pandemic

Snakes On A Plane: Another Weird Pandemic Effect

In these pages, I have commented on some unexpected consequences of the pandemic, to wit: With reduced restaurant business, farmed fish are not selling and the fish are getting too big for the restaurants to buy--a vicious circle. And with the switch from sit-down dining to take-out, there has been a run on ketchup packets, creating an expensive secondary market for the packets on ebay. Now we learn that as a result of the pandemic, planes are having a problem with snakes—rattlesnakes to be precise.

Since the start of the pandemic, thousands of planes from airlines around the world have been grounded in hot, arid deserts, which are ideal for long-term aircraft storage. Australian airline, Qantas, stored about a dozen of its A380 superjumbos in an airfield near Victorville, in California's Mojave Desert. It is an area well known for feisty rattlers who love to curl up around the warm rubber tires and in the aircraft wheels and brakes. The maintenance workers use a low-tech solution, giving each plane its own designated 'wheel whacker' as part of the engineering kit, complete with the aircraft's registration number written on it. The whacker is a repurposed broom handle.

Prior to any landing gear inspections, the workers walk around the plane whacking the wheels and landing gear with the broom stick to scare off any slumbering snakes. Some scorpions have also been rousted.

It takes more than 100 man-hours to make a wide-body aircraft airworthy after storage—now they have to add a few more minutes for “whacking” the tires and landing gear.

It puts a new meaning on “check your luggage.”


What Caused India’s Devastating Second Wave?

Understanding what contributed to a second, more intense COVID-19 surge in India can inform the rest of the world on how to avoid a similar surge for this and future pathogens. This outbreak threatens to extend the pandemic itself and drive world-wide infections to new highs, creating an enormous a breeding ground for new and potentially more dangerous viral variants. If variants emerge that are not touched by the current vaccines, the world will be at square one with the pandemic. What a depressing thought.

It appears that the second wave arose due to a combination of three things: 1) India’s relaxing quarantine measures back in January, 2) the emergence of more rapidly spreading viral variants, including one that first appeared in India, and 3) a very poor rollout of vaccines to protect India’s population from spread of the virus. These are further discussed below.

  1. Relaxed safety measures. India’s second surge came after loosening restrictions, which let public complacency set in, which, in turn, was exacerbated by government officials like Prime Minister Modi and Health Minister Harsh Vardhan declaring that the pandemic was defeated. Life returned to normal. Masks went away, as did social-distancing. Weddings and parties resumed, which usually are large events in India. A new season of state-level elections ushered in big political rallies and street parades. A massive religious festival known as the Kumbh Mela took place, bringing an estimated 5 million Hindu pilgrims to the banks of the river Ganges in April. By mid-March, cases started gradually climbing again—then suddenly accelerated, becoming a vertical line rather than an upward sloping curve. The government was slow to respond. It was not until late April that Modi finally acknowledged the urgency of the situation. Local containment measures are beginning to be enacted, including shutting down the capitol of Dehli, and a few Indian states. However, Modi remains reluctant to enact country-wide restrictions like he did during the first wave. Without a more aggressive vaccine campaign, that could be a bad decision.

The more the virus spreads throughout India, and even into its neighboring countries of Nepal, Pakistan, and Bangladesh, the greater the risk that it will generate more infectious and dangerous viral variants that will not be affected by the current vaccines. If that happens, well vaccinated countries will have to start over. That is not a pleasant prospect, and is further discussed below.

  1. More infectious viral variants. India’s more deadly second wave of the CoV-2 virus can also be attributed to more infectious and more persistent viral variants. In this second wave, India, like many other countries, has been inundated with viral variants first identified in the UK and South Africa that were recently discussed in these pages. The UK variant has a mutation in its spike protein that makes it more infectious than its parent virus. The South African variant has a different mutation in its spike protein that makes the virus more resistant to some vaccines.

India’s second surge also has introduced the world to a unique viral variant dubbed the "double mutant," which was first identified in October. It is now the dominant strain in the state of Maharashtra, home to India’s financial center, Mumbai.

“Double mutant” is actually a misnomer for this variant since it has 13 mutations throughout its genome. However, it acquired that sobriquet because it has joined the UK and South African spike protein mutations in the same virus. It is a double whammy.

