1,587 thoughts on “General Discussion – 2

  1. https://www.sabcnews.com/sabcnews/more-children-admitted-with-covid-19-symptoms-to-hospitals/

    ‘More children admitted with COVID-19 symptoms to hospitals’

    Health care workers are raising concern about the growing number of children being hospitalised with moderate to severe symptoms of the Omicron variant of the coronavirus.

    Head of Intensive Care at Chris Hani Baragwanath hospital, Dr Rudo Mathivha says the situation is worrying because the hospital isn’t built to admit a high number of sick young children.

    She says a 15-year-old died after the child’s condition deteriorated rapidly following a COVID-19 infection, and a 17-year-old is in ICU with coronavirus-related pneumonia.

    Mathivha has urged parents to get their children vaccinated.

    South Africa is currently in the fourth wave of the pandemic, fuelled by the newly discovered Omicron variant of the virus. Mathivha has warned that they may soon not be able to accommodate any more children.

    This is not something that we had observed with the first, second and third wave. In the past, the children used to get COVID-19 infection. It wouldn’t really send them to hospital in big numbers to be admitted. Our hospitals were not built to house a lot of children. We will not be able to accommodate them, and I’m not saying this to make people panic,” says Mathivha.


  2. Hospital Admissions continue more than doubling every week in Gauteng and deaths last week were more than double the week before for the first time in their 4th wave. If the deaths chart is following the admissions chart with a roughly 2 week delay then big trouble ahead so let’s hope it isn’t.

    Gauteng Admissions

    Gauteng Deaths

    Note the data gets backfilled and it is likely that both reported admissions and deaths for week 48 will still increase.

    Source: https://www.nicd.ac.za/diseases-a-z-index/disease-index-covid-19/surveillance-reports/daily-hospital-surveillance-datcov-report/

    So if anybody tells you “There have been no reported deaths from Omicron” ask them why the covid deaths in Gauteng more than doubled last week from the week before.

  3. Just a very mild doubling to over 2000 excess deaths in South Africa in one week.


    Omicron Wave Sees South Africa’s Weekly Excess Deaths Almost Double

    (Bloomberg) — South African excess deaths, a measure of mortality above a historical average, almost doubled in the week ending Nov. 28 from the preceding seven-day period as a new coronavirus variant spread across the country. During the period 2,076 more people died than would normally be expected, the South African Medical Research Council said in a report on Wednesday. That compares with 1,091 the week earlier.

    …Excess deaths are seen as a more accurate measure of the impact of Covid-19 than official deaths. While South Africa’s official coronavirus death toll is just over 90,000 the number of excess deaths during the pandemic is 275,000. During the week to Nov. 28 just 174 deaths were officially attributed to the respiratory disease. Still, the weekly deaths are well below their peak of about 15,500 in mid-January, at the height of the second wave of infections.

  4. I think the Bloomberg story has the dates wrong and the latest week excess deaths are for the week beginning Sunday Nov 28 not ending November 28 as the actual report says data through to week 48 ending Saturday 4th December. Doubling then fits exactly with the approximate doubling (55 to 102) in national hospital deaths over the same week 47 to 48. Of course we need more than one week to see if this is the start of a concerning trend or noisy data (or both). But there looks to be at least some signal there to me.

    Actual report at https://www.samrc.ac.za/sites/default/files/files/2021-12-08/weekly4Dec2021.pdf

  5. Google translated


    Covid after a trip to South Africa – two children seriously ill

    District of Kleve: The first omicron mutations in the district of Kleve have been confirmed for sure. There are now numerous corona cases that are related to the outbreak after trips to South Africa. These include two children who are seriously ill.

    The district of Kleve has the first clear evidence of the Omikron variant. The full sequence analysis of a laboratory has now confirmed the suspicion for two index cases. This is a South Africa traveler and a contact person. At the weekend, a laboratory for two other people who were in South Africa confirmed the suspicion of the omicron mutation, but not yet finally confirmed it.

