Pediatric hospital admissions rise with omicron SARS-CoV-2 variant

The Omicron variant of concern of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported on November 24, 2021, from a sample collected on November 9, 2021, in Gauteng Province of South Africa (SA).Simultaneously, there was a sudden rise in cases from this province. This rapidly spread to the other provinces, forming the fourth wave of COVID-19 in the country.

Study: Rapid rise in paediatric COVID-19 hospitalisations during the early stages of the Omicron wave, Tshwane District, South Africa. Image Credit: Sergii Sobolevskyi/ShuttershockStudy: Rapid rise in paediatric COVID-19 hospitalisations during the early stages of the Omicron wave, Tshwane District, South Africa. Image Credit: Sergii Sobolevskyi/Shuttershock

A new preprint on the medRxiv* server examines the impact of this variant on hospitalizations among children in South Africa.


Pediatric SARS-CoV-2 infections in South Africa, and elsewhere in the world, have been largely asymptomatic or mild, but some have developed more severe symptoms. Largely, however, children have been spared during the first three waves.

However, from the middle of November 2021, Tshwane district, an urbanized part of Gauteng Province, began to report higher rates of pediatric COVID-19. This district has a population density of over 500 people/sq. km, and home to over 3.5 million people. Largely uninsured, the people are served by nine general hospitals and four specialized hospitals, as well as private hospitals that cater mostly to the ~25% who are insured.

Altogether, data from over 40 hospitals were gathered for the current study on pediatric COVID-19 during the fourth wave in SA. It makes use of testing data, genomic sequencing data, hospitalization data and pediatric COVID-19 admission data. The DATCOV surveillance system keeps tabs on hospital admissions from all the public and private sector hospitals in Tshwane, and this data, supplemented by clinical data, was also mined.

What did the study show?

Any person who tested positive for SARS-CoV-2 infection and was then admitted to hospital was counted for hospitalization. The researchers found that COVID-19 case numbers went up rapidly from week 45 of the year, beginning November 7, 2021. This was 8 weeks from the end of the third wave, in week 37.

By December 11, COVID-19-positive cases had crossed 202,000 and included over 36,000 admissions and over 7,000 deaths. From October 31 to December 11, 2021, there were ~6,300 cases among children, with over 2,000 each occurring in children 10-14 and 15-19 years old, 1,200 in children 5-9 years old, and 870 in children younger than 5 years.

This represented a sudden rise in cases, reflecting a rise in testing numbers, as expected during any wave. The fourth wave showed the most rapid rise of all, with test positivity rising to over 40% within a period of days.

Genomic sequencing was performed on 75 specimens of COVID-19-positive patients between November 7 and November 29, 2021, with all but one returning the presence of the Omicron VOC, indicating that the current wave was driven by this variant, the earliest such sample in this district having been collected on 12 November.

Interestingly, overall hospitalization rates decreased during the fourth wave, even as overall admissions increased. Even at the peak, the cumulative numbers were lower than in any previous wave. The exception was with pediatric hospitalizations.

While there were 2,550 admissions due to COVID-19 in the study period of six weeks, one fifth of the infections occurred in children below 19 years, coinciding with the COVID-19 testing and test positivity increase, during week 46. This rise was seen in both private and public sector hospitals, though the former saw a much larger proportion despite serving a much smaller segment. Admissions waned, including pediatric hospitalizations, during the last week, week 45, from December 5-11, 2021.

During the fourth wave, pediatric hospitalizations rose ahead of adult admissions, especially among children under 5 years. This surprising reversal of earlier trends confirmed clinical impressions that pediatric infections had risen unexpectedly before adult admissions began to increase with the Omicron-driven surge.

The mean age of pediatric admissions was 4 years, and over a third occurred in infancy while more than 60% occurred in the under-5 age group. Fever and cough were reported in almost half and over 40% of cases, respectively, while a quarter reported vomiting and difficulty in breathing. One in five had diarrhea and seizures, respectively.

Other than four children, who had other diagnoses requiring prolonged hospitalization, all pediatric admissions were released within two weeks. These four had burns, malnutrition, or tuberculosis.

