Virus

Here's how mutations in #SARSCoV2 Nu variant (B.1.1.529) will affect polyclonal and monoclonal antibodies targeting RBD. These assessments based on deep-mutational scanning experiments; underlying data can be explored interactively at https://t.co/uP3IKvnDw0 (1/n)

— Bloom Lab (@jbloom_lab) November 25, 2021

But I'd expect the Nu variant to cause more of a hit on vaccine- and infection-elicited antibody neutralization than anything we've seen so far. (6/n)

— Bloom Lab (@jbloom_lab) November 25, 2021

However, it appears the AstraZeneca AZD7442 cocktail and Vir's S309 are likely to hold up better against the Nu variant. See below. (9/n) pic.twitter.com/PNlJjHc5fT

— Bloom Lab (@jbloom_lab) November 25, 2021

Today 2 suspected B.1.1.529 (Nu variant) samples were analyzed. Samples were flagged as suspicious because of an S gene dropout qPCR. 1 sample was confirmed to be the new Nu variant. This patient was not vaccinated and developed mild symptoms 11 days after returning from Egypt.

— Piet Maes (@MaesPiet) November 26, 2021

What vaccine makers are saying about B.1.1.529 (cont):

-lab data will tell BioNTech whether B.1.1.529 could be an escape variant

-Pfizer/BioNTech can adapt mRNA vaccine within 6 weeks, ship initial batches within 100 days in event of escape variant (2/2)

— Meg Tirrell (@megtirrell) November 26, 2021

Agreed. By the time you've identified a new variant, it's already global.

— robertcerff (@robcerff1) November 26, 2021

Belgium's first case of new COVID variant is a young, unvaccinated woman who returned from Egypt on Nov. 11 and developed symptoms 11 days later - RTBF

— BNO Newsroom (@BNODesk) November 26, 2021

WATCH: Passengers on South African flight not allowed to get off in Amsterdam amid concern about new COVID variant; testing and quarantine expected pic.twitter.com/iTnaeYaVim

— BNO Newsroom (@BNODesk) November 26, 2021

Another, a hotel worker from Malawi, had her second dose of AZ in mid-July. A third had her second J&J dose two months ago.

— Arieh Kovler (@ariehkovler) November 26, 2021

Tiny sample size of course, very early days, etc. We still no next to nothing about this variant.

— Arieh Kovler (@ariehkovler) November 26, 2021

While some degree of immune escape is possible, and the presence of the E484K mutation is suggestive of change in that direction, immune escape alone cannot explain the rapid the increase in prevalence. If that's not some of founder effect, it must have higher transmissibility.

— Carl T. Bergstrom (@CT_Bergstrom) November 26, 2021

I'd be careful not to overinterpret the following graph from @jburnmurdoch.

Yes, the fraction of B.1.1.529 is increasing faster. But I think that is that is largely due to different denominators. pic.twitter.com/NDhSqJpLlw

— Carl T. Bergstrom (@CT_Bergstrom) November 26, 2021

The bad news, of course, is that B.1.1.529 is increasing in South Africa at a time when Delta has been is decreasing. *If* the turn-around is due to increased transmissibility, instead of other e.g. behavior factors, it's going to a rough winter.

Obviously we'll know more soon.

— Carl T. Bergstrom (@CT_Bergstrom) November 26, 2021

Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern
26 November 2021 
Statement
Reading time: 2 min (616 words)

The Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE) is an independent group of experts that periodically monitors and evaluates the evolution of SARS-CoV-2 and assesses if specific mutations and combinations of mutations alter the behaviour of the virus. The TAG-VE was convened on 26 November 2021 to assess the SARS-CoV-2 variant: B.1.1.529.
The B.1.1.529 variant was first reported to WHO from South Africa on 24 November 2021. The epidemiological situation in South Africa has been characterized by three distinct peaks in reported cases, the latest of which was predominantly the Delta variant. In recent weeks, infections have increased steeply, coinciding with the detection of B.1.1.529 variant. The first known confirmed B.1.1.529 infection was from a specimen collected on 9 November 2021.
This variant has a large number of mutations, some of which are concerning. Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other VOCs. The number of cases of this variant appears to be increasing in almost all provinces in South Africa. Current SARS-CoV-2 PCR diagnostics continue to detect this variant. Several labs have indicated that for one widely used PCR test, one of the three target genes is not detected (called S gene dropout or S gene target failure) and this test can therefore be used as marker for this variant, pending sequencing confirmation. Using this approach, this variant has been detected at faster rates than previous surges in infection, suggesting that this variant may have a growth advantage.
There are a number of studies underway and the TAG-VE will continue to evaluate this variant. WHO will communicate new findings with Member States and to the public as needed.
Based on the evidence presented indicative of a detrimental change in COVID-19 epidemiology, the TAG-VE has advised WHO that this variant should be designated as a VOC, and the WHO has designated B.1.1.529 as a VOC, named Omicron.
As such, countries are asked to do the following:

• enhance surveillance and sequencing efforts to better understand circulating SARS-CoV-2 variants.
  
• submit complete genome sequences and associated metadata to a publicly available database, such as GISAID.
  
• report initial cases/clusters associated with VOC infection to WHO through the IHR mechanism.
  
• where capacity exists and in coordination with the international community, perform field investigations and laboratory assessments to improve understanding of the potential impacts of the VOC on COVID-19 epidemiology, severity, effectiveness of public health and social measures, diagnostic methods, immune responses, antibody neutralization, or other relevant characteristics.
  

Individuals are reminded to take measures to reduce their risk of COVID-19, including proven public health and social measures such as wearing well-fitting masks, hand hygiene, physical distancing, improving ventilation of indoor spaces, avoiding crowded spaces, and getting vaccinated.
For reference, WHO has working definitions for SARS-CoV-2 Variant of Interest (VOI) and Variant of Concern (VOC).
A SARS-CoV-2 VOI is a SARS-CoV-2 variant:

• with genetic changes that are predicted or known to affect virus characteristics such as transmissibility, disease severity, immune escape, diagnostic or therapeutic escape; AND
  
• that has been identified as causing significant community transmission or multiple COVID-19 clusters, in multiple countries with increasing relative prevalence alongside increasing number of cases over time, or other apparent epidemiological impacts to suggest an emerging risk to global public health. 
  

A SARS-CoV-2 VOC is a SARS-CoV-2 variant that meets the definition of a VOI (see above) and, through a comparative assessment, has been demonstrated to be associated with one or more of the following changes at a degree of global public health significance:

• increase in transmissibility or detrimental change in COVID-19 epidemiology; OR
  
• increase in virulence or change in clinical disease presentation; OR
  
• decrease in effectiveness of public health and social measures or available diagnostics, vaccines, therapeutics
  

Variants could be named after star constellations when Greek alphabet runs out, says WHO Covid chief

There is considerable uncertainty related to the transmissibility, vaccine effectiveness, risk for reinfections and other properties of the Omicron variant. However, given its immune escape potential and potentially increased transmissibility advantage compared to Delta, we assess the probability of further introduction and community spread in the EU/EEA as HIGH. In a situation where the Delta variant is resurgent in the EU/EEA, the impact of the introduction and possible further spread of Omicron could be VERY HIGH. In conclusion, the overall level of risk for the EU/EEA associated with the SARS-CoV-2 variant Omicron is assessed as HIGH to VERY HIGH. Options for response Based on the mutation profile of Omicron, partial immune escape is likely.

At least 15 passengers on the two KLM flights from South Africa that arrived at Schiphol earlier today have tested positive for the corona virus. There were a total of more than 600 passengers on the planes, all of whom had to be tested. According to the GGD Kennemerland, the first 110 test results have now been received, of which 15 are positive.
Based on that outcome, the GGD expects a "finding percentage" of 13.6 percent. "That means that we take into account approximately 85 positive corona tests in total." It is not yet known with which variant of the corona virus the positively tested travelers are infected.