How Omicron came to light – Covid-ARG separates fact from fiction

What happened since this tweet

B.1.1.529, or Omicron, was designated as a variant of concern by the World Health Organization (WHO) on Friday 26th November due to its “concerning” mutations and because “preliminary evidence suggests an increased risk of reinfection with this variant”.

With scientists still unsure whether Omicron poses a greater danger than other variants,

  • Thousands of UK nationals face paying thousands of pounds for mandatory hotel quarantine on their return from South Africa, Botswana, Lesotho, Eswatini, Zimbabwe and Namibia after Sunday. Non-UK and non-Irish nationals from those countries will be banned, while people arriving in England before 4am on Sunday will have to take PCR tests and quarantine at home.
  • The EU agreed there was a need to suspend flights from countries in southern Africa following restrictions announced by countries including the UK, Japan, Germany, Italy and Spain. The US and Canada also brought in travel curbs on Friday night.
  • South Africa said it was “unjustified” for other countries to impose travel bans and Boris Johnson held a call with the country’s president, Cyril Ramaphosa, to discuss the restrictions.
  • The FTSE 100 had its worst day since June 2020, closing down 3.6%, with £72bn wiped off the index. The British Airways owner, IAG, ended the day nearly 15% lower, while Rolls-Royce slumped more than 11%.

What follows is the report on the Covid Actuaries website, you can read the original here

New variant B.1.1.529

This week this new variant has been identified in ten genome sequences from Southern Africa (mainly Botswana and South Africa)

It first came to our attention in a Twitter thread by virologist Tom Peacock:


This thread and the discussion on the website’s GitHub highlight a large number of spike protein mutations that raises concerns about potential immune escape. The variant has now been included on the website.

Increase in cases in South Africa

On 23 November 2021 South Africa reported over 18,500 cases.

It looks like South Africa had a recent massive jump in cases, but there is important context. The South African National Institute for Communicable Diseases (NICD) states:

As of today, retrospective antigen tests are being loaded to fill in gaps that existed while antigen test providers put systems in place to report to the National Department of Health (NDoH). The NICD and NHLS optimised the systems to accurately reflect these reports. Please refer to the media statement that was released by the NDoH on 23 November 2021.

The increase in cumulative cases in today’s report is attributed to the retrospective addition of 18 586 antigen tests, that include the reporting of 868 positive cases recorded in the past 24 hours. The incorporation of antigen tests follows ongoing improvements to report as accurately as possible from all provinces and all testing facilities throughout South Africa. 19 244 585 tests have been conducted in both public and private sectors as per the table below.

NICD, Latest Confirmed Cases of COVID-19 in South Africa (23 November 2021)

In other words the large spike in cases results from a processing issue – the inclusion of cases not previously reported, that can now be included due to system improvements. It would not be correct to link the spike to the new variant.

By my estimates the true picture of cases in South Africa does show an increasing trend, but far far below the numbers above. Below I plot estimated 7-day moving average of cases by date the specimen is received at the laboratory. Cases have not grown anything like as rapidly as the chart above suggests, though they do show a concerning upward trend.

Daily Cases for Last 30-days (7-day moving average)Daily Cases in South Africa (7-day moving Average)



In this video update by the Department of Health of South Africa’ information about the variant B.1.1.529 is shared. In the presentation Dr. Tulio de Oliveira (Director of CERI: Centre for Epidemic Response & innovation, South Africa) and Dr. Richard Lessels discuss this variant, a summary of which is presented in this thread

In the video, Oliveira and Lessels expand on the timeline of discovery of this variant. It was discovered on Tuesday, 23 November 2021 when it showed different results on a qPCR test.

The mutation profile of this variant is then presented in the update, details below:

  • It has more than 30 mutations on the spike protein.
  • Mutation profile is very different from other variants of concern or variant of interest.
  • Some of the mutations are characterised to be affecting transmissibility and immune evasion.
  • The significance of many of the mutations remains uncertain.

They go on to show that B.1.1.529 is already becoming the dominant variant with it being a significant proportion of recently sequenced genomes (in blue) apparently outcompeting Delta (in red). C.1.2 is also a variant that posed some concern.

It should be noted that during the last week all sampling had been focussed on Gauteng, (given the observed increase in cases), and hence almost all the recent genomes are from Gauteng.

Cases continue to rise across Gauteng province as can be seen the chart by district below:

Gauteng Daily Cases for Last 30-days by District Municipality (7-day moving average)

R in Gauteng is similarly estimated to have increased to 2 (or higher):

This is further affirmed by test positivity rates observed in Gauteng.

Due to the virus also resulting in S gene target failure on particular PCR assays, (similar to Alpha), it is detectable via this particular PCR assay and based on this, they establish that this variant is already circulating in many provinces in South Africa and may be an estimated 90% of cases in Gauteng. This creates a link between the rise in cases in Gauteng with this variant.

The researchers also highlight that much is unknown and continue to encourage those who have not vaccinated yet to get vaccinated. Oliveira and Lessels a focus of research on transmissibility, impact on protection of vaccines, risk of reinfection, disease severity and diagnostics.

This news is hugely concerning and seems to clearly indicate that the surge in cases observed in Gauteng is associated with this variant. This raises serious questions about the expected 4th wave of COVID-19 which was generally expected to be milder than the wave preceding it.

Report by Louis Rossouw
Segment Head of Research & Analytics – Gen Re

As Head of Research and Analytics in his segment Louis Rossouw is based in Gen Re’s Cape Town office and him and his team support life insurance clients in the UK, South Africa, Canada, Australia and New Zealand with research and analytics. He has previously worked on individual pricing and product development, group pricing and reserving. Louis joined Gen Re in 2001. He has also worked for two years in Gen Re’s Singapore branch as Regional Chief Actuary. He currently serves on the Actuarial Society of South Africa’s Continuous Statistical Investigation Committee.


About henry tapper

Founder of the Pension PlayPen,, partner of Stella, father of Olly . I am the Pension Plowman
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