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Gordo

Just curious, anyone have a plan, or preps for global pandemic?

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Public immunity to COVID-19 is probably higher than shown by antibody tests

 

New research from Karolinska Institutet and Karolinska University Hospital in Sweden shows that many people with mild or asymptomatic COVID-19 demonstrate so-called T-cell-mediated immunity to the new coronavirus, even if they have not tested positively for antibodies.

According to the researchers, this means that public immunity is probably higher than antibody tests suggest. The article is freely available on the bioRxiv preprint server and has been submitted for publication in a scientific journal.

"T cells are a type of white blood cells that are specialized in recognizing virus-infected cells, and are an essential part of the immune system," says Marcus Buggert, assistant professor at the Center for Infectious Medicine, Karolinska Institutet, and one of the paper's main authors.

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The UK government are looking at the connection between vitamin D and mortality from COVID-19.

https://www.theguardian.com/world/2020/jun/17/uk-ministers-order-urgent-vitamin-d-coronavirus-review

"It comes amid growing concern over the disproportionate number of black, Asian and minority ethnic people contracting and dying from the disease, including a reported 94% of all doctors killed by the virus."

I wonder if we're experiencing a reduction in mortality due to higher levels of vitamin D? Sounds simplistic, but I hope they get an answer soon. Maybe things could get much worse in the winter months.

 

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15 minutes ago, Matt said:

The UK government are looking at the connection between vitamin D and mortality from COVID-19.

LOL.  A bit late.  Scientists and public health policy officials have known that vitamin-D deficiency impacts the susceptibility to infections and outcomes, for decades now.

Here is an example paper from 2006, and there are many more:

Epidemic influenza and vitamin D

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35 minutes ago, Matt said:

The UK government are looking at the connection between vitamin D and mortality from COVID-19.

Matt,

That Guardian article was from last week. They have a story dated yesterday with the results of the review of the vitamin D and covid link. Here is the meat of the government report (pdf):

Effectiveness and safety

Evidence was from 5 published studies in peer-reviewed journals. One observational cohort study (D'Avolio et al. 2020), 3 observational prognostic studies involving published data sets using correlation or regression (Hastie et al. 2020, Ilie et al. 2020 and Laird et al. 2020) and 1 case-control survey (Fasano et al. 2020) looked retrospectively at the association between vitamin D status and development of COVID 19. None of the studies were intervention trials of vitamin D supplementation for the prevention or treatment of COVID-19.


Four of the studies found an association or correlation between a lower vitamin D status and subsequent development of COVID-19. However, confounders such as body mass index (BMI) or underlying health conditions, which may have independent correlations with vitamin D status or COVID-19, were not adjusted for (D'Avolio et al. 2020, Fasano et al. 2020, Ilie et al. 2020 and Laird et al. 2020). Vitamin D status was based on serum 25-hydroxyvitamin D (25(OH)D) levels in 3 studies and the proportion of participants taking a vitamin D supplement in 1 study. The largest UK study (Hastie et al. 2020) found an association between vitamin D status and COVID-19 only in a univariable analysis (with this single potential causative factor). Importantly, no causal relationship between vitamin D status and COVID-19 was found after adjustment for confounders such as comorbidity, socio-demographics, ethnicity, BMI and other baseline factors.

The evidence was pretty weak since there were no interventional studies.  So vitamin D can't be ruled out as effective against the virus. But the UK scientific establishment doesn't sound very optimistic.

--Dean

 

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This new paper [1] in Nature found 42.5% of people who tested positive in Vo' Italy never developed symptoms. These asymptomatic folks had just as high a viral load as symptomatic people. This is exactly the same percent of asymptomatic people I discussed here based on a study from China. 

--Dean 

---

[1] Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo’
Enrico Lavezzo, Elisa Franchin, […]Andrea Crisanti 
Nature (2020)

Abstract
On the 21st of February 2020 a resident of the municipality of Vo’, a small town near Padua, died of pneumonia due to SARS-CoV-2 infection1. This was the first COVID-19 death detected in Italy since the emergence of SARS-CoV-2 in the Chinese city of Wuhan, Hubei province2. In response, the regional authorities imposed the lockdown of the whole municipality for 14 days3. We collected information on the demography, clinical presentation, hospitalization, contact network and presence of SARS-CoV-2 infection in nasopharyngeal swabs for 85.9% and 71.5% of the population of Vo’ at two consecutive time points. On the first survey, which was conducted around the time the town lockdown started, we found a prevalence of infection of 2.6% (95% confidence interval (CI) 2.1-3.3%). On the second survey, which was conducted at the end of the lockdown, we found a prevalence of 1.2% (95% Confidence Interval (CI) 0.8-1.8%). Notably, 42.5% (95% CI 31.5-54.6%) of the confirmed SARS-CoV-2 infections detected across the two surveys were asymptomatic (i.e. did not have symptoms at the time of swab testing and did not develop symptoms afterwards). The mean serial interval was 7.2 days (95% CI 5.9-9.6). We found no statistically significant difference in the viral load of symptomatic versus asymptomatic infections (p-values 0.62 and 0.74 for E and RdRp genes, respectively, Exact Wilcoxon-Mann-Whitney test). This study sheds new light on the frequency of asymptomatic SARS-CoV-2 infection, their infectivity (as measured by the viral load) and provides new insights into its transmission dynamics and the efficacy of the implemented control measures.

