18 Feb 2021 Variants vaccines and evolution

Thu, 02/18/2021 - 21:27

Dear colleagues,

In this Episode, I will give some short comments about recent info on variants and vaccine progress

  1. Variants


  • The medRxiv paper by Hodcrof (Ep 111-1) describes several clusters in the US, which share a polymorphism in position 677 of S, which is associated with other mutations in ORF1a, ORF1b, ORF 3 and N (see Fig 4 p. 22 and Table p.24).  Since position 677 is close to the S1-S2 polybasic cleavage site, the hypothesis is that it could enhance “fusion fitness’, just like N501Y (in the British, S-A and Brazilian variants) enhances “binding fitness”.


  • The short paper by Kissler et al (Ep 11-2) suggests that SARS-CoV-2 variant B.1.1.7 may cause longer infections with  similar peak viral concentration compared to non-B.1.1.7 SARS-CoV-2, and this extended duration may contribute to B.1.1.7 SARS-CoV-2’s increased transmissibility. A longer isolation period than the currently recommended 10 days after symptom onset5 may be needed to effectively interrupt secondary infections by this variant. Similar analyses should be performed for other SARS-CoV-2 variants such as (South-African) B.1.351 and (Brazilian) P.1.


  • The Nature paper by Kemp et al (Ep 111-3) warns against the risk of repeated convalescent plasma in a chronically infected immunosuppressed COVID case: it induced a mutation in D796H, reducing fitness, which was compensated by the 69-70 deletion (also present in the B117 variant).  In view of the doubtful beneficial effects of convalescent plasma, the authors propose that it should be limited to clinical studies with extensive virological and immunological monitoring and not be administered lightly to T and B immunosuppressed patients  


  1. Vaccines
  • The comment in Nature of 16 Feb (Ep 111-4) provides some preliminary info on side effects, based on the experience with mRNA (mainly US data) and Astra-Zeneca (mainly UK).  The figures of only 372 per million “non-serious reaction reports” for the mRNA seems extremely low, since in the trials, where 80 % reported local pain.  The reactions were at 4000 per million for AZ, but again substantially lower than in the trial (more than 50 %).  Anaphylactic reactions are extremely low (5 per million) and all recovered.  Nevertheless, side effects are more common than with flu vaccines….
  • A comment by Kai Kupferschmidt (Ep 111-5) on the growing inequity with limited access to life-saving equipment (ventilators, oxygen) in Sub-Saharan Africa and no access to COVID vaccines. Nobody knows how many health care workers have died in Africa.  
  • Speculations on “endemic future” of COVID-19 (Ep 111-6).

Best wishes,

Guido Vanham