Thread by @LyngseF

New Preprint Out!
“Transmission of SARS-CoV-2 Omicron VOC subvariants BA.1 and BA.2: Evidence from Danish Households”
We investigate the secondary attack rate (SAR) in #Omicron BA.1 vs. BA.2 households in Demark, 20 December 2021 – 18 January 2022.
medrxiv.org/content/10.110…
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We conclude that Omicron BA.2 is inherently substantially more transmissible than BA.1. It also possesses immune-evasive properties that reduce the protective effect of vac. against infection, but do not increase its transmissibility from vac. persons with breakthrough infect.
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To set the stage, here is the 14-day SAR for different Variant of Concerns (VOC).
“New” #Omicron BA.2 (red): 42%
“Original” #Omicron BA.1 (blue): 35%
#Delta VOC (purple): 33%
Unknown VOC (no WGS results on sample) (gray): 33%
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What is #Omicron BA.2 and why do we care?
Omicron BA.2 is genetically very different from BA.1. They differ by approximately 40 mutations.
@mobdjek has told me told that BA.2 differs more from BA.1 genetically than #Alfa differs from the original Wuhan strain!
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Omicron BA.2 has increased rapidly in Denmark (and other countries).
06DEC2021: Omicron BA.2=0%, Omicron BA.1=5%, Delta=95%.
20DEC2021: Omicron BA.2=5%, Omicron BA.1=64%, Delta=30%.
11JAN2022: Omicron BA.2=47%, Omicron BA.1=53%, Delta=0%.
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We include households with a primary case 20DEC2021—11JAN2022.
We have 2,122 households with BA.2 with 4,587 potential secondary cases and 1,792 positives within 1-7 days: SAR=39%
We have 6,419 households with BA.1: SAR=29%.
Distributions across subvariants are comparable.
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We follow all potential secondary cases for 7 days.
84% are tested once, 60-61% are tested twice (panel a). The testing propensity is comparable across subvariants.
Omicron BA.2 households, SAR=39% on day 7.
Omicron BA.1 households, SAR=29% on day 7.
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First, we compare the effect of vaccination within Omicron BA.2 households and within BA.1 households.
Lower susceptibility for unvaccinated, higher susceptibility for booster vaccinated.
Lower transmissibility for booster vaccinated.
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Next, we compare the effect of living in an Omicron BA.2 household vs. BA.1 household across individuals with the same vaccination status.
Increased susceptibility for BA.2 across all vaccination statuses.
Increased transmissibility from unvaccinated primary cases with BA.2.
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DK has random sampling of positive RT-PCR tests for WGS.
Note, all hospitalized patients are tested for SARS-CoV-2; and all positive tests are WGS’ed for treatment purposes. This gives a sampling bias at Hospitals (panel b). Problem, if we investigated e.g. hospitalizations.
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Lastly, we have more results in the appendix:
- Background
- More descriptive statistics
- Alternative presentation of main results
- Robustness analyses 
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This work has been done extremely fast. Started looking at the data 20JAN2022.
This is only possible, because DK is highly digitized with linkable databases, random sampling for WGS with quick turnaround time, and many people across the country working way too much. 
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@udansk, @CarstenKirkeby, @KareMolbak, @TyraGroveKrause, @RskSkov, @mobdjek,@MarcStegger
@Economics_UCPH, @CEBI_UCPH, @ssi
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Så er der også en populærvidenskabelig artikel på @videnskabdk: videnskab.dk/krop-sundhed/b…

@videnskabdk Published in @NatureComms:
nature.com/articles/s4146…