Thread by @NathanGrubaugh

B.1.1.529 PCR detection 🧵

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)

https://twitter.com/Tuliodna/status/1463911577544011780?s=20

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)

Fortunately, the (research-use only) multiplexed qPCR that we developed in collaboration with scientists in South Africa and Brazil in early 2021 to help discriminate among variants can be helpful again (4/8)

Link to the paper 👉
journals.plos.org/plosbiology/ar…

Our "VOC" PCR assay targets 3 regions - ORF1a, N, Spike - and can produce target-failure signatures to discriminate between variants. Previously, Alpha = S & ORF1a dropouts; Beta/Gamma = ORF1a dropout; non-variants = no dropouts (5/8)

B.1.1.529 has both the ORF1a 3675–3677 (genome positions 11,287-11,295) and spike 69–70 (21,766-21,771) deletions similar to Alpha, which Delta has neither (6/8)

So when using our PCR assay,
- "Potentially B.1.1.7" could be replaced with "Potentially B.1.1.529"
- "Other lineages" could be replaced with "Potentially Delta" (7/8)

Here is a link to our VOC assay protocol. We'll work to update the interpretations on here soon. Please don't hesitate to reach out to @VogelsChantal, @JosephFauver, or myself with questions (8/8)

protocols.io/view/multiplex…