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The Brazil 
Manaus #COVID19 epidemic is getting epically worse. And many scientists suspect it might be because of the new Brazil P1 variant of #SARSCoV2, which has many multiple mutations. Quick thread 
https://www.theguardian.com/world/2021/jan/14/brazil-manaus-amazonas-covid-coronavirus
Manaus #COVID19 epidemic is getting epically worse. And many scientists suspect it might be because of the new Brazil P1 variant of #SARSCoV2, which has many multiple mutations. Quick thread https://www.theguardian.com/world/2021/jan/14/brazil-manaus-amazonas-covid-coronavirus
2) Brazil has been hit really hard already. In Oct 2020, someone estimated Manaus already have hit potentially 76% already infected — some saying it’s basically been plowed so hard, it’s now at herd immunity levels (getting there the dangerous way). https://science.sciencemag.org/content/371/6526/288
already have hit potentially 76% already infected — some saying it’s basically been plowed so hard, it’s now at herd immunity levels (getting there the dangerous way). https://science.sciencemag.org/content/371/6526/288
3) yet suddenly mortality is suddenly spiking again after a period of relative flatness. And Manaus is even skews younger than other areas. So this is odd.... https://www.reuters.com/article/us-health-coronavirus-brazil/amazon-city-resorts-to-mass-graves-as-brazil-covid-19-deaths-soar-idUSKBN22B35Z
4) So what is new in Manaus ? They have the worrisome B1128 / P1 lineage. It has a crap ton of mutations in the all important spike; and moreover mutations in the spike’s critical binding domains...
And most of all the most worrisome E484K mutation that can evade antibodies
? They have the worrisome B1128 / P1 lineage. It has a crap ton of mutations in the all important spike; and moreover mutations in the spike’s critical binding domains... And most of all the most worrisome E484K mutation that can evade antibodies
5) I’ve been trying to sound the alarm on B1128 (previously called B11248 by Japan), but it’s the same lineage — now renamed P1 because there are actually two B1128’s types in Brazil. https://twitter.com/drericding/status/1348606324901359619
6) To be clear on nomenclature (naming), the two Brazil variants are:
B.1.1.28(K417N/E484K/N501Y) 
this is the one renamed P1.
There is another one called B.1.1.28(E484K)
...both have the problematic E484K mutation that can escape antibodies!
B.1.1.28(K417N/E484K/N501Y) this is the one renamed P1. There is another one called B.1.1.28(E484K)...both have the problematic E484K mutation that can escape antibodies!
7) Why are we so worried about this one? Because like the SA B1351 variant, this new one also has the E484K mutation. In a recent study by @jbloom_lab, E484 mutation (inside the #SARSCoV2’s spike’s critical receptor binding domain) seemed to escape neutralizing antibodies—bad.
8) There has even been a new case of reinfection of a person with #sarscov2 with the E484K mutation too. https://twitter.com/alinouriphd/status/1347016588579508224
9) How much affect? the E484K shows a 10x reduction of neutralization (“neutralization” = stopping the virus)
by various antibodies compared to wildtype (common #SARSCoV2) in some patients —a rather bad thing. It means the virus with E484K is worrying for “immune escape”.
by various antibodies compared to wildtype (common #SARSCoV2) in some patients —a rather bad thing. It means the virus with E484K is worrying for “immune escape”.
10) Bottomline: despite overwhelming #COVID19 already in Manaus , cases and deaths surging again possibly because of the new P1 variant. Many epidemiologists are getting worried too. And many are now saying reinfection possible if high immune escape from previous antibodies.
, cases and deaths surging again possibly because of the new P1 variant. Many epidemiologists are getting worried too. And many are now saying reinfection possible if high immune escape from previous antibodies.
11) this is also why UK is even closing off all travel from LATAM and from Portugal (because of Brazil network). https://twitter.com/drericding/status/1349862952913022977
12) and now WHO is even sounding the alarm because of the new Japan-discovered Brazil variant. https://twitter.com/drericding/status/1348710699036516355
variant. https://twitter.com/drericding/status/1348710699036516355
13) to be clear on vaccines, the existing vaccine will still work. Though some scientists suspect maybe a few % drop in efficacy. But not sure yet. We are awaiting studies. Researchers are backlogged with also studying the South Africa 
B1135 variant that also has E484K.
B1135 variant that also has E484K.
14) Someone asked, isn’t is just lack of Brazil mitigation? I don’t think it’s just that:
—no real major change in mitigation measures suddenly like in Ireland
—crisis uniquely increasing more in Manaus than in other parts of Brazil.
—reinfection case above also supports
—no real major change in mitigation measures suddenly like in Ireland
—crisis uniquely increasing more in Manaus than in other parts of Brazil.
—reinfection case above also supports
15) And for those who try to say, “but reinfections are rare”... experts are now thinking that’s not necessarily true. They are “lower” than new infections but “not rare” as Dr Andersen, a leading virus mutation expert points out. https://twitter.com/k_g_andersen/status/1349918512056205317
16) As for some who say “but reinfections are mild”, that’s not always true. New UK study finds that 1/3 of reinfections still have symptoms.
17) E484K mutation is also not a 1 time fluke. 
virologists decided to see what mutations can help virus escape from patients w/ convalescent plasma immunity. So they soaked virus w/ CP over 12x times to speed evolution—80 days later *E484K arose*! https://twitter.com/ncholia/status/1347555563400519682
virologists decided to see what mutations can help virus escape from patients w/ convalescent plasma immunity. So they soaked virus w/ CP over 12x times to speed evolution—80 days later *E484K arose*! https://twitter.com/ncholia/status/1347555563400519682
18) And the E484K mutation is carried by many #SARSCoV2 variants—both Brazil variants that arose *independently*, the South Africa B1135 variant, and the experimental forced evolution study. Converging evolution is worrisome—it means nature discovered repeatedly it works.
B1135 variant, and the experimental forced evolution study. Converging evolution is worrisome—it means nature discovered repeatedly it works.
19) That said, the UK B117 variant that is more infectious doesn’t have the E484K variant. It’s not more severe nor escapes antibodies, but #B117 is worrisome for different reason — its speed of domination. See thread below. https://twitter.com/drericding/status/1346899021621813249
below. https://twitter.com/drericding/status/1346899021621813249
