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Rule-extracted, not adjudicated. The grade says what may be done with each one; read the document above before relying on any of them.

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1. 2021-02-20 08:19 Andrew Rambaut open
   My current favourite hypothesis is that all of this is about increasing transmissibility in the face of global implementation of NPI which is why we have simultaneous explosive 2nd waves (Doug & Phil) and then the 3rd waves (VOCs). In particular I am wondering if partially-effective measures may have driven evolution for transmissibility in the same way that ineffective vaccines can. Doug & Phil arose in China during the first lock down period (but possibly outside of Wuhan in somewhere like Shanghai) but really took off in Italy. Displacedeverything globally except for areas like Africa where there was not much reported incidence and not much response and lineage A persisted. Then as incidence started to rocket, NPI were implemented and the lineage AVOCs were selected for.
2. 2021-02-20 08:20 Andrew Rambaut open
   This would be an explosively political hypothesis given all the anti-lockdown stuff going on.
3. 2021-02-20 08:25 Kristian G. Andersen open
   I agree with the first part - not sure about the VOCs. I think the selection pressure there is more complicated with RSA/BRA selecting more for evasion, than inherent transmission. The fixation of mutations was probably due tointrahost selection, but I agree the near-fixation in the population likely has more to do with transmission (in apopulation with high levels of immunity - so reinfections).
4. 2021-02-20 08:27 Kristian G. Andersen open
   B.1.1.7 just looks different to me - again, mutations fixed intrahost in the first place, then near-fixation in the population because of being inherently more transmissible. I think partial immune escape adds to its success aswell.
5. 2021-02-20 08:28 Kristian G. Andersen
   But overall, yes, I agree with the hypothesis and think the distinction of different waves being due to differentmitigation efforts is a good one - but as you say, massively politically charged.The fourth wave will likely be driven almost entirely by vaccine escape.
6. 2021-02-20 08:29 Robert F. Garry open
   Makes a lot of sense to me.
7. 2021-02-20 08:30 Kristian G. Andersen open
   (this ain't the flu, btw). Bob, I'll look at the document today!
8. 2021-02-20 09:18 Andrew Rambaut open
   @Kristian Andersen I generally agree - I am 100% convinced that B.1.1.7 is different from everything in its origin story but has converged on the same peak.
9. 2021-02-20 09:23 Andrew Rambaut open
   I guess the first question to demonstrate is that has there been a shift in the adaptive landscape (rather than just alot more unusual stuff happening because there are shed loads of cases - although that too). Possible reasons for awide-spread shift in the population level landscapes are 1) NPI, 2) deployment of anti-viral treatments, 3) increasing seroprevalence 4) ? anything else? Then there is the possibility of a shift in within host landscapes - more chronic infections, possibly inimmuno-compromised, possibly treated. Here it is a numbers game - more infections mean more of these and more chance some of them hit this population-fit fitness peak and then transmit onwards.

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