Neither In Nor Out

https://science.sciencemag.org/content/368/6493/808
Links to an article in Science magazine about modeling disease spread. The authors, from the London School of Hygiene write about the k number, which is as important as the much-discussed R number, as reflects the dispersal of the virus. The lower the k number, the smaller the number of people the virus spreads from. The flu had a k number of 1 but SARS and MERS had a much lower k number reflecting that infection clusters played less of a role in flu. An estimate of the k number of Covid-19 is 0.1, meaning that 10% of the cases lead to about 80% of the spread. Another estimate from this number is that the virus has to be introduced undetected into a new country at least 4 times before it establishes itself. Patients' characteristics also have a role to play in that some patients will shed virus more virus for a longer period time than others.

https://www.nytimes.com/2020/05/27/health/coronavirus-spread-united-states.html
This is a Carl Zimmer article from the NYT about the spread of the coronavirus in US. A computational biologist from Scripps Institute an evolutionary biology from the U of Arizona and a geneticist at Hutchinson, are quoted in the article. A new analysis of the genomes of coronavirus established that the first case, called WA1 and the second case, WA2, different in 2 mutations. It would have been about 6 weeks to accumulate those mutations and it is believed that the virus circulated in Washington for six weeks but it is likely that it would have taken more than six weeks to accumulate 2 mutations since the coronavirus mutates slowly. A computer modeling experiment showed that the WA1 couldn't have seeded the outbreak there.  The implication was that the WA2 was introduced in Washington by travelers from China, meaning that the epidemic was set off by the WA2, after Trump's travel ban from China. They went over the Italian outbreak the same way. The implication is that the epidemics were seeded later than previously believed and that there was time to take advantage of the delay before the virus took off by testing and contact tracing.

https://geneticliteracyproject.org/2020/05/29/viewpoint-believing-that-well-have-a-coronavirus-vaccine-anytime-soon-is-naive-at-best/ This is a link to an opinion in the Genetic Literacy Project, written by a senior fellow of the Pacific Research Institute. Operation Warp Speed notwithstanding, it is unlikely that we will have a Covid-19 vaccine inside of a year, or even a year-and-a-half. The history of vaccines describes obtaining pus from smallpox and using it as the inoculum. It’s actually much more complicated as the opinion describes. How much of the vaccine should be in each dose? Does one dose elicit immunity, or do you need two (as is the case for Shingrix)?  How well does it work in the elderly, who are highly vulnerable to COVID-19 infection but tend to mount a poor immune response? Does immunity last long enough to make immunizing billions of people worthwhile? A rush to inoculate could produce side effects that could impede progress for years (RSV vaccine, for example).

Asymptote to Normalcy

https://www.nytimes.com/2020/05/18/nyregion/coronavirus-deaths-nyc.html
This is a NYT article recording the death rates in NYC per zip code from data provided by the NYC Health Department. Neighborhoods with high populations of black and Latinos and low income people  have the highest death rates, while zip codes where the wealthy reside have almost no deaths. A city councilwoman from Starrett City (Crooklyn) explains that there are multigenerational families in Starrett City who don't have the luxury of going to their vacation homes. As you might imagine looking at the starkness of the data, it is actually much worse. The city's zip code data doesn't reflect the disparities in testing. And, in not-so-recent memory, I recall the closing of several city hospitals, Harlem, Sydenham among others, and the relocation of a hospital on Central Park West to Valhalla, NY. leaving many poor areas underserved even at that time, 40 years ago.

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https://www.nytimes.com/2020/05/19/us/politics/hydroxychloroquine-trump-coronavirus.htm
This is a NYT article about the ascendancy of "anecdotal evidence" into the pantheon, where it clearly doesn't belong. A good quote on This Week In Virology was that "the plural of anecdote is anecdotes, not data". If our chief executive, the oxidizer in chief, is promoting hydroxychloroquine, a malaria drug, for Covid-19, how does that compete with drug efficacy testing? Dr. Hernandez, director of the Clinical Research Institute at Duke U said "When we have this playing out in the media instead of the scientific and clinical communities, people don't know what the right answer is..." An analysis of veterans treated with hydroxychloroquine found that 28% compared with 11%  who had routine care dies. No matter how you round the numbers, it is criminal to promote this drug.  There is no substitute for randomized controlled clinical trials. I ran some of those trials of cancer drugs and it makes a difference how the subjects are selected and matched and how the stats are done.