While scientists are still learning about the double mutant variant, India is seeing people who were previously infected become re-infected with this new variant. Also, younger and healthier people are being hospitalized in greater numbers. These observations are concerning. Similar observations of re-infection have also been seen in Brazil with yet another viral variant that was first identified there (more about Brazil in a future post). The ability of viral variants to re-infect people can be an important driver of future pandemic waves even in countries where the population is well vaccinated, but where isolation measures have been lifted or ignored.

For the country overall, the double mutant virus made up 70.4% of the samples collected during the week ending March 25, and that is compared with 16.1% just three weeks earlier, according to Covid CG, a tracking tool from the Broad Institute of MIT and Harvard. The tool mines data from the GISAID Initiative, a global database for coronavirus genomes. These data also show that the double mutant virus has already hopped to at least 21 countries including the US. In Australia viral genome sequencing showed that the double mutant made up 40% of the samples collected over the week ending April 15, compared with 16.7% a month earlier. It accounted for 66.7% of samples from New Zealand for the week that ended April 8, up from 20% a month ago. It also has been detected in California, according to Dr. Benjamin Pinsky, director of the Clinical Virology Laboratory at Stanford University. Clearly, where the double mutant virus appears, it quickly achieves dominance.

  1. Poor vaccine distribution. As of 4/30, India had only administered 15 million vaccinations, a tiny proportion of its population of 1.4 billion people. The country is the primary producer of the AstraZeneca vaccine that has run into supply chain problems causing delays in vaccine delivery. In February, Biden signed the Defense Production Act to boost U.S. COVID-19 vaccine production but that decision cut off US exports of raw materials that India needs in order to maintain its vaccine production capabilities. Thus, vaccine makers around the world, including the Serum Institute of India (SII), the largest vaccine manufacturer in the world, face a shortage of materials to make COVID-19 vaccines. The ban has garnered much criticism as resource hoarding that threatens global vaccine production. On April 16, SII appealed directly to Biden to lift the embargo of raw material exports so that vaccine production could continue. Several days later, the White House announced it would partially lift the ban for materials the Indian company needed to manufacture the AstraZeneca vaccine, specifically.

The US also inexplicably has a large stockpile of millions of doses of the AstraZeneca vaccine, that were made here, even though it is not approved for use in the US. If we are not using it, why not release the stores to the world? The Biden administration also has faced criticism for hoarding these doses that could help India and other countries around the world that also are experiencing a new surge in infections. On Friday, April 30th, the U.S. Chamber of Commerce called on Biden release the AstraZeneca vaccines to India and other hard-hit countries.

There is some irony in all of this since India is a huge manufacturer of vaccines and pharmaceuticals for the world, and likes to bill itself as the “pharmacy of the world.” India produces 60 percent of the world’s vaccines, but cannot supply its own country, partly because of reduced production due to the supply chain problems, but also because it failed to order sufficient vaccine doses. India almost completely halted vaccine exports last month in order to divert supplies to its domestic population, which is affecting supply in the rest of the world. Rather than rely on its own manufacturers for vaccines, India approved Russia’s Sputnik vaccine, and has fast-tracked the approval process for other vaccines manufactured in foreign countries. That means that while the industrialized world was being vaccinated with vaccines produced in India, the country was still looking at approving foreign-made vaccines for use in its country.

Bottom line. The combination of relaxed safety protocols, the appearance of deadlier viral variants, and poor distribution of vaccines to its people has left the country as the world’s epicenter for the pandemic. As the virus races through its huge population, all of this provides an enormous breeding ground for new variants to arise, which is worrisome even for countries that have had successful vaccine rollouts and have begun to see reduced viral spread. Let us hope this is not a perfect storm for restarting the pandemic with vaccine-resistant variants.

And India is not the only problem. In Africa, vaccination is also off to a slow start. Just 6m doses have been administered in sub-Saharan Africa, fewer than in New Jersey. Just 1% of African adults have received a first jab, versus a global average of 13%. Prepare for Africa to become the next hot-spot and breeding ground for troublesome variants, if Brazil and South America do not beat them to the punch.

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The Coronavirus Condiment Conundrum

The vexing thing about a novel pathogen and its attendant disease is that we expect it to behave like earlier pathogens and maladies we have experienced. But, sometimes historic diseases poorly predict the new problems that novel pathogens can raise. One such unexpected fallout from the current coronavirus pandemic was that farmed fish were getting too big for restaurant plates as discussed earlier in these pages. Now, the current pandemic has us facing another unpredicted conundrum, a critical shortage of ketchup packets!

