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Thread: Modeling coronavirus spread, or why are there different numbers of expected deaths?

  1. #61
    tWebber shunyadragon's Avatar
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    I looked more closely at the reports of possible 'herd immunity' in California, and found them inconclusive. I consider it a greater possibility in the Orient, but at present awaiting further extensive testing and research. Stanford University is proposing extensive testing in California to determine the extent of COVAG 19 virus infection.
    Last edited by shunyadragon; 04-13-2020 at 08:19 AM.
    Glendower: I can call spirits from the vasty deep.
    Hotspur: Why, so can I, or so can any man;
    But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

    go with the flow the river knows . . .

    Frank

    I do not know, therefore everything is in pencil.

  2. #62
    tWebber shunyadragon's Avatar
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    New genetic research narrows down the most likely source of the COVAG-19 Virus that caused the pandemic.
    Source: https://www.sciencedaily.com/releases/2020/03/200326144342.htm



    Missing link in coronavirus jump from bats to humans could be pangolins, not snakes

    As scientists scramble to learn more about the SARS-CoV-2 coronavirus, two recent studies of the virus' genome reached controversial conclusions: namely, that snakes are intermediate hosts of the new virus, and that a key coronavirus protein shares "uncanny similarities" with an HIV-1 protein. Now, a study in ACS' Journal of Proteome Research refutes both ideas and suggests that scaly, anteater-like animals called pangolins are the missing link for SARS-CoV-2 transmission between bats and humans.

    Understanding where SARS-CoV-2 -- the virus that caused the COVID-19 pandemic -- came from and how it spreads is important for its control and treatment. Most experts agree that bats are a natural reservoir of SARS-CoV-2, but an intermediate host was needed for it to jump from bats to humans.

    A recent study that analyzed the new virus' genome suggested snakes as this host, despite the fact that coronaviruses are only known to infect mammals and birds. Meanwhile, an unrelated study compared the sequence of the spike protein -- a key protein responsible for getting the virus into mammalian cells -- of the new coronavirus to that of HIV-1, noting unexpected similarities. Although the authors withdrew this preprint manuscript after scientific criticism, it spawned rumors and conspiracy theories that the new coronavirus could have been engineered in a lab. Yang Zhang and colleagues wanted to conduct a more careful and complete analysis of SARS-CoV-2 sequences to resolve these issues.

    Compared to the previous studies, the researchers used larger data sets and newer, more accurate bioinformatics methods and databases to analyze the SARS-CoV-2 genome. They found that, in contrast to the claim that four regions of the spike protein were uniquely shared between SARS-CoV-2 and HIV-1, the four sequence segments could be found in other viruses, including bat coronavirus.

    After uncovering an error in the analysis that suggested snakes as an intermediate host, the team searched DNA and protein sequences isolated from pangolin tissues for ones similar to SARS-CoV-2. The researchers identified protein sequences in sick animals' lungs that were 91% identical to the human virus' proteins. Moreover, the receptor binding domain of the spike protein from the pangolin coronavirus had only five amino acid differences from SARS-CoV-2, compared with 19 differences between the human and bat viral proteins. This evidence points to the pangolin as the most likely intermediate host for the new coronavirus, but additional intermediate hosts could be possible, the researchers say.

    The authors acknowledge funding from the National Science Foundation, the National Institute of General Medical Sciences, the National Institute of Allergy and Infectious Diseases and the Extreme Science and Engineering Discovery Environment.

    © Copyright Original Source

    Glendower: I can call spirits from the vasty deep.
    Hotspur: Why, so can I, or so can any man;
    But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

    go with the flow the river knows . . .

    Frank

    I do not know, therefore everything is in pencil.

  3. #63
    tWebber shunyadragon's Avatar
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    By the way the fatality rate from country to country and region to region in the West is more correlated to the elderly age percentage and vulnerability of the population then any difference in the efforts of the individual countries implemented to reduce impact of the COVAG-19 pandemic. Northern Italy has the highest average age than most countries. at 79.9 See: https://ourworldindata.org/coronavirus
    Glendower: I can call spirits from the vasty deep.
    Hotspur: Why, so can I, or so can any man;
    But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

    go with the flow the river knows . . .

