Prof Salim Abdool Karim Weekly COVID-19 UPDATES

14 April 2022

Globally, the downward trend continues (slide 6). BA.2 transmission is now picking in New York and surrounding areas. I am somewhat surprised that it took so long for the BA.2 uptick to occur in the USA; and even then it is mostly in the northeast part of the country. But the higher transmissibility of BA.2 is likely to see that change as it is likely to spread more widely across the USA causing a temporary uptick in cases before continuing its downward decline if it follows the trends that BA.2 has generated in several other countries.

So, if BA.2, BA.4, XE, etc are not going to cause the next wave, what is the next variant of concern going to look like? Looking at Slide 7, we have spent most of the pandemic with either the D614G variant or the Delta variant with shorter periods of ancestral strain, alpha and omicron. To date, we have only had 3 truly global variants – D614G, Delta and Omicron. Ancestral, alpha, beta and gamma did not gain enough traction to become globally dominant and so remained restricted to a few regions. So, how long before Omicron is replaced by the next variant? If the next variant is going to displace omicron, it will likely become the 4th global variant. In anticipating the next variant, there are 2 excellent articles (slide 8 & attached articles). I particularly like Katherine Wu’s outline of the 4 options possible in the next variant, including her use of descriptive titles – The Sharpshooter, The Escape Artist, The Sprinter, etc.

In case you heard someone say that new variants are unlikely because of widespread vaccination, think again. In slide 9, this article from JID, shows that vaccinations are not generating protective immunity in a high proportion of immunocompromised people – ie. they are at risk of getting infected and if they do get infected with persistent infection, there is a good chance that the virus will be exposed to low levels of vaccine-induced antibodies, driving immune escape. And this is the group we are most concerned about – because immunocompromised individuals may be a source of new variants.

On excess deaths, there was a small increase last week in the total number of excess deaths in South Africa (Slide 15). It is too early to make anything of this – it could just be random variation. If you have not seen it, this week’s Lancet has a fascinating article on the global excess death estimates. Slide 16 shows the level of each country’s under-reporting of Covid-19 deaths. It compares excess deaths with reported Covid-19 deaths. Note that this is not a like-to-like comparison as not all excess deaths are Covid-19 deaths, though it is likely that most are. Keeping this shortcoming in mind, the map shows the high level of Covid-19 death under-reporting in Africa and Asia. While this problem has been suspected for a while, this study quantifies the scale and extent of the problem.

Excess death rates vary quite substantially across countries. Slide 17 provides a graphical presentation of excess death rates, showing very high rates in several countries while a few countries, like Singapore, Australia, etc have actually saved lives during Covid-19 – most likely because Covid-19 public health measures are reducing other diseases. The Lancet article also provides age-adjusted excess death rates – age accounts for 74% of the variability in excess deaths across countries. 

Some people have been inappropriately comparing excess deaths in South Africa with reported Covid-19 deaths in other countries (which is not comparing like to like) and then making inaccurate statements like South Africa has the world’s highest death rate from Covid-19. The Lancet article clarifies South Africa’s under-reporting of Covid-19 deaths may be as much as 3-fold, which is just below the global average for under-reporting and it further clarifies that South Africa’s excess mortality rate is high, but not anywhere near the highest in the world. 

Finally, for those of you in the invidious position of providing science advice on Covid-19, herewith attached is an article in Nature – Humanities and Social Sciences Communications that provides an assessment (actually, a critique) of the role of the Public Health Agency’s scientific advice to the government of Sweden on how to respond to Covid-19. You may recall that Sweden’s science advisors recommended that the country chose a different path from most of the rest of the world, including refusing to use masks when it was standard practice almost everywhere else. This article is a stinging rebuke of Anders Tegnell (and Johan Carlson to a lesser extent) and their role in taking Sweden down a path that did not try to slow the spread of the virus and instead laid the basis for the Great Barringdon Declaration. I gather that Anders Tegnell has now resigned from the Public Health Agency in Sweden. 


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