Omicron is probably the most covered virus variant in the history of virus variants. There have been a multitude of highly technical hot takes which mostly distill down to “this thing spreads really fast but we don’t know much else yet”. And then some people want to do bad math to calculate R0, make conjectures about reinfection rates, and make pedantic arguments about transmission advantage versus transmissibility advantage.
However, yesterday there was an analysis posted by a Dr. Fareed Abdullah, a member of the COVID clinical team at the hospital system at the epicenter of the outbreak in South Africa.
I think his perspective is worth summarizing because it represents a firsthand “boots on the ground” assessment and highlights some points which may not have made their way into the mainstream media (but honestly the MSM isn’t part of my media diet so maybe this has been widely broadcast already).
His perspective also isn’t particularly well organized so I’m going to attempt to reorganize Dr. Fareed’s words into the big themes.
Issues other than Omicron are driving hospitalizations
[….] the majority of hospital admissions are for diagnoses unrelated to COVID-19. The SARS-CoV-2 positivity is an incidental finding in these patients and is largely driven by hospital policy requiring testing of all patients requiring admission to the hospital.
Sixty-three patients were admitted to high care, but our anecdotal information is that the majority of high care admissions were for a diagnosis other than COVID.
76% of patients at the SBAH/TDH complex are incidental COVID admissions. This very unusual picture is also occurring at other hospitals in Gauteng.
Hospital stays are shorter
A significant early finding in this analysis is the much shorter average length of stay of 2.8 days for SARS-CoV-2 positive patients admitted to the COVID wards over the last two weeks compared to an average length of stay of 8.5 days for the past 18 months. The NICD reports a similar shorter length of stay for all hospitals in Tshwane in its weekly report. It is also less than the Gauteng or National average length of stay reported by the NICD in previous waves.
Omicron affects the Young more than the Old
In the last two weeks, no fewer than 80% of admissions were below the age of 50 years. This is in keeping with the age profile of admissions in all public and private hospitals in Tshwane and throughout the Gauteng Province in the last two weeks as reported by the NICD and the Gauteng Provincial Government.
Omicron patients have significantly less pulmonary issues
The main observation that we have made over the last two weeks is that the majority of patients in the COVID wards have not been oxygen dependent. SARS-CoV-2 has been an incidental finding in patients that were admitted to the hospital for another medical, surgical or obstetric reason.
Only a single patient on oxygen was fully vaccinated but the reason for the oxygen was Chronic Obstructive Pulmonary Disease.
Vaccinations are still great.
This is a picture that has not been seen in previous waves. 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.
This very unusual picture is also occurring at other hospitals in Gauteng. On 3 December Helen Joseph Hospital had 37 patients in the COVID wards of whom 31 were on room air (83%); and the Dr George Mukhari Academic Hospital had 80 patients of which 14 were on supplemental oxygen and 1 on a ventilator (81% on room air).
Mortality may be far lower than previous waves (but pay attention for a 2 week data lag)
The best indicator of disease severity is measured by the in-hospital death rate. There were 10 deaths in the SBAH/TDH cohort in the past two weeks, making up 6.6% of the 166 admissions. Four deaths were in adults aged 26 – 36 and five (5) deaths were in adults over 60. One death was in a child in whom the cause of deaths was unrelated to COVID. There were no COVID related deaths among 34 admissions in the paediatric[sic] COVID wards over the last two weeks. This compares favorably to the proportion of deaths at the complex over the past 18 months which was 17%.
Basically, a 17% death per hospitalization rate is now 6.6%. I suppose some of that could be from an overall improvement in COVID standards of care.
The trend over the next two weeks will be clarified as the number of deaths is currently low, and sufficient time will have elapsed for the development of greater severity of disease and the number of deaths might be expected to increase. For now, the death rates over the last two weeks.as[sic] well as over the past 18 months at the SBAH/TDH complex are lower than the overall in-hospital death rate of 23% for the country over all previous waves, as reported by the NICD.
Deaths are particularly laggy so wait a week or two before feeling good about that data.
So there you have it. If you were looking for Omicron “good news”, these are the themes you should pay attention to and see if they emerge in other geographies.
Important caveats
This is still early days.
Dr. Fareed’s analysis is just basic summary statistics. No adjustments have been made for anything. He’s dividing numerators by denominators of things his team can count. There are typos everywhere and that’s probably because none of their team has slept in weeks.
I don’t think it’s unfair to acknowledge that Dr. Fareed’s team is probably incentivized to minimize severity of Omicron given it originated in their backyard. Rule of law and anti corruption isn’t high on South Africa’s core values but maybe these doctors are saints.
Check out Dr Fareed’s post here and their data addendum here.
I really appreciate that you did all the work to put this together. But there's an issue. We already know that younger patients are going to have milder cases. This was true with Delta; there's no reason to believe that it won't be true with Omicron. South Africa has a very young population (average age 26.) There's no reason why we would expect to see more severe cases in these much younger people. We'd also expect to see vaccine protection against severe outcome. It all says nothing about whether the virus itself has become intrinsically milder or not. That's something that we simply don't yet know.