Nine medical researchers, primarily in South Africa, but also including Professor Jonathan Dushoff at McMaster University, have released a preprint of a paper in which they report that their analysis of South African data shows that “the Omicron variant is associated with substantial ability to evade immunity from prior infection.” The paper by Pulliam et al. (2021) concludes that this “has important implications for public health planning, particularly in countries like South Africa with high rates of immunity from prior infection.” They leave unanswered whether Omicron is also able to evade vaccine-induced immunity, because vaccination coverage in South Africa was very low during much of the study period.
The researchers looked at data on 35,670 suspected reinfections among 2,796,982 individuals with laboratory-confirmed SARS-CoV-2. Individuals having sequential positive tests at least 90 days apart were considered to have suspected reinfections. They identified 35,670 individuals with at least two suspected infections, 332 individuals with suspected third infections, and one individual with four suspected infections. They found that reinfection was lower during waves driven by the Beta and Delta variants than for the first wave. In contrast, the spread of the Omicron variant was associated with an increase in reinfection, and a spike in the number of daily new infections. Pulliam et al. (2021) believe both are driven by the emergence of the Omicron variant.
Importantly, while previous infection gave protection against reinfection by the Beta variant and the Delta variant, it doesn’t protect against the Omicron variant. Whether Omicron can also evade vaccine derived immunity will have important implications. Interestingly, current vaccines which have given protection against the Beta variant and the Delta variant are based on the original strain. A pessimist would argue that if previous infection doesn’t prevent reinfection by Omicron, then a vaccine based on the earlier strain won’t prevent infection by the Omicron variant. However, the 'experts' are telling us it doesn't necessarily follow that while prior infection doesn't protect against the Omicron variant that a vaccine based on the original variant won't provide some protection against the Omicron variant, particularly if people are double vaccinated and boosted.
South Africa is reporting a surge of COVID infections with laboratory testing showing that three-quarters of new cases are the new variant. Over the last few days various news sources reported that the number of COVID cases in South Africa almost tripled between Tuesday and Thursday, and increased five fold between Monday and Thursday. This is much faster than the spread of COVID infections reported by China in January and February, 2020 when new cases were doubling every two days. The following chart shows how much faster the new variant infects. The first column show new cases doubling every two days. After ten doubling periods (twenty days) you have 1,024 active case. The second column shows the new cases tripling every two days. After ten doubling periods (twenty days) you have 59,049 active case. The third column shows a five fold increase in cases every four days. After twenty days you have 3125 active case
1 1 1
2 3
4 9 5
8 27
16 81 25
32 243
64 729 125
128 2187
256 6561 625
512 19683
1024 59049 3125
For the original variant, a further ten doubling periods (twenty days) led to over a million infections. This resulted in the worldwide lockdown in the third week of March (about 50 days after the first cases were reported in the USA and Canada).
If prior infection and vaccination do not prevent infection by the Omicron variant and the variant grows by tripling every two days the result could be catastrophic. If cases of the Omicron variant grow by tripling every two days then a further ten doubling periods (twenty days) could lead to over 3.49 billion cases unless steps (including lockdowns, masks, social distancing) are taken to prevent the spread. Where cases of the Omicron variant grow by a five fold increase every four days then a further 20 days could produce 9.7 million cases unless steps (including lockdowns, masks, social distancing) are taken to prevent the spread. For those that do not believe this is possible, I’ve provided the numbers below. It is simple exponential growth.
1024 59,049 3125
2048 177,147
4096 53,1441 15,625
8192 1,594,323
16384 4,78,2969 78,125
32768 14,348,907
65536 43,046,721 390,625
131072 129,140,163
262144 387,420,489 1,953,125
524288 1,162,261,467
1,048,576 3,486,784,401 9,765,625
The world can handle a five fold increase every four days as the Beta variant appears to spread at this rate. The world probably can't react fast enough to deal with Omicron variant cases tripling every two days. (It is worth noting that measles spreads five times faster than SARS-CoV-2, that measles is preventable through vaccination, that about 7.5 million unvaccinated people contract measles each year, that about 150,000 die from measles each year, and that measles has a mortality rate similar to COVID.)
If prior infection and vaccination do not prevent infection by the Omicron variant and cases grow either by tripling every two days or with a five fold increase every four days then the case load will overwhelm most hospitals. Early reports suggest that early cases appear mild, and many experts advise not to panic or worry. However, the ‘experts’ could just be repeating the same mistake made when COVID first appeared in North America and Europe in January and February, 2020. Most cases of the original strain of COVID, and most cases of the Beta and Delta variants, are mild cases and one would expect most cases of the Omicron variant to be mild cases. Deaths and severe cases lag two weeks behind the exponential growth of cases. Further, for the original strain it took five weeks before there were sufficient cases in the community to generate the significant deaths that started to appear at seven weeks. Within two to four weeks we should know whether the Omicron variant produces only mild cases or is like the earlier strains and has similar mortality rates. We will also have better data on the growth rate.
There is a troubling circumstance surrounding early reports of Omicron variant cases from South Africa. This is that while South Africa is reporting mild cases, the hospitals are filling up with cases.
Another troubling aspect of the Omicron variant is that while the coronavirus pandemic has largely spared children, the Omicron variant is putting a disproportionately large numbers of children under 5 years old in hospitals in South Africa. It is behaving more like the seasonal flu, which mainly affects the very young and the very old.
One point worth mentioning is that because South Africa has a high HIV case load studies from South Africa may not be applicable to the rest of the world. Patients with HIV have a compromised immune system that makes it difficult for them to fight COVID and makes them more susceptible to infection and reinfection. South Africa also differs from Canada, the United States and most countries in Europe because vaccination coverage in South Africa was very low during much of the study period and is still very low. In addition South Africa has a much younger population than Canada, the United States and most countries in Europe.
For those that missed the reference to “We're back in the car again”, it is from the movie Jurassic Park. I'd like to be able to say "At least we're out of the tree.", the responding line from the movie, but we are not out of the tree. If prior infection and vaccination do not prevent infection by the Omicron variant, then we are back in the car stuck in the tree.
Christopher Brett
Ottawa
Reference
Juliet R.C. Pulliam , Cari van Schalkwyk , Nevashan Govender, Anne von Gottberg, Cheryl Cohen, Michelle J. Groome, Jonathan Dushoff, Koleka Mlisana, Harry Moultrie, 2021
Increased risk of SARS -CoV-2 reinfection associated with emergence of the Omicron variant in South Africa
https://www.medrxiv.org/content/10.1101/2021.11.11.21266068v2.full.pdf
https://doi.org/10.1101/2021.11.11.21266068
