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Denmark SSI: Omicron Subvariant BA.2 Now Accounts For Nearly Half Of All Danish Cases + Rising in Norway, Sweden & UK

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  • sharon sanders
    bump this

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  • Michael Coston
    And now the UK . . . .

    UKHSA: Omicron Sublineage BA.2 Designated as A VUI (Variant Under Investigation)


    Although we first looked at it's growing diversity in mid-December (see The Omicron Uncertainty Principle), the now dominant Omicron variant is actually comprised of four closely-related viral lineages; B.1.1.529, BA.1, BA.2 and BA.3.

    While B.1.1.529 was the progenitor of the Omicron lineage, BA.1 has been, by far, the most commonly reported version (> 99%).

    BA.3 remains the rarest of the four, but the BA.2 sublineage has in recent weeks begun to make a move in several scandinavian countries (Denmark, Norway, Sweden).

    Yesterday, in Denmark SSI: Omicron Subvariant BA.2 Now Accounts For Nearly Half Of All Danish Cases and in Norwegian Institute of Public Health Also Reports A Rapid Increase In Omicron BA.2 Subvariant) we looked at these reports.

    At this time, we have zero information on how BA.2 infection might differ from BA.1, assuming it does at all. But there are concerns that BA.2 may prove even more transmissible.

    Today the UK's Health Security Agency (UKHSA) has taken notice of a low, but rising number, of BA.2 cases in the UK, and has designated BA.2 as a VUI.

    Unlike BA.1 - which has the SGTF (Spike Gene Target Failure) which helps identify it with certain PCR tests - BA.2 simply tests positive as COVID, and requires additional genomic sequencing to identify its lineage.

    This from the UKHSA.

    Omicron sub-lineage BA.2 designated as a variant under investigation (VUI)

    The Omicron variant sub-lineage known as BA.2 has been designated a variant under investigation ( VUI-22JAN-01) by the UK Health Security Agency (UKHSA).

    Overall, the original Omicron lineage, BA.1, is dominant in the UK and the proportion of BA.2 cases is currently low. The designation was made on the basis of increasing numbers of BA.2 sequences identified both domestically and internationally. There is still uncertainty around the significance of the changes to the viral genome, and further analyses will now be undertaken.

    To date, there have been 426 cases of Omicron BA.2 confirmed by Whole Genome Sequencing (WGS), with the earliest dated 6 December 2021.

    The areas with the largest number of confirmed cases are London (146) and the South East (97). Data for the devolved administrations will follow in due course.

    Early analyses suggest an increased growth rate compared to BA.1, however, growth rates have a low level of certainty early in the emergence of a variant and further analysis is needed.

    In total, 40 countries have uploaded 8,040 BA.2 sequences to GISAID since 17 November 2021. At this point it is not possible to determine where the sublineage may have originated. The first sequences were submitted from the Philippines, and most samples have been uploaded from Denmark (6,411). Other countries that have uploaded more than 100 samples are India (530), Sweden (181), and Singapore (127).

    Omicron BA.2 lacks the genetic deletion on the spike protein which produces S-gene target failure (SGTF) in some polymerase chain reaction (PCR) tests, which has been used as a proxy for Omicron cases previously.

    Dr Meera Chand, COVID-19 Incident Director at UKHSA, said:

    It is the nature of viruses to evolve and mutate, so it’s to be expected that we will continue to see new variants emerge as the pandemic goes on. Our continued genomic surveillance allows us to detect them and assess whether they are significant.

    So far, there is insufficient evidence to determine whether BA.2 causes more severe illness than Omicron BA.1, but data is limited and UKHSA continues to investigate.

    Case rates remain high throughout the UK and we must remain vigilant and take up vaccinations. We should all continue to test regularly with LFDs and take a PCR test if symptoms develop.

    Health and Social Care Secretary, Sajid Javid, said:

    We are learning to live with this virus – and thanks to our world-leading surveillance system we can rapidly detect and carefully monitor any genetic changes to COVID-19.

    Our exceptional vaccine rollout means the number of people severely affected by COVID-19 is low, and the UK’s innovation and research has discovered life-saving treatments for those most at risk from COVID-19.