    The Kleve district has now identified 19 index cases that are related to this outbreak. The contact persons also include children who have not yet been vaccinated. The adults are all fully immunized. Two children are seriously ill. An adult has a severe course of the disease. All other people who tested positive so far have had a comparatively mild course of the disease. Some are asymptomatic.

    And official statement confirming two children seriously ill at https://www.kreis-kleve.de/de/aktuelles/vollstaendiges-laborergebnis-bestaetigt-eindeutig-zwei-omikron-indexfaelle-im-kreis-kleve/

  6. Long thread here worth reading the whole thing. Bottom line is nothing in the South Africa data so far suggests Omicron is intrinsically “milder” than other variants but read the entire thread.

  7. Look we all want it to be milder. I’d certainly love it to be milder but there don’t seem to be any features of the genetic code of the Omicron variant that would suggest it could be milder as far as the experts can see. Now they could be missing something of course and I’ve not seen anything definitive as to whether part of the spike is still seen as super-antigenic and I’m not sure there was much consensus on how much of a role that played anyway.

    Still I’m going to continue to hope for good news on any front because with 34% of London samples Omicron on 8th December (that’s likely over 50% today) London and overall UK covid case counts are heading into orbit soon.

  8. Two weeks ago I wrote

    So mild in fact that admissions with covid almost quintupled in 2 weeks in Gauteng Province. (I previously said it had only quadrupled but additional cases have been added for week 47)

    A week later I wondered if the hospital deaths were following admissions with a 2 week delay. So how do deaths compare after that two week delay?

    Yep, just a very mild five times increase in hospital deaths over the last two weeks. And that’s based on still partial data for week 49 (Their Week 50 started yesterday). Deaths for week 49 still likely to increase considerably as data is back-filled.

    These figures are just for Gauteng Province and yet everyone seems to think nobody has died of omicron in South Africa.

    Source: https://www.nicd.ac.za/diseases-a-z-index/disease-index-covid-19/surveillance-reports/daily-hospital-surveillance-datcov-report/

  9. So we must all be happy and rejoice that across South Africa only a few hundred people so far are mildly dead from Omicron on official figures. Based on previous waves many hundreds more will have died even more mildly (without even troubling a hospital!) unofficially of omicron.

    And jolly good show for the thousands more who will also mildly die in South Africa (and of course more elsewhere) in the coming weeks in support of the dream of herd immunity.

  10. And hospital admission in London now leading the way up

  11. https://www.imperial.ac.uk/news/232698/modelling-suggests-rapid-spread-omicron-england/

    Modelling suggests rapid spread of Omicron in England but same severity as Delta

    The new report from the Imperial College London COVID-19 response team estimates that the risk of reinfection with the Omicron variant is 5.4 times greater than that of the Delta variant. This implies that the protection against reinfection by Omicron afforded by past infection may be as low as 19%.

    …The study finds no evidence of Omicron having lower severity than Delta, judged by either the proportion of people testing positive who report symptoms, or by the proportion of cases seeking hospital care after infection. However, hospitalisation data remains very limited at this time.

    Full report https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/covid-19/report-49-omicron/

  12. COVID-19 hospital admissions in London continue to accelerate, with 7-day average now up 42% week-on-week.

  13. As we seem to be locked into one massive surge of Omicron I’m trying my best to cling on to anything that might reduce the final death toll. I like this pre-print and just hope it doesn’t turn out to be another false hope.