https://www.nytimes.com/2020/05/19/climate/coronavirus-climate-change-survey.html
Another NYT article about perspectives on climate change among Americans. This is a survey by Yale and George Washington Universities, published on Tuesday showing that 73% of Americans polled believed that climate change was happening, similar to polling in 2019. This was not expected because of a psychological hypothesis in psychology called the finite pool of worry, which suggests that when people’s level of concern about one issue rises, concern about others tends to fall.










https://www.nytimes.com/2020/05/17/opinion/mount-st-helenscoronavirus.html?searchResultPosition=3
This is an article from the NYT about how the Mt. St Helen's blast, 40 years ago, changed volcanology.  David Johnson, a geologist and one of the first scientists summoned to monitor new warning signs from the mountain, was barred from meeting the press, based on his dire predictions of a cataclysmic event. Like the probability of a pandemic, it was well-established that one of the dozen or so volcanoes in the 800-mile Cascade Range might soon turn active and this was, in fact, overdue.Mr. Johnson died in the explosion.

      

https://www.nytimes.com/2020/05/22/us/politics/coronavirus-tests-cdc.html
This is an article in NYT pointing out the consequences  of including diagnostic tests and serological tests, not the least of which is that some individuals may experience both tests, artificially inflating the numbers of those who have been tested. Two other reasons, equally significant, are that diagnostic testing attempts to quantify the amount of active disease in the population and that serological testing can be unreliable, as some of the tests have shown to be with a 50% accuracy rate. This has been attributed to confusion and fatigue in state and local boards of health.

 

https://www.nytimes.com/2020/05/22/health/coronavirus-polio-measles-immunizations.html
More from the NYT about the concerns that routine immunization services have been disrupted due to the you-know-what. The article reports a WHO survey of 129 poor and middle-income countries and found that 68  were experiencing a disruption of their large-scale vaccination services through clinics and other interventions. Polio, recently, has all but been eradicated, a tremendous accomplishment, that now is under threat. Before the pandemic, measles cases were already rising, in 2017, there were seven and a half million estimated cases with 124,000 deaths. In 2019 the US alone reported 1282 measles cases, its highest in more than 25 years.

 

https://jamanetwork.com/journals/jama/fullarticle/2766367

This is a link to JAMA article about serological testing done in LA County. Thirty-five individuals out of 865 tested positive. After adjusting for test sensitivity and specificity, the unweighted and weighted prevalence of SARS-CoV-2 antibodies was 4.34%, which would imply that approximately 367 000 adults had SARS-CoV-2 antibodies, which is substantially greater than the 8430 cumulative number of confirmed infections in the county on April 10. Therefore, death rates based on confirmed cases may be higher than rates based on number of infections. By implication, contact tracing methods to limit the spread of infection will be challenging.

 

https://www.nytimes.com/2020/05/20/health/coronavirus-vaccine-harvard.html

This is a NYT article about animal experiments done at Beth Israel Deaconess and published in science which show in principle that a vaccine may be protective against Covid-19 in monkeys. In one set of experiments, the monkeys were infected with the coronavirus and developed lung inflammation, recovered and made antibodies to the coronavirus, which were shown to be neutralizing. When the monkeys were challenged by a second dose of the virus, they produced neutralizing antibodies which defeated the virus in the monkeys’ nasal passages. In a separate experiment, prototype vaccines were tested on monkeys. The monkeys received pieces of DNA, which their cells turned into viral proteins which were intended to train the monkeys’ immune systems to recognize the virus. Several variations of a viral challenge were attempted. Some vaccines gave only partial protection but others, specifically the vaccine that trained the immune systems to recognize the entire spike protein, worked best. 

https://www.nejm.org/doi/full/10.1056/NEJMp2005687?query=TOC
This links to an article in NEJM about Covid-19 in incarcerated populations. The authors advise that improved preparation is "essential" for minimizing impacts of Covid-19 on incarcerated persons, correctional staff, and surrounding communities. Racial minorities, homeless people and mentally ill are overrepresented in incarcerated populations and are housed in close proximity in prisons, making them exceptionally vulnerable to infection. These populations already have an increased rate of HIV, HCV and TB Social distancing in nigh-near impossible in prisons. In order to "flatten the curve" the authors advise“decarcerating,” or releasing, as many people as possible, including those who are least likely to commit additional crimes, but also on the elderly and infirm. Incarcerated people who are infected should be separated from the general prison population. People who have recovered from Covid-19 could help with custodial and care efforts since they may be immune.