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That study is pretty significant in that almost the entire community, a small town, was tested. So it might be considered a representative sample of the whole population (might, because conditions might be different in other areas). 42% asymptomatic sounds like a lot, close to half the infected population.

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2 hours ago, Dean Pomerleau said:

This new paper [1] in Nature found 42.5% of people who tested positive in Vo' Italy never developed symptoms.

This is actually a rather old study, from mid-April, and if I am not mistaken, it might have been posted here earlier. 

Suppression of COVID-19 outbreak in the municipality of Vo, Italy

This appears to deal with active infections, half of which are completely asymptomatic, which jives with other studies that show a similar lack of any symptoms among many of those with active infections.  Given that more recent results indicate a much wider prevalence of infections, as well as likely earlier spread (as early as March 2019?!), it raises the likelihood that a large portion of Vo' population has been exposed to the virus at some point.

More significant is the study from Karolinska Institutet and Karolinska University Hospital in Sweden, also posted above, which shows that infection rates may be much higher, as the antibodies tests fail to identify all those who have developed T-cell immunity, who for all we know, maybe the majority of those infected.

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Here is another study, from Germany, which supports the study from Karolinska Institutet and Karolinska University Hospital in Sweden on T-cell Covid-19 immunity.

SARS-CoV-2 T-cell epitopes define heterologous and COVID-19-induced T-cell recognition

This is the first work identifying and characterizing SARS-CoV-2-specific and cross-reactive HLA class I and HLA-DR T-cell epitopes in SARS-CoV-2 convalescents (n = 180) as well as unexposed individuals (n = 185) and confirming their relevance for immunity and COVID-19 disease course. SARS-CoV-2-specific T-cell epitopes enabled detection of post-infectious T-cell immunity, even in seronegative convalescents. Cross-reactive SARS-CoV-2 T-cell epitopes revealed preexisting T-cell responses in 81% of unexposed individuals, and validation of similarity to common cold human coronaviruses provided a functional basis for postulated heterologous immunity[9] in SARS-CoV-2 infection.

This one seems to use a different methodology and the Swedish study above found about 30% T-cell immunity in addition to those who had antibodies.  Either way, when combined with the recent models estimating 20%-45% immunity needed for herd immunity, this is very good news.

 

 

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Oops, did not notice your post, Gordo, I searched for the authors.

Anyway, maybe the below pertains too:

Estimation of Excess Deaths Associated With the COVID-19 Pandemic in the United States, March to May 2020
Daniel M. Weinberger, PhD1; Jenny Chen, BS2; Ted Cohen, MD, DPH1; Forrest W. Crawford, PhD3,4; Farzad Mostashari, MD5; Don Olson, MPH6; Virginia E. Pitzer, ScD1; Nicholas G. Reich, PhD7; Marcus Russi, BS1; Lone Simonsen, PhD8; Anne Watkins, BS1; Cecile Viboud, PhD2
Author Affiliations Article Information
JAMA Intern Med. Published online July 1, 2020. doi:10.1001/jamainternmed.2020.3391
https://sci-hub.tw/10.1001/jamainternmed.2020.3391
Key Points
Question  Did more all-cause deaths occur during the first months of the coronavirus disease 2019 (COVID-19) pandemic in the United States compared with the same months during previous years?
Findings  In this cohort study, the number of deaths due to any cause increased by approximately 122 000 from March 1 to May 30, 2020, which is 28% higher than the reported number of COVID-19 deaths.
Meaning  Official tallies of deaths due to COVID-19 underestimate the full increase in deaths associated with the pandemic in many states.
Abstract
Importance  Efforts to track the severity and public health impact of coronavirus disease 2019 (COVID-19) in the United States have been hampered by state-level differences in diagnostic test availability, differing strategies for prioritization of individuals for testing, and delays between testing and reporting. Evaluating unexplained increases in deaths due to all causes or attributed to nonspecific outcomes, such as pneumonia and influenza, can provide a more complete picture of the burden of COVID-19.
Objective  To estimate the burden of all deaths related to COVID-19 in the United States from March to May 2020.
Design, Setting, and Population  This observational study evaluated the numbers of US deaths from any cause and deaths from pneumonia, influenza, and/or COVID-19 from March 1 through May 30, 2020, using public data of the entire US population from the National Center for Health Statistics (NCHS). These numbers were compared with those from the same period of previous years. All data analyzed were accessed on June 12, 2020.
Main Outcomes and Measures  Increases in weekly deaths due to any cause or deaths due to pneumonia/influenza/COVID-19 above a baseline, which was adjusted for time of year, influenza activity, and reporting delays. These estimates were compared with reported deaths attributed to COVID-19 and with testing data.
Results  There were approximately 781 000 total deaths in the United States from March 1 to May 30, 2020, representing 122 300 (95% prediction interval, 116 800-127 000) more deaths than would typically be expected at that time of year. There were 95 235 reported deaths officially attributed to COVID-19 from March 1 to May 30, 2020. The number of excess all-cause deaths was 28% higher than the official tally of COVID-19–reported deaths during that period. In several states, these deaths occurred before increases in the availability of COVID-19 diagnostic tests and were not counted in official COVID-19 death records. There was substantial variability between states in the difference between official COVID-19 deaths and the estimated burden of excess deaths.
Conclusions and Relevance  Excess deaths provide an estimate of the full COVID-19 burden and indicate that official tallies likely undercount deaths due to the virus. The mortality burden and the completeness of the tallies vary markedly between states.