    SARS-CoV-2 Omicron spike mediated immune escape, infectivity and cell-cell fusion

    The Omicron variant emerged in southern Africa in late 2021 and is characterised by
    multiple spike mutations across all spike domains. Here we show that the Omicron spike
    confers very significant evasion of vaccine elicited neutralising antibodies that is more
    pronounced for ChAdOx-1 adenovirus vectored vaccine versus BNT162b2 mRNA
    vaccine. Indeed neutralisation of Omicron was not detectable for the majority of
    individuals who had received two doses of ChAdOx-1. Third dose mRNA vaccination
    rescues neutralisation in the short term. Despite three mutations predicted to favour
    spike S1/S2 cleavage, observed cleavage efficiency is lower than for wild type Wuhan-1
    D614G and Delta. We demonstrate significantly lower infectivity of lung organoids and
    Calu-3 lung cells expressing endogenous levels of ACE2 and TMPRSS2 but similar
    infection as compared to Delta when using H1299 lung epithelial cells. Importantly,
    fusogenicity of the Omicron spike is significantly impaired, leading to marked reduction
    in syncitia formation. These observations highlight that Omicron has gained immune
    evasion properties whilst compromising on properties associated with replication and

    However nobody seems to have a good answer yet as to why Omicron has such a high observed transmissibility compared to all other variants if it has “compromised” its replication ability and is not good at infecting some cells unless it has much, much better ability to enter other cells (and how does that fit in with “compromised” replication). Another study found much better ability to enter bronchial cells than previous variants but it seems there’s still too much unknown.

    Meanwhile in South Africa deaths continue to pile up, just not at the truly horrendous rates they reached previously. Based on the daily hospital data about 500 people a week are dying at the moment as backdated deaths fill in – Just 4 weeks ago there were only 55 recorded covid deaths in one week. So Delta was only managing to kill about 50 people a week then along came “mild” Omicron and increased that ten fold in a month.

    And remember almost everyone catching covid in South Africa has already caught it before. Most of their most vulnerable age groups are vaccinated and a high proportion are both previously infected AND vaccinated which is thought to give very good protection against serious illness.

    I want to believe South African deaths are lower because of some intrinsic property of this variant but there are also very seemingly convincing arguments that most or all of the decreased severity in South Africa is due to prior infection and vaccination compared to earlier waves. We now know that plenty of people are getting sick in the UK from Omicron and seemingly many are ending up in hospital. Possible even worse many seem to be catching it in hospital (both staff and patients) and critical services in London already with escalating staff shortages…

    I can only hope it is spectacularly less lethal in the UK than Delta currently, or news really will be grim by Christmas.

  14. Oh dear. The paper I quoted last comment well things may not be as they seemed and perhaps Omicron really did grow just as well.

  15. Oh Just great


    SARS-CoV-2 infection and persistence throughout the human body and brain

    COVID-19 is known to cause multi-organ dysfunction in acute infection, with prolonged symptoms experienced by some patients, termed Post-Acute Sequelae of SARS-CoV-2 (PASC). However, the burden of infection outside the respiratory tract and time to viral clearance is not well characterized, particularly in the brain. We performed complete autopsies on 44 patients with COVID-19 to map and quantify SARS-CoV-2 distribution, replication, and cell-type specificity across the human body, including brain, from acute infection through over seven months following symptom onset. We show that SARS-CoV-2 is widely distributed, even among patients who died with asymptomatic to mild COVID-19, and that virus replication is present in multiple extrapulmonary tissues early in infection. Further, we detected SARS-CoV-2 RNA in multiple anatomic sites, including regions throughout the brain, for up to 230 days following symptom onset. Despite extensive distribution of SARS-CoV-2 in the body, we observed a paucity of inflammation or direct viral cytopathology outside of the lungs. Our data prove that SARS-CoV-2 causes systemic infection and can persist in the body for months.

  16. Covid obviously affecting the brain as Scotland loses ability to do basic arithmetic


    2,434 new cases of COVID-19 reported*
    52,022 new tests for COVID-19 that reported results*
    13.0% of these were positive

    * Public Health Scotland (PHS) are aware that today’s reported positive case numbers are lower than expected. PHS are investigating this, and will provide updates in future reports.

    I remember when 13% of 52,022 used to be 6,763

  17. This is very interesting. While I’d expected the measures in England would have reduced R I didn’t think that would be below 1.

