Prof Salim Abdool Karim Weekly COVID-19 UPDATES

17 May 2022

First – let’s briefly deal with fatalism/defeatism before going into the latest trends in SARS-CoV-2 infections. 

Several people wrote to me after last week’s missive, about my comments on fatalism in the Covid-19 response. In last week’s missive, I briefly discussed how defeatism (or fatalism) was creeping into the Covid-19 discourse. Often this was done under the guise of “living with the virus” which is sometimes wilfully extended to the “the pandemic threat is over (as omicron is mild) and so we can get back to living ‘normal’ lives”. The important concept of “living with the virus”, which we all need to do is being used as code for “let the virus spread – public health measures should not be imposed to slow or impede it.” Sometimes, it can be even more defeatist, “let the virus spread – anything we do is pointless!” In simple terms, this is a passive surrender to the virus – or worse, an active surrender when accompanied by a belief that any defensive action should deliberately NOT be taken in the belief that it has no prospect of success. 

In a local South African newspaper, Mail & Guardian, a scientist is quoted last week as saying, “ We should stop pretending as if the mask mandate does work in South Africa, it hasn’t worked in South Africa. It might work in other settings where people are more adherent to this sort of mandated regulation and are able to wear the right type of masks but in a South African context the starting point is that masks haven’t done much in preventing infection.”

This comment that we as South Africans (or Africans more broadly) do not know how to use masks, how to choose the right type of masks or how to adhere to masks reminds me of comments made a while ago in the AIDS pandemic, that Africans cannot tell time, do not have watches and so will not be able to adhere to complex regimens of ARVs.  Reminds of a colonial mentality…

Around the same time, another scientist was quoted in Business Day explaining the scientific evidence for masks, “…a clinical trial carried out in 2020 in Bangladesh, compared three groups - wearing surgical masks, cloth masks and no mask. It showed that wearing a mask is better than not, and a medical mask is better than cloth. It reduces the risk of transmission of the virus, as well as the (secondary) attack rate of new infections…. Another reason to carry on protecting your mouth and nose… in 2020/21, we did not have a flu season because masks played a critical role in combating airborne infections. An issue most of us do not fully appreciate is that masks are much more effective in protecting a positive person from spreading the virus than protecting a negative person from being infected. If you have Covid, wearing a mask is a big plus to those around you. This is especially important because most people who have it (Covid-19) don’t know they have it.”

The quoted comments above provide a stark contrast between an opinion with prejudice and a scientific explanation in dealing with the question of whether masks should still be used indoors in South Africa. This kind of defeatism is most unfortunate, especially when it deliberately conveys disinformation that “prevention just does not work – so why bother”.  This kind of sentiment is gaining legitimacy as if it is a scientifically validated fact rather than being seen for what it is - a personal opinion.

To help counter this, I prefer to talk about “living with the virus” as “living smartly with the virus” in order to differentiate it from the Barringdon-declaration like approach of simply going about our business while the virus spreads unchecked. For me, “living smartly with the virus” means knowing when transmission is high/low and what my most risky activities are, so that I can adjust my willingness to participate in riskier activities like attend indoor gatherings but not let it stop me from essential activities like going to work everyday and undertake most of my usual low risk or mitigated risk activities. Living smartly with the virus is about adjusting my use of public health measures in response to the (changing) prevailing risk of infection. At a community level, living smartly with the virus is captured most simply in the “Vaccination Plus” maxim, which calls for the adoption of selected public health measures (selected as appropriate to the setting) in addition to being vaccinated. The Public Health Task Force of the Lancet Commission on Covid-19 made this recommendation of a Vaccination Plus strategy in March 2021. 

But this problem of defeatism is not restricted to South Africa. My thanks to Barry Schoub who sent me Eric Topol’s blog where he articulates the fatalism (or defeatism) as ‘capitulation’ in his blog:
“The United States is now in the midst of a new wave related to Omicron variants BA.2 and BA.2.12.1 with over 90,000 confirmed new cases a day and a 20% increase in hospitalizations in the past 2 weeks. That belies the real toll of the current wave, since most people with symptoms are testing at home or not testing at all; there is essentially no testing for asymptomatic cases….The bunk that cases are not important is preposterous. They are infections that beget more cases, they beget Long Covid, they beget sickness, hospitalizations and deaths. They are also the underpinning of new variants. Meanwhile, the CDC propagates delusional thinking that community levels are very low…Not only does this further beget cases by instilling false confidence, but it is conveniently feeding the myth that the pandemic is over—precisely what everyone wants to believe.”

