1.There has been a lot of anticipation about Omicron and T cell responses. T cells epitopes are largely conserved and this suggest that most of the T cell response might still be on hand to fight the virus @Alba_Grifoni @aetarke @profshanecrotty @Dani6020 @ljiresearch
2. Scientists all over the world have identified T cell epitopes in the past year, we analyzed the number and fraction of CD4 and CD8 epitopes 100% conserved in various variants sciencedirect.com/science/articl…
3. In general the vast majority of T cell epitopes are totally conserved and is not different when we consider the early (alpha, beta, gamma, epsilon), or late variants (kappa, eta, lambda, iota, Mu etc…) such as delta.
4. T cell epitopes in natural infection? The analysis of the full proteome here show that on average 98% of CD8 and 95% of CD4 epitopes are totally conserved. 
5.When we get to Omicron presumably because of the higher number of mutations, the fraction of CD8 epitopes that are 100% conserved drops significantly to 95% for CD8 and 88% for CD4 whole proteome. Still very high conservation.
6. T cell epitopes and vaccination? Here is the analysis of spike-only data. Since many variant mutations are in spike, we expect naturally a higher number of mutated T cell epitopes. On average 94% of CD8 and 91% of CD4 epitopes are still totally conserved.
7. For spike and Omicron the fraction of conserved epitopes is 86% for CD8 and 72% for CD4. Still a majority of epitopes are conserved. Bear in mind that a mutation in an epitope does not preclude cross reactive recognition, so these are conservative estimates.
8.Bottom line; the fraction of 100% conserved epitopes drops in omicron compared to other variants BUT still the majority of the epitopes are conserved.
9. An important caveat is that we do not know what level of conservation is likely to preserve functional T cell responses, but from the data available it seems likely that T cell activity will be far less impacted that neutralizing antibody responses.
10. Experimental data assessing T cell responses in details are cooking. Stay tuned.
• • •
Missing some Tweet in this thread? You can try to
force a refresh