 

Excess Deaths From COVID-19 and Other Causes, March-April 2020
Steven H. Woolf, MD, MPH1; Derek A. Chapman, PhD1; Roy T. Sabo, PhD2; et alDaniel M. Weinberger, PhD3; Latoya Hill, MPH1
Author Affiliations Article Information
JAMA. Published online July 1, 2020. doi:10.1001/jama.2020.11787
https://jamanetwork.com/journals/jama/fullarticle/2768086?guestAccessKey=a41c1ad0-ef8f-41aa-b478-e3eff3f1e566&utm_source=silverchair&utm_campaign=jama_network&utm_content=covid_weekly_highlights&utm_medium=email
https://sci-hub.tw/10.1001/jama.2020.11787

Edited by AlPater

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Of course. total death rates include those who died from non-Covid causes who were two afraid to go to a hospital -- and also suicides.

  --  Saul

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1
1 hour ago, AlPater said:

Findings  In this cohort study, the number of deaths due to any cause increased by approximately 122 000 from March 1 to May 30, 2020, which is 28% higher than the reported number of COVID-19 deaths....

Conclusions and Relevance  Excess deaths provide an estimate of the full COVID-19 burden and indicate that official tallies likely undercount deaths due to the virus. The mortality burden and the completeness of the tallies vary markedly between states.

Well, well....  This is a study that seeks a headline and presents the data accordingly (and in fact it made headlines in all the major media). 

It picks a period that is generally marked by a declining mortality rate, as the "flu" season, which accounts for a large portion of the annual deaths, especially among the elderly, usually peaks between December and early February.  I don't feel like pulling the data for the US to show the manipulative nature of this, but here is what I had posted for the EU, which applies to this nonsense as well:
 

 
 
 
1
 
 
 
1
On 6/29/2020 at 5:55 PM, Ron Put said:

Let's look at the select EU data on excess mortality which is used by FT.  Hover over the current week 25 for 2016 and the cumulative excess mortality is 31, 516.  Hover over the same week in 2018 and the excess mortality is 104, 002, showing an increase of 72,486.  Now hover over the same week in 2020 and the excess mortality is 194,745 (unadjusted), showing an increase of 90, 514.  So far, that's an increase difference of just over 18,000 compared to the 2018 increase.

Now, compare the above numbers to the aggregate number of annual deaths in the EU for 2016, which is 5,100,000.  Note that respiratory diseases accounted for 8% of these 5.1 million deaths, or 422,000 deaths.  This can be adjusted for the reporting countries above, as well as for population growth, but I hope that you get the point I am trying to make.  

We should also keep in mind that approximately 6 million people die annually in the US, so we should keep the 60,000 or so excess death in perspective.

Just as importantly, reported deaths from strokes and heart attacks are way, way down, which suggests that many who were frightened by the media and their "leaders" and skipped going to the emergency room, and then died in their homes, ended up counted as "possible" Covid-19 deaths.

This politicized mess will take years to clean up, assuming that an impartial body does the final tally.

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From the CovidTrackingProject:

Hospitalization_Social__8_.png?w=900&fl=

timeline-death-lag__2_.jpg?w=1600&h=450&

image__14_.png?w=1990&h=1340&q=50

But there’s reason to hope that hospital mortality rates are declining. That’s the news from Milan, where hospital fatality rates fell from 24 percent to 2 percent from March to May (and the percentage of hospitalized patients who needed to be admitted to intensive care units also dropped). In England, the hospital fatality rate fell from 6 percent in April to 1.5 percent in June.

