Thread by @Tuliodna

Summary of BA.4 & BA.5 in South Africa
- 100% of infections
- Fuelling 5th wave
- Low testing & high positivity ratio
- Increasing number of hospitalizations, however still much lower than in previous waves
- SA may guide the world on the future of the pandemic

South Africa had multiple waves of infections, the first dominated by multiple lineages (> 50 614G lineages), the second by Beta, them Delta, Omicron BA.1, BA.2 and Omicron BA.4 and BA.5.

The multiple variants and lineages of Omicron fulled 5 waves of infections. With decreasing qPCR testing in South Africa and the world, test positivity ratio or other proxy markers may be better than infections to identify waves of infections

Test positivity ratio (and infections) is on a very upward trajectory in South Africa. Positivity ratio is as high as at the peak of the other waves.

However, hospitalization and deaths are low. We believe that the high population immunity of South Africa helped to decrease the effect of the 4th Omicron BA.1 wave and the current, 5th Omicron BA4/5 wave. However, BA4/5 wave of hospitalization is still in the start.

Omicron BA.4 and BA.5 do break easily through immunity of previous BA.1 infections, but less in hybrid immunity (vaccination & previous infections). If South Africa, and other countries, want to stop waves we need to increase vaccination & boost also previously infected

South Africa's restrictions are very low and we are, potentially, doing an experiment that can help the whole world. The main question that SAmay answer is: Will new lineages and variants cause much hospitalization and deaths or only infections?

It is like playing with fire. One may have a lot of fun and enjoy a night next to a warm fire or may get burned. The main thing that SA and other countries should be doing is to increase vaccination so the fire 🔥 gets controlled.

There were two interesting pieces this week on the serious scientific literature on what the future may look like for the COVID-19 pandemic and the new Omicron lineages (thelancet.com/journals/lance…) and (nature.com/articles/d4158…)

At present, low restrictions are appropriate South Africa needs full economic activity. We will keep a laser-sharp focus on the science and following metrics of hospitalization and deaths in SA. The identification of BA.4 and BA.5 before a wave really helped to keep focused.

Lots of scientists and labs to thanks. Variant plots produced by @houzhou, neutralization by @sigallab genomics data by NGS-SA, @krisp_news @ceri_news @nicd_sa @UCTIDM @WitsUniversity @StellenboschUni up-to-date epi-graphs thanks to unsupervised.online/static/covid-1…