Covid-19 Weekly Updates

This is the last month that I will sending out the weekly Covid-19 emails. The grant funding for this initiative comes to an end this month - it is 2 years since the weekly emails started.  I have unfortunately not yet been able to secure new funding to continue beyond June. Suggestions on potential avenues for assistance for this public service would be welcome.

 

New cases have continued to decline in this mini-wave (slide 2) dipping to below the threshold of 5 cases per 100,000 population (Slide 3) that I use to define the start and end of waves. Test positivity is dropping below 10% (slides 7 and 8). Hospital admissions continue to be elevated (slide 4) – it seems that admissions started rising slower in relation to cases and seem to be dropping slower in relation to cases in this wave. 

 

Phylogenetic data (slide 5) indicate that the BA.4 / BA.5 takeover in South Africa is almost complete – they comprise well over 90% of the available sequences from May. Higher transmissibility is key to gaining this dominance. But it will have difficulty gaining dominance in settings where BA.1 or BA.2 have spread within the last 3-4 months due to the cross-immunity protection (you may recall Alex Sigal’s data on this) – so, delayed introduction (and not early introduction) of BA.4 or BA.5 more than 3-4 months after the initial omicron wave ended may lead to mini-waves like the one we just experienced. Crossing fingers though that this does not happen. Even if mini-waves do occur, the positive feature is that the deaths did not rise significantly (slides 10-12) – reported Covid-19 deaths, in-hospital deaths and excess deaths showed only slight increases. 

 

If you want to calculate when your country (or state) is at risk of a wave if there is a BA.4 / BA.5 introduction, you can calculate this quite easily by adding 3 months to the date of the end of the last wave – let Marothi know if you need any help with this calculation. Using this approach, I was able to accurately estimate (several months in advance) the date on which the 4th and 5th waves would start in South Africa (slides 14 and 15). In fact, I had a deluge of social media accusations that I was spreading the virus – how else could I have known on 17th August that the date of 2nd December would see the start of the 4th wave driven by a new variant. For the 5th wave, I was off by 1 day – South Africa crossed the threshold for the 5th wave on 7th May and not 8th May. Please note that the calculation may not be useful in countries that do not follow a similar trend to the South African epidemic, especially in countries without regular waves. 

 

Given the key role of higher transmissibility that enables new variants or sub-variants to displace past ones, knowledge of transmission is important.  An article this week in Clinical Infectious Diseases (Slide 13) provides useful insights on transmission by aerosols. In this study, they made Covid-19 positive people breathe, talk and sing into a machine that collected the aerosol droplets. Note that some of the participants were asymptomatic or pre-symptomatic. The study confirmed 3 points:

The take home message (especially in the midst of variants or sub-variants with immune escape causing breakthrough infections in vaccinated or previously infected people) is that masks remain important in poorly ventilated indoor settings.  This problem is particularly difficult to mitigate in indoor settings where people (including those who do not know that they have Covid-19) are talking without masks eg. pubs.  I am particularly concerned about the potential super-spreading that could occur in an indoor wedding with several hundred guests without masks, moving around and speaking with other guests without masks. It also points to the importance of places where masks are not worn, like restaurants, needing to ensure that the windows are open and that outdoor serving should be prioritised. Fortunately, South Africa has maintained an indoor mask requirement, though this is being undermined to some extent by complacency and Covid fatigue.

 

Cases continue to rise in North America, mostly due to BA.2 and BA.1.12.1 - though the rise is at a slower rate than it was for Omicron BA.1 (slide 19). Cases are now also starting to rise in South America (Slide 19). These increases are not large enough to alter the overall global trajectory (slide 18), which continues in decline. I was relieved to see that cases have also been coming done in Shangai and Beijing – omicron is not an easy virus to slow down due to its high infectiousness.