Update on the new B.1.1.529 variant spreading rapidly in South Africa.

Cases are increasing nationally with R=1.47 after recent decline. Cases are not growing everywhere. They are growing particularly in Gauteng.

Gauteng is a small province containing Johanesburg, the largest city in South Africa. The Test positivity has been at about 1% and is still at 1% in much of the province, but one area, Tshwane, has part with positivity at 30%.

This increase happened within two weeks.

The estimated R value of the local increase is 1.93, significantly larger than the national value (1.47).

The genetic analysis of the new variant (from over 100 genomes) shows that it has 30 mutations in the spike protein.

In the receptor binding area
Beta had 3,
Delta had 2,
B.1.1.529 has 10, just in the receptor binding domain.

Analysis of the mutations:

Resistance to current antibodies due to multiple mutations in the spike protein.

Enhanced transmissibility

Evasion of immunity

Increased infectivity

Compare rate of increase compared to previous variant of Beta (green), Delta (red), B.1.1.529 (blue)!!

Using a PCR signature of the new variant they can see the rapid increase in multiple provinces.

Circled plot (third down on the left) is Gauteng. Other provinces showing the same rapid increase can be seen in the other plots.
Content and figures from the presentation by Prof. Tulio de Oliveria

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More from @yaneerbaryam

27 Nov
Global Response to Omicron Variant: Better but needs to be stronger.

@TheWHN worldhealthnetwork.global/omicron

1/ Image
Nov 27, 2021: In response to the new variant outbreak growing in the southern part of the African continent, Europe as a unit, the US and many other countries, have limited travel from South Africa and adjacent countries.

The World Health Network thanks South Africa for sounding the alarm and congratulates countries for responding rapidly, much faster and more decisively than with the original spread of the Coronavirus and the successive variants.

Read 17 tweets
26 Nov
International passenger traffic from Johannesburg O.R. Tambu airport: 188,530

If the proportion of infected individuals is like the recent report from Netherlands:

Almost 6,000 infected travelers in the last week.

Number of airplanes: 3,246 in October, or about 733 per week. ImageImage
Airports with direct flights from Johannesburg

2/ Image
List of largest airport destinations

flightsfrom.com/JNB/destinatio… ImageImageImage
Read 6 tweets
26 Nov
Japanese government: Japanese nationals traveling from Eswatini Zimbabwe Namibia Botswana South Africa Lesotho must quarantine at gov accommodations for 10 days and take COVID tests on 3rd, 6th, 10th days. Japan has not yet opened up to foreign nationals

“The last thing we need is to bring in a new variant that will cause even more problems,” German Health Minister Jens Spahn said. The member nations of the EU have experienced a massive spike in cases recently.

"EU Commission President Ursula von der Leyen said flights will have to “be suspended until we have a clear understanding about the danger posed by this new variant, and travelers returning from this region should respect strict quarantine rules.”

Note: Great!

Read 5 tweets
26 Nov
Very rough estimate of Nu variant mortality is 8X original variant based upon the current rough estimate of transmissibility, assuming they track each other.

Corrections welcome.

(Figure type labeled Nu) Image
Error range (estimated in this way) is 3X-12X
Transmission rate depends significantly on the density of viral particles in airborne particles, which depends on the rate of generation of the virus. The severity of the disease also depends on the replication rate of the virus. Previous variants are consistent with this.
Read 6 tweets
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New variant = new pandemic
We do not know that the existing vaccines will prevent infection or severe disease. The extent of mutation indicates the opposite. Just as at the beginning of the COVID pandemic, uncertainty means risk should not be taken. Have we learned the lesson?
Infections we know about today happened a few days to two weeks ago.

Infections that happened today will only be known in a few days to two weeks from now.

Where should we stop travel from? Everywhere.

Only then will we stop it from getting most places.
Read 5 tweets
24 Nov
"Part of the problem is that honest COVID risk analysis doesn’t allow us to live in denial, a place many people like to dwell..."

From: "The latest advice on COVID is so clear! Definitely gather with your family! Or maybe don’t!"


"What? You’re fearful of long COVID? Come back later for more information. In the meantime, stop being so paranoid!"

"Welcome to the season of COVID confusion. We’re bombarded with statistics. Infections, breakthrough cases, death tolls, vaccine effectiveness rates.

"COVID-19 cases have jumped 59 percent in New England in the past 2 weeks

[Note: Apparently, the virus has not gotten its script]

Read 4 tweets

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