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C_Althaus's profile
Christian Althaus
Christian Althaus
Christian Althaus
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@C_Althaus

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Christian AlthausVerified account

@C_Althaus

Computational epidemiologist, cyclist, and citizen. Views are my own. @INPUTBern @ISPMBern @MCIDBern @unibern @chplusplus

Zurich, Switzerland
calthaus.github.io
Joined June 2011

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    1. Christian Althaus‏Verified account @C_Althaus 28 Nov 2021

      The mutational profile of Omicron suggests a potentially significant transmission advantage. But can we already say something about increased transmissibility or immune evasion? I'll give it a try. Warning: Preliminary and based on VERY limited data. 1/15pic.twitter.com/6v72viJBjk

      54 replies 638 retweets 1,692 likes
      Show this thread
    2. Christian Althaus‏Verified account @C_Althaus 28 Nov 2021

      Christian Althaus Retweeted Tulio de Oliveira

      The observed rapid replacement of Delta by Omicron in the province of Gauteng in South Africa is suggestive of a transmission advantage. 2/15https://twitter.com/Tuliodna/status/1463911571176968194 …

      Christian Althaus added,

      Tulio de Oliveira @Tuliodna
      This new variant, B.1.1.529 seems to spread very quick! In less than 2 weeks now dominates all infections following a devastating Delta wave in South Africa (Blue new variant, now at 75% of last genomes and soon to reach 100%) pic.twitter.com/Z9mde45Qe0
      Show this thread
      7 replies 44 retweets 258 likes
      Show this thread
    3. Christian Althaus‏Verified account @C_Althaus 28 Nov 2021

      Fitting a multinomial logistic regression model to the proportion of different variants in South Africa results in an estimated growth advantage of Omicron of 0.43 (95% CI: 0.15-0.72) per day compared to Delta. 3/15pic.twitter.com/VPHsRQPJqw

      10 replies 54 retweets 259 likes
      Show this thread
    4. Christian Althaus‏Verified account @C_Althaus 28 Nov 2021

      Christian Althaus Retweeted Tom Wenseleers

      .@TWenseleers obtained a similar estimate of 0.38 per day. There are lots of caveats: Targeted sequencing, stochastic effects in low incidence settings, and successive superspreading events could significantly bias these estimates. But let’s continue from here. 4/15https://twitter.com/TWenseleers/status/1464673722640568327 …

      Christian Althaus added,

      Tom Wenseleers @TWenseleers
      Replying to @Emmanuel_microb
      I also don't believe it is less severe. The growth rate advantage of Omicron vs Mu based on GISAID & SGTF data works out at 0.38/day [0.33-0.43] 95% CLs, which would correspond to it infecting ca. exp(0.38*4.7)=6.0 [4.7-7.5] x more people than Delta within one GT of the virus. pic.twitter.com/8hOj7MznxP
      1 reply 31 retweets 225 likes
      Show this thread
    5. Christian Althaus‏Verified account @C_Althaus 28 Nov 2021

      Assuming the same generation time, the transmission advantage could act at two levels: 1) increase in transmissibility, 2) immune evasion. We recently developed a mathematical framework to relate differences in growth rates to these properties. 5/15https://doi.org/10.1101/2021.06.10.21258468 …

      4 replies 31 retweets 237 likes
      Show this thread
    6. Christian Althaus‏Verified account @C_Althaus 28 Nov 2021

      A potential increase in transmissibility can be expressed as ρD/R_w, where X is the estimated growth advantage (0.43 per day), D the generation time (5.2 days), and R_w the effective reproduction of the previous variant (~ 0.8 in RSA during October). 6/15 https://ibz-shiny.ethz.ch/covid-19-re-international/ …

      6 replies 16 retweets 159 likes
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    7. Christian Althaus‏Verified account @C_Althaus 28 Nov 2021

      This would result in an increased transmissibility of 280% (95% CI: 98-468%). With Delta having an R_0 = 5-6 in the Northern Hemisphere during winter, the R_0 of Omicron would be around 10-30. Not impossible, but such a jump seems rather unlikely. 7/15

      5 replies 57 retweets 299 likes
      Show this thread
    8. Christian Althaus‏Verified account @C_Althaus 28 Nov 2021

