GISAID or Global Initiative on Sharing Avian Influenza Data is a website where gene sequences of coronaviruses and influenza viruses are shared.
Genetic sequences from all over the world are submitted to GISAID. Based on the gene sequences, scientists can identify and categorize different strains of coronaviruses and influenza viruses.
The table below shows the number of omicron variants from all the countries that submitted as of today.
#GR/484A and B.1.529 are other names for omicron. The data is from GISAID.
You can trace below the spread of the omicron variant around the world. The tree starts from the left. Each color represents a country.
Below is the 3D Structure of the omicron variant with the spike with amino acid changes labeled. Omicron has 50 genetic changes, with 30 of them in the spike protein.
SARS-CoV-2 spike glycoprotein trimer (3 units shown, gray ribbons) is attached with the human host cell receptor ACE2 (1 unit shown, green ribbon).
Positions with changes in the B.1.1.529 lineage are indicated as colored balls. Changes with documented phenotypic effects from literature are colored light orange or cyan for insertions/deletions, while others without documented phenotypic effects are colored in green.
Pheno is short for the phenotype. Phenotype is the expression of a gene. Genetic can cause a change in the property or function of the virus. Not all mutations can cause a functional change.
Omicron numbers will go higher
I suspect that the omicron numbers will skyrocket. One reason is that it is more transmissible. The other is scientists will sequence previously collected PCR samples from the nasal swabs. That will show that the omicron has been around earlier than when it was announced. This is what happened in the Netherlands as reported here.
The Netherlands’ RIVM health institute found omicron in samples dating from Nov. 19 and 23. The WHO said South Africa first reported the variant to the U.N. healthy agency on Nov. 24.
Still early to say if the omicron is more deadly
It is still early to say what the genetic changes mean and how they will work in combination to affect disease severity and mortality.
Usually, the viruses that survive are less lethal.
I will update this page regularly.
Be careful out there.
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Should I be afraid of the omicron variant?
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