    Frank

    I do not know, therefore everything is in pencil.

  4. #64
    tWebber shunyadragon's Avatar
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    There are distinct differences in the percentage of the population in different countries and regions that have been infected by COVID 19: (1) the traffic pattern of humanity shows how the spread hit certain ares first, such as large cities where particularly travel from the Orient was dominant. (2) The percentage of the elderly and vulnerable population. Northern Italy has the probably the highest percentage of elderly and vulnerable in the world, and it had the highest percentage of cases and fatalities. (3) The health of the elderly population, with the Orient has the healthiest elderly population.

    There is the 'other' more controversial cause of the percentage of the population infected by the COVID 19 Virus, and that is the long term regional 'herd immunity' and co-evolution of the host population and the virus in the endemic source region or country of origin. I posted a research article before that documented the coevolution immunity in regional population. These factors do possible explain some of the differences in the percentage of infection rates in different regions and countries of th world.

    Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945372/



    Mortality patterns associated with the 1918 influenza pandemic in Mexico: evidence for a spring herald wave and lack of pre-existing immunity in older populations
    Gerardo Chowell,1,2 Cécile Viboud,2 Lone Simonsen,2,3 Mark A. Miller,2 and Rodolfo Acuna-Soto4

    Abstract
    Background
    While the mortality burden of the devastating 1918 influenza pandemic has been carefully quantified in the US, Japan, and European countries, little is known about the pandemic experience elsewhere. Here, we compiled extensive archival records to quantify the pandemic mortality patterns in two Mexican cities, Mexico City and Toluca.

    Methods
    We applied seasonal excess mortality models to age-specific respiratory mortality rates for 1915–1920 and quantified the reproduction number from daily data.

    Results
    We identified 3 pandemic waves in Mexico City in spring 1918, fall 1918, and winter 1920, characterized by unusual excess mortality in 25–44 years old. Toluca experienced 2-fold higher excess mortality rates than Mexico City, but did not have a substantial 3rd wave. All age groups including those over 65 years experienced excess mortality during 1918–20. Reproduction number estimates were below 2.5 assuming a 3-day generation interval.

    Conclusion

    Mexico experienced a herald pandemic wave with elevated young adult mortality in spring 1918, similar to the US and Europe. In contrast to the US and Europe, there was no mortality sparing in Mexican seniors, highlighting potential geographical differences in pre-existing immunity to the 1918 virus. We discuss the relevance of our findings to the 2009 pandemic mortality patterns.

    Prior immunity helps to explain wave-like behaviour of pandemic influenza in 1918-9.

    Mathews JD1, McBryde ES, McVernon J, Pallaghy PK, McCaw JM.
    Author information
    Abstract
    BACKGROUND:
    The ecology of influenza may be more complex than is usually assumed. For example, despite multiple waves in the influenza pandemic of 1918-19, many people in urban locations were apparently unaffected. Were they unexposed, or protected by pre-existing cross-immunity in the first wave, by acquired immunity in later waves, or were their infections asymptomatic?

    METHODS:
    We modelled all these possibilities to estimate parameters to best explain patterns of repeat attacks in 24,706 individuals potentially exposed to summer, autumn and winter waves in 12 English populations during the 1918-9 pandemic.

    RESULTS:
    Before the summer wave, we estimated that only 52% of persons (95% credibility estimates 41-66%) were susceptible, with the remainder protected by prior immunity. Most people were exposed, as virus transmissibility was high with R0 credibility estimates of 3.10-6.74. Because of prior immunity, estimates of effective R at the start of the summer wave were lower at 1.57-3.96. Only 25-66% of exposed and susceptible persons reported symptoms. After each wave, 33-65% of protected persons became susceptible again before the next wave through waning immunity or antigenic drift. Estimated rates of prior immunity were less in younger populations (19-59%) than in adult populations (38-66%), and tended to lapse more frequently in the young (49-92%) than in adults (34-76%).

