARS-CoV-2 and show no symptoms.

In January 2022, the CDC updated the guidelines, reducing the isolation period to five days and permitting infected adults/children to return to workplaces/schools if afebrile; nonetheless, masking was mandatory for five more days. Furthermore, in February 2022, the FDOH permitted the return of infected children after five days of isolation without taking tests or using masks.

About the study

In the present study, researchers characterized the prevalence and infectivity of SARS-CoV-2 Omicron among children. Those with a positive SARS-CoV-2 result in a polymerase chain reaction (PCR) or rapid antigen test (RAT) were identified from the University of Florida (UF) Health pediatric clinics or referred by school nurses at a local public school.

They enrolled kids who showed symptoms for five days or longer with sampling between December 20, 2021, and February 21, 2022. Parents’ samples were also collected when multiple children from the same family were enrolled in the study. After enrolment, nasal swab samples were obtained from 31 children (16 years or younger) and eight from three parents.

The team collected two specimens from each participant. One sample was immediately tested with a BinaxNOW RAT, and the other was frozen until subsequent reverse-transcriptase quantitative PCR (RT-qPCR), culture tests, determination of viral load, and genome sequencing.

Those with a positive test result during the first follow-up returned on days 7, 10, or until a negative result was recorded. Different cell lines were used for viral cultures, such as LLC-MK2, Vero E6, A549, and HEK293T cells. They observed cells for a month, and the presence of the virus was verified by an RT-PCR test when cytopathic effects (CPE) became evident.


Two-thirds of the children were boys, and the median age was seven. Ten had negative RAT results at enrolment that corresponded to their fourth day (or later) of symptom onset or after initial positive result (from UF Health or school referrals). They observed at least one positive RAT for the remaining children; subsequently, 14 tested negative.

Assuming that all children would be SARS-CoV-2-positive before their last positive result, the authors calculated that more than a third of them would be SARS-CoV-2-positive on day 5, and 48% would still test positive on RAT by day 7. Next, the team estimated the duration of children being positive over time by fitting a parametric survival model.

The model predicted that children would remain positive for 7.74 mean days, with a 10% drop in the probability of being positive by day 12. SARS-CoV-2 cultures were performed on 23 samples. Virus cultures were positive for 16 samples, and all were RAT-positive. Seven culture-negative samples were also RAT-negative. Moreover, a significant correlation was noted between RAT and culture results.

Forty samples were RAT-positive, and all tested positive in RT-qPCR tests. Of the 25 RAT-negative samples, nine were RT-qPCR-positive; four of these samples were cultured and produced negative results. Sequencing revealed that all positive samples were of Omicron BA.1 variant. The phylogenetic analysis did not find much variability, consistent with the circulation of a single SARS-CoV-2 clade.


The authors reported that nearly half the infected children would have been SARS-CoV-2-positive for a minimum of two days had they returned to schools based on the CDC’s January 2022 guidelines. Although masks would have reduced the transmission, masking practice was controversial in Florida, given the FDOH’s February 2022 recommendations.

From a public health perspective, limiting SARS-CoV-2 transmission by infected children in schools is essential. Thus, extending the five-day isolation period before returning to school should be considered with the requirement of a negative RAT result.

*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.

Journal reference:
  • Lohse, Z. et al. (2022) "Persistence of SARS-CoV-2 omicron variant in children and utility of rapid antigen testing as an indicator of culturable virus". medRxiv. doi: 10.1101/2022.06.21.22276668.

Posted in: Medical Science News | Medical Research News | Disease/Infection News

Tags: Antigen, Cell, Children, Coronavirus, Coronavirus Disease COVID-19, covid-19, Genome, Omicron, Polymerase, Polymerase Chain Reaction, Public Health, Respiratory, SARS, SARS-CoV-2, Severe Acute Respiratory, Severe Acute Respiratory Syndrome, Syndrome, Virus

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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.

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