CNN recently reported that restaurants have descended into a mad search for ketchup packets. One Denver tavern owner admitted to purloining ketchup packets from nearby McDonald’s and Wendy’s fast food franchises in order to meet his customers’ needs. Adding to his emergency, the tavern is across from Coors Field, to which the baseball All Star Game has been moved, thanks to Georgia’s new voter reform laws. As a 30+ year Wisconsinite (or “Sconnie” for short) and, thereby somewhat expert in brats, and hot dogs, I offer a suggestion to reduce this ketchup shortage--never, ever put ketchup on brats or hot dogs. Mustard is the proper condiment for these tubes of tasty processed meat. Admittedly, if everyone took this advice it could cause a deficit of that tangy yellow or brown topping and add to our COVID misery. There is nothing sadder than a bare brat, unless it is one slathered with ketchup. Folks in Chicago likely agree. Have you ever seen a Chicago dog with ketchup? It will have a luminescent green relish, but never ketchup.

This shortage of ketchup packets began last summer when the CDC began discouraging dine-in service at sit-down restaurants and encouraging delivery and takeout instead. Sit-down restaurants coast-to-coast began packing food for people who expected condiment packages with their meals. Suddenly, this packet packing by formerly traditional restaurants competed with fast food places for ketchup packets. As a result, demand went up, prices increased, and supply went down for those little 1/3 ounce packets. That is called economics.

In response, Heinz, the biggest ketchup producer in the country, just days ago announced it was increasing production of ketchup packets to 12 billion a year. A condiment Warp Speed?

This ketchup shortage also has fueled an underground market for the old packets you might have hoarded in a kitchen or desk drawer, or baked in your car’s glove box or under the seats. Entrepreneurial diners with a cache of ketchup packets are selling their treasures on eBay and Facebook Marketplace. One Indianapolis entrepreneur sold 20 Heinz ketchup packets for $8 shortly after the Wall Street Journal reported on the ketchup shortage. This too is called economics.

While all this reflects entrepreneurial principles, it is not exactly an efficient market. The prices in dozens of ketchup-packet listings posted online ranged from a quarter to $5 per packet. The latter was offered in a lot of 20 packets for $100. On eBay a week ago, an acupuncturist from NY posted “Assorted Ketchup packets for Apocalypse Survival,” with a starting bid of 99 cents for three packets. They soon were up to $11.50. Who knew ketchup was essential during an apocalypse?

What is next--a shortage of relish, mayo, and mustard packets? Maybe sugar and fake-sugar packages? It might not be too late to begin stocking up on condiments in case of an apocalypse. Make sure to store your bounty in a secure place, maybe along with your toilet paper and hand sanitizer.

Amazingly, people fret about vaccine safety during this ketchup shortage. Who ever heard of a vaccine protecting anyone from an apocalypse?

Is it time for lunch?


Paying The Piper

In the face of a pandemic caused by a new and deadly virus, states and local governments enact social-distancing measures, bans on crowds, closure orders, and mask mandates in an effort to flatten the curve and prevent health care systems from being overwhelmed with critically infected people. Initially, people are fairly compliant with the order, but, as the days of restriction turn into weeks, then months, compliance wanes. Theater owners complain about financial losses. Clergy bemoan church closures. People argue whether children are safer in classrooms or at home, and many rebel at having to wear face masks in public, complaining that the government has no right to infringe on their civil liberties. Sound familiar?

But this is not about the 2020-21 coronavirus pandemic; these are descriptions of the US response to the deadly Spanish flu pandemic between 1918 and 1920. In many ways our current pandemic mirrors the one that occurred a century ago, and that is presciently described in the book, The Great Influenza, by John M. Barry. Like CoV-2, the H1N1 “Spanish” flu killed less than 1% of the people it infected, but during a third wave of infection with a more virulent strain, that flu killed more people around the world in just 24 weeks than were killed in the 10 years of WWI and WWII combined! In remote areas with little access to health care, the flu wiped out entire villages.

