Thread by @NathanGrubaugh

🧵 Brief update on impact of #Omicron on the CDC #SARSCov2 primers/probes that are commonly used in PCR assays in the US and abroad (1/6)

https://twitter.com/NathanGrubaugh/status/1464369814407892996

(2/6) The CDC N1 probe mismatch in Omicron is a C28311T mutation. Of the 91 B.1.1.529 sequences on GISAID:
- 48 have a T (mismatch)
- 19 have a C (exact match)
- 26 have no coverage (NNNs)

(3/6) All of the Omicron sequences with a C at 28,311 (exact match to N1 probe) are from the CERI-KRISP group, so maybe @Tuliodna can provide some info if these are potentially a sequencing artifact (which we've seen with Delta) or if this site is variable within the lineage

(4/6) This is something to keep an eye on, but anecdotally at least I am hearing that the C28311T mutation doesn't have a major impact on CDC N1 PCR detection.

(5/6) Currently, of the 91 available B.1.1.529 sequenced, there are 0 detected mismatches in the CDC N2 primer/probe set (which is ~900 nt downstream of N1). So this set will work just fine 👍

(6/6) This type of analysis can only be done because the following laboratories rapidly made their #Omicron data available to the public. A very sincere, thank you! 🙏