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25 Nov, 49 tweets, 25 min read
Summary & presentation markers for what is known about the NEW, VERY CONCERNING #VARIANT B.1.1.529 per South African Ministry of Health live streamed briefing today.
Holiday travel could spread this variant exponentially across the world if countries don’t act fast.
There r 2 international airports in Gauteng, region of Africa hardest hit w/ B11529. Already found in 3 countries so far: Botswana, South Africa & Hong Kong (returning traveller).
8:15- Prime Minister briefing

SA had a big Delta surge over June-July. Case rates since were very low. B11529 causing sudden, early, unanticipated surge, with a high number of cases in Guateng.

There is no gradual slope to that line. Vertical spike.
SA has low level of vax @ 4% fully vax’d while high levels of infection from 3 large waves.
12:00- Presentation of scientific findings

In South Africa it has been detected in Guateng province - positivity rates in Tshwane (part of Guateng) have increased particularly fast in the last 3 weeks from less than 1% to over 30%.
90% of all new cases in Gauteng are now this new variant which is causing an observable significant surge in a matter of 3 or so weeks.
B11529 is rapidly taking over Delta (red) and C.1.2 (yellow) in the setting of low case rates overall in SA. Are the low case rates in SA leaving a void in which a new variant can spread more easily? These preliminary findings here says it is likely outperforming/more fit…
…than Delta and C.1.2 w/ the caveat that most sequencing was focused on Gauteng when they saw the spike in cases.
It has many MORE mutations than other variants and has mutations seen in other variants that are associated w/ BOTH HIGHER TRANSMISSIBILITY AND IMMUNE ESCAPE. Some mutations we know relatively little about and are actively studying these as fast as we can, as we speak.
We are not yet clear how much immune evasion this variant has especially since only ~4% of Africa is vax’d. Important to keep in mind that mutations often work together. We can’t perfectly predict what this combination may mean. Wait for lab work. Can take weeks….
S-gene drop out data suggests it's rapidly increasing across S Africa. Luckily we can track it well bc particular mutations in spike can be detected through S-gene dropout by PCR.
Same vertical spike in surrounding provinces which means it’s already significantly spread.
Circled is Guateng. Already starting to spread to other areas of the world as evidenced by case found in China (traveller visited SA).
36:30- Summary of concern

39:00- not just a variant of concern, “A variant of serious concern”

B.1.1.529 is very likely more fit and has significant advantages over Delta and C.1.2 as it is rapidly taking these over in Gauteng.
51:00- “Matter of days and weeks” before most areas of Africa will be having significantly rising case numbers w/ B11529 as Gauteng is a major hub of activity. It has transportation lines coming and going from all over the country.
53:20- SA accelerating resurgence plans now, much earlier than anticipated

56:30- 90% of new cases in Gauteng are now this new variant
Likewise, the United States needs to get ahead of this now. International travel has already brought B11529 outside Africa’s borders. Act fast and act now per past discussions by Mike Ryan of the WHO.

arabianbusiness.com/videos/442939-…
58:15- We know we need to protect ourselves w/the non-pharmaceutical interventions (restrictions on incoming travelers, ⬆️ quarantine measures, strict adherence to NPI’s especially in airports and on transport, etc) NOW as we wait for laboratory data which will take weeks…
…to better understand how much neutralizing antibodies are evaded & how much T cell function is impacted. We already know what many of the mutations generally tell us when we compare them to what the same mutations did in other past variants.
59:30- how severe is this variant? Should know in next few weeks & do not be fooled that it’s milder disease bc that’s how it can initially spread even though it is ultimately more severe. Need to also see what happens as it moves out of the younger individuals into the older.
1:04:00- “More transmissible variant” with multiple genetic markers for immune evasion.

