Virus variants – how are they recognized?

Virus variants have already replaced the original type of SARS-CoV-2. But how are the mutations detected and why are some easier to spot than others?

Which virus variant is present can usually be determined using the PCR test: This is how the procedure works.

How does a PCR test work?

A PCR test is a laboratory method and is also referred to as the gold standard of test procedures due to its reliability. With the help of this test method, the genome of viruses can be directly detected and characterized. The test is carried out in several steps. The procedure briefly explained:

  • Taking the sample:  Usually a short smear of the pharyngeal wall and/or the nasal mucous membranes is taken. Secretions, rinses or samples from the deep airways can also be used. The responsible doctor decides which method is chosen. The sample is then sent to the responsible laboratory for analysis.
  • Duplication of the genetic material:  The genetic material of  SARS –  CoV-2 is multiplied by   means of the polymerase chain reaction . This makes it possible to examine even the smallest traces of DNA.
  • Sorting of the genetic material:  The existing genetic material is separated, analyzed and characterized based on various attributes. A detailed “profile” of the virus DNA is thus created.

PCR test specifically for virus variants

Variant-specific PCR tests were developed in order to be able to quickly and easily identify existing and dangerous virus variants. As part of the special test procedure, characteristic features of the genetic material are recorded and analyzed for variants – in Germany this should be possible especially for the current Delta variant and Omicron.

If a specific PCR test is carried out, the variant can be detected in the laboratory without further complex tests.

While a specific PCR test only detects certain virus variants that are already known, new variants can be identified using genome sequence analysis.

The responsible doctor decides which test should be carried out. In some cases, infected people can find out whether and with which variant they have been infected, others only receive a positive or negative test result.

Sequencing genome analysis: alert system for new variants

A sequencing genome analysis is a detailed and complex analysis of the genetic material. Here, the exact sequence of the RNA building blocks within the virus DNA is analyzed.

Overall, the entire DNA of the genome is decoded and then compared with the wild type of SARS-CoV-2 and other existing variants.

This method shows, for example, various mutations in the spike protein and other parts of the virus.

The disadvantage of genome sequencing is that it is very expensive and time-consuming. Thus, not every sample can be sequenced. Experts usually decide on a random sample – sequencing can also be carried out if the infection process is particularly conspicuous or if there are indications of variants.

The sequences are stored in an international database to quickly identify dangerous virus variants, prevent their spread and examine them more closely. However, since there are different requirements worldwide, not all sequences can be recorded reliably and quickly.


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