    Don’t want to get my hopes up just yet but it is certainly interesting. Let’s hope it isn’t a testing limit or backlog

  18. Oh well that hope didn’t last long as back up again today.

    If behaviour changes have brought R substantially below 1 for Delta but still left Omicron above 1 perhaps a fast drop off in Delta masked the slower, but still ongoing march of Delta, with some testing capacity issues as well?

  19. Preliminary analysis from Edinburgh University suggests you are 2/3 less likely to be admitted to hospital with Omicron. There are so many caveats in the report and based on such small numbers that it could be completely misleading but I want to believe it. However if they are correct that would seem to imply that today’s London hospital admissions would have been closer to 900 (if same as Delta) than the 300 announced and no model was predicting anything like that just yet based on case lag.

    Report at https://www.research.ed.ac.uk/en/publications/severity-of-omicron-variant-of-concern-and-vaccine-effectiveness-

    Anyway latest UK Omicron hospital report. In England so far 195 hospitalizations and 18 deaths so far – and that’s backdated. There have been almost 1000 covid admissions to London hospitals in 4 days to 20th December and the ever increasing majority of these will be Omicron. UK daily Omicron report at https://www.gov.uk/government/publications/covid-19-omicron-daily-overview

  20. And Imperial looking at England data suggest a 15-20% reduced chance of hospitalisation compared to current Delta wave and 40-45% reduction in hospital stays over 1 day. Given that a lot of current infections are re-infections that Delta couldn’t re-infect but does reduce severity they calculate that the the actual reduction between risk of hospitalisation for someone not previously infected and not vaccinated is between 0 and 30%.

    So if that Imperial report is correct if you are not vaccinated and not yet infected, Omicron is at least almost as likely to send you to hospital as Delta with the added bonus it is far more likely to infect you soon. Not enough data yet to say anything about death rates.


    However, after adjusting estimates to account for only one in three reinfections being identified, the estimated difference in intrinsic hospitalisation risk (i.e. defined for primary infections in unvaccinated people) between Delta and Omicron is reduced (ie, 0-30% reduced risk of any hospitalisation) but the estimated reduction in risk of hospitalisation due to previous infection is increased (around 55-70% reduction

  21. As the news continues to bombard us with how mild Omicron is I find the common belief “but only 1 person has died WITH it in the UK not FROM it”

    Out of the first 668 identified Omicron hospital patients in England, 49 of them are already mildly dead.

  22. RIP Trowbridge H Ford


    Trowbridge Ford
    Died: July 26, 2021
    Trowbridge Harris Ford, professor and writer on British constitutional history as well as gadfly independent investigator, died peacefully at his home in New Haven, Connecticut on July 26, 2021. Trow was born in El Paso, TX, on November 9, 1929 to the late Brig. Gen. William Wallace Ford and Alice Trowbridge Harris Ford.

  23. Worth reading the entire quoted thread

  24. Meanwhile hospital covid deaths in South Africa continue to mildly pile up

    Total excess deaths in South Africa even worse at about 3,000 per week last 2 weeks.

  25. Bulgaria looks like it will be first country to pass the 1% of population dead mark in excess deaths. Currently at 0.87% and that’s before Omicron just starting there. Next is Russia at 0.74% then Novax Serbia at 0.71%. UK currently 0.22% USA 0.32%. Bulgaria’s Delta wave peaked at 2,000 excess deaths a week just a couple of months ago. That would be about equivalent to 20,000/week in UK by population ratio. Chart from https://www.nsi.bg/en/content/18121/basic-page/deaths-bulgaria-weeks

  26. But, but Sweden…


    Sweden rolls out new Covid restrictions to curb ‘record high’ infection rate

    Joined by Health Minister Lena Hallengren and the directors-general of the Public Health Agency and National Board of Health and Welfare at a press conference at noon, Andersson announced a several new restrictions to curb Sweden’s “record high spread of infection”.

