PCR Testing - Credit CDC PHIL
#16,051
While the news cycle in the United States is somewhat subdued this morning because of the the long 4th of July weekend, we do have reports coming in from other regions, including three recent updates on COVID variants from Denmark's Statens Serum Institut.
Because of their relatively small population (5.8 million), a well-monitored universal healthcare system, and a high degree of genomic testing, Denmark's ability to track both the spread and impact of different COVID variants has been remarkable.
Some of the past studies we've looked at from the SSI include:
SSI Study: Denmark's Cluster-5 mink Variant Had Increased Antibody Resistance
Denmark: Statens Serum Institut Announces 1st Detection of AY.1 Variant (Delta with K417N)
Denmark: SSI Reports Encouraging Numbers On COVID Vaccine Breakthroughs
Denmark SSI: Assessment of Protection Against Reinfection with SARS-CoV-2
Today, they have a follow up - and a summary of a recently published LANCET article - that appears to validate their original conclusions.
New study confirms: The alpha variant (B.1.1.7) is associated with a greater risk of hospitalization
The Statens Serum Institut (SSI) has published a research study in the journal Lancet. This confirms that there is a greater risk of being admitted to hospital if you become infected with the covid-19 alpha variant.
Last edited July 5, 2021
If you become infected with the covid-19 variant alpha (B.1.1.7), which was first detected in the UK in December, there is a greater risk that the infection will lead to hospitalization than for other variants in January, February and March. 2021. Exactly 42% greater risk.
This is the conclusion of a new study from SSI, Aalborg University and the Danish Covid-19 Genom Consortium. It has just been published in the scientific journal Lancet.
Read the new study here: Risk of hospitalization associated with infection with SARS-CoV-2 lineage B.1.1.7 in Denmark: an observational cohort study
Already published in February
The conclusion about the increased risk of hospital facilities was already clear in the latter part of February, when the alpha variant had reached 60% of the detected covid-19 cases in Denmark.
Therefore, instead of waiting for the results to be published in a scientific journal, they chose to send them to an international preprint server so that they became publicly available immediately.
At that time, a total of 35,887 people were included in the register-based survey. They were all tested positive for SARS-CoV-2 in the period from January 1 to February 6, 2021.
The result of SSI's investigation pointed in the same direction as several reports from the UK during the same period.
Investigated even more
Since February, the research article and results have been evaluated by peers and then adopted and published in the Lancet.
During this period, SSI's researchers continued to investigate even more Danish covid-19 cases. The finished research article therefore covers a month and a half further from 1 January to 24 March.
A total of 50,958 people ended up in the new study, which tested positive for SARS-CoV-2. From them, a virus genome was detected for 30,572 people, and among them, 10,544 were infected with B.1.1.7.
One looked at how many of these individuals were admitted within a 14-day period after they tested positive. A total of 1,944 people did so. Of these, 571 were infected with the alpha variant, while 1,373 were infected with other variants.
Expectations held true
The final study concludes that people infected with the alpha variant of SARS-CoV-2 have a 42% higher risk of being admitted (safety range 25% -60%).
“We have now been able to carry out our analyzes with even more people at a time when 95% of the covid-19-infected in Denmark were infected with the alpha variant, which at that time had taken over almost completely. The study clarifies how valuable Danish covid-19 data is - also in an international context, because we have a high test and sequencing rate per inhabitant, detailed health data, and perform high-quality epidemiological analyzes, ”says SSI's technical director Tyra Grove Krause and continues:
“With the updated analyzes, the result is even more accurate. And we can see that our expectations that it would lead to more hospitalizations when the alpha variant became dominant in Denmark, and that it was therefore necessary to keep the country closed longer to avoid overloading the hospitals, proved to be true " .
Read more
Read the new study here: Risk of hospitalization associated with infection with SARS-CoV-2 lineage B.1.1.7 in Denmark: an observational cohort study
B.1.1.7 in Denmark - as it already has in the UK, and is in the process of doing in the United States - is quickly giving way to the even more transmissible Delta (B.1.617.2) variant. Late last week the SSI warned that Delta was about to become the dominant COVID strain there, as well.
