Omicron appears to have emerged around Oct 1 and has taken 8 weeks of exponential growth to "suddenly" have sizable impacts on case counts and hospitalizations in Gauteng. This "suddenly" is the nature of exponential growth. 2/6
Exports from the South African epidemic are now being detected across the world and these exports are sparking local transmission. Figure from nextstrain.org/groups/blab/nc… using data generously shared to @GISAID. 3/6
As a broad analogy if it took ~8 weeks for Omicron to grow from initial spark into local epidemic in South Africa, I would expect very roughly 8 weeks from today for secondary epidemics to begin to manifest. 4/6
This is assuming rate of spread is similar across populations, which may not be the case. Population immunity differs quantitively (proportion with some immunity) and qualitatively (vaccine derived vs infection derived) across geographies. This may well impact rate of spread. 5/6
I expect we'll know more about the extent of worldwide seeding and epidemic growth rates in different geographies in just a couple weeks. 6/6
• • •
Missing some Tweet in this thread? You can try to
force a refresh
Following up here with speculative estimates of the rate of spread of Omicron and a stab at how to apportion this rapid rate of spread between intrinsic transmissibility and immune escape. 1/18
Monday's post was mainly meant to emphasize that observed rapid spread of Omicron can be influenced by both intrinsic transmissibility and immune escape. Here, I'll try to put (speculative) numbers on this rate of spread. 2/18
Key datapoints include rapid displacement of existing Delta viruses by Omicron in Gauteng and South Africa. Estimates of logistic growth rate here by @TWenseleers imply Omicron has ~5X current transmission rate of Delta. 3/18
I think there's perhaps been some confusion regarding transmissibility vs immune escape in Omicron. The apparent rapid increase in frequency of Omicron in Gauteng does not mean that Omicron is necessarily more intrinsically transmissible than Delta. 1/15
This diagram shows estimated increase in intrinsic transmissibility from work by @marlinfiggins (
) along with fold drop in neutralization titer compiled from Uriu et al (biorxiv.org/content/10.110…) and similar papers. 2/15
We see that previous variants have showed only modest potential for escape from immunity engendered by vaccination or infection with circulating SARS-CoV-2 viruses, but have varied considerably in their intrinsic transmissibility with Delta outpacing others. 3/15
There have been a number of overview threads on the emerging variant designated as @PangoNetwork lineage B.1.1.529, @nextstrain clade 21K and @WHO Variant of Concern Omicron. I'm not going to attempt to be comprehensive here, but will highlight a few aspects of the data. 1/16
Global systems for identifying novel variants and rapidly sharing data are working well with 91 genomes from Omicron viruses shared to @GISAID from specimens collected between Nov 11 and Nov 23 from Botswana, South Africa and Hong Kong. 2/16
These viruses are visible on @nextstrain as "21K (Omicron)" shown here in red (nextstrain.org/ncov/gisaid/af…). They do not descend from previously identified "variant" viruses and instead their closest evolutionary connection is to mid-2020 viruses. 3/16
Did vaccination drive the evolution of variant (Alpha, Beta, etc...) SARS-CoV-2 viruses? This is a legitimate scientific question, but after looking into it I don't believe this to be the case. 1/19
Grenfell et al. 2004 (science.org/doi/10.1126/sc…) lays out the conceptual foundations for thinking about this problem. This figure is a bit hard to parse, but basically vaccination will increase population immunity and move rightward on the x-axis. 2/19
This will increase the strength of selection for immune escape (blue line), but will decrease viral abundance (red line). The rate of viral adaptation (black line) depends on both selection and abundance and so is maximized at an intermediate level of population immunity. 3/19
I support making boosters broadly available for those 18 and older. Even if breakthrough cases are generally mild in younger age groups, there is significant societal benefit to reducing circulation. 1/6 nytimes.com/2021/11/16/us/…
Currently Washington State is seeing almost 30% of cases as breakthrough cases (doh.wa.gov/Portals/1/Docu…). 2/6
Here, I think of @alexismadrigal's piece on the implications of a positive COVID test (theatlantic.com/health/archive…). It's crazy to me that we're saying to healthy younger individuals they must isolate for 10 days after a positive test, but that they're not eligible for a booster. 3/6
The evolution of SARS-CoV-2 in the past year has been remarkable with Delta increasing transmissibility by perhaps 2.2X over "non-variant" viruses. 1/14
We should expect this evolution to slow as SARS-CoV-2 continues to adapt to the human host, but when should we expect this? Here, I propose that we've already seen slowing between 2020 and today. 2/14
One very important concept here that I keep coming back to in thinking about evolution is @GreatDismal's quote that "the future is already here. It's just not evenly distributed yet". 3/14