Thread by @trvrb

Rapid growth and early crest compared to simple Rt estimate can perhaps be explained by a shortened generation interval. We observe a 2-3 day doubling, but calculating the number of secondary infections requires a generation interval assumption. 8/17

The Norway Christmas party case study by Brandal et al (eurosurveillance.org/content/10.280…) shows a clear 3-day incubation period vs ~4.3 days for Delta and ~5.0 days for other variants (thelancet.com/journals/lanep…). 9/17

Similar values of initial epidemic growth rate r can have different values of Rt based on generation interval and lower Rt results in waves that break with fewer individual's infected. 10/17

Omicron continues to spread rapidly in the US and other countries. Here, @marlinfiggins and I estimate breakdown of Delta vs Omicron cases from genomic data from @GISAID and case counts from @OurWorldInData (further results at github.com/blab/rt-from-f…). 11/17

Some countries like the UK are farther ahead in their Omicron waves and Omicron cases have eclipsed Delta cases. Other countries like the US are just hitting the point where Omicron begins to rapidly increase overall case counts. 12/17

Omicron wave across the US and other Western countries will be difficult to track over the next 11 days to Jan 3 because of holiday under-reporting due to decreased test seeking, decreased testing capacity and delays in reporting. 13/17

More detailed estimates of severity have now come in with @mrc_outbreak estimating perhaps a 30% reduction in intrinsic severity, ie hazard ratio for hospitalization of unvaccinated Omicron case relative to unvaccinated Delta case (imperial.ac.uk/mrc-global-inf…). 14/17

With Omicron cases being primarily reinfections or breakthrough infections the overall severity in terms of risk of hospitalization is perhaps 3X lower for an Omicron case than for a Delta case. This number will differ by region based on population immunity. 15/17

So far London daily hospital admissions have been lower in absolute terms during this wave than the winter 2020-2021 wave, but are exceeding daily hospital admissions for the Delta wave (coronavirus.data.gov.uk/details/health…). 16/17

To summarize, Omicron wave will be fast and intense across geographies, but is expected to burn through quickly. Even if individual potential of severe outcomes are lower for Omicron, regions with already strained hospital capacity are particularly at risk. 17/17

Follow up #1: In tweets 6 and 7 I use estimate of 7.5% of London with reported Omicron and multiply by assumed under-reporting to arrive at 30-38% of London with Omicron infection. However, the 7.5% is 3X too high due to bug as described here:

https://twitter.com/seabbs/status/1474168339320688648

Follow up #2: According to coronavirus.data.gov.uk/details/cases?… there were 280,317 cases (Omicron and otherwise) in London from Dec 1 to Dec 20. Based on population of 8.982 million, this is 3.1% cumulative cases (which won't all be Omicon).

Follow up #3: Correcting this error to give 3X lower cumulative cases would suggest total Omicron infections in London to be more like 10% rather than 30%. I apologize for the confusion.

Follow up #4: Tweet 7 quoting 30% of London having been infected with Omicron was being shared outside of context of thread that includes correction. I've deleted this tweet to hopefully reduce confusion.