The Solipsist Sans Soiree

https://scitechdaily.com/new-artificial-intelligence-diagnostic-can-predict-covid-19-without-testing/
This is an article from Scitech Daily, about a group from King's College London, Mass General, and a company called Zoe (why would I trust a company with a dog's name) that are working to develop AI to diagnose Covid-19 based on symptoms. This may be of use in communities where access to testing is limited (NJ?) and will be tested in UK and US.  The researchers analyzed data gathered from about 2.5 million people in the UK and US who had been regularly inputting their health status in a COVID symptoms study app, around 0.3 of whom had logged symptoms associated with COVID-19. Of these, 18,374 reported having had a test for coronavirus, with 7,178 people testing positive. They then investigated which symptoms associated with COVID-19 were most likely to be also associated with a positive test. Loss of taste and smell (anosmia) was particularly striking, with two thirds of users testing positive for coronavirus infection reporting this symptom compared with just over 0.5 of the participants who tested negative.  They created a mathematical model that predicted with nearly 80% accuracy whether an individual is likely to have COVID-19 based on their age, sex and a combination of four key symptoms: loss of smell or taste, severe or persistent cough, fatigue and skipping meals. Applying this model to the entire group of over 800,000 app users experiencing symptoms predicted that just under a fifth of those who were unwell (17.42%) were likely to have COVID-19 at that time.

https://www.nytimes.com/2020/04/30/opinion/coronavirus-leadership.html

This is an article from NYT about the female leaders of several countries who have demonstrated effective and compassionate leadership, decency, and respect for science, including  Ardern, Merkel, Frederiksen, Marin and Solberg, according to the NYT editors, “dulling the impact of disease upon their people.” Angela Merkel, herself a scientist, acted quickly and calmly to get testing underway for the German people. In Iceland, Prime Minister Katrin Jakobsdottir led the government in offering free testing for all and organizing a thorough tracking system. The editors further suggest that there are “qualities beyond politics, economics and science, qualities of character that can’t be faked, chiefly compassion” that make a good leader in a crisis.  


https://www.washingtonpost.com/health/2020/05/15/lancet-editorial-trump-administration-coronavirus-response/
Article from the Washpost reporting the Lancet's editorial advoating Trump's replacement by someone who supports the role of the CDC and doesn't allow partisan politics to guide public health policy at the expense of human lives. The editors of the Lancet, in the history-making editorial decry the fact that the CDC “has seen its role minimised and become an ineffective and nominal adviser” and lament the removal of a major CDC offical in China last year which left an intelligence vacuum.

https://www.nytimes.com/interactive/2020/05/13/opinion/inequality-cities-life-expectancy.html

This is a Sunday Review NYT article with useful graphics of features of cities compared across various cities (wages differentials, life expectancies, educational attainment, portion of work commutes an hour or longer, broadband access, venture capital investments.  Physical mobility is to a great extent controlled by income levels. Average income has soared over the past 50 years in nearly every metro area but have risen largely because incomes for affluent have increased greatly but the graphics tell all.

 https://www.nature.com/articles/d41586-020-01449-8

This is an article from Nature magazine about the small likelihood that scientists will ever discover how the coronavirus got into people. Since Chinese scientists published the genetic sequence of the virus, scientists have been searching genomic databases of animals. They identified RATG13, the horseshoe bat, which is 96% similar to humans. The phylogenetic tree suggests that 50 years have elapsed since the horseshoe bat virus and the human virus shared a common ancestor. This suggests that there was an intermediate host and the pangolin has not been ruled out. Computational biologists and other computer modelers are working on this problem.