    As we cautiously return to Plan A, I encourage you to give yourself and your loved ones the best protection possible and Get Boosted Now.

    As is routine for any new variants under investigation, UKHSA is carrying out laboratory and epidemiological investigations to better understand the characteristics of this variant. We will continue to monitor this situation closely and recommend appropriate public health measures if needed.

    More detail will be available in UKHSA’s regular
    variant technical briefings.

    While there is considerable consternation in the media, and on some social media sites, over this BA.2 lineage, it is still too early to know how much of an impact it will have on the pandemic. It does remind us, however, that SARS-CoV-2 continues to evolve, and that more surprises may lay ahead.

    Stay tuned.

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  • sharon sanders
    bump this

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  • Michael Coston
    It also appears to be happening in Sweden and Norway.

    Norwegian Institute of Public Health Also Reports A Rapid Increase In Omicron BA.2 Subvariant


    Following the posting of today's earlier blog (see Denmark SSI: Omicron Subvariant BA.2 Now Accounts For Nearly Half Of All Danish Cases), I've found another Scandinavian country reporting a sharp increase in the Omicron BA.2 subvariant; Norway.

    For additional background on the BA.2 subvariant, you'll want to refer to my previous blog, butin short BA.1 has been the dominant Omicron variant (>99%) globally for the past couple of months, but now its sibling (BA.2) is suddenly making major inroads in northern Europe.

    It isn't known what - if any - difference infection with BA.2 may have over BA.1, although there are hints that BA.2 may be more transmissible.

    Yesterday Norway's NIPH published their (week 2) Epidemiological summary of COVID, which finds BA.2 outpacing BA.1 over the past couple of weeks. While they report a reduction in hospital admissions over the previous week, it is too soon to know what impact BA.2 will have on their COVID wave.


    Weekly report covid-19 for week 2 has been published

    Published 19.01.2022
    So far, 218 new patients have been admitted to hospital with covid-19 detected in week 2, of which 112 (51%) with covid-19 as the main cause. This is a preliminary 23% decrease in new admissions with covid-19 as the main reason after 145 in week 1.

    Summary for week 2
    Severe covid-19 disease
    • So far, 218 new patients have been admitted to hospital with covid-19 detected in week 2, of which 112 (51%) with covid-19 as the main cause. This is a preliminary 23% decrease in new admissions with covid-19 as the main reason after 145 in week 1. The number of new patients admitted to hospital last week can be adjusted upwards. Small adjustments in figures for previous weeks may also occur.
    • The number of admissions for covid-19 (the main cause) continues to decline, probably because the omicron variant causes less serious illness and more are well protected through vaccination. The number of hospitalizations of people infected with SARS-CoV-2, but who have another main cause of hospitalization, is increasing. This is because there is widespread infection in the community, including among those who have to be hospitalized for reasons other than covid-19. These patients now make up half of the new admissions.
    • Last week, there was an increase in the number of new hospital admissions in the age group 0-17 years, a stable trend in the age group 18-29 years, otherwise there has been a decrease in other age groups.
    • The number of new patients admitted to the intensive care unit is currently 18 in week 2, a 42% decrease from week 1 (31).
    • Among 112 new patients admitted to hospital in Norway with covid-19 as the main cause in week 2, 47 (46%) were unvaccinated, 24 (24%) were vaccinated with two doses and 27 (26%) were vaccinated with three doser. Primary vaccinated people who have been admitted to hospital with covid-19 as the main reason for hospitalization have a higher median age, and a larger proportion of them have underlying medical conditions that give a moderate or high risk of a serious course of covid-19, compared with the unvaccinated.
    • So far, 24 covid-19 associated deaths have been registered in week 2 after 22 in week 1. The number for week 2 can be adjusted upwards. In week 2, the median age was 81 years (lower-upper quartile: 74 - 87 years).
    Virological monitoring
    • Omikron became dominant in Norway through Christmas and there has been a rapid increase in all counties. The proportion of omicron cases increased rapidly from around 6% in week 49 to 89% in week 1 and 94% in week 2. There are regional differences, but an increase in most counties.
    • A variant of SARS-CoV-2, so far defined as an omichronic subvariant, BA.2, is increasing rapidly in Norway. From 7 detections on 4 January to a total of 611 detections on 19 January (mainly in Oslo), this edition of omikron is growing strongly compared to the original omikron, BA.1. The properties of the virus are not known other than that it is more contagious than BA.1 and increases correspondingly in Denmark and Sweden and may appear to take over for BA.1 already.