    CONCLUSIONS:
    Our model for pandemic influenza in 1918-9 suggests that pre-existing immune protection, presumably induced by prior exposure to seasonal influenza, may have limited the pandemic attack-rate in urban populations, while the waning of that protection likely contributed to recurrence of pandemic waves in exposed cities. In contrast, in isolated populations, pandemic attack rates in 1918-9 were much higher than in cities, presumably because prior immunity was less in populations with infrequent prior exposure to seasonal influenza. Although these conclusions cannot be verified by direct measurements of historical immune mechanisms, our modelling inferences from 1918-9 suggest that the spread of the influenza A (H1N1) 2009 pandemic has also been limited by immunity from prior exposure to seasonal influenza. Components of that immunity, which are measurable, may be short-lived, and not necessarily correlated with levels of HI antibody.

    © Copyright Original Source

    Glendower: I can call spirits from the vasty deep.
    Hotspur: Why, so can I, or so can any man;
    But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

    go with the flow the river knows . . .

    Frank

    I do not know, therefore everything is in pencil.

  5. #65
    tWebber
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    https://thediplomat.com/2020/04/covi...e-japan-model/

    Japan has a large elderly population---it is practicing limited (Short)partial lockdowns but otherwise using a cluster-based approach---containing the infected clusters.
    the approach may be workable in Japan because people have been regularly using masks ---the country has a regular flu season and close exposure to China so gets hit with respiratory illnesses coming out of China....
    If Japan is any indication of the future---then masks and social distancing are here to stay from here on out....but lockdowns are not workable longterm solutions to future epidemics/pandemics....

    pneumonia from flu or other respiratory illness such as Sars etc can be caused by the cytokine storm---an over-reaction of our immune system to the virus.
    https://www.newscientist.com/term/cytokine-storm/

    Indonesian citizens are taking matters into their own hands and trying to find ways to survive....
    https://thediplomat.com/2020/04/indo...ld-is-missing/

    Korea, Taiwan etc are relying on tracing and containing measures to limit spread to manageable levels.
    If spread is not "managed" it can overwhelm healthcare systems.

  6. #66
    tWebber shunyadragon's Avatar
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    More daily data is making the progress of the CVOD 19 pandemic clearer. The USA is over the hump of the peak in late April, and in gradual recovery like China did and recovered, and France and other European countries. Russia's bumpy peak will be in a week or so. The paths of the viruses are closely related to when each region or country was first infected, and they are approaching the peak and going over in the order they were infected.

    See this cite for the latest data: https://ourworldindata.org/coronavir...HN+FRA+DEU+KOR.
    Last edited by shunyadragon; 04-29-2020 at 05:04 PM.
    Glendower: I can call spirits from the vasty deep.
    Hotspur: Why, so can I, or so can any man;
    But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

    go with the flow the river knows . . .

    Frank

    I do not know, therefore everything is in pencil.

  7. #67
    tWebber Roy's Avatar
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    Quote Originally Posted by shunyadragon View Post
    I realize there are only estimates without firm figures in the number of cases, and particularly in China the deliberate underreporting under reporting of fatalities and cases.
    Nonetheless my one BIG concern now is the outrageous fear based figures put out by Fauci concerning fatality estimates of 100,000 to as much as 240,000.
    Not fear based after all.
    Jorge: Functional Complex Information is INFORMATION that is complex and functional.

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  8. #68
    tWebber TheLurch's Avatar
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    Quote Originally Posted by Roy View Post
    Not fear based after all.
    Yeah, that post has certainly not aged well.
    "Any sufficiently advanced stupidity is indistinguishable from trolling."

  9. #69
    tWebber shunyadragon's Avatar
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    Quote Originally Posted by Roy View Post
    Not fear based after all.
    I admit my estimate of cases and fatalities were to low, but my predictions concerning the curve of the virus infection were accurate. I anticipated a better organized effort to consistently control the spread of the Pandemic when compared to other countries that were infected earlier.. I was wrong.

    To add: I did not know Trump refused to accelerate the manufacture of PPE, and thought Fauci was more in control of the government efforts.
    Last edited by shunyadragon; 05-17-2020 at 05:47 PM.
    Glendower: I can call spirits from the vasty deep.
    Hotspur: Why, so can I, or so can any man;
    But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

    go with the flow the river knows . . .

    Frank

    I do not know, therefore everything is in pencil.

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