Omicron, South Africa on November 24th, 2021
Omicron diverged from the lineage roughly in mid-2020
Mutations not found in:
Alpha, Beta, Gamma, and Delta
SARS-CoV-2 variants isolated from three chronically infected patients
The variants showed the highest sequence similarities to Omicron
Normal rate of mutations in spike protein RNA
∼ mutations per month
During missing time for Omicron
27 mutations accumulated in spike protein RNA (in Branch O) during 18 months
∼1.5 mutations per month
∼3.3 times faster than the average rate of other variants
First hypothesis
Omicron could have “cryptically spread” and circulated in a population
Second hypothesis
Omicron could have evolved in a chronically infected COVID-19 patient
Third hypothesis
Omicron could have accumulated mutations in a nonhuman host and then jumped into humans
Mice
Evidence for a mouse
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