This week I'd like to check in on the @OhioStateFB team, hoping that they are doing ok. They had a pretty rough time in The Game last weekend. Lucky for them that they have an open weekend coming up to heal 🙏. (6/6)
(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
Like Alpha (B.1.1.7), B.1.1.529 has the spike 69-70 deletion that causes a S-gene target failure (SGTF) when using the ThermoFisher TaqPath COVID-19 assay. Because most other variants didn't have the deletion, this was helpful for tracking Alpha (1/8)
Likewise, reporting SGTFs will be extremely helpful again for tracking the spread & growth of B.1.1.529, like the amazing folks in South Africa are already demonstrating (2/8)
While the ThermoFisher TaqPath COVID-19 assay is very common, not everyone is using it; and while sequencing is required to confirm B.1.1.529 cases, slow turn-around times can delay its tracking. Here is where other PCR screening assays can be helpful (3/8)
The Delta sublineage leaderboard remained virtually unchanged this week (boring is good), though things could get very interesting through the holidays. (2/4)
Unfortunately, we are going into the holidays with transmission and infections estimated to be rising in Connecticut (and across the US). (3/4)
Much of the discussion is still about AY.4.2, which is still slowly 📈 in the UK, which they have designated as a 'variant under investigation' (VUI). (2/6)
Effective reproductive number (Rt) estimates for the top Delta lineages in Connecticut.
➡️All are now <1, suggesting that transmission is 📉.
➡️The relative similar Rt values suggest that they are of similar transmissibility. (2/12)
Last week we reported AY.4 was ~27%, and this week its 4%. The sudden 📉 is not due to more refined classifications. Its hard to distinguish between closely related sequences, and a dropout in some Delta spike sequences makes it even harder. (3/12)
B.1.617.2 is decreasing primarily because these sequences are being classified as other sublineages. Otherwise, the Delta AY sublineage frequencies are remaining very stable and there is currently *no evidence that any are more transmissible* in Connecticut. (3/6)