Viral load kinetics of the severe acute respiratory syndrome coronavirus 2 Omicron variant in children aged 0 to 3 years and their parents : Chinese Medical Journal

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Clinical Observation

Viral load kinetics of the severe acute respiratory syndrome coronavirus 2 Omicron variant in children aged 0 to 3 years and their parents

Zhou, Jianguo1; Lu, Yanming2; Wang, Libo3; Yu, Hui4; Zhang, Ting5; Chen, Yiwei6; Zhou, Wenhao1

Editor(s): Ni, Jing

Author Information
Chinese Medical Journal ():10.1097/CM9.0000000000002326, December 26, 2022. | DOI: 10.1097/CM9.0000000000002326

The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first confirmed in November 2021 in South Africa[1] and is more transmissible than other sub-variants.[2] The influence of Omicron in children has been recognized with increased hospital admission rate than Delta wave.[3,4] But severe clinical outcomes and comorbidity of Omicron are less than Delta in children.[5] Hospitalized children during the Omicron period were more likely to be younger than that in the pre-Omicron period.[6]

Children aged 0 to 3 years were not eligible for coronavirus disease 2019 (COVID-19) vaccination and accounted for >60% of hospitalized pediatric cases in the current wave of SARS-CoV-2 Omicron (BA.2) variant infection in Shanghai, China since March 2022.[7] A study suggested that younger children may be more likely to transmit SARS-CoV-2 infection than older children, and the highest odds of transmission were observed for children aged 0 to 3 years.[8] However, the dynamics of viral load and required isolation and quarantine time in infected children are inconclusive. We hypothesize children shed viruses longer than adults. As such, we performed this prospective viral load comparison study. The result is expected to guide quarantine time and optimal frequency of reverse transcription-quantitative polymerase chain reaction tests for SARS-CoV-2 infected children.

Study design, setting, and patients’

This observational cohort study was conducted in a dedicated medical center for admitting COVID-19 infected children and adults with 890 beds, of which 470 were for children aged 0 to 14 years and their companion parents. All medical caregivers including pediatricians and nurses were deployed from three children's hospitals and one general hospital in Shanghai.

Infected children aged 0 to 3 years and their 1:1 matched infected parents admitted from April 12 to 30, 2022, were eligible for the study. In the matching process, most families have one kid and one parent. For those children accompanied by two parents, we chose the same-gender parent with the child. No parent took care of more than one child. If either the child or the parent had underlying diseases, both were excluded. Clinical data of age, gender, symptoms, severity of the disease, and vaccination were retrieved from medical records.

Virus load kinetics and the management of COVID-19 infection

Reverse transcription-polymerase chain reaction (RT-PCR) tests provide semiquantitative results in the form of cycle threshold (Ct) values, which are inversely correlated with viral loads and are useful in determining the need for isolation and quarantine.[9]ORF1ab gene of the SARS-CoV-2 genome was detected every other day in all recruited cases. Nasal swab specimens were collected by standard procedures. Diagnosis and treatment of COVID-19 infection were based on the universal Chinese national domestic guidelines.[10] All samples with a Ct <35 were recognized as active COVID-19 infections. Patients with two consecutive Ct values >35 with intervals of >24 h are eligible for de-isolation. The dynamics of the Ct value and the time interval (days requiring isolation, [DRI]) between the onset of symptoms and the first Ct value of >35 were compared between children and their parents.[11] This study was approved by the institutional review board of the Children's Hospital of Fudan University (No. 2022–82) and gained informed consent from the parents.

Categorical variables were expressed as n (%) and compared using the Chi-squared test or Fisher's exact test. Continuous variables were expressed as mean ± standard deviation or median (interquartile range). The Kaplan–Meier survival curve was drawn in the R software (version 4.1) to reflect the change in the probability of positive PCR tests between the two groups. The log rank was used to test the difference in the survival curves. We used local polynomial regression fitting to get the trend curve with a 95% confidence interval. Analysis of variance, t-test, and Fisher's exact test with adjustment for multiple testing using the false discovery rate method in the R version 4.1.

Recruited children and parents

We enrolled 203 children and 203 matched parents [Supplementary Figure 1,]. The basic clinical characteristics of children and parents were demonstrated in Supplementary Table 1, For both children and parents, fever was the dominant phenotype (97.5% vs. 78.8%) followed by cough (63.1% vs. 80.8%). Children had a significantly higher rate of vomiting than parents (15.8% vs. 6.9%; P = 0.022). All children were mildly-to-moderately ill. No children were vaccinated. Of 203 parents, 85 (41.9%), 14 (6.9%), 61 (30.0%), and 43 (21.1%) received no vaccine or 1, 2, and 3 doses of inactivated SARS-CoV-2 vaccine.

Virus load kinetics

Chronological Ct value and DRI analyses in children and parents were demonstrated in Figure 1. Ct values were significantly lower in children compared with those in their parents from day 4 to day 14 after the onset of symptoms and therefore with higher quantities of viral RNA [Figure 1A].