Over 60% of admissions in the pediatric age group had no underlying chronic conditions, and of those who had, none was found to be a common risk factor. About 44% of hospitalized children were admitted with COVID-19, with the infection being a contributory factor or incidental to the admission illness in less than one in five, and 38%, respectively. There were no cases of multi-system Inflammatory Syndrome in Children (MIS-C) during this time.

Standard care was given to most children, with a quarter being put on oxygen. Three children required high-flow oxygen and 6% (seven children) were on ventilation for neonatal sepsis and other infectious conditions. Only one child was thought to have COVID-19 pneumonia requiring ventilation, a baby who had been born prematurely with bronchopulmonary dysplasia and new-onset pneumonia without other identified infectious causes.

Four deaths occurred during this period, all in children aged 0-10 years with complex illnesses. Three of these occurred soon after presentation with non-COVID-19 reasons requiring admission, and one of neonatal sepsis, with no deaths occurring primarily due to COVID-19.

None of the children were known to be vaccinated, and among the parents with vaccination data, 92% were vaccinated.


Children aged less than 19 years experienced a quick surge in test positivity for COVID-19 and hospitalizations in Tshwane district, Gauteng, with the Omicron rising to dominance over the Delta variant and spreading rapidly at community level from the middle of November 2021. Omicron evades antibodies elicited by earlier variants, spreads more rapidly, is more infective, and causes more breakthrough infections and reinfections.

Most children in SA are unvaccinated, and among adults, at the beginning of the outbreak, just over a quarter had been fully vaccinated, and less than a third partially vaccinated. Boosters were not being given. The patchy vaccination data makes it hard to confirm or rule out protection via natural infection or because of vaccinated adults living among the unvaccinated.

The fourth wave started from a low-test positivity rate which shot up rapidly. Pediatric admissions surged from the middle of November, before adult hospitalizations began to increase, and reached much higher rates than with any of the three earlier waves. This led to some pressure on pediatric COVID-19 hospital bed capacity, along with staff shortages due to isolation and quarantine protocols.

The highly infectious nature of the variant was obvious from the high-test positivity rates, but almost four in ten pediatric COVID-19 diagnoses were incidental. Most other respiratory viruses began to show the more common seasonal patterns from November 2021, including influenza A, rhinovirus, and adenovirus, despite the presence of Omicron.

The reasons for the high and early spread of Omicron in children could be due to the rapid generation time, low pediatric vaccination rates, immune evasion characteristics, and less frequent mask use in children compared to adults, while the school closures may have prevented the normal acquisition of immunity to other common childhood pathogens such as the flu.

Reassuringly, over 90% of children hospitalized with COVID-19 required normal care and 85% had been discharged by the time the paper was written. Most children stayed only a few days, three on average. A few children presented with seizures that could not be ascribed to simple febrile seizures, being outside the typical age group; this may have been due to COVID-19-associated encephalitis.

The absence of MIS-C does not imply that this complication was absent, since it is known to occur late in the course of the illness, mostly during convalescence.

Further studies will be required to tease out the mechanisms responsible for the greater transmission of Omicron among younger individuals. It is interesting that seropositivity among adults for SARS-CoV-2 antibodies, induced by vaccination or prior infection, or both, stood at 65-80% in October 2021, vs 50% among children. With low-level immunity among children, Omicron can spread rapidly in this niche population.

Conversely, with high immunity among adults, Omicron’s immune-evasion properties are more apparent in its ability to cause reinfections and breakthrough infections.

Although our initial experiences in this fourth wave do not suggest that there is increased severity of COVID-19 disease amongst hospitalized children, infections and hospitalisations will be monitored in the district and updates provided. To date, the data have been reassuring.”

*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:
Dr. Liji Thomas

Written by

Dr. Liji Thomas

Dr. Liji Thomas is an OB-GYN, who graduated from the Government Medical College, University of Calicut, Kerala, in 2001. Liji practiced as a full-time consultant in obstetrics/gynecology in a private hospital for a few years following her graduation. She has counseled hundreds of patients facing issues from pregnancy-related problems and infertility, and has been in charge of over 2,000 deliveries, striving always to achieve a normal delivery rather than operative.


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