    “It is undoubtedly the case that the situation has deteriorated. The spread of infection in Sweden is at historically high levels,” she said.

    The new rules, which will come into force on January 12th, will force bars and restaurants to close at 11pm. They also have to limit groups to eight people, seated at least a metre apart and only have table service, but vaccine passes will not be rolled out for restaurants at this stage.

    …”I want to strongly emphasise that everyone who can work from home should do so,” said Andersson.

    Indoor public events with more than 20 attendees will only be allowed to go ahead if everyone is seated and limited to groups of eight people, seated at least a metre apart. Public events with more than 50 attendees must additionally require a valid Covid vaccine pass.


    Swedish Crown Princess and Prince catch Covid-19 for the second time

    Sweden’s Crown Princess Victoria and her husband Prince Daniel have both tested positive for Covid-19 for the second time, although the pair have very mild cold symptoms.

    Sweden’s Royal Court announced that Prince Daniel had tested positive in a press release issued on Sunday, while Crown Princess Victoria’s second infection was revealed in another release on Saturday.

    The royal couple, who are both fully vaccinated, first tested positive for the virus in March last year, and have only mild symptoms.

  27. Preliminary analysis from New York does suggest Omicron is more severe in young children than previous variants

    Report at https://health.ny.gov/press/releases/2022/docs/pediatric_covid-19_hospitalization_report.pdf

  28. And in the UK

  29. Nobody seems to have told Omicron it isn’t supposed to kill people.


    Meanwhile South Africa excess deaths continue to run at about 3,000 per week for last 3 weeks. Now in normal times most countries running 30% excess deaths for 3 weeks would indicate a big problem but in the new normal – that’s mild apparently. Well I suppose if compared to their staggeringly bad previous waves…


  30. Maria Van Kerkhove, Infectious Disease Epidemiologist; COVID-19 Technical Lead @WHO, WHO Health Emergencies Programme says Omicron is not mild. Obviously she’s a fool because everyone else knows it is apparently.

  31. New data from South Africa finds Omicron likely has, for unvaccinated and previously uninfected adults, a 25% reduced risk of hospitalization or death within 14 days of admission compared to Delta but that it appears as intrinsically severe as their first “Wuhan” wave. That’s for adults – Data from South Africa and elsewhere continues to point to Omicron actually being more severe than Delta in under 12s.


    Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa

    Conclusions: In the Omicron-driven wave, severe COVID-19 outcomes were reduced mostly due to protection conferred by prior infection and/or vaccination, but intrinsically reduced virulence may account for an approximately 25% reduced risk of severe hospitalization or death compared to Delta.

    …Notwithstanding, the similarity in risk of admission suggests that in the absence of immunity, Omicron could be as severe as the ancestral strain.

    That fits with Imperial’s research.

    Omicron may not target the lungs as much (reduced ability to enhance entry with TMPRSS2 – relevant to lungs) but evidence appears to be growing that damage to heart, kidneys, post-infection diabetes, auto-immune disorders, long covid etc. is at least as bad as Delta and might even be worse due to enhanced fundamental ACE2 entry.

  32. https://www.nature.com/articles/s41590-021-01113-x?s=09

    Immunological dysfunction persists for 8 months following initial mild-to-moderate SARS-CoV-2 infection

    In summary, our data indicate an ongoing, sustained inflammatory response following even mild-to-moderate acute COVID-19, which is not found following prevalent coronavirus infection. The drivers of this activation require further investigation, but possibilities include persistence of antigen, autoimmunity driven by antigenic cross-reactivity or a reflection of damage repair. These observations describe an abnormal immune profile in patients with COVID-19 at extended time points after infection and provide clear support for the existence of a syndrome of LC (Long Covid). Our observations provide an important foundation for understanding the pathophysiology of this syndrome and potential therapeutic avenues for intervention.

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