Eric Topol has nicely articulated the subtle ways in which the message that the pandemic is over is being fostered. I am not sure why so many are convinced that SARS-CoV-2 is not going to mutate with greater immune escape, when the current omicron sub-variants are proving to be wily escape artists. This is evident from the Andrews study (NEJM, 2022) that showed that vaccine effectiveness against BA.1 omicron after two BNT162b2 doses was 65.5% (95% CI: 63.9 to 67.0) at 2 to 4 weeks, dropping to 8.8% (95% CI: 7.0 to 10.5) at 25 or more weeks after the 2nd dose (without a 3rd dose booster). Yes, your eyes are not deceiving you, the same 2 doses of Pfizer vaccine that was 95% efficacious against the initial variants is now only 9% efficacious against BA.1 at 6 months post-vaccination!

Further, the accumulation of multiple mutations is turning out to be a much more complex issue than we first thought. Some of the individual mutations in omicron are actually harmful to the virus but when they occur in combination with several other mutations, they convey an advantage to the virus. It is getting more difficult to predict the behaviour of new variants or sub-variants based on individual mutations. Combinations of mutations seem to have synergistic effects. This opens a whole new world of variability for the virus, ie. to gain an advantage that goes beyond individual mutations. For example, BA.2.12.1 has a key immune escape mutation in L452Q, and it seems, as an immune escape artist, to also be more transmissible than BA.2.  BA.2.12.1 is rapidly replacing BA.2 as the dominant variant in the US. To go further, BA.4 has even more mutations L452R, F486V and R493Q in the spike protein enabling it to be more transmissible with more immune escape capabilities. We have to be vigilant that new variants are going to arise and that they are not readily predictable in terms of clinical severity or extent of immune escape.

Are you also finding an increase in fatalism? Or is this problem being over-played? Feel free to email me and/or Marothi with your thoughts.

While the pandemic has continued its global decline, omicron sub-variants are showing possible early signs that they may change this trend (Slide 15), though it is too early to tell for sure. In South Africa, BA.4 and BA.5 continues to drive the 5th wave (Slide 2). Testing is at a much lower level in this 5th wave than we have seen in previous waves (Slide 3) – at this stage in other waves, SA would be doing over 50,000 tests per day compared to about 30,000 being done daily at present. This is a global trend – but lower testing does not mean that the wave is not real, rather it means that the actual wave is much bigger than what we are seeing in the case numbers. In South Africa, hospitalisations have been increasing but at a much lower rate and in-hospital deaths are showing a only a very slight increase (Slide 4). At a provincial level, the increase in cases is slowing in some provinces (Slides 21 and 22).

Incidentally, Geneviève Chene, the Executive Director of Public Health (Sante Publique) France, has been sharing an informative weekly newsletter that summarises the Covid-19 situation in France with me – I am sharing the link here as I think you may be interested in how the situation is evolving in France.

Talking of reports, the ISC released its Covid-19 future scenarios report in which several important recommendations are made (Slide 17). I have attached the full report here. The report was released by President of the ISC Peter Gluckman at the WHO headquarters in Geneva (Soumya Swaminathan, WHO’s Chief Scientist was also present). I think the 3 scenarios outlined in this report are very helpful and shine a light on the fact that the future is not cast in stone and our choices as the global community will determine which scenario will unfold in reality.

The latest NEJM has an article on the lack of benefit from home use of personal pulse oximetry (Slide 18). I could not help, but sit up at this finding – here I was in mid-2020, strongly advising every home to get a pulse oximeter. Medical insurance companies in South Africa, like Discovery Health, have been providing pulse oximeters for free to their clients. But it turns out that this intervention had no effect on hospitalisation rates or length of stay. This result is a stark reminder, pointing out that conventional approaches, even when they seem so obviously effective, need rigorous evaluation.

The question that we would like an answer to is whether BA.2.12.1, BA.4 and/or BA.5 are likely to spread globally like BA.1 did. It is still too early to answer this question as there are too many factors at play to predict how this will play out. But we should have an answer in a few weeks.

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