The delta variant (B.1.617.2), which was first found in India and which has since spread to the rest of the world with great force, is also on the rise in Denmark. The Statens Serums Institut follows the development closely. Extensive test activity with coronapas, high sequencing capacity and intensive contact detection help to limit the spread of the delta variant in Denmark.
Last edited July 2, 2021The delta variant was first detected in India and has since spread to the rest of the world. In the UK, it now accounts for more than 90% of genome-sequenced samples. The delta variant has thus taken over the place as the dominant variant.The same development is expected in the rest of Europe, where the Delta variant accounts for an increasing share of the positive samples.The Danish strategyThe Statens Serum Institut (SSI) closely monitors the development of the Delta variant.“There is great international concern about the clearly more contagious Delta variant, and we are now seeing an increasing number of cases infected with this variant. Our strategy has been to delay the emergence of the Delta variant as much as possible, and spend time getting as many people vaccinated as possible. So it's a bit of a race, ”says SSI's director Henrik Ullum.Why are we aware of the Delta variant?
The Delta variant has raised concerns about increased infectivity compared to the Alpha variant (B.1.1.7). There are also a few studies from the UK that indicate an increased risk of hospitalization for infection with the Delta variant, but at present there is not enough data to assess whether this will also apply in Denmark. Finally, the Delta variant shows a decreased sensitivity to antibodies after the first vaccine injection. After two bites, however, the vaccine effect should have been preserved.
The delta variant is on the rise in Denmark
In Denmark, the Delta variant was detected for the first time in week 13. Since then, 664 cases of the variant have been found in this country. There has been an increasing trend both in the number and proportion of whole-genome-sequenced samples since week 20 (see Figures 1 and 2).
Figure 1. Number of Delta variant cases by calendar week and region (data for 26 are not complete yet)Figure 2. Proportion of Delta variant cases out of whole-genome-sequenced samples in Denmark (data for 26 are not complete yet)
The development follows in line with a new note from the expert group for mathematical modeling (pdf), which estimates that the delta variant will be dominant - ie. make up more than 50% of the genome-sequenced samples - in early July.Denmark's active efforts against the Delta variantThe large sequencing capacity in Denmark means that we can quickly find the Delta variant, and that the Danish Agency for Patient Safety can quickly intervene with an intensified infection detection of cases with this variant.In addition, TestCenter Denmark has developed another option for screening positive samples for the Delta variant. Thus, it is now possible to find cases with the mutation L452R, which is present in the Delta variant, among other things. This will mean that infection detection can be initiated more quickly.
Although there have been preliminary reports out of the UK suggesting that the Delta variant may have an even greater risk of hospitalization than Alpha, the data has been mixed, and there is - as yet - no consensus. Hopefully Denmark's surveillance system will provide us with a more definitive answer as Delta becomes dominant there.
In our last stop, today Denmark's SSI announced that Delta was now dominant, and outlined their strategy to deal with it. I'll have a brief postscript after the break.
