PCR Tests Don’t Identify the Variant

With the news of a new SARS-Cov-2 variant named ‘Omicron’, or rather B.1.1.529 with it’s technical designation on the horizon, it bears repeating, that your usual PCR test is not capable of determining which variant of the virus was detected in a positive test.
That’s what “Whole Genome Sequencing” is for, or more specifically, next-generation sequencing (NGS) as noted by the CDC. So what is NGS:

Next-generation sequencing (NGS) is a massively parallel sequencing technology that offers ultra-high throughput, scalability, and speed. The technology is used to determine the order of nucleotides in entire genomes or targeted regions of DNA or RNA. NGS has revolutionized the biological sciences, allowing labs to perform a wide variety of applications and study biological systems at a level never before possible.  

Source: illumina.com

The method has been used to detect other variants of SARS-Cov-2.
Here’s a good opportunity to clear up the terms “variant” and “strain”.
In the process of replicating the viral RNA errors occur, i.e. during copying, one or more constituents of the RNA genetic code are replaced with other constituents. This is called a mutation. Viruses with mutations are called “variants” and differ slightly from the original virus. Some mutations have no effect at all, others change the behaviour of the virus, in which case the mutation is called “strain”, a “strain” is also a “variant”, but not vice versa – see here for a nice introduction to this topic.
Previous strains were the UK variant (B.1.17), the (previous South African variant (B.1.351).
The current newly identified South African variant (B.1.1.529) is most likely also a strain, since it has increased transmission rates.
Now, it would be interesting to know, when NGS are performed, how many are performed and how long they take.
I haven’t found numbers so far, so I can only guess. Given my understanding of the technology, I have to assume that not every sample is tested (a test takes time and cost money). Or in the words on an article on the Roche website, published June 1, 2021:

While there have been significant technological and cost-effective advances in analyzing the genome with NGS, the method has not yet been widely used in routine clinical practice for diagnosis. This suggests that there remain many challenges and uncertainties that clinical laboratories, regulatory agencies, payers and other stakeholders need to address before NGS becomes standard for diagnosing diseases or biomarker testing.

Source: roche.com


This would lead me to believe that it is usually not determined scientifically, which variant of SARS-Cov-2 someone has tested positive for.
So, if media and politicians claim that such-and-such variant was rapidly spreading, that is largely an assumption, in my view. Of course, there can always be information I’ve missed…