Sequencing and virus strains
Although we know from the media that there are currently 59 cases of the Omicron strain in Lithuania, it is very important to understand that this number does not say anything about the prevalence of the strain in Lithuania. Why?
[kelios sąvokos: viruso buvimas nustatomas PGR tyrimo būdu bet kurioje laboratorijoje, viruso atmaina nustatoma sekoskaitos būdu mokslinėse laboratorijose]
All of these 59 samples were not selected at random, but by targeted searching for an omicron strain among positive PCR samples with certain features of the viral genome that increase the likelihood that the strain is an omicron. Samples could also be selected by chance if a person who had recently traveled in Lithuania received a positive PCR (the probability of omicron is increased because the strain is already widespread in other countries).
Random (representative) sample
Conclusions about the prevalence of the omicron strain in Lithuania can be drawn from other sequencing data – samples that were randomly selected for the sequencing project, regardless of any characteristics, in order to avoid multiple members of the same family and to represent all regions of Lithuania. In December, 600-700 samples per week were selected and sequenced in this way. In the illustration, we publish their results.
It is important to note that sequencing work is not performed in a single day as a PCR test. Sample sequencing can take several weeks. Only in exceptional cases (for a small number of samples, when an omicron strain is suspected in advance) is the sequence counted “lightning fast” (with a lot of effort and the work of many people) – within six days.
VIDEO: The Omikron variant: what is known about it and why is it a cause for concern?
–
–
Prevalence of Omikron in Lithuania
No omicron strain has ever been detected in a random sample. Of the 97 samples from the last available week (12/13/2021 to 19/12/2021), all 97 were Delta.
It is important to remember that this does not mean that the prevalence of the omicron strain in Lithuania is exactly 0%, as we conclude on the population from a relatively small random sample. Correct conclusion: with a relatively high level of confidence (95% confidence) it can be stated that the prevalence of omicron in Lithuania in that week was somewhere between 0.0% and 2.8%.
This text is published in the Facebook account State Data Analytics
– .
