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Although Denmark's overall number of confirmed B.1.1.7 COVID variants remains small (n=208), the percentage of sequenced viruses that match this more transmissible variant continues to rise each week.
These numbers are considered major undercounts, as current PCR testing can't differentiate between the old COVID lineage and newer variants, and only a limited number of cases can be sequenced.
Just over a week ago, Denmark's Statens Serum Institute (SSI) estimated the B.1.1.7 variant would likely become dominant in their country by mid-February.
While we are still learning about the full capabilities of this (relatively) new variant, early reports suggest it is 70% more transmissible than the previous variant, and with this biological advantage, there are fears it may become the dominant variant world-wide in the months to come.
Denmark's SSI released two updates yesterday; one on the introduction of a new PCR test, which will help them narrow the search for COVID variants, and the other updating the rise in variants detected over the past week.
The new PCR test will detect some - but not all - of the recent variants of concern, but will not differentiate between them. It will, however, flag them for sequencing.
Additional tests are being developed for the South African 501Y.V2 variant, as explained below:
The Delta PCR test has not been developed to detect the South African 501Y.V2 variant, which, like B.1.1.7, is more contagious and therefore poses a potential risk in the coming months. Instead, SSI is currently working on developing another method that targets changes in viral nail protein. It will be able to determine whether a given person is infected with B.1.1.7, N439K, the South African variant or the mink variant. In addition, the method will also provide information on other possible variations in the nail protein.
Even before these improvements, Denmark was well ahead of most other nations in the testing of suspected COVID cases, and the genomic sequencing of a significant percentage of positive tests.
Translated excerpts from both reports follow:
New PCR tests will strengthen control of mutated variants
TestCenter Denmark is now using a new PCR test in response to the worrying development of mutated variants of the SARS-CoV-2 virus. The Delta-PCR test can detect whether a positive sample contains B.1.1.7 and other variants that are being monitored. It provides new and better opportunities for infection detection, strengthens surveillance - and ultimately control of the epidemicLast edited January 13, 2021
(SNIP)
An effective tool
The new Delta PCR test can be an effective tool in the fight against mutated variants. The Delta PCR test can show whether a positive covid sample contains a selection of virus variants that can challenge efforts to maintain control of the epidemic.
Among these variants is B.1.1.7, which was first found in England, but also the variant N439K, which has its origins in Romania, but has since, like B.1.1.7, spread to a number of other countries, including Denmark. Delta-PCR can also detect the Danish mink variants, which are still in circulation to a lesser extent. This ultimately leads to a strengthened control of the epidemic.
"It is a really good step to strengthen the monitoring and provides opportunities to intensify the detection of infection more specifically after the problematic variants," says academic director Tyra Grove Krause from the Statens Serum Institut (SSI)
Not the solution to everything
However, she stresses that Delta-PCR is not the solution to everything. It has its limitations.
“12.1% of all sequenced samples in week 53 are of the originally Romanian strain N439K, and only 2.7% are so far of B.1.1.7. Both give a positive signal when tested with Delta-PCR. So we will not with one stroke from tomorrow be able to say anything very precise about the prevalence of B.1.1.7. But we will be able to do that with delay when the samples that are "Delta positive" are sequenced ", says Tyra Grove Krause.
She points out that SSI is simultaneously working on developing new methods, so that you know more quickly exactly which variant a person is infected with. Also when it comes to the South African tribe, for example, which Delta-PCR is not geared to detect.
Moving on, the SSI also published an update on the B.1.1.7 variant in Denmark.
Status of development of B.1.1.7 in Denmark
The latest figures show that the trend continues with an increasing proportion of detected cases of the mutated variant B.1.1.7 among the sequenced samples.Last edited January 13, 2021
In the following, you can read the latest figures on how the situation has developed in Denmark and the individual regions. The figures are based on current statements, and adjustments can therefore be made as sequencing responses come in. In addition, the figures for week 1 are not complete and are therefore subject to uncertainty.
The latest count of the number of confirmed infections with the mutated covid-19 virus variant B.1.1.7, which was first discovered in England, shows a clear continued development. The variant thus fills an ever-increasing proportion of the sequenced samples among Danish covid-infected.
This is a development that is being closely monitored by the Statens Serum Institut (SSI), and which is expected to increase with increasing strength in the coming months.
B.1.1.7. in Denmark
In total, the variant has now been found in 208 Danes in the period from 14 November to 6 January.
In the weeks 46-1, 17,305 samples have now been sequenced. B.1.1.7 has been found in 1.1% of the samples.
In week 53, 52 cases of B.1.1.7 were detected throughout the country, and they accounted for 2.4%, of the sequenced samples. For week 1, 12 samples with the variant have so far been found, which is 3.6% of the 1,176 samples that have been sequenced so far.
192 of the detected cases were found in random samples, while 16 of the cases were found as household contacts for infected with B.1.1.7
Among all the samples, there are 3 cases with travel history from England, 2 have come from the United Arab Emirates incl. Dubai, 1 from Barbados and 1 from Lebanon. It is unknown whether they are infected in Denmark or abroad.
Infection in the regions of the country
Infection has been detected with B.1.1.7. in all regions of the country. Where there is the most infection seems to vary slightly from week to week, and in week 1 between 1-15 cases were found among the samples in the respective regions, the fewest in North Jutland.
If one compares the situation in week 53 with the situation in week 1., then the highest percentage of detected was among the samples in week 53 in Southern Denmark, where B.1.1.7. were found in 5.8% of the samples. That trend seems to be continuing. In week 1, the incomplete data so far show a percentage of samples from Southern Denmark with B.1.1.7 of 9.0%
See Status of development of B.1.1.7 in Denmark, 13 January 2021 (pdf)
With new COVID Variants popping up around the globe, the need for better tests grows greater with every passing day.
While most of these variants will probably amount to little more than a `flash in the pan' - being unable to compete with more biologically `fit' versions - it just takes one overachiever be a game changer.
