Currently, the US is reporting about 54k daily cases of COVID-19 (16 per 100k per capita) and the UK is reporting about 4k (6 per 100k). This seems comfortingly low compared to even this summer's BA.5 wave and let alone last winter's BA.1 wave. Figure from @OurWorldInData. 1/16 However, at this point, nearly all infections will be in individuals with prior immunity from vaccination or infection and this combined with a roll back in testing makes it unclear how to interpret current case counts compared to previous time periods. 2/16

Largely through partial immune escape, lineage BA.5 viruses resulted in sizable epidemics throughout much of the world. However, in most countries these epidemics are now beginning to wind down. What do we expect after BA.5? 1/10 Lineage BA.2.75 (aka 'Centaurus') has been high on watch lists due to sustained increase in frequency in India combined with the presence of multiple mutations to spike protein. We now have enough sampled BA.2.75 viruses from outside India to make some initial conclusions. 2/10

Based on the experience in winter 2020/2021, seasonal influence on SARS-CoV-2 transmission is quite clear, but much of the Northern Hemisphere is currently experiencing large summer epidemics driven the spread of evolved BA.5 viruses. 1/11 It's necessarily fraught to try to make predictions of seasonal circulation patterns going forwards, but we can gain some intuition from simple epidemiological models. 2/11

There seems to be a worry that telling people we've exited the "pandemic phase" will lead to further reduced precautions. As always however, I think it's best not to conduct messaging for intended behavioral effect and just try to make scientifically accurate statements. 1/5 Given vaccination and infection, the US and global population now has widespread immunity to SARS-CoV-2 and deaths per-infection are about 10 times lower than they were pre-immunity in 2020 with a ballpark IFR of 0.05% (though this will vary by immunity and age demographics). 2/5

The @US_FDA VRBPAC committee will be meeting tomorrow to discuss variant-specific COVID-19 vaccines (fda.gov/advisory-commi…). Based on present observations, I would argue that the most important metric to optimize are titers against BA.4/BA.5 viruses. 1/10 We've seen repeated replacement of SARS-CoV-2 variants during 2022, first of Delta by Omicron BA.1 and then by sub-lineages of Omicron, with BA.2 replacing BA.1 and now with BA.4/BA.5 replacing BA.2. 2/10

Global monkeypox confirmed and suspected cases compiled by @globaldothealth show initial rapid increase as case-based surveillance comes online, followed by slower continued growth. 1/10 This is data from github.com/globaldothealt… and has had a 7-day smoothing applied and all y-axes are shown on a log scale. 2/10

We now have enough co-circulation of Omicron sub-lineages BA.4, BA.5 and BA.2.12.1 in the US to make an assessment of relative fitness between these viruses. 1/12 Pango lineages BA.4 and BA.5, corresponding to @nextstrain clades 22A and 22B, were first described in South Africa by @Tuliodna et al and possess key spike mutations L452R and F486V. 2/12

Non-travel related monkeypox cases were announced by @UKHSA just 10 days ago on May 14 and first viral genome shared by @irj_pt 5 days later on May 19. It's remarkable how far pathogen genomic sequencing has come, in part spurred by the pandemic. 1/9

https://twitter.com/borges__vitor/status/1527436883093078029

There are now over 300 confirmed and suspected cases globally and at least 15 viral genome sequences shared publicly. The extent and trajectory of the outbreak is still incredibly hazy. Here, I wanted to give a word of caution on genomic epidemiology of monkeypox. 2/9

We're now starting to see the evolution of new potentially impactful sublineages of Omicron with particular focus on mutations at spike residue 452. Here, I'd like to highlight lineages B.2.12.1 in New York, as well as BA.4 and BA.5 in South Africa. 1/17 Stepping back, Omicron emerged as three distinct lineages BA.1, BA.2 and BA.3 and despite the head start of BA.1, we've seen BA.2 overtake BA.1 across the world over the course of January to April. 2/17

Today, I presented to @US_FDA VRBPAC with an overview of SARS-CoV-2 evolution up to this point and a brief perspective for what to expect going forward. Slides are here: bedford.io/talks/sars-cov… and my slot in the full recording is viewable here: . 1/13 My main point was really how fast evolution has been proceeding. We see that SARS-CoV-2 variants have (1) displaced existing genetic diversity and (2) accumulated amino acid changes in the relevant domain much faster than seen in the fastest seasonal flu subtype H3N2. 2/13

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

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

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

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

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

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

I fully agree that the single best action individuals (and governments) can be taking to reduce impact of the Omicron wave is to get booster dose if already vaccinated and to get vaccinated if not. 1/14 However, I absolutely think we need to be moving forward with clinical trials for a possible future swap to an Omicron-specific or bivalent vaccine (nytimes.com/2021/12/20/hea…). 2/14

The extremely rapid rate of spread of Omicron clearly visible since the beginning of December will now be acutely felt in many geographies as local epidemics amplify to the point of eclipsing Delta circulation. 1/12

https://twitter.com/trvrb/status/1467245887357210624

Continuing previous methods, if we partition case counts from @OurWorldInData using sequence data from @GISAID and apply a modeling approach from @marlinfiggins we get rapid rises in Omicron cases in South Africa, Denmark, Germany, the UK and the US. 2/12

It seems that the common assumption has been that Omicron will displace Delta, just as Delta displaced Alpha, Beta, Gamma, etc... before it. This may well be the case, but it's by no means definite. 1/15 Depending on Omicron's mix of intrinsic transmissibility and immune escape (and what happens with continued evolution), we could see:
1. Displacement of Delta by Omicron
2. Long-term co-circulation
3. Omicron wave followed by resurgence of Delta and extinction of Omicron
2/15

There is now enough genomic data from the US and Germany to repeat this approach to estimating Omicron-specific rate of epidemic spread. Here, we observe similar initial rapid spread in the US and Germany. 1/10

https://twitter.com/trvrb/status/1469157770716872708

As before, we partition case counts from @OurWorldInData using sequences from @GISAID into estimated Omicron, Delta and other cases, and we use this partitioning to infer variant-specific Rt and epidemic growth rate r (methods and code here github.com/blab/rt-from-f…). 2/10

We've seen exceptionally rapid spread of Omicron in South Africa. Although we should expect this rapid spread to follow in other geographies, we've mostly lacked data to confirm this until recently. 1/21

https://twitter.com/trvrb/status/1467245887357210624

Because of significant travel connections (

https://twitter.com/MOUGK/status/1464141177226158094

) and extremely strong genomic surveillance by @CovidGenomicsUK, we should have early data from the UK about rate of spread outside of South Africa. 2/21