Trevor Bedford Profile picture
Feb 8, 2020 4 tweets 3 min read
Insight into the spatial behavior of epidemics from @ohallats and colleagues. An initial outbreak will grow in its highly connected environment and subsequently seed outbreaks in other locations. These other outbreaks resemble a transposed copy of the first. 1/4
@ohallats #nCoV2019 in Wuhan went from an index case in ~Nov 2019 to several thousand cases by mid-Jan 2020, thus going from initial seeding event to widespread local transmission in the span of ~10 weeks. 2/4
@ohallats We believe that international seeding events started to occur in mid-Jan. Thus we have a critical ~10 weeks from then to late-March to contain these nascent outbreaks before they become sizable. 3/4

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More from @trvrb

Jan 28
Omicron viruses can be divided into two major groups, referred to as PANGO lineages BA.1 and BA.2 or @nextstrain clades 21K and 21L. The vast majority of globally sequenced Omicron have been 21K (~630k) compared a small minority of 21L (~18k), but 21L is gaining ground. 1/15
Omicron clades 21K and 21L differ at ~40 amino acid sites, which is substantial in the context of SARS-CoV-2 evolution. 2/15
For comparison Alpha, Beta and Gamma are each about as divergent from each other in terms of amino acid changes across the genome as Omicron 21K and 21L are from each other. Figure from @nextstrain (nextstrain.org/ncov/gisaid/gl…). 3/15
Read 15 tweets
Jan 20
Case counts for the US appear to have peaked at a 7-day average of 806k on Jan 14. Omicron grew from approximately 35k daily cases on Dec 14 to ~800k daily cases in ~4 weeks. 1/9
Looking at cases per 100k population per day across states, downturns are clear in NY, NJ, MA, FL, etc..., but many states are not yet at peak case loads. 2/9
If we partition @CDCgov cases between Delta and Omicron using @GISAID sequence data following approach by @marlinfiggins (bedford.io/papers/figgins…) we can see clear Omicron epidemics. 3/9
Read 9 tweets
Jan 10
With Omicron, case counts in the US and many other countries have skyrocketed. The US 7-day average is now ~680k cases per day, or 0.2% of the population recorded as confirmed cases each day. 1/15
However, a large fraction of infections, symptomatic and otherwise, don't end up reported as cases due to lack of testing (either the individual doesn't seek testing or testing is desired but not readily found). 2/15
Historically, I have assumed that around 30% of infections in the US are reported as cases. This number was derived from seroprevalence and modeling estimates from sites like (no longer updated) covid19-projections.com. 3/15
Read 15 tweets
Jan 5
The impact of Omicron on case counts in the US is now abundantly obvious with 885k reported cases yesterday alone. Figure using @CDCgov data and showing daily reported cases with 7-day smoothing on log scale. 1/12
We can partition state-level cases between Delta and Omicron using sequence data from @GISAID. This is made possible by 1.6 million genomes from the US from viruses sampled since Oct 15. This remarkable dataset is thanks to a large number of labs throughout the country. 2/12
Genomic data will necessarily be lagged by about 10 days, but we can use modeling framework from @marlinfiggins to project forward variant-specific frequencies and epidemic growth rates to the present. 3/12
Read 13 tweets
Dec 23, 2021
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
Read 14 tweets
Dec 23, 2021
An update on Omicron epidemic dynamics and where we stand today. Exponential growth cannot go on forever, but predicting when a wave will crest ahead of observing slowing in case growth is very difficult. 1/17
That said, we have a fundamental prediction from basic epidemic modeling that epidemics with higher initial Rt (number of secondary infections caused by one infection) should result in larger epidemic waves in terms of total infections. 2/17 Image
Estimates of initial Omicron Rt of ~3.5 suggested the potential for a very large wave in terms of cases, with significantly more cases than Delta wave just based on comparison of initial Rt. 3/17
Read 17 tweets

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