[aardvark92]

We're working on it! Demultiplexing the signal is tricky though.

Currently, labs have two main tools available - RT-qPCR and tiled amplicon sequencing. RT-qPCR provides cycle threshold (Ct) values which quantify the amount of virus RNA in a sample. RT-qPCR is not practical for finding and quantifying de novo variants as it relies on standard primer sets. Sequencing based approaches are less quantitative but provide more insight into the diversity of RNAs and mutations present in a sample - and thus which variants are present.

https://www.gisaid.org/hcov19-variants/ has a variant dashboard based on sequencing data, including Omicron. It's not as quantitative qPCR, but still may be of interest.

[yread]

Couldn't you run RT-qPCR twice with two different sets of primers? Does RT-qPCR give you the spike gene target failure rate?

[aardvark92]

Yes! Looking for gene target failure rates is a valid, albeit indirect way of quantifying variants. You will only be able to detect variants this way if the variant contains a mutation within the primer binding region and if that mutation happens to affect primer binding causing signal drop-off (a lot of 'ifs'!).

Some labs quantify amount of variant by running multiple RT-qPCRs using primers specific to mutations unique to each variant (see https://www.promega.com/products/pcr/qpcr-and-rt-qpcr/sars-c...).

Both of these strategies leave much to be desired. For one, it's terribly costly to run multiple RT-qPCRs in parallel. It also fails to account for any novel variants whose mutations lie outside your primer binding region(s).

From what I've gathered, RT-qPCR is useful for quantifying what is already known while sequencing helps you discover what is unknown.

I guess if you had unlimited time and money you could order new primer/probe sets from IDT every time a new variant comes into play...kind of like a home-brew microarray? Honestly, I'm kind of surprised there aren't SARS-CoV-2 variant microarrays on the market yet...we're all just spitballing here.