Prof Salim Abdool Karim Weekly COVID-19 UPDATES

8 May 2022

Just to be clear – I have no authority to declare a new wave of infections in South Africa. It is up to the Minister of Health to declare a new wave and I look forward to learning what his decision will be. I am simply conveying my interpretation of the current data – the cases have now risen to 10 cases per 100,000 population per day ie. around 6,000 cases per day on a 7 day moving average (Slide 2). The actual number of cases in the last 3 days were 6,170 cases (27,310 tests / 23%) on 4th May,  9,757 cases (37,618 tests / 26%) on 5th May and 9,253 cases (34,817 tests / 27%) on 6th May. Cases (and test positivity) are high and going up in almost all provinces after the brief holiday effect (Slide 21). 

I had been hoping that the increases in cases we saw 2 weeks ago would just be a short-lived uptick and some of the indications from last week suggested that this may be the case – but the true situation revealed itself once the holidays were over and testing went back up during this week. I must point out that interpretation of cases is not straightforward though, as testing patterns have changed and rapid tests are more widely used. Also, the vast majority of infections in South Africa are either asymptomatic or mildly symptomatic with the infected person being none the wiser about his/her infection and so is not coming forward for testing. I have also seen lots of people just isolating without testing once they become symptomatic.  Notwithstanding these limitations, the overall trend in cases provide us a reasonable tip-of-the-iceberg impression of the situation.

I was wrong that a new variant was essential for a new wave. This new wave is being driven by omicron sub-variants and not a completely new variant. I explained last week that Delta’s over 150 sub-variants did not lead to new surges but omicron has so many mutations and variations that its sub-variants can also lead to surges when immunity to the parent omicron variant has waned sufficiently. 

This situation has one major significance – it now means that new waves of infection are not only caused by a new variant, new waves can now also be caused by a sub-variant of an existing virus. The virus has just indicated that we have both variant and sub-variant possibilities to be concerned about as potential causes of future new waves of infection! 

We are also now far enough along the wave to say with some confidence that the BA.4 / BA.5 variants are causing only a few cases of severe disease. Hospitalisations have gone up slightly nationally (Slide 3) but there has been almost no measurable increase in in-hospital deaths (slide 3) or excess deaths (slide 12). This trend is seen consistently in the largest provinces (BA.4 in Gauteng in slides 22 and 23; BA.5 in KwaZulu-Natal in slides 25 and 26).  The low clinical severity is likely to be due to BA.4 and BA.5 being less virulent like BA.1. This combined with higher levels of T-cell immunity both from vaccination (49%) and natural infection (add another 25-30%) in South African adults is probably maintaining low numbers of hospitalisations (Slide 3). But with all this immunity present, why are people still getting infected and why are we seeing a new wave if immunity is this high? There is no simple answer to this but 3 key factors probably contribute to this – a) immunity from natural omicron BA.1 infection is often “weak” with low levels of antibodies immediately following infection as most infections were asymptomatic (which is associated with lower Ab levels); b) the Abs from BA.1 infections may have been high some 4-5 months ago but they have waned over time and are much lower now (this problem of waning Abs is more significant in those who were not vaccinated – vaccinees who got BA.1 have hybrid immunity which is very high Ab levels) and c) BA.4 and BA.5 have new mutations that are not in BA.1 or BA.2 and these mutations confer additional immune escape as I explained based on Alex Sigal’s important study in the emails of the last 2 weeks.

Whatever the reasons for the new surges of infection, South Africa experiences a new wave after a 3-month inter-wave gap. Simply adding 94 days to the end of the last wave gives you a predicted start of the next wave – provided past trends continue.  In September 2021, I predicted a 4th wave on 2 December for the Moseneke Commission. The 4th wave was declared by the Department of Health on 2 December 2021 as predicted. Using the same elementary calculation, I predicted that the 5th wave would start on 8 May 2022 in an important briefing I did about 6 weeks ago (the slide I used in that briefing is Slide 5 and I also included it in my weekly Covid-19 emails several weeks ago). I have been desperately trying to be wrong this time as today is 8 May!  