Figure 1:
(A) Chronological Ct value and DRI analyses in children aged 0 to 3 years and their parents. The upper panel of the scatter plot shows ORF1ab gene Ct values in children (dark cyan) and parents (orange) after the onset of symptoms. The lines show the fitting curve by polynomial regression. The 95% CI of the regression curve is displayed as shaded confidence bands. The lower panel of the scatter plot showed the Ct value difference between children and matched parents (blue). The lines show the fitting curve by polynomial regression. The 95% CI of the regression curve is displayed as shaded confidence bands (pink). From day 4 to day 14, the deviation of Ct value between parents and children had a significant difference by paired Student's t-test (adjusted P < 0.05). The adjustment for testing using the FDR method. (B) Time gap from symptom onset to negative PCR test results in children and parents. Ct trajectory of infected children (dark cyan) and 1:1 matched parents (orange). CI: Confidence interval; Ct: Cycle threshold; DRI: Days requiring isolation; FDR: False discovery rate; PCR: Polymerase chain reaction.

Virus shedding time comparisons between groups

DRI in children was significantly longer than that in their parents (13.4 ± 2.7 days vs. 11.4 ± 3.0 days, P < 0.001) [Figure 1B]. Subgroup analyses demonstrated that DRI was significantly longer in mothers than that in fathers, unvaccinated than vaccinated parents, and children than unvaccinated parents [Table 1].

Table 1 - Virus shedding time (DRI) of subgroups.
Group DRI P value
 Male vs. female 13.5 ± 2.5 vs. 13.3 ± 3.3 0.575
 Mild vs. moderate 13.4 ± 2.7 vs. 13.3 ± 3.2 0.894
 Age at 0–6 months vs. 6–12 months 13.8 ± 2.3 vs. 13.5 ± 2.7 0.668
 Age at 6–12 months vs. 12–36 months 13.5 ± 2.7 vs. 13.2 ± 2.9 0.462
 Age at 0–6 months vs. 12–36 months 13.8 ± 2.3 vs. 13.2 ± 2.9 0.961
 Fathers vs. mothers 10.2 ± 2.3 vs. 11.4 ± 3.0 0.019
 Mild vs. moderate 11.1 ± 2.9 vs. NA NA
 Vaccinated 0 vs. 1/2 12.3 ± 3.5 vs. 11.0 ± 2.3 0.015
 Vaccinated 0 vs. 3 12.3 ± 3.5 vs. 10.1 ± 2.7 <0.001
 Vaccinated 1/2 vs. 3 11.0 ± 2.3 vs. 10.1 ± 2.7 0.551
 Children vs. adults 13.4 ± 2.7 vs. 11.4 ± 3.0 <0.001
 Children vs. unvaccinated adults 13.4 ± 2.7 vs. 12.3 ± 3.5 <0.001
Data are shown as mean ± standard deviation; DRI: Days requiring isolation; NA: Not applicable.

In this study, we found that it took longer to reach a Ct value of >35 for young children compared with adults, which implied that children shed viruses much longer and required longer quarantine time. In the pandemic, children could be a source of infection for family members, especially the elderly with comorbidities predisposed to the severe form of COVID-19 infection.[12,13] Therefore, for children aged 0 to 3 years, a strict quarantine strategy and particular contact caution for the elderly in the same family could potentially minimize the risk of secondary household transmission.

In our study, we used the Ct value detected by RT-PCR as a proxy of viral load. The exact duration of COVID-19 patients being infectious is unclear and is likely dependent on many factors, but in particular, the individual's disease severity, the viral load, and the patient's immune status. A positive viral culture has been correlated with viral loads quantified by RT-PCR. The likelihood of a positive viral culture decreases with increasing Ct values.[14] In one study, no positive culture of SARS-CoV-2 from samples was detected when Ct was 28 to 30.[15] In other studies, the negative culture threshold of Ct values was >24 or >34.[14,16] Currently, Ct > 35 is used as the criteria for discharge in China, which seems safe in preventing subsequent community transmission by infected patients.

As most SARS-CoV-2 Omicron variant-infected children were mild and moderate, home quarantine may be suitable without overwhelming hospital capacities in the pandemic. Based on our data, the optimal time for PCR test in infected children aged 0 to 3 years can be performed on the 11th to 16th (13.4 ± 2.7) day after the onset of symptoms with the best chance to get a negative result. This strategy can be cost-effective and significantly reduce the frequency of PCR tests in children.

Due to >30 mutations on the spike protein, the SARS-CoV-2 Omicron variant demonstrates a greater breakthrough against vaccine-induced immunity as compared to the delta. However, the administration of COVID-19 vaccines, no matter the mRNA vaccine, inactivated vaccine, or other forms of vaccines, is still the most effective public health strategy for preventing severe forms of COVID-19. Additionally, our study found that the duration of shedding viruses in vaccinated adults was much shorter than that in unvaccinated counterparts, which gives extra evidence for vaccination in all eligible populations.

In conclusion, based on our comparison study of children and parents, we found that children aged 0 to 3 years tend to shed virus longer than their parents, which implies a longer quarantine duration for young children is needed and the optimal PCR testing time for detecting a negative result with the purpose of de-isolation is around 2 weeks. For all eligible populations, vaccination is strongly recommended, not only for preventing infection but also for shortening viral shedding time in vaccine-breakthrough infections.


This study was funded by the National Key Research and Development Program of China (Nos. 2021YFC2701800 and 2021YFC2701801) and the Shanghai Municipal Science and Technology Major Project (No. ZD2021CY001).

Conflicts of interest



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