1/ You’ve probably heard the #Omicron “stealth” sub-variant, BA.2, is spreading rapidly in places like Denmark. We’re tracking the signal and, while there’s a lot of uncertainty, a picture is emerging. A thread on what we’re learning. @RickABright @jessicamalaty @amymaxmen @Tuliodna
2/ Like most VoCs, #Omicron can be divided into multiple sub-variants. The most common one–often just referred to as #Omicron–is BA.1. Unlike BA.1, BA.2 can’t be easily distinguished from Delta using PCR. So, for this analysis we relied on genome sequences shared in @GISAID.
4/ But, there are A LOT of ways that data biases can “trick” us into thinking a variant is spreading faster. We’ll rule them out as we walk you through our findings.
5/ First, labs could rush genomes they think are stealth #Omicron (BA.2). We saw this with BA.1 in the US. In Denmark, the data show no evidence for this bias, with time between collection and posting to @GISAID being nearly identical for BA.1 and 2.
6/ Second, the surge in BA.2 might only be happening in a single city or region of Denmark. Think early days of #COVID19 in the US being largely confined to NYC/Boston. Again, this is not what’s happening in Denmark. How can we tell?
7/ Across Denmark, BA.1 #Omicron waves preceded BA.2 in every region, and despite these BA.1 waves, we find that BA.2 is increasing exponentially. This analysis relies on a rough estimate of variant prevalence, but Denmark has very good surveillance.
8/ We estimate that BA.2 is quickly replacing BA.1 in Denmark (in more technical terms it has a doubling time of 4–5 days relative to BA.1). Said differently, the epi data show that BA.2 is outcompeting BA.1. This is a worrying trend and one that we are watching closely.
9/ We are not the only ones reporting a growth advantage of BA.2 in Denmark. Multiple groups finding similar patterns is the kind of evidence we look for with newly emerging variants. Consensus is one way to build confidence in results.
10/ Concerningly, we find similar growth rates of BA.2 in India vs. other variants (doubling every 4 days). This is a sign we look for when a variant has a competitive advantage, spread in multiple countries despite the high prevalence of other variants. Important caveat follows.
11/ The data from India are noisier (it’s a *much* bigger country than Denmark & has lower prevalence). The dynamics of Delta vs BA.1 vs BA.2 don’t look exactly the same either. We wouldn’t hang our hat on these results, but they are consistent with the emerging BA.2 pattern.
12/ In Germany researchers have again found similar patterns.
13/ And also in the UK.
14/ Genome sequences from individuals arriving in Japan that test positive for SARS-CoV-2 show evidence for widespread BA.2 across South East Asia. These findings are consistent with genomes from in-country-based surveillance outside of Japan.
15/ Finally, it might also be that there are mutations present in Denmark BA.2 that make these viruses unique from other BA.2s (a sub-sub-variant). Based on recent data, this again does *not* seem to be the case.
16/ Our partners in the US are scanning for BA.2 in wastewater & clinical samples. Right now, BA.2 is rare.
17/ BUT wastewater testing from Marc Johnson’s lab at @mumedicine shows that BA.2 is in the US, and spreading fast. This aligns with what we would expect given trends in other countries. As our environmental surveillance manager, @megan_b_diamond says, “Waste before case.”
18/ There’s no data yet on BA.2 severity nor on its risk for vaccine breakthroughs. However, we need to watch the science here very closely over the next few days.
19/ What’s next? As with the currently dominant #Omicron (BA.1) the advantage for BA.2 could be because it’s better at spreading (higher R0) and/or it’s able to re-infect individuals w/ immunity to BA.1 (immune escape). We’re investigating this now w/ epi data & will report out soon.
20/ Huge thanks to the @GISAID initiative and their incredible community that makes these kinds of analyses possible.
21/ Our analysis, along with others on Twitter, are only possible because data and insights are being shared publicly. Join the network we’re building @ppi_insights, share your information with the world, and help us create a #PandemicFreeFuture.