Like COVID-19, the Spanish flu pandemic hit hard and fast, going from a handful of reported cases in a few cities to a nationwide outbreak within a few weeks, then with increased mobility due to WWI, it quickly spread around the world, from America to Europe and back. Many communities, responding to the ebbs and flows of the epidemic waves, issued several rounds of closure in an attempt to keep the disease in check. These social-distancing orders worked to reduce cases and deaths. However, just as today, they often proved difficult to maintain. By the late autumn of 1918, just weeks after wide-spread social-distancing orders went into effect, the pandemic seemed to be coming to an end as the number of new infections declined. People clamored to return to their normal lives. Businesses pressed officials to be allowed to reopen. Believing the pandemic was waning, some state and local authorities began rescinding public health edicts. Sound familiar?

Americans hurried to return to their pre-pandemic routines. In some cities, they packed into movie theaters and dance halls, crowded into stores and shops, and gathered with friends and family for holidays and celebrations. Meanwhile, officials warned the nation that cases and deaths likely would continue for months to come, but the warnings fell on increasingly deaf ears, as people enjoyed a return to normalcy. The nation carried on, inured to the toll the pandemic was taking. But as health officials warned, the pandemic wore on, stretching into a third deadly wave that lasted through the spring of 1919, with a fourth wave hitting in the winter of 1920. Some blamed those world-wide resurgences on careless Americans.

The different responses and experiences of two large American cities are noteworthy here. In Denver, local business interests lobbied heavily to get rid of the quarantine measures that had shut down schools, churches, libraries, pool halls, businesses, and theaters. The city capitulated. The city opened up and was hammered by the deadly third wave of the flu. On Armistice Day, November 11, 1918, residents poured out of their homes to celebrate the end of World War I. A few days later, many were dead, victims of the pandemic flu. Two weeks later, a headline in the Denver Post captured the devastation: “All Flu Records Smashed in Denver in Last 24 Hours.”  An editorial in the Denver Monthly Magazine said, “For some reason, even the most enlightened citizens will not take the influenza epidemic seriously. They know that it is the most widespread epidemic that has ever visited America. They know the disease is a deadly menace and snuffs out life almost before the victim realizes he is ill. Yet when health officers try to impress upon people the necessity of following essential rules and regulations, the average citizen simply refuses to heed these admonitions.”

In contrast to Denver, St. Louis enacted and maintained strong social distancing measures, including in-home quarantines for infected people. They experienced a fraction of the deaths that Denver saw. The quarantine measures worked there.

The similarities in our responses to the 1919-20 flu and 2020-? coronavirus pandemics are noteworthy. But, there is one big, hopefully defining difference between the two pandemics that might make the outcomes quite different. Vaccines. There were no flu vaccines to rescue the world from the ravages of the Spanish flu. In fact, the influenza virus would not even be discovered for another 15 years, and a vaccine was not available until 1945. For the first 12 or so months of the current coronavirus pandemic, we were in the same boat—we faced a novel virus with no vaccine or effective medicine. When there is no available medical response to a pathogen, we must rely on protective public health measures to provide a buffer against the pathogen while we learn how to respond to it.

Today, we have significant advantages with a much better understanding of virology and epidemiology then we did in 1918. We know that both social distancing and masking work to help save lives. Most critically, we now have multiple safe and effective anti-CoV-2 vaccines that are being deployed, with the pace of vaccinations increasingly weekly.

Still, the deadly third wave of influenza shows what can happen when people prematurely relax their guard against viruses that can mutate and become more deadly. That is why we must remain vigilant while the coronavirus vaccines roll out. We are still learning about this virus and are only beginning to learn about the variants spawned by the virus. We still need a public health buffer from the virus to keep us safe until we better understand its full capabilities and can vaccinate more people.

Be smart. Stay safe. Get the vaccine.


The Post-Thanksgiving Surge Is Underway

As the pandemic surges, newly released data from the US Department of Health and Human Services show at least 200 hospitals across the country were at full capacity last week. One third of all hospitals have 90-100% occupancy of ICU beds, and coronavirus patients now take up almost 50% of all staffed ICU beds in the US--up from 37% in the first week of November. Hospitalizations in the US reached a record high of 107,248 on Thursday, Dec 10, according to the Covid Tracking Project.  This is the post-Thanksgiving surge we were warned would happen.

