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Forum: COVID-19
Last Post: M_T
10 hours ago
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Wastewater & a possible p...
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New variant: omicron
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It ain't over
Forum: COVID-19
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01-11-2022, 03:22 AM
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Hospitalization (Omicron)
Forum: COVID-19
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Forum: COVID-19
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  Reproduction numbers of different variants in US
Posted by: M_T - 12-12-2021, 04:51 PM - Forum: Research - No Replies

(This does not include Omicron)
SARS-CoV-2 variant dynamics across US states show consistent differences in effective reproduction numbers

Quote:Here, we extend methods for inferring the effective reproduction number of an epidemic using confirmed case data to jointly estimate variant-specific effective reproduction numbers and frequencies of co-circulating variants using case data and genetic sequences across states in the US from January to October 2021. 

The reproductive number is affected by numerous factors: variant, population density, size of families, steps taken to reduce spread, adherence to those steps, completeness of infection numbers.  This group tries to compute this and to pull out the reproduction number for each variant, and then to compute a fixed growth advantage for each variant.   I'm trying to understand the state-to-state differences.

In other (colorful!) graphs in the paper they show the time-varying R for the variants.

[Image: COVID-R-by-Variant.png]

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  Estimates of Vaccine Effectiveness against Omicron hospitalization, etc.
Posted by: M_T - 12-12-2021, 04:33 PM - Forum: Research - No Replies

Estimates of reduced vaccine effectiveness against hospitalization, infection, 
transmission and symptomatic disease of new SARS-CoV-variant, Omicron 
(B.1.1.529), using neutralizing antibody 

Quote:Omicron increased the risk of hospitalization four to five-fold and increased the risk of symptomatic disease seven to ten-fold for mRNA vaccinees, with similar relative effects for recently vaccinated, or individuals with waned antibody titers. Third doses restored titers and protection to levels similar to waned immunity against Delta. Overall, these analyses indicate that vaccine effectiveness against severe disease is significantly diminished for waned individuals, and protection against infection, symptomatic disease and transmission is nearly eliminated. However, third doses significantly ameliorate these reductions but only restore protection to levels equivalent to waned protection against the Delta variant. The invasion of Omicron is likely to result in widespread infection, and substantial hospitalizations unless widespread boosting of immunity occurs.
(bold and italics are mine)

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  Natural&Vaccine-produced Antibodies against variants including Omicron
Posted by: M_T - 12-12-2021, 04:25 PM - Forum: Research - No Replies

SARS-CoV-2 B.1.1.529 variant (Omicron) evades neutralization by sera from vaccinated and convalescent individuals

Quote:Neutralization capacity against B.1.1.529 [Omicron] was maintained best against sera from super immune individuals (infected and vaccinated or vaccinated and infected).

Vaccines & natural immunity versus Alpha, Beta, Delta, Omicron.  This shows the neutralization for various vaccines or prior infections against Alpha, Beta, or  Delta.   It doesn't look great.  Best was for people that got sick & then vaccinated; followed by those that got sick after vaccination.

Spikevax = Moderna
ChAdOx1 = AstraZeneca
BNT162b2 = Pfizer
ChAdOx1/BNT162b2  means full vaccination with AZ and a Pfizer booster.
B.1.1.7 = Alpha (UK variant)
B.1.351 = Beta (South Africa)
B.1.617.2 = Delta
B.1.1.529 = Omicron

Higher numbers indicate better immunity.

[Image: COVIDab-Rossler.png]

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  Antibodies for vaccinated with/without natural infection
Posted by: M_T - 12-12-2021, 04:04 PM - Forum: Research - Replies (5)

Delta breakthrough infections elicit potent, broad and durable neutralizing antibody responses

Quote:However,  we  show  that  Delta  breakthrough  cases,  subjects  who  were  vaccinated  after  
SARS-CoV-2  infection  and  individuals  vaccinated  three  times  (without  infection)  have  
serum  neutralizing  activity  of  comparable  magnitude  and  breadth  indicate  that  multiple  
types of exposure or increased number of exposures to SARS-CoV-2 antigen(s) enhance 
spike-specific antibody responses.

Graph A shows the  level of antibodies over time (30, 60, ... days)
B, C, and D show different kinds antibodies at the same time (shortly after infection or vaccination)

A thru D are measures of how effective the antibodies were against one particular culture of COVID.
E and F are the same  graph as D but against two other cultures of COVID.

In each graph are different groups of people.  Purple triangles are vaccinated people that got Delta (so probably recently).
The cyan diamonds are people who were infected with COVID (original or other) and then got vaccinated.
The orange circles are people who have been vaccinated but not had COVID.
The gray squares are people that were infected (in WA in 2020) but not vaccinated.
The white circles are people that were not vaccinated and not had COVID.
2X means two vaccinations.  3X means three vaccinations

[Image: COVIDab-Walls.png]

Quote:Figure 1: Repeated exposures to  SARS-CoV-2 antigens through  vaccination  or infection enhance S-specific serum IgG and IgA binding titers. 

(A) Serum IgG binding titers at 30 or 60 days post infection or 10, 112, or 180 days post second or third vaccine dose were evaluated
for longitudinal samples by ELISA using prefusion-stabilized SARS-CoV-2 S Hexapro as
antigen. Serum samples were obtained from  individuals who had a Delta breakthrough infection
(n=15, magenta triangle), were previously infected then vaccinated (n=15, teal diamond), have
only  been  vaccinated  (n=15,  orange circle),  were  infected in  2020 in Washington  State  (n=15,
gray  square),  or  were  SARS-CoV-2  naive  (samples  taken  prior  to  vaccination,  n=15,  open

(B)  Serum  IgA  binding  titers  at  30  days  post  infection  or  10  days  post  second
vaccine  dose  were  evaluated  by  ELISA  using  prefusion-stabilized  SARS-CoV-2  S  Hexapro  as

© Serum IgM binding titers at 30 days post infection or 10 days post second vaccine
dose  were evaluated by ELISA using prefusion-stabilized SARS-CoV-2 S Hexapro as antigen. 

