The non-omicron variants column in the hospitalization table of the daily Danish omicron reports (which one can found on here, with the most recent one via the big “Download her” button and the older ones under “Arkiv”) was changed from the previous one to the last report. Until the report from the December 15, they only reported cases for which a variant PCR test was carried out, i.e. hospitalizations of people who tested positive for coronavirus, but where no variant PCR test result is available was not counted (which makes sense, as it is then not known whether the case is omicron or not!). Starting with the current report from December 16 they are counting positive tests without a variant PCR result as “other variants”. At least that is how I understand the explanation on page 1. So here is how I read the two tables:
Report
Column
Which cases are counted
Dec 15
Other variants
PCR test positive, variant PCR result negative for Omicron
Dec 15
Omicron
PCR test positive, variant PCR result positive for Omicron
Dec 16
Other variants
PCR test positive, variant PCR result negative for Omicron OR no variant PCR result available
Dec 16
Omicron
PCR test positive, variant PCR result positive for Omicron
The previous report had 95,245 other variant cases of which 715 were hospitalized with positive tested earlier than 48 hours after (abbreviated <48h from now on), and 4 with test after (48+h). Now, with one extra day of data plus the added cases that did not have a variant PCR done (or no result available yet), they report 115,017 other variant cases with 1,560 (<48h) and 222 (48+h) of those hospitalized cases. This doesn’t make sense unless a large number of hospitalized cases did not have a variant-PCR test done? In particular, those could still turn out to be omicron, so this makes concluding things about virulence from the new table more difficult. It confuses me why (even though the total number of other variant cases went up only moderately by the change in definition for that column, corresponding to the fact that variant PCR test coverage in general is very high) so many hospitalized cases seem not to have a variant PCR result, with the difference particularly drastic in the 48+h category. The only explanation I can come up with that fits this is the following: Hospitals have their own labs to analyze covid tests they carry out. Originally, in February / early March 2020, I think tests were essentially done in those labs, now the mass testing program has two big central labs in which the PCR tests for the whole country is analyzed. But presumably hospitals still analyze their own PCR tests in their own labs. Perhaps hospitals tend to not be equipped with the variant PCR test? I think this would explain the data. Up to the report before the current one, the numbers in the 48+h category were not changing much for other variants and omicron, (eg. staying at 8-9 cases for omicron). I dimly remember in the early days of omicron (1-2 weeks ago) that it was said (in a press conference or interview for the news) by someone responsible for contact tracing that there had been an omicron outbreak at a hospital, so that is probably why there originally were a couple of omicron cases identified in the 48+h category. My conclusion is that the 48+h row in that table is essentially useless to compare variants, as there seems to be very little variant testing to be done for those cases so far, or with a big delay (I would assume that the hospital labs are either going to set up variant tests or forward positive tests to the central labs for variant testing, but this might introduce extra delays, so this is not really reflected in the data yet?). In the <48h row there also must be quite a few cases that don’t have a variant result, though the difference is less drastic than for the 48+h row. Which makes sense because <48 hours includes tests done at the hospital (which I suspect correlates strongly with no variant PCR test result available) as well as tests done before admission (for which there seems to be good coverage of variant PCR tests, though with a little extra delay until results are ready).
The previous table from the December 15 report shows 0.6% of omicron cases being hospitalized in the <48h category and 0.8% of non-omicron cases being hospitalized in the <48h category, which is quite disappointing regarding virulence; as omicron is still rapidly rising and hospitalizations are delayed we would expect a lower rate currently even if virulence is the same, so this little difference in hospitalization is not good news.
The table from December 16 report still shows 0.6% of the omicron cases hospitalized (<48h) and 1.4% of the other variant cases (<48h). But by my discussion above I think the additional difference likely can be explained by people who were tested positive at the hospital and for which we don’t (yet) have a variant PCR test result.
Thanks for writing these posts on corona Zvi, I really appreciate them!
Regarding the Danish hospitalization numbers:
The non-omicron variants column in the hospitalization table of the daily Danish omicron reports (which one can found on here, with the most recent one via the big “Download her” button and the older ones under “Arkiv”) was changed from the previous one to the last report. Until the report from the December 15, they only reported cases for which a variant PCR test was carried out, i.e. hospitalizations of people who tested positive for coronavirus, but where no variant PCR test result is available was not counted (which makes sense, as it is then not known whether the case is omicron or not!). Starting with the current report from December 16 they are counting positive tests without a variant PCR result as “other variants”. At least that is how I understand the explanation on page 1. So here is how I read the two tables:
The previous report had 95,245 other variant cases of which 715 were hospitalized with positive tested earlier than 48 hours after (abbreviated <48h from now on), and 4 with test after (48+h). Now, with one extra day of data plus the added cases that did not have a variant PCR done (or no result available yet), they report 115,017 other variant cases with 1,560 (<48h) and 222 (48+h) of those hospitalized cases. This doesn’t make sense unless a large number of hospitalized cases did not have a variant-PCR test done? In particular, those could still turn out to be omicron, so this makes concluding things about virulence from the new table more difficult. It confuses me why (even though the total number of other variant cases went up only moderately by the change in definition for that column, corresponding to the fact that variant PCR test coverage in general is very high) so many hospitalized cases seem not to have a variant PCR result, with the difference particularly drastic in the 48+h category. The only explanation I can come up with that fits this is the following: Hospitals have their own labs to analyze covid tests they carry out. Originally, in February / early March 2020, I think tests were essentially done in those labs, now the mass testing program has two big central labs in which the PCR tests for the whole country is analyzed. But presumably hospitals still analyze their own PCR tests in their own labs. Perhaps hospitals tend to not be equipped with the variant PCR test? I think this would explain the data. Up to the report before the current one, the numbers in the 48+h category were not changing much for other variants and omicron, (eg. staying at 8-9 cases for omicron). I dimly remember in the early days of omicron (1-2 weeks ago) that it was said (in a press conference or interview for the news) by someone responsible for contact tracing that there had been an omicron outbreak at a hospital, so that is probably why there originally were a couple of omicron cases identified in the 48+h category. My conclusion is that the 48+h row in that table is essentially useless to compare variants, as there seems to be very little variant testing to be done for those cases so far, or with a big delay (I would assume that the hospital labs are either going to set up variant tests or forward positive tests to the central labs for variant testing, but this might introduce extra delays, so this is not really reflected in the data yet?). In the <48h row there also must be quite a few cases that don’t have a variant result, though the difference is less drastic than for the 48+h row. Which makes sense because <48 hours includes tests done at the hospital (which I suspect correlates strongly with no variant PCR test result available) as well as tests done before admission (for which there seems to be good coverage of variant PCR tests, though with a little extra delay until results are ready).
The previous table from the December 15 report shows 0.6% of omicron cases being hospitalized in the <48h category and 0.8% of non-omicron cases being hospitalized in the <48h category, which is quite disappointing regarding virulence; as omicron is still rapidly rising and hospitalizations are delayed we would expect a lower rate currently even if virulence is the same, so this little difference in hospitalization is not good news.
The table from December 16 report still shows 0.6% of the omicron cases hospitalized (<48h) and 1.4% of the other variant cases (<48h). But by my discussion above I think the additional difference likely can be explained by people who were tested positive at the hospital and for which we don’t (yet) have a variant PCR test result.
Thanks for writing these posts on corona Zvi, I really appreciate them!