The delta variant (B.1.617.2), which was first found in India and which has since spread to the rest of the world with great force, now dominates in Denmark. The incipient societal infection means that the Statens Serum Institut (SSI) recommends adapting the infection detection, e.g. so close contacts close contacts no longer need to be isolated if they have no symptoms but are still being tested.Last edited July 5, 2021The delta variant is about twice as contagious as the alpha variant, and it is spreading rapidly throughout the world. In Europe, major outbreaks and societal infections are being seen, and restrictions are being reintroduced in several places. The European Center for Disease Control (ECDC) predicts that the infection will increase over the summer. It will especially affect the unvaccinated, including children and young people when the summer holidays end. The ECDC predicts that this will lead to an increase in hospital admissions, including among the fully vaccinated, but that more serious illnesses will be reduced by the large - and ever-increasing - proportion of the elderly and people at risk who have been vaccinated.Developments in DenmarkIn Denmark, there are currently few daily covid-19 cases and a very low number of hospitalized patients, but the delta variant now accounts for more than 2/3 of all positive cases, and it is estimated that it will be all-dominating within a short time. The delta variant has a large infection potential, and a number of major outbreaks have already been observed, some of which have the character of super-spreading events. There are also incipient signs of societal infection, where new cases cannot be linked to travel or concrete outbreaks. An increasing number of cases are expected in the near future.SSI assesses that we are in a fordSSI assesses that we are in a ford where the delta variant goes from being a variant where we can delay the transmission of society, to being an all-dominating variant, with more widespread societal transmission. The previous delay strategy therefore changes its character to a strategy with infection control measures while at the same time speeding up vaccines as much as possible. It has succeeded in delaying the transmission of the infection, but the very intensive infection detection changes character as the transmission of the infection increases.Infection control measuresIn a situation of more widespread societal infection, it no longer makes sense to isolate close contacts of close contacts without symptoms. Instead, it is recommended that unvaccinated contacts to contacts be tested on days 4 and 6, whereas vaccinated contacts to contacts are tested only on day 4 after their contact with the close contact. For practical reasons, all new positive cases will be detected in this way regardless of variant, now that the delta is on its way to being all-dominant.Use the infection stop appAt the same time, everyone in Denmark is encouraged to use the infection stop app and remember to activate it again if you have switched it off after being vaccinated. With more widespread societal infection, you can not know if / where you are exposed to infection, and unfortunately it is also possible to become infected and test positive, even if you have been fully or partially vaccinated. Fortunately, all indications are that you will very rarely get seriously ill if you have been vaccinated. Especially if you have been vaccinated. It is also expected that you become less infected if you have been vaccinated and tested positive.The spread of infection in Denmark is at the same time dampened by the accelerated roll-out of vaccines, coronapas, easy access to testing, entry screening, seasonal effect with many outdoor activities, continued contact tracking and outbreak management and the large sequencing activity. In addition, the local closure model benefits based on incidence, number of infections and positive percentage. Time will tell whether further action is needed.The goal is within reachIn the current phase, all those who can and will be vaccinated as soon as possible are vaccinated while the infection is reduced. This delays the delta variant so that as few non-vaccinated people as possible, or who do not tolerate the vaccine or have the effect of it, become infected. When everyone who can and wants to has been vaccinated, which is now within reach, the delta variant's opportunities to reach the vulnerable groups are reduced.Professor Troels Lillebæk, SSI and chairman of the SARS-CoV-2 variant risk assessment group says:
“No one can predict exactly where we end up with the delta and possibly other new variants, but we are much better equipped now than when covid-19 first hit us about a year and a half ago. It is encouraging that vaccines are being rolled out at a rapid pace and that they continue to have an effect against serious illness ”.
Read moreUpdated professional note regarding. contact tracing of special SARS-CoV-2 variants, 4 July 2021 (pdf)
The United States is several weeks behind the UK and Denmark in the spread of Delta, but we will likely see B.1.617.2 become dominant sometime during the month of July.
Currently, daily cases in the US remain relatively low - likely muted by the warmer weather and high early vaccine uptake - and so its immediate impacts may be harder to assess.
Lagging behind the UK and Denmark may give us an advantage going forward, as they could provide us with a preview of what we might expect in the weeks ahead.
But there are differences between the United States, and Denmark or the UK, which could alter our respective outcomes. Vaccinations in the United States have fallen off sharply over the past 60 days, there seems to be little appetite for wearing face masks in public anymore, and a great many people believe the COVID crisis has ended.
Whether we end up being a success story this fall, or serve as a cautionary tale for other countries, will depend largely on our ability to assess new information as it comes in, and pivot if necessary.
Anything less will simply provide the virus with fresh opportunities to thrive.