(D) Serum  IgG binding titers were evaluated by ELISA at 30 days post infection, 10 days post 
second  or  third    vaccine  dose  or  prior  to  SARS-CoV-2  exposure  (SARS-CoV-2  naive)  using  
prefusion-stabilized SARS-CoV 2P S as antigen. 

(E-F) Serum IgG binding titers were evaluated 
at 30 days post infection,  10 days post second or third vaccine dose, or prior to SARS-CoV-2 
exposure (SARS-CoV-2 naive) by ELISA using OC43 S (E) or HKU1 2P S (F) as antigen. # of 
doses:  number  of  vaccine  doses  received. 

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  Your brain on COVID-19
Posted by: M_T - 12-06-2021, 01:14 PM - Forum: COVID-19 - Replies (2)

A couple of not-yet-reviewed studies on effects on the brain related to COVID-19 infection.
  "Brain imaging before and after COVID-19 in UK Biobank"
    Posted in August.  Comparison of brain scans of 401 patients (and 384 controls) where brain scans had been done before infection.
    Post-COVID, there was a reduction in grey matter thickness in some areas, markers of tissue damage, decrease in brain size.

Quote:These brain imaging results may be the in vivo hallmarks of a degenerative spread of the disease — or of the virus itself — via olfactory pathways (a possible entry point of the virus to the central nervous system being via the olfactory mucosa), or of neuroinflammatory events due to the infection, or of the loss of sensory input due to anosmia. 

"Brain Injury in COVID-19 is Associated with Autoinflammation and Autoimmunity"

Quote:During hospitalisation, patients with COVID-19 demonstrated elevations of NfL and GFAP in a severity-dependant manner, and there was evidence of ongoing active brain injury at follow-up 4 months later. Raised NfL and GFAP were associated with both elevations of pro-inflammatory cytokines and the presence of autoantibodies; autoantibodies were commonly seen against lung surfactant proteins as well as brain proteins such as myelin associated glycoprotein, but reactivity was seen to a large number of different antigens. Furthermore, a distinct process characterised by elevation of serum total Tau was seen in patients at follow-up, which appeared to be independent of initial disease severity and was not associated with dysregulated immune responses in the same manner as NfL and GFAP.

Stay well.

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  Weather & COVID
Posted by: M_T - 12-04-2021, 03:37 AM - Forum: COVID-19 - Replies (1)

New Hampshire is #1 in cases/100K in the last week at 539.5.
New Hampshire is #1 in vaccination rate at 88.5% of the total population having had at least one vaccination.

Cases/100K population in last 7 days
[Image: COVIDcase-Rate20211203.png]
To me, this looks like the weather map, showing a cold front coming down from the north.  Maybe the outdoor temperature or the side-effects of cold weather (indoors; heating with little recycling of air; wood smoke somehow helping the virus to get into airways) are contributing to this.

Vaccination rate:[Image: COVIDvac-Rate20211203.png]

ME, NH, VT, MA, CT, RI, PA are the states with > 80% vaccination (of total population)
NJ is 79.7%, CA is 79.3%, NY is 78.8%  Every other state is lower.

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  Booster Hesitancy
Posted by: ChrisGreene - 12-03-2021, 08:37 AM - Forum: Vaccine - Replies (1)

My wife, 58, did not want to get the booster because she felt extremely sick for two days after the second dose. The symptoms were all extreme and included nausea and weakness. Only at the end of the second day could she hold down water, in the form of ice chips that I would feed to her every few minutes. (Doctor's recommendation).

After the Omicron thing I asked her to speak to her doctor about the booster. The doctor recommended it and also prescribed anti-nausea medicine. It made my wife say she will schedule a shot. So if you know someone who is hesitant to get a booster due to a previous reaction, a conversation with their physician may be helpful. 

Are there cases where boosters are contra indicated?

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  It ain't over
Posted by: M_T - 11-28-2021, 04:17 AM - Forum: COVID-19 - Replies (2)

We grow tired of a constant fight.  However,  ....

As of November 2021, Europe's number one cause of death is COVID.

Here are the current world and US levels of COVID weekly cases and deaths. 
I wouldn't count on the cases being actual, but the deaths are probably closer.
The fact that the number of cases in the US is on the rise means that deaths will
soon be on the rise.  But for now, there are just over 50,000 COVID deaths a week in the
world, with approximately 8,000 COVID deaths a week in the US (out of a normal 60K deaths).

[Image: Covid20211128.png]
(Sorry, the right-hand side of the thumbnail is truncated.  Click on it to see the full image.)

Approximately the middle of each graph is where vaccines first came available.

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  New variant: omicron
Posted by: Hurlburt88 - 11-26-2021, 11:52 AM - Forum: COVID-19 - Replies (24)

I think the latest variant is referred to by "omicron" although yesterday morning one article called it "nu".   Potentially more transmissible and with 50 mutations some concern about evading established immunity--although one article this morning implied that the vast majority of hospitalized cases in South Africa are unvaccinated persons.   To me it will be interesting to see if it fizzles or if it truly takes hold and challenges delta's current dominance.   I am also interested if it gives rise to boosters tweaked to this variant.


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  Detox after vaccination
Posted by: Hurlburt88 - 11-13-2021, 09:24 AM - Forum: Humor - Replies (1)


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