Thread by @SternLab, Finally excited to share our work with @KoelleLab @m_a

Finally excited to share our work with @KoelleLab @m_a_martin and many others on features of SARS-CoV-2 spread.
https://www.medrxiv.org/content/10.1101/2020.05.21.20104521v1
What did we find:
1. Sequenced 212 genomes from Israel @GISAID @nextstrain

Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel

Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequenced 212 SARS-CoV-2 sequences and use...

https://www.medrxiv.org/content/10.1101/2020.05.21.20104521v1

2. Vast majority of introductions are from US (70%), exceeding their relative proportion in incoming infected travellers (27%)

3. Super-spreading is a feature of viral spread: 1-10% of infected individuals responsible for 80% of secondary infections

4. Under the most extreme scenario (1% superspreaders) we find cumulative incidence of ~1% of Israeli population, and this is our upper bound estimate. Far from herd immunity.

5. We estimate R0 dropped from 2-2.6 down to about 0.7 following shelter-in-place restrictions, enforcing their effectiveness.

Led by the wonderful @Daniellemlrs @m_a_martin @taliakustin and Noam Harel, Omer Tirosh

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