Prof Salim Abdool Karim Weekly COVID-19 UPDATES
- The rise in cases over this last week could reflect a short-lived uptick in cases due to a new sub-variant of omicron. The omicron BA.1 wave started in South Africa on 2 December 2021 and was well on its decline when the opening of schools in January saw a brief uptick in cases due to omicron BA.2 before the original wave continued its decline. So, we know that omicron sub-variants can lead to short-term increases in cases – BA.2 has been causing similar upticks in many parts of the world that have completed their BA.1 waves. Since the January uptick in cases by BA.2, this sub-variant quickly became the dominant variant most likely due to its higher transmissibility (which has not been proven yet but has been estimated through modelling). But BA.2 did not have sufficient escape from BA.1 immunity, especially when BA.1 antibody titres are high so soon after the wave, and so it has continued spreading at a low level to the few susceptibles available.
But now, 2 new omicron sub-variants BA.4 and BA.5 are spreading in South Africa (Slide 11). Omicron BA.1 was dominant in December 2021, but by February, omicron BA.2 had taken over as the dominant circulating sub-variant and by April, BA.4 and BA.5 are on their way to becoming dominant, reducing BA.2 to about half of the circulating viruses. Note how BA.1 has been almost entirely squeezed out in April – comprising just 3% of circulating sequenced viruses (Slide 11) – barely 3 months after it caused a massive wave in SA (and in most of the world). So, the current increase could be a second short uptick in cases due to omicron sub-variants BA.4 and BA.5. Why the uptick now? It is now just over a week since Easter, Ramadan and Passover took place (an uncommon overlap). The Easter long weekend hosted many weddings, church services and gatherings that can lead to such a drastic increase in cases. In 2021, SA had an increase in cases about 2 weeks after Easter. Personally, I am aware of 2 Easter weekend weddings this year where most of the guests became infected. Hence, there is a chance that this increase in cases could be related to gatherings being held with few public health measures – if it is gathering-related, it could be short-lived, especially with vaccination lowering secondary attack rates (recall my past slides on the Science & NEJM papers showing a 72% and 68% reduction in secondary attack rates due to 2 doses of Pfizer).
2. Alternatively, it could indicate the start of a sustained increase creating the 5th wave due to omicron BA.4 or BA.5 or both. Several indicators increase the likelihood of this being the case – a) the increase is across all provinces (slide 22 with a magnification of the last few weeks shown in slide 23) and not just the major cities, b) SA is due for a 5th wave about now based on the past cyclical waves of infection (while we do not know for sure why the virus spreads in waves, it is thought to be related principally to waning immunity from the past wave – and since omicron causes mostly asymptomatic infection, which is associated with lower antibody levels, this early start of the wave could be due to the omicron wave immunity waning to low levels more quickly having started at a lower peak), and c) BA.4 / BA.5 look circumstantially like they have higher transmissibility and immune escape, while we await the epidemiological data on transmissibility and lab data on immune escape.