      If the transmission advantage acted via immune evasion only, the level of immune evasion would be ρD(1-Ω)/(ΩR_w), with Ω being the proportion of the population that has fully protective immunity against infection with earlier variants. 8/15

      6 replies 20 retweets 194 likes
      Show this thread
      Christian Althaus‏Verified account @C_Althaus 28 Nov 2021

      South Africa records an excess mortality of 230k during the pandemic, which corresponds to 0.39% of the overall population (https://github.com/dkobak/excess-mortality …). We earlier estimated the infection fatality ratio for the population of South Africa to be 0.35% (https://doi.org/10.1007/s10654-020-00649-w …). 9/15

      3:42 AM - 28 Nov 2021
      • 52 Retweets
      • 254 Likes
      • Dave Limited Kinnaird McQuade💥🌩 Derek Homeier Klaus Masuch Moritz S. Per Prins Luisa Regula Nebel ZC 🇺🇲
      6 replies 52 retweets 254 likes
        1. New conversation
        2. Christian Althaus‏Verified account @C_Althaus 28 Nov 2021

          Hence, it is likely that almost everyone in South Africa has been infected with #SARSCoV2 and developed partial immunity against reinfection. In addition, 24% of the population have been fully vaccinated. 10/15pic.twitter.com/ygL5IrIfwa

          8 replies 53 retweets 279 likes
          Show this thread
        3. Christian Althaus‏Verified account @C_Althaus 28 Nov 2021

          Thus, the proportion of the population that is fully protected (‘immune’) against infection and further transmission must be quite high. If we assume Ω = 75%, we get an immune evasion of 93% (95% CI: 32-100%), i.e., Omicron evades protective immunity in 93% of individuals. 11/15

          14 replies 80 retweets 370 likes
          Show this thread
        4. Christian Althaus‏Verified account @C_Althaus 28 Nov 2021

          For Ω = 90%, we obtain an immune evasion of 31% (95% CI: 11-52%) ‘only’. This clearly illustrates the current level of uncertainty about Omicron, and I want to emphasize again the preliminary character of these calculations. 12/15

          6 replies 51 retweets 286 likes
          Show this thread
        5. Christian Althaus‏Verified account @C_Althaus 28 Nov 2021

          Still, I do expect partial immune evasion to be the main driver of the observed dynamics, but increased transmissibility cannot be ruled out so far. 13/15

          9 replies 40 retweets 306 likes
          Show this thread
        6. Christian Althaus‏Verified account @C_Althaus 28 Nov 2021

          The developments in South Africa and observations from other countries during the coming days and weeks will allow us to shed more light on the properties of Omicron. 14/15

          3 replies 23 retweets 215 likes
          Show this thread
        7. Christian Althaus‏Verified account @C_Althaus 28 Nov 2021

          Finally, thanks for the amazing work from @Tuliodna, @houzhou, @rjlessells, and their colleagues in South Africa, @firefoxx66 from @ISPMBern at @unibern for http://covariants.org , @richardneher and @trvrb for @nextstrain, and the many others working around the clock. 15/15

          21 replies 42 retweets 430 likes
          Show this thread
        8. End of conversation
        1. KooZooK.com‏ @koozookit 28 Nov 2021
          Replying to @C_Althaus

          Have you considered latest case fatality rate by age cohort, fatality strongly influenced by older age? SA has a low 65+ population, a higher stratified vax uptake in older cohorts (64% in 65+) & use a large % of J&J. The Gauteng vax rates are also lower than SA rates?pic.twitter.com/C8pTbqn0Fj

          0 replies 2 retweets 6 likes
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        2. MacGregor Cox‏ @CoxMacgregor 28 Nov 2021
          Replying to @C_Althaus

          How are excess deaths due to aspects of the pandemic other than the virus accounted for here?

          1 reply 0 retweets 0 likes
        3. Janosch‏ @Janosch21565665 29 Nov 2021
          Replying to @CoxMacgregor @C_Althaus

          How should that be quantified?

          0 replies 0 retweets 0 likes
        4. End of conversation
        1. Alaska‏ @Alaska74073229 29 Nov 2021
          Replying to @C_Althaus

          Omg.

          0 replies 0 retweets 1 like
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