Frederik Plesner Lyngse Profile picture
Jan 31, 2022 15 tweets 9 min read Read on X
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…
1/ ImageImage
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.
2/
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%
3/ Image
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!
4/
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%.
5/ Image
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.
6/ Image
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.
7/ Image
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.
8/ Image
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.
9/ Image
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.
10/ Image
Lastly, we have more results in the appendix:
- Background
- More descriptive statistics
- Alternative presentation of main results
- Robustness analyses 
11/
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. 
12/
Så er der også en populærvidenskabelig artikel på @videnskabdk: videnskab.dk/krop-sundhed/b…

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More from @LyngseF

Sep 26, 2022
Very happy that this work is finally out in a peer reviewed journal: @NatureComms
“Household transmission of the SARS-CoV-2 Omicron variant in Denmark”
Read it here: nature.com/articles/s4146…

A short thread with the new/updated results.
1/
We investigate the secondary attack rate (SAR) in households infected with #SARSCoV2 #Omicron vs #Delta in Demark, 9-22 December 2021.
2/
Conclude:
Omicron has a higher SAR than Delta. While vaccination and booster vaccination does confer protection against Omicron, we conclude that the rapid spread of Omicron is likely due to immune evasiveness and to a lower extent an increase in the basic transmissibility.
3/
Read 34 tweets
Jan 10, 2022
New Preprint Out!
Effect of Vaccination on Household Transmission of SARS-CoV-2 Delta VOC
We investigate the secondary attack rate (SAR) in #Delta households in Demark, June-November December 2021.
medrxiv.org/cgi/content/sh…
1/N
We have 24,693 primary cases (33% fully vaccinated) and 53,584 potential secondary cases (49% fully vaccinated).
The SAR was generally lower among vaccinated potential secondary cases than among unvaccinated.
2/N
We found that the vaccine effectiveness against susceptibility (VES) was 61% (95%-CI: 59-63) and that the vaccine effectiveness against transmissibility (VET) was 42% (95%-CI: 39-45).
3/N
Read 10 tweets
Dec 29, 2021
New Preprint Out!
SARS-CoV-2 Omicron VOC Transmission in Danish Households
We investigate the secondary attack rate (SAR) in #Omicron vs #Delta households in Demark, 9th-19th December 2021.
medrxiv.org/content/10.110…
1/N Image
Overall, our findings confirm that the rapid spread of Omicron can primarily be ascribed to the immune evasiveness rather than an inherent increase in the basic transmissibility.
2/N
We identify primary cases 9-12 December 2021. This gives us 11,937 households (2,225 with Omicron) living with 27,874 potential secondary cases. We identified 6,397 positive secondary cases during a 1-7 day follow-up period.
3/N Image
Read 24 tweets

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