-On the UK vaccination data, the 79% number is for Pfizer and AZ combined. Since the vast majority of US vaccinations are Pfizer or Moderna, the Pfizer number should be much closer to the truth. Their EV is 87.9%, with a confidence interval from 78.2 to 93.2%.
-Looking at Israel’s Delta/vaccination document linked to in my other comment, they don’t have many hospitalizations or severe disease cases for either vaccinated or unvaccinated. So I don’t expect their expected value number to be very meaningful, due to huge confidence intervals.
-When you compare predictions to reality in “Transmissibility”, you seem to assume vaccine efficacy (VE) from cases should equal VE from R. Vaccinations seem to reduce peak viral load by a lot, regardless of conditioning on symptoms. So we should not expect the R to be very predictive of VE.
Various points on Delta and R:
-When I dig into R estimates for new variants, I find lots of disagreement comes from the serial interval estimate. Personally I convert everything to weekly growth now so I don’t have to hold that information in my head.
-I’ve been doing a similar estimate for the US based on weekly proportions of delta and it’s descendants, albeit with a shoddier method because time constraints & heterogeneous data. The best fit is usually a relative growth rate of ~1.85 per week (although it can vary by +/- 0.1 depending on the day). I’ve been surprised because the US overall growth rate has been faster than 1.85 times the pre-delta rates. It might be that the highest-transmission states are now contributing much more than before? Data from https://outbreak.info/situation-reports?pango=B.1.617.2&loc=USA&selected=USA and equivalents for the AY’s.
Various points on Delta & vaccination:
-On the UK vaccination data, the 79% number is for Pfizer and AZ combined. Since the vast majority of US vaccinations are Pfizer or Moderna, the Pfizer number should be much closer to the truth. Their EV is 87.9%, with a confidence interval from 78.2 to 93.2%.
-Looking at Israel’s Delta/vaccination document linked to in my other comment, they don’t have many hospitalizations or severe disease cases for either vaccinated or unvaccinated. So I don’t expect their expected value number to be very meaningful, due to huge confidence intervals.
-When you compare predictions to reality in “Transmissibility”, you seem to assume vaccine efficacy (VE) from cases should equal VE from R. Vaccinations seem to reduce peak viral load by a lot, regardless of conditioning on symptoms. So we should not expect the R to be very predictive of VE.
Various points on Delta and R:
-When I dig into R estimates for new variants, I find lots of disagreement comes from the serial interval estimate. Personally I convert everything to weekly growth now so I don’t have to hold that information in my head.
-Regarding the calculation you did in “Transmissibility”, there’s pretty good data from the UK. While Delta was taking over, they estimated that the natural log of the Delta/Alpha ratio increased by 0.91/week to 0.93/week (a factor of ~2.5). I trust this value more because it is less biased by the control system. See for example Table 7 on pg 25 of https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/993879/Variants_of_Concern_VOC_Technical_Briefing_15.pdf
-I’ve been doing a similar estimate for the US based on weekly proportions of delta and it’s descendants, albeit with a shoddier method because time constraints & heterogeneous data. The best fit is usually a relative growth rate of ~1.85 per week (although it can vary by +/- 0.1 depending on the day). I’ve been surprised because the US overall growth rate has been faster than 1.85 times the pre-delta rates. It might be that the highest-transmission states are now contributing much more than before? Data from https://outbreak.info/situation-reports?pango=B.1.617.2&loc=USA&selected=USA and equivalents for the AY’s.