Across the country, more hospitals are running out of health care workers and/or ICU beds, forcing some doctors to send patients out of state. This does not just affect COVID-19 patients, it affects anyone who needs hospital care. When hospitals run out of beds and staff, all patients are turned away, making difficulty in obtaining hospital care very egalitarian.

Thursday was encouraging as an FDA committee recommended that a COVID-19 vaccine be authorized for emergency use. But it was also a day of loss. The single-day death toll from COVID-19 reached a record high of 3,124 according to Johns Hopkins University. That's more deaths than suffered in the 9/11 attacks. We are now suffering the equivalent of a 9/11 attack and more every day, and it is getting worse.

A composite forecast from the US Centers for Disease Control and Prevention projects a total of 332,000 to 362,000 Covid-19 deaths by January 2, and up to 500,000 dead by April. That forecast combines modeling from 40 independent research groups. As I reported a few days ago in these pages, COVID-19 has now become the leading cause of death in the US.

Yet, the mortality statistics do not tell the full story. Many more people who survive COVID-19 suffer long term health problems, usually neurological or cardio-pulmonary. This will continue to be a drain on health resources, finances, families, and lead to reduced life-spans in many long after the pandemic wanes. These problems also are common in younger, healthier survivors, and in those who only had mild disease. This is the long-term cost that too many people ignore.


CoV-2 In Animals

Coronaviruses are promiscuous critters. We know that the several coronaviruses that cause significant human disease passed from bats to other species and then to people. The virus that caused SARS came from a bat that infected a civet that then infected a human who passed it on to other people. MERS was similar—a bat virus infected a camel that spread it to people. There is good evidence that the SARS-CoV2 virus also came from a bat to infect humans, but we are not sure what animal was the intermediate vector.

Usually there is a biological barrier that limits virus spread between species. When viruses do jump between species, it usually is a result of chance mutation that makes a different non-host species a more hospitable home. That doesn’t seem to be the case with many coronaviruses, which seem to jump between species without markedly changing their genome. Notably, early in this pandemic, we realized that humans were spreading the virus to lions and tigers in the Bronx zoo. Since then, there have been increasing reports of pet cats and dogs catching the virus from their owners and even spreading it to other animals. Also there are reports that monkeys, ferrets and hamsters have caught the virus.

Human to animal spread is not confined to zoo and pet mammals. It has devastated mink farming activities around the world as well. Denmark recently announced plans to cull one million mink after finding extensive spread of the virus in several mink farms. Last May, Spain ordered the culling of 93,000 mink at one farm. The Netherlands also undertook a large cull after two, maybe four people, were reported to have caught the virus from infected mink. Several cats that roamed the affected mink farms were also infected, meaning that the virus was spreading between three different species. And on October 9, it was reported that 10,000 mink died at fur farms in Utah and Wisconsin following COVID-19 outbreaks. It was noted that the virus progressed quickly in mink, with most infected animals dying in one day.

Mink

It is unclear why mink seem more susceptible to the virus than other animals, but it is concerning. Similarly, we also do not fully understand why some people, but not other others are highly susceptible to the disease. What would it take for the virus to change and become even more deadly to more humans like it is in mink?

All this suggests that animals that are in very close contact with humans might become a growing reservoir for the virus. So, when a vaccine for humans is available, should we also vaccinate our pets to also give them herd immunity, which would protect them and us? That probably would be easier than trying to make your cat wear a face mask! Experts also are advising people to keep their pets safe by avoiding contact with other people and animals. They even advise to isolate pets from household members who catch the virus.

Another concern is that as viruses pass between animal species, they often acquire new behaviors via genetic drift and rearrangement between different viral genomes. It is believed that a simple mutation increased the ability of CoV-2 to infect human cells. We have found about 500 different coronaviruses in bats alone, while other animals often carry coronaviruses typical to their species. There might be thousands of different coronaviruses out there. When a coronavirus from one species enters a cell from another species that has its own endogenous coronavirus, the viruses can shuffle their genes creating new strains with new capabilities. And when we are talking about viruses infecting an animal, we are talking about billions of virions being produced that are capable of shuffling genomes with endogenous viruses. All it takes is one particularly nasty and overly competitive virion to emerge and find a new host that has not seen it before.

