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Printable Handouts
Navigable Slide Index
- Introduction
- Brief timeline of Omicron
- What do we know?
- Chapter 1: South Africa and the origins of Omicron
- South Africa
- Covid-19 in South Africa
- Average daily tests and proportion of positive tests
- Wastewater measurements
- Covid-19 in South Africa: fourth wave
- Vaccination status 31st January 2022
- Chapter 2: Omicron
- Covid-19 in South Africa: Omicron
- S-gene target failure
- Network for genomic surveillance – South Africa
- 5 SARS-CoV-2 VOC from 4 continents
- Omicron mutation profile
- Spike protein mutations
- SARS-CoV-2 variant lineages
- Cladogram of SARS-CoV-2 variants
- Where do these variants come from?
- Variants in immunocompromised individuals
- Chapter 2: transmissibility
- The fourth wave: Omicron
- Reproduction (R) number
- R number of Covid-19 in South Africa
- Receptor binding
- Omicron can bind to mice receptors
- Chapter 2: immune evasion
- Decreased antibody-mediated neutralisation
- Estimates of infection and reinfection hazards
- Rapid global spread of Omicron
- Chapter 2: two properties of Omicron
- Proportion and number of clades in South Africa (1)
- Chapter 2: clinical expression
- Wave 4: hospital admissions and reported cases
- Clinical expression of the 3 variants
- Clinical expression
- Chapter 3: round up
- Round up
- Omicron global map
- High virus load in highly vaccinated countries
- South Africa and UK data
- Testing levels
- Omicron: why a South African perspective?
- Population immunity
- Population immunity in South Africa
- High proportion of individuals with previous natural infection after third wave
- The road to endemicity: positive signs
- Viral fitness
- Myxomatosis in rabbits in Australia
- Proportion and number of clades in South Africa (2)
- Omicron infection is faster in the bronchus
- Omicron produces smaller plaques than delta
- Forming giant cells
- Omicron infected genetically engineered mice
- The road to endemicity: negative signs
- Viral evolution
- What do we know?
- Thank you!
Topics Covered
- Omicron
- South Africa and the origins of Omicron
- The fourth wave
- Properties of Omicron
- 5 SARS-CoV-2 variants of concern
- Omicron mutation profile
- Omicron spike protein
- Omicron transmissibility
- Reproduction (R) number
- Omicron immune evasion
- Clinical expression of SARS-CoV-2 variants
- The spread of Omicron
- Population immunity
- Viral fitness
- Viral evolution
Links
Categories:
Therapeutic Areas:
External Links
Talk Citation
Schoub, B. (2022, March 30). The Omicron variant: a South African perspective [Video file]. In The Biomedical & Life Sciences Collection, Henry Stewart Talks. Retrieved December 27, 2024, from https://doi.org/10.69645/TKDS3494.Export Citation (RIS)
Publication History
Financial Disclosures
- Prof. Barry Schoub has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.
A selection of talks on Microbiology
Transcript
Please wait while the transcript is being prepared...
0:00
My name is Barry Schoub.
I'm a Professor Emeritus of Virology at
the University of the Witwatersrand,
which is the university
in Johannesburg.
I retired from that post but I am
trained as a medical virologist,
and currently I chair the Ministerial
Advisory Committee on COVID vaccines.
We advise our government on
aspects related to COVID vaccines.
What we are talking about
is the Omicron variant.
The latest, the fifth, of
the variants of concern,
which are spread
around the world,
basically causing havoc
around the world,
and I'll looking at predominantly
from a South African perspective.
You might ask why a South
African perspective?
The virus was first
discovered in South Africa,
and a lot of the science has come from
scientists in South Africa as a result of it.
0:49
This is a brief timeline of
Omicron in South Africa.
It was first detected or first
alerted to in early November
by what's called a
S-gene target failure.
What we mean by that is that
the specific PCR tests,
that is a Thermofisher TaqMan® test
for those who are in the field,
it picks up various
genes of the virus,
and with this
particular variant,
the Omicron variant,
it fails to pick up the
S-gene in that test.
That's a very good alerting signal
or a screen test for the Omicron.
It was picked up by a junior
medical technologist
in one of the
semi-rural laboratories
private laboratories in
Africa, just out of interest.
Anyway, that was
in early November.
In mid-November,
the first actual detection of
Omicron was made in Botswana,
which is a neighboring country,
north west of South Africa,
and probably came
from South Africa.
12th November, the first detection
of Omicron in South Africa.
It was then described
by scientists,
and published on
24th of November.
The World Health Organization
designated it as
the fifth variant
concern, or VOC,
as Omicron from the
Greek letter ο.
On the 7th of December,
the first neutralizing
antibody test
revealed that this particular Omicron variant
was relatively resistant to antibodies,
either from past infection
or from vaccines.
On the 14th, we had the first
clinical vaccine effective studies.
Just a brief timeline of the early
stages of Omicron in South Africa.