“Concerned by the jump of evolution”
This jump in evolution was foretold by Dr. Ugur Sahin. We were told not to only focus on the spike.
@VirusesImmunity @MBVanElzakker @edyong209 @lukeliao1 @ravgup33_ravi @ravgup33_ravi @PeacockFlu @ochealth @ashishkjha @theAliceRoberts @Dr_FarrisD @trvrb @jburnmurdoch @CT_Bergstrom @Bob_Wachter @SaadOmer3 @Craig_A_Spencer @cmyeaton @DrEricDing @PeterHotez @DrTomFrieden
@EricTopol @evolutionarypsy @segal_eran @florian_krammer @neil_ferguson @ScottGottliebMD @Laurie_Garrett @ahandvanish @itosettiMD_MBA @JessicaYellin @michaelmina_lab @JHSPH_CHS @KatrinaFoley @kprather88 @linseymarr @long_covid @LongCovidSOS @LauraMiers @StevePhillipsMD
@AndrewNoymer @stuartjdneil @profshanecrotty @SystemsVirology @vnminin @fitterhappierAJ @RadCentrism @TWenseleers @GYamey @yaneerbaryam @Kit_Yates_Maths @ZiikZiiii @JoannaTeglund @DrZoeHyde @emilygraymd_mph
B.1.1.529 appears to be outcompeting other variants including Delta.
Correction of typo: South Africa 24% fully vax’d
Sorry. One more typo found. This info at 41:00.
The Brits aren’t taking any chances:

cnbc.com/amp/2021/11/25…
Now it’s been found in Israel. 1 confirmed individual and 2 presumed (awaiting final testing results).
Also reportedly in Egypt.
“…B11529 has the potential to b very dangerous. We r raising a red flag. We understand that we are on the verge of a state of emergency. [Omicron] is a variant that spreads faster & requires us to respond faster. Now is the time to act fast, early, hard, & strong….”
- Israel PM
Israel ran a sort of emergency drill for a worsened variant just two weeks ago. Israel has led the way so many times in this pandemic. Listen and heed the words of Naftali Bennett, Prime Minister of Israel.
Talk about a jump in evolution.
Look at that leap.
"In conclusion, the overall level of risk is assessed as HIGH TO VERY HIGH."
“The Omicron variant is the most divergent variant that has been detected in significant numbers during the pandemic so far, which raises concerns that it may b associated w/ ⬆️ transmissibility, significant reduction in vaccine effectiveness and increased risk for reinfections.”
“…a precautionary approach is important and the timely and urgently reinforced implementation of non-pharmaceutical interventions (NPIs) in the [the world] is strongly advised.”

ecdc.europa.eu/en/publication…
List of Airport destinations from Johannesburg. These cities best be on high alert…and wherever their connecting flights went.
Disaster Emergency Declared in NY Over Rising Covid-19 Infection Rates

Let’s all guess what’s happening in NY. It’s one of the major airports to receive numerous passengers from Johannesburg.

reuters.com/world/us/new-y…

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Marya Alexander, MD Profile picture
13 Oct
Singapore is surging. We will have multiple “Singapores” here in the US. Their surge is higher than any they’ve had. 83% fully vax’d @ the time of this graph.

Does this look like u can’t surge if u have a significant amount of vax in your country or state? US is 57% fully vax’d. Image
What say you? But is it impacting their healthcare services? YES. “Singapore ministers told a media briefing on Friday that the jump in COVID-19 cases in the island of 5.7 million people had put ‘tremendous’ pressure on its healthcare system.”
reuters.com/world/asia-pac…
But has it required them to increase mitigations again? YES. Long lines started forming at the emergency departments @ several hospitals. With cases doubling every 8-10 days, the government limited social gatherings to 2 people & told people once again they should work from home.
Read 19 tweets
Marya Alexander, MD Profile picture
29 Jul
Time for a thread on: What Do We Know About Outdoor Transmission of Delta? @linseymarr @Daltmann10 @LongCovidKids @Ayjchan @VirusesImmunity @dgurdasani1 @ScottGottliebMD @kprather88 @DrEricDing @IndependentSage @michaelzlin @segal_eran @ashishkjha @Bob_Wachter @PeterHotez @CDCgov
1. Delta behavior indoors & outdoors: they saw fleeting proximity transmission in the Bondi Junction outbreak. Only needed 5-10 seconds proximity or 1-3 inhalations if briefly within 2 ft of someone else.
These kinds of transmission occurred when just “brushing past” someone & was well documented for indoor cases by genomic testing and CCTV. They also had a case of a woman sitting outdoors at a cafe who was infected by a man who visited the cafe when she was not inside.
Read 16 tweets

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