It is relevant here that a new coronavirus that causes gastrointestinal distress in pigs has emerged in China. It is especially lethal to baby pigs, killing 90% of them. It is called swine acute diarrhea syndrome virus, or SADS-CoV and is 98.48% genetically identical to a virus collected from horseshoe bats in China. Research recently published in the Proceedings of the National Academy of Science (PNAS) show that the virus can also infect human cells, but, so far as your humble blogger knows, no human disease has been associated with SADS-CoV. Yet.

Seeing as how coronaviruses readily transmit between different species, I predict that we can expect more novel human coronavirus disease in the future. Hopefully, things we continue to learn about the current CoV-2 virus and COVID-19 disease will translate to more rapid and effective responses to new coronavirus pathogens that are likely to pop up in pigs, people and pets.

We will see.


Higher-Than-Normal Death Rate In The US Since March

Some people insist on viewing the coronavirus pandemic through a subjective political lens and downplay the seriousness of the disease and assert that the COVID-19 mortality rate is overblown. Then there are those of us who view the pandemic through an objective scientific lens and come to a diametrically different conclusion. Earlier in these pages, I reported on two studies, one done in the UK and the other in the US, that used actuarial and hospital data to show a 35% increase in all deaths compared to a comparable period of time before the pandemic. Both papers concluded that the COVID-19 deaths were, in fact, being undercounted.

Continuing to look through the science lens, we see recent confirmation of those studies in a paper published Oct 12, in the Journal of the American Medical Association (JAMA). While total US deaths usually are remarkably consistent from year to year, this study reported a 20% increase in total deaths between March 1 and August 1 this year compared to historical data. States with the highest rate of excess deaths included NY, RI, NJ, MA, LA, AZ, MS, MD DE and MI. Excess deaths in these states ranged from 22% in RI and MI, to 65% in NY. States that reopened earlier saw greater increases in total extra deaths.

67% of the excess deaths across the country were associated with COVID-19. The 33% of deaths unrelated to COVID-19 were statistically elevated for patients with heart disease and Alzheimer disease. Deaths not linked to COVID-19 were probably due either to unrecognized COVID-19 disease, or to disruption of normal health and personal care due to pandemic-related shutdowns.

The current JAMA study analyzed death data for 2014-2020 from the National Center for Health Statistics to conclude that the excess US death rate is 20%, while the previous studies used actuarial and hospital data to conclude that the excess death rate was 35%. The different conclusions regarding death rates could reflect using different sources of data, or different science filters.

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Timeline Of Early COVID-19 Events

Late 2019: In November 2019, analyses of wire and computer intercepts, coupled with satellite images leads the US National Center for Medical Intelligence to suspect that a contagion was emerging in China’s Hubei Province, specifically in Wuhan, China's 10th largest city with a population of ~11 million (for comparison, NYC has a population of just over 8 million). This intelligence is shared with the US Defense Intelligence Agency, the Pentagon’s Joint Chiefs, and the White House. Around Thanksgiving, analysts report that China’s leadership is aware of a growing epidemic, but decided to keep the details secret from the world.

Dec 31, 2019: Chinese officials inform the WHO about a cluster of 41 patients with a mysterious pneumonia.

In the middle of the night on the 31st, Wuhan officials quietly begin disinfecting its wet market.

Jan 1, 2020: A Chinese CDC team from Beijing arrived in Wuhan and collected 585 “environment” samples from a garbage truck, drains and sewers in the market. They report that 33 of samples test positive for the virus. 14 of the positive samples are from the area of the market where wildlife was traded.

The Wuhan market closes.

The Chinese government prohibits genome sequencing of new coronavirus samples and orders existing viral samples destroyed.

Jan 1-3: Wuhan police silence eight medical doctors they call “rumor mongers,” warning them against talking about the novel disease. One of them, Dr. Li Wenliang, an ophthalmologist, contracts the virus on Jan 8 and dies Feb 7.

Jan 2: The Central Hospital of Wuhan prohibits staff from publicly discussing the disease.

Jan 6: The US CDC issues a Level 1 travel watch with recommendations on washing hands, avoiding animals, animal markets, and contact with unwell people if travelling to Wuhan.

Jan 7: Chinese scientists report that the cause of the Wuhan flu is a novel coronavirus.

Jan 11: China records it first death linked to the new virus.

Jan 12: The Shanghai Public Health Clinical Center, the facility that published the first genome sequence of the virus, closes without reason.

