Genomic surveillance update for the prior week. Still virtually all Delta according to the CDC modeling.
Given what we are seeing internationally I expect we will have an Omicron case this week in the US. But if it is here its prevalence is low. So we fortunately have time to learn more and prepare.
The CDC is strengthening genomic surveillance at major travel hubs in the meantime. At present the CDC is sequencing about 1 in 7 positive PCR tests. A significant improvement from earlier in the pandemic when we'd be lucky to sequence 1 in 50 or worse.
Dutch authorities investigated older antigen tests and found Omicron cases as early as November 19th, a week before South Africa announced Omicron cases.
This doesn't mean the Netherlands is the source of the variant. We don't know the provenance of the new variant yet. It may still be Southern Africa given the high prevalence of the variant there. But this should underscore how the travel bans are more for show than anything. They'll likely only slow the spread a small amount in the short term. Omicron is likely in many countries beyond Southern Africa.
We should incentivize proactive genomic surveillance not punish it. There will be more variants in the future and our ability to confront them will rely on early discovery before these variants are widespread. This isn't a months long problem, but a years long problem.