Just out of interest, at that same briefing, I suggested that the strategy needed going forward should focus on 5 things – a) increased testing/surveillance,  b) Some indoor mass gathering capacity restrictions, c/d) indoor mask and vaccine requirement in public spaces, and e) steps for the next wave (Slide 7). These public health measures, all of which have good evidence for their efficacy, are less intrusive and have fewer unintended harmful effects than past measures like curfews or school closures. There is no justification for a lockdown or any of the more stringent measures, based on the trends we have seen so far.  The 5 proposed public health measures are intended to avoid super-spreading events and reduce the spread of the virus in high risk indoor settings. As this week’s Lancet Editorial eloquently captured – while public health measures are being eased/removed, there is still a need for some public health measures as we are still living in the midst of a pandemic. 

I have been concerned about growing fatalism internationally and in South Africa in dealing with the pandemic, where some of the Barringdon declaration (a discredited view that the virus should be allowed to spread while protecting the elderly) arguments are re-surfacing - even some scientists are saying what is the point of trying to prevent infections as everyone is going to get infected anyway.  Let’s just let the virus spread and do little or nothing about it. They argue that their freedom from the restrictions of public health measures is more important. Everyone is going to get infected because public health measures like masks don’t work in Africa - is a comment I have read this week.  This position is defeatist and has no scientific rationale that I am aware of. We are living in the midst of a pandemic that has killed about 16 million people in 2 years according to the WHO estimate this week based on excess deaths - This is far worse than what we saw with AIDS deaths in the first 2 years of that pandemic. The argument that almost all South Africans have been infected or are going to get infected is not true. The first D614G wave infected only about 20% of the population while Beta and Delta pushed this initial seroprevalence up to above 50% and omicron is even higher – but seroprevalence surveys indicate that about 1 in 4 to 1 in 5 South Africans have not been infected (like me).  The retort argument that past infection or vaccination ensures that the person does not get severe disease and so we should just let the virus spread because it will not lead to hospitalisations is not grounded in what we know about long Covid or the long term cardiovascular, neurological and endocrine effects of Covid-19. New variants are likely to have some immune escape and infect those with past infection immunity or with waning vaccine immunity. We should be trying to prevent and/or slow the spread of infection as every person who does not get infected is saved from the risk of not only acute infection consequences but its many long-term consequences.

Low antibody levels are associated with breakthrough infections. In this regard, 3rd dose boosters help, as they push up antibody levels and so Ab levels in boosted people a few months later are higher even though they are also waning. 4th dose boosters do not push the peak Ab levels above those obtained from the 3rd dose booster and so provide very short-term increase when given several months after the 3rd dose when Ab levels have waned again. While this repeated boosting seems to be Israel’s preferred approach, it is not an appropriate public health strategy as it will require taking boosters twice a year and is only recommended for those at very high risk, like the elderly or immune-compromised people.

New waves were expected to stem from more transmissible viruses – you may recall the Mary Bushman article in Cell that I explained in a February 2022 email (I have included it here for ease of reference – Slide 6). It is not clear if BA.4 /BA.5 are more transmissible than BA.1 or BA.2 – looking at the trajectories (Slide 4), it does not seem like the new sub-variants are more transmissible as cases are not rising as fast (but this may be due to fewer susceptible people being available even if the virus is transmitting faster). We will have to wait for the estimates of their transmissibility which will only become available much later – higher transmissibility would increase the chances of BA.4 / BA.5 spreading well beyond our country’s borders.

At this time, cases are declining globally (Slide 15), as expected.  The increase in cases in Africa and China are too small to change this downward trend. There is a reasonable chance that BA.4 / BA.5 may cause an increase in cases globally – if this happens, I would expect it to occur only in about 4-6 weeks from now, which is the gap we saw between South Africa’s BA.2 uptick and global uptick in cases caused by BA.2. 

Finally, what can we expect from this wave in South Africa – I think that the number of susceptible people without sufficiently high levels of BA.1 / BA.2 antibodies may not be very high and so this wave may not rise to high numbers of cases and may not last as long as past waves – but this is just speculation. Let’s wait to see what happens with this surge of infections in South Africa. 


Salim S. Abdool Karim, FRS
Director: CAPRISA
CAPRISA Professor of Global Health: Columbia University