Prof Salim Abdool Karim Weekly COVID-19 UPDATES

2 May 2022
A quick recap of last week’s missive. I raised concern about the rapid rise in cases, explaining that some markers of the start of a wave had been met but that it was too early to tell if South Africa is actually entering the 5th wave. I presented 2 options – a) that the rise could just be a small short-lived uptick that would settle within a few weeks without rising to become a fully fledged wave or b) that this rapid rise in cases could be the start of South Africa’s 5th wave. I explained that we needed to see what the trend looks like after a week. 
Well, it is now a week later – but I am sorry to say that we still don’t have a clear answer as to which of the 2 options is occurring in South Africa. The reason – holidays! There were 2 national holidays in South Africa in the last week (Freedom Day and Worker’s Day). Many people made it a long weekend and so testing numbers are down and we do not have a comparable set of data for the last 7 days in relation to the previous week’s data.
But there are some early and tentative indications regarding which way the trend is leaning towards:
  1. A week ago, the 7-day moving average was 3,097 (slide 2) – today it is 52% higher at 4,693 (slide 3). If we were in a wave, the 7-day moving average would have doubled every 2-3 days (and so we would have expected over 10,000 cases per day a week later), given the high transmissibility of omicron and its sub-variants. We have only seen a modest rise in cases. However, the problem could be that the increased case numbers are not evident because the holidays have led to a situation where testing has not increased as expected.  That testing is so low that we are only seeing a 52% rise in cases even though cases are going up much more than this.
  2. The slow increase (perhaps more aptly referred to as a meandering increase) is evident in slide 5 – compare the green and red lines after they each hit the threshold of 5 cases per 100,000 population per day.  Looking inside the red circle on slide 5, the slow increase is evident when comparing it to the omicron BA.1 increase we saw in SA in December last year.
  3. The slowing of the increase in cases (provided it is not an artifact of the holidays) is evident across the board in most provinces. While the increases looked steady and rapid the previous week (slide 22), they are slowing this week and are not following a rocket-like upward trajectory (slide 23), we would expect in a 5th wave. 
  4. A few weeks ago, I shared the Rossler data (slide 6) from the NEJM showing that omicron generated good immunity to the past variants of concern. I pointed out that omicron has spread quite widely due to its high level of infectiousness and so many people (most, in some countries) have been infected by BA.1 and so have immunity to Delta, BA.1 (and BA.2) which would make it difficult for one of the past variants of concern to return to cause a new wave of infection. Incidentally, I have seen some data from Penny Moore that suggest that BA.1 immunity may not be as good against some of the other variants of concern in unvaccinated people. Regardless, BA.1 has probably generated enough immunity to prevent a new wave with BA.1 or BA.2. But what about BA.4 and BA.5? Alex Sigal is a miracle worker in the lab – he has already produced data from his live virus assay – he grew BA.4 and BA.5 in his lab. He tested the serum of vaccinated and unvaccinated people who got infected with BA.1 to see if the BA.1 immunity neutralised live BA.4 and BA.5 viruses.  His answer is available in the preprint on slide 7.  Vaccinated people who had BA.1 breakthrough infection have good neutralisation of BA.4 and BA.5 – so, we can expect only a few BA.4 or BA.5 infections in this group. In unvaccinated people who had BA.1 infection, they have reasonable neutralisation of BA.4 and BA.5 in their blood but much less than the levels we see in vaccinated individuals. So, we can expect some BA.4 and BA.5 infections in unvaccinated people who had BA.1 infection (like children who do not yet qualify for vaccination) – more than we will likely see in vaccinated individuals. But, in both instances, the number of new BA.4 and BA.5 infections will likely be quite limited in those who had BA.1 infection a few months ago.
While it is too early to say for sure, the 4 indicators above are making a short-lived uptick (option 1) a more likely option that a fully-fledged wave (option 2). I would like to have case data from a holiday-free week before we can say for sure, recognising the challenges with PCR case numbers as fewer people come forward for testing and rapid tests are becoming more widespread. Given these shortcomings with case data, it is more useful to look at trends rather than absolute changes.
One piece of good news is that excess deaths are not rising (slide 13) like we saw in the first 3 waves. This is notwithstanding the challenges in death reporting in 2 provinces related to the floods in KwaZulu-Natal and Eastern Cape.
So, overall, the early indications are that we may not be going into a 5th wave – but this is very tentative and may change when we have case data from days that are not holidays. So, it is too early to say either way for sure or to break out the champagne. Rather, wait one more week for a clearcut answer.
Regarding the vaccination programme, most countries still recommend postponing Covid-19 vaccination until after childbirth. This was due to the lack of clinical trial data on safety since pregnant women were not enrolled in the original vaccine efficacy trials. But a range of data are becoming available showing that Covid-19 vaccines are not increasing any negative perinatal outcome indicators (slide 11). Data from Canada, Sweden and Norway as well as other countries have recently been published – Nikita (my assistant) summarised the set of papers on this question in the Journal of the American Medical Association to make it easier for you to see that Covid-19 vaccines are safe in pregnancy. Regulatory advice is now awaited on whether pregnant women can be vaccinated. This will help reduce one of the contra-indications to vaccines and help increase vaccinations, at least, a little.
Finally, just a word on the global situation – cases are declining (post-omicron BA.1 and BA.2) across all regions of the globe. Case rates are still somewhat high in Australia and some European countries but most of these countries have declining trends.
Once again, sorry that I do not have a definitive answer on the 5th wave. The holidays intervened making it difficult to provide a categorical answer on whether South Africa is in the 5th wave due to BA.4 and BA.5 omicron sub-variants.
Salim S. Abdool Karim, FRS
Director: CAPRISA
CAPRISA Professor of Global Health: Columbia University