    While the future course of the COVID pandemic is unknowable, two European countries reporting a sudden surge in the BA.2 subvariant - and predicting it will soon overtake the dominant Omicron strain - is worth noting.

    Stay tuned.

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  • yielddude
    this is interesting. Denmark seems to be having a second omicron surge in the same month. Not sure if there is a correlation here.

    Leave a comment:

  • Denmark SSI: Omicron Subvariant BA.2 Now Accounts For Nearly Half Of All Danish Cases + Rising in Norway, Sweden & UK

    Denmark SSI: Omicron Subvariant BA.2 Now Accounts For Nearly Half Of All Danish Cases

    Credit NIAID


    In mid-December, in The Omicron Uncertainty Principle, we looked at the discovery of a significant sibling variant to Omicron - dubbed BA.2 - which lacked Omicron's signature SGTF (S-gene target failure), making it more difficult to detect without full sequencing.

    According to the latest WHO Weekly COVID epidemiological report (Jan 18th):

    The Omicron variant includes Pango lineages B.1.1.529, BA.1, BA.2 and BA.3. BA.1 accounts for >99% of sequences submitted to GISAID as of 18 January 2022. All these variants are being monitored by WHO under the umbrella of ‘Omicron’

    While siblings, these `4 flavors' of Omicron may not all act the same. BA.1 appears to be the most transmissible right now, but without SGTF, the BA.2 sublineage may be spreading `under the radar' in some countries. BA.2 has been detected in over 30 countries, while BA.3 remains very rare.

    Other potential differences(if any)- in terms of transmission, or severity - have yet to be determined. It also seems likely that other sublineages of Omicron will emerge over time.

    With the BA.1 subvariant believed to be theoverwhelmingly dominant (> 99%) version of Omicron, the following report from Denmark's Statens Serum Institut (SSI) - finding nearly half of all Danish infections due to BA.2 - will likely raise a few eyebrows.

    A subvariant of omicron, BA.2, now accounts for almost half of all Danish omicron cases

    So far, 3 subvariants of omicron have been described: BA.1, BA.2 and BA.3. Worldwide, BA.1 accounts for the vast majority of cases. In Denmark, however, BA.2 wins at the expense of BA.1.

    Last edited 19 January 2022

    The subvariant BA.2 accounted for 20% of all cases of infection in Denmark in week 52, while in week 2 it accounts for approx. 45%. At the same time, the share of BA.1 has fallen.

    There is also an increase in BA.2 cases in other countries, i.a. Great Britain, Norway and Sweden, but apparently not quite at the same level as in Denmark.
    Different mutations

    BA.1 and BA.2 have many differences in mutations in the important areas. In fact, the difference between BA.1 and BA.2 is greater than the difference between the original variant and the alpha variant.

    Such differences can lead to different characteristics which, for example, may relate to infectivity, vaccine effect or severity. There is as yet no final clarification of whether BA.1 and BA.2 have different properties, but SSI is continuously working to investigate this.
    So far no difference in admissions

    Preliminary analyzes from SSI show that there is no difference in the risk of admission with BA.2 compared to BA.1. Analyzes regarding infectivity and vaccine effectiveness etc. has been initiated, just as attempts are also being made to grow BA.2 so that antibody neutralization studies can be performed. The expectation is that vaccines also have an effect against serious illness when it comes to BA.2.

    Many people are convinced that Omicron (specificallyBA.1) signals the last gasp of the COVID pandemic and the virus will soon become an endemic, likely seasonal, respiratory virus.

    While this would be the best possible outcome at this point, it is far from guaranteed.

    The rise of BA.2 in Denmark may be a fluke, or ultimately of little consequence to the course of the pandemic - but it is a reminder that SARS-CoV-2 continues to evolve and adapt - which is why reports of COVID's imminent demise may be premature.