Jan 13: Thailand reports the first coronavirus infection outside China.

Jan 14: The first confirmed case of COVID-19 in the US appears in the Seattle area in a 35 year old man who had recently arrived from Wuhan. However, a recent UCLA examination of its hospital records shows that there was an unexpected 50% spike in patients with respiratory illness beginning Dec. 22 and continuing through the end of February. This raises the possibility that COVID-19 might have been in the US at least a month before this patient was diagnosed with it.

The WHO states that there is no evidence of person-to-person transmission of the virus.

Jan 17: The US CDC sends 100 people to three US airports to screen travelers from Wuhan.

Jan 20: Since health care workers have come down with COVID-19, the WHO announces that there is person-to-person transmission of the virus.

Jan 21: Anthony Fauci, head of the National Institute for Allergy and Infectious Disease says that “this is not a major threat for the people of the United States, and this is not something that the citizens….should be worried about.”

China reports COVID-19 cases across several major cities including Beijing and Shanghai.

Jan 22: Countries begin closing borders and restricting travel. This includes North Korea, Singapore, Vietnam, Russia, Hong Kong, Mongolia, Pakistan, Malaysia, Mexico, Philippines, Sri Lanka, Thailand, UK, Papua New Guinea, Palau, Vanuatu, Kazakhstan, Nepal, Tibet, Canada, Italy, Trinidad, Tobago, Jamaica, Poland, Iraq, and Turkey.

The US State Department issues a Level 4 travel advisory to not travel to China. It also advises that Americans in China should consider departing, and authorizes American diplomatic staff and their families to evacuate China.

Jan 23: China completely isolates Wuhan—no traffic, including planes, and trains, is allowed in or out of the city, and all public transportation within the city is suspended. A few days later the entire Hubei province is shut down. The day before the Wuhan travel ban, 100,000 people leave the city on trains. An estimated 5 million people travel out the area in the days prior to the quarantine.

The WHO declares that the virus is not a Public Health Emergency of International Concern.

Jan 24: Chinese doctors publish in the medical journal, Lancet, the first report on “Clinical Features of Patients Infected With 2019 Novel Coronavirus in Wuhan, China.” It includes the first description of symptom-free infected people. It also reports that 13 of the original 41 cases had no link to the Wuhan wet market, indicating probable human transmission of the virus.

Another report in the same issue of Lancet describes person-to-person of the virus within a family and the WHO documents another case of person-to-person transmission in Vietnam.

The WHO changes its mind and warns the world of a possible pandemic.

Jan 25: The beginning of the Chinese New Year (the year of the Rat). Nancy Pelosi and NYC mayor de Blasio encourage Californians and New Yorkers to participate in Chinese New Year Parades and to visit China Towns in NYC and San Francisco.

Jan 26: Fauci advises, “The American people should not be worried or frightened by this. It’s a very low risk to the United States, but it’s something that we, as public health officials, need to take very seriously.”

China bans all wildlife trade and the Chinese CDC begins developing vaccines against the novel coronavirus.

Chinese police drop their case against eight people accused on January first of spreading false rumors about a new SARS-like virus.

Jan 30: WHO reverses its decision from one week earlier to declare the coronavirus outbreak a Public Health Emergency of International Concern and advises "all countries should be prepared for containment, including active surveillance, early detection, isolation and case management, contact tracing,…”

US health experts agree that a ban on travel from epidemic hot areas is needed.

Jan 31: Trump announces a travel ban from China and declares a Public Health Emergency. US borders close to all foreign nationals who pose a threat of transmitting the virus. U.S. citizens returning from Hubei province in China are quarantined for two weeks.

Feb 1: Joe Biden and Nancy Pelosi accuse Trump of fearmongering and xenophobia for the travel ban.

Feb 3: Fauci predicts that because of travel restrictions, the danger to Americans was “just minuscule.” He also warns against “outlandish extrapolations of fear” and advises that “…there is no reason whatsoever to wear a mask.”

Feb 4: Italians embark on a campaign to hug Chinese to encourage them in the coronavirus fight and as an anti-prejudice statement.

Feb 12: COVID-19 cases begin to spike in S. Korea.

Feb 19: COVID-19 cases begin to spike in Iran.

Feb 21: COVID-19 begins to spike in Italy.

Feb 25: The US CDC warns that