South African data offers preliminary insights into Omicron variant
Little more than a week after the World Health Organization formally labeled a recently emerged SARS-CoV-2 variant of concern as Omicron it has been detected in at least 38 countries around the globe. A pair of new reports out of South Africa are offering some very early insights into how this new variant could behave in humans as it rapidly spreads.
A patient profile from researchers in the South African district of Tshwane, an epicenter of the Omicron outbreak, indicates the new variant may lead to less severe illness compared to prior variants. And a reinfection study is suggesting Omicron is causing high rates of SARS-Cov-2 cases in people previously infected with the virus.
A new report from the South African Medical Research Council (SAMRC) offers a snapshot of patients currently in hospital with COVID-19 in the Tshwane District Hospital Complex. Authored by Fareed Abdullah, a doctor working with the SAMRC, the report offers preliminary insights into the profile of hospitalized patients experiencing COVID-19 from the omicron variant.
Abdullah is cautious to note the report is only based on patients seen in the first two weeks of the omicron wave, so it is entirely possible this patient profile will change over the coming weeks. However, the early signs indicate this Omicron wave is very different to prior waves seen in the local Tshwane region.
The main observation reported in this analysis is the majority of patients in COVID wards are not oxygen dependent. Few patients currently need supplemental oxygen and Abdullah reports this is markedly different to what was seen in hospitals in prior COVID-19 waves. Interestingly, most of these patients were initially admitted into hospital for other medical reasons and routine testing picked up the SARS-CoV-2 infection.
“This is a picture that has not been seen in previous waves,” the report states, “In the beginning of all three previous waves and throughout the course of these waves, there has always only been a sprinkling of patients on room air in the COVID ward and these patients have usually been in the recovery phase waiting for the resolution of a co-morbidity prior to discharge. The COVID ward was recognizable by the majority of patients being on some form of oxygen supplementation with the incessant sound of high flow nasal oxygen machines, or beeping ventilator alarms.”
Complicating these promising indications is the fact that most COVID-19 hospitalizations in Tshwane are in younger people. In fact, according to the SAMRC report, 80 percent of hospitalized COVID-19 in the last two weeks are in those under the age of 50.
Abdullah speculates the higher rates of positive cases in younger people could be a sign vaccines are working against Omicron. He notes 57 percent of those over 50 in the local region have been vaccinated whereas the rate for those under 50 is only 34 percent.
Of course, it may also be that the virus simply hasn't yet started spreading through more vulnerable older communities. Speaking to STATNews, Baylor College of Medicine’s Peter Hotez reads the new data as promising but stresses it is way too early to claim this is the definitive behavior of Omicron.
“Potentially it means that the severity of illness is less with Omicron,” Hotez said to STAT while commenting on the SAMRC report. “But I think we have to be very cautious about making any definitive statement. Right now, it’s an interesting anecdote as much as anything else. And we’ll see as Omicron accelerates in the United States whether if falls along a similar pattern.”
Another new study on Omicron comes from the South African Centre of Excellence in Epidemiological Modelling and Analysis. Published as a preprint and yet to be peer-reviewed, the research reports on an ongoing surveillance study tracking the rate of COVID-19 reinfections in the local region.
The study began at the start of 2021, and the initial findings published as a preprint in early November tracked rates of reinfection across Beta and Delta variant waves. That study, also not yet peer-reviewed or published in a journal, concluded there was no evidence those particular variants led to unusual rates of reinfection in those individuals with prior encounters with the virus.
Over the course of October the researchers started seeing a shift in the data. Reinfections were increasing rapidly in some South African regions. When Omicron was recently identified the researchers quickly updated their study to include data up to the end of November.
This new data paints a very different picture to the initial findings, suggesting Omicron may behave differently to prior Beta and Delta variants. Rapid increases in SARS-CoV-2 reinfections across October and November were seen to correlate with the emergence of Omicron.
“We find evidence of a substantial and ongoing increase in the risk of reinfection that is temporally consistent with the timing of the emergence of the Omicron variant in South Africa, suggesting that its selection advantage is at least partially driven by an increased ability to infect previously infected individuals,” the researchers conclude.
Francois Balloux, a researcher from University College London, calls the reinfection study “competently performed and timely.” He does, however, point out the research offers no indication as to the relationship between Omicron and vaccine effectiveness. Plus, the study does not look at infection severity so there is no data on what kind of disease reinfected patients may experience.
“… since the study is strictly correlative, some confounders such as waning levels of immunity could not be taken into account,” notes Balloux. “It remains that it provides a plausible estimate for the increased rate of reinfection by the omicron variant.”
Bill Hanage, an epidemiologist from the Harvard T.H. Chan School of Public Health, stresses it is too early to understand what kind of impact Omicron may have on the trajectory of the pandemic. He is not surprised Omicron can lead to higher rates of reinfection, but until the variant spreads through more diverse populations it is impossible to know what kind of disease it can cause.
“Those thinking about the severity of omicron please remember we think it has only been transmitting since about mid October,” Hanage writes on Twitter. “There has literally not been enough time for enough severe cases to progress and get severe so we can measure that.”
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