Saturday, November 14, 2020

Denmark: SSI Update On COVID-19 Mutation & Relaxation Of North Jutland Restrictions

Credit ECDC


Ten days ago Danish authorities raised the alarm when they announced the discovery of 5 mutated strains of COVID-19 that had arisen in mink and had transmitted to humans - including a `5th cluster'  they feared could evade vaccines currently under development (see Denmark Orders Culling Of All Mink Following Discovery Of Mutated Coronavirus).

While `mutation' reports in emerging viruses are rarely as dire as they sound - in this case, Danish authorities were unusually strident in expressing their concerns for public health - and ordered a full 4 week lockdown, and emergency testing of all residents in North Jutland, where the virus had emerged. 

Since then, we've seen several risk assessments (from the WHO, ECDC, Serum Statens Inst.), but hard evidence concerning the spread of this mutation - and its actual risks to public health - have been hard to find.  

Nevertheless, on Nov. 7th the UK instituted a travel ban to and from Denmark over concerns of the potential international spread of this mutation.

Between a lack of new, confirmatory information and a push back on the lockdowns and culling of 17 million mink, last week Denmark began to moderate its response to this perceived threat. 

First stop, the (translated) unexpected announcement on the lockdown in North Jutland. 
A number of local restrictions in North Jutland are eased
PRESS RELEASE - On the basis of new data, the Task Force for Covid-19 handling assesses that a number of local restrictions in seven North Jutland municipalities can be relaxed. The government has decided to follow the recommendation.
In order to reduce the development of infection with Covid-19, a number of local restrictions and measures have been implemented in seven North Jutland municipalities.
Based on new infection data and results from sequencing, the Task Force for Covid-19 management, including the health authorities, assesses that there is a basis for easing some of the restrictions within the seven municipalities. The task force includes emphasis that:
  • In the 7 North Jutland municipalities, 72 infected per 100,000 in the last week, when the number a week ago was 115.
  • In the North Jutland municipalities, 41,713 have been tested from 7.-10. October, when the number the week before was 12,816, corresponding to more than a tripling.
  • Results of the sequencing show a marked decrease in the proportion of people infected with mink variants in the North Jutland Region. In week 44, 21% of all sequenced samples were positive for mink variants compared to 53% in week 42.
  • All mink in the 7 municipalities are expected to be killed on Monday 16 November 2020.
The Government has decided to follow the Task Force's recommendations to ease certain restrictions. The reductions will apply from Monday 16 November 2020.

The easing means concretely:
Geographical mobility It is no longer called for to restrict mobility between the 7 municipalities. This means that the residents of the affected municipalities are no longer encouraged to cross municipal boundaries between the affected municipalities alone in special cases. Public transport, etc. It will again be possible to use public transport across the affected municipalities. Day care, primary school, youth and adult education, boarding, post-secondary and folk high schools Children in 5.-8. grade level must return to school. See fact sheet

The task force follows the development very closely, including with a view to assessing whether there are grounds for further easing of the restrictions in the North Jutland municipalities, and whether further restrictions may be needed in other municipalities.

Based on new sequencing figures for North Jutland during week 47, the task force will assess whether there is a basis for changing the professional attitude fsva. the remaining restrictions in the seven municipalities.

Continued health professional basis for killing mink

In relation to mink keeping as a reservoir for Covid-19 infection, the health authorities' assessment is that continued mink breeding in Denmark entails a significant risk to public health during the ongoing pandemic.

There is thus a significant health professional basis for the killing of the Danish mink population.

The Serum Statens Institute issued an update yesterday (LINK), and the following press release. 

The recent development of covid-19 on mink farms and among humans

The proportion of people infected with a mink variant of covid-19 is declining. At the same time, the probability that cluster 5 has died out has increased. It shows a new note from the Statens Serum Institut.