Researchers have suggested a variety of reasons for this decline in hospital deaths. The authors of the Milan paper suggested several factors, including a better understanding of the disease’s effects, a reduction in the severity of the local outbreak, and a decline in simultaneous infections with seasonal illnesses. “Patients with COVID-19 in late March and early April included a significant proportion of patients who caught the infection in hospital,” the authors of the British Medical Journal report on the decline in hospital mortality rate in England wrote. “These patients, because they were in hospital, were more likely to be sicker and more vulnerable than patients who acquired infection in the community and so more likely to die from COVID-19.” 

But as the share of patients with infections from community transmission increases, the mortality rate has still declined. Several factors might explain this: Current patients are younger and less likely to die, hospitals are admitting less severe cases because more beds are available, and doctors and nurses have learned from experience. Bob Wachter, chair of the University of California-San Francisco Department of Medicine, posted a list of “Things We’ve Gotten Better At Since March”; it includes a number of improvements that could affect in-hospital mortality, such as better monitoring of vital signs and a more effective use of prone (face-down) positioning, which has been observed to improve oxygen levels in severely ill COVID-19 patients.

We still don’t know how the death curve will respond to increasing hospitalizations in the United States. In certain states, the rise in hospitalizations has been very sharp. Between June 2 and July 2 in Arizona, the number of people hospitalized with COVID-19 rose from 1009 to 2,938. During the same period in California, COVID-19 hospitalizations rose from 4,393 to 6,812. For the same dates In Texas, COVID-19 hospitalizations jumped from 1,773 to 7,382. 

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And this, from saner times, before the politicization of epidemics:

Can surgical masks protect you from getting the flu?

"Basically, there is no strong evidence to support well people wearing surgical masks in public. Or as the US Centers for Disease Control and Prevention put it: "No recommendation can be made at this time for mask use in the community by asymptomatic persons, including those at high risk for complications, to prevent exposure to influenza viruses."

The best thing you can do to stop getting the flu is to regularly wash your hands, and try to avoid touching your face."

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1 hour ago, Gordo said:

From the CovidTrackingProject:

Hospitalization_Social__8_.png?w=900&fl=

timeline-death-lag__2_.jpg?w=1600&h=450&

image__14_.png?w=1990&h=1340&q=50

But there’s reason to hope that hospital mortality rates are declining. That’s the news from Milan, where hospital fatality rates fell from 24 percent to 2 percent from March to May (and the percentage of hospitalized patients who needed to be admitted to intensive care units also dropped). In England, the hospital fatality rate fell from 6 percent in April to 1.5 percent in June.

Researchers have suggested a variety of reasons for this decline in hospital deaths. The authors of the Milan paper suggested several factors, including a better understanding of the disease’s effects, a reduction in the severity of the local outbreak, and a decline in simultaneous infections with seasonal illnesses. “Patients with COVID-19 in late March and early April included a significant proportion of patients who caught the infection in hospital,” the authors of the British Medical Journal report on the decline in hospital mortality rate in England wrote. “These patients, because they were in hospital, were more likely to be sicker and more vulnerable than patients who acquired infection in the community and so more likely to die from COVID-19.” 

But as the share of patients with infections from community transmission increases, the mortality rate has still declined. Several factors might explain this: Current patients are younger and less likely to die, hospitals are admitting less severe cases because more beds are available, and doctors and nurses have learned from experience. Bob Wachter, chair of the University of California-San Francisco Department of Medicine, posted a list of “Things We’ve Gotten Better At Since March”; it includes a number of improvements that could affect in-hospital mortality, such as better monitoring of vital signs and a more effective use of prone (face-down) positioning, which has been observed to improve oxygen levels in severely ill COVID-19 patients.

We still don’t know how the death curve will respond to increasing hospitalizations in the United States. In certain states, the rise in hospitalizations has been very sharp. Between June 2 and July 2 in Arizona, the number of people hospitalized with COVID-19 rose from 1009 to 2,938. During the same period in California, COVID-19 hospitalizations rose from 4,393 to 6,812. For the same dates In Texas, COVID-19 hospitalizations jumped from 1,773 to 7,382

Thanks Gordo, I have been wondering about this so this post really got my attention. As we learn more let’s hope we can make progress against this little bastard! This article seems to suggest that may already be happening!

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Hi Mike!

Probably an over-vigorous immune cell response  --  aka inflammation -- may be more relevant, as this often leads to blood clot formation -- which is a stroke, when it occurs in blood vessels in the brain.

Uncontrolled hypertension is of course a negative.

  --  Saul

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recalling what had been vigorously debated:

https://www.nytimes.com/2020/07/07/business/sweden-economy-coronavirus.html?referringSource=articleShare

The data in The Norwegian countries does not, at this point, support those who argued for opening up the economies.

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