Last edited November 13, 2020
The number of mink farms infected with covid-19 is increasing in the Central Jutland Region and the Southern Denmark Region. At the same time, there is also an increase in the number of covid-19 infected people working in mink production in the two regions.
It shows a new note from the Statens Serum Institut (SSI) on the development of covid-19 on mink farms and among humans.
The new figures also show that the proportion of people infected with a mink variant of covid-19 is falling nationwide. This is due in particular to a decline in the North Jutland Region. However, there is an incipient increase in the proportion infected with mink variants in the Central Jutland Region. Finally, the figures show that no new cases of the so-called cluster 5 mink variant have been detected since 15 September.
"This is good news, as it increases the likelihood that the cluster 5 variant is extinct," said department head Tyra Grove Krause of SSI.
Development in infected persons associated with mink production

The number of newly infected mink farms has fallen in recent weeks in the North Jutland Region, where the number has increased in Central Jutland. If you look at people associated with mink production who are infected with COVID-19, the same pattern follows. The number of infected decreases in Region North Jutland, but increases in Region Central Jutland and now also in Region South Denmark.

SSI's inventory is based on positive covid-19 samples from persons residing at the production or owner address of mink farms. It therefore does not include sequencing results.
Result of sequenced samples

As for the sequenced samples, from week 24-44, a total of 7,108 positive covid-19 samples have been sequenced. This corresponds to almost 19% of the total number of positive covid-19 samples.

Among them, a total of 326 samples were found with a mink variant of covid-19 - corresponding to 4.6%.

The vast majority of samples with finds of covid-19 mink variant - a total of 272 - originate from the North Jutland Region. In weeks 41-43, covid-19 mink variants accounted for about half of the sequenced samples in the region. In week 44, however, only 1 in 5 sequenced samples are mink variants.

In the Central Jutland Region, covid-19 mink variants were only very sporadically found in the sequenced samples before week 41. Thereafter, the number of detected cases with mink variants increased to approximately 12% in week 44.

In the other regions in Denmark, only sporadically cases of covid-19 with the mink variants have been detected.
Developments in cluster 5
The much talked about cluster 5 mink variant has been detected on five mink farms in the North Jutland Region in August and September. The minks on all five farms have now been killed.
A total of 12 people have been diagnosed with covid-19 infection with the cluster 5 variant. Of these, 8 people have a direct connection to four of the farms, either as owner, employee or family member. The last 4 people have no known connection to mink farms, but come from the same areas where there have been infected farms.
However, no cases of the cluster 5 mink variant have been detected since 15 September.
"It increases the probability that it has died out, but we continue the planned increased test effort and sequencing of all positive samples in North Jutland to be completely safe," says Tyra Grove Krause.

          (Continue . . . )

Based on the numbers provided, the reduced spread of these mutations in North Jutland is encouraging, although the spike in Central Jutland region is worth watching.  (Note: I'm jaded enough after 15 years of blogging to take both `good' and `bad' news with with equally-sized grains of salt). 

Even if - as suggested - the `cluster 5 mink variant' has been successfully eradicated in Denmark, it may be a fleeting victory.  

We continue to see fresh reports of mink infected with SARS-CoV-2 around the world (see FluTrackers thread Greece - Mink and minkworkers tested positive for Covid-19 - Media - Outbreak in 2 farms), and spillovers of the virus into other non-humans hosts could open the door to other mutations. 

And even without the help from another intermediate host, COVID-19 has shown the ability to evolve and adapt in humans (see Study: SARS-CoV-2 D614G Variant Exhibits Efficient Replication Ex Vivo and Transmission in Vivo).

The good news is that not all mutations are bad. In fact most end up being relatively benign. 

And it is possible that, over time, mutations in SARS-CoV-2 could help attenuate its virulence or transmissibility in humans. We've certainly seen evidence of that with HPAI H5N1 in Indonesia and Egypt - where human infections once were common and often deadly - but in recent years have all but disappeared. 

While no one can predict the future course of COVID-19 - or any other emerging infectious disease for that matter - there is one constant that we can be sure of; evolution never stops. 

Which is why we need to be prepared for surprises going forward. Both with COVID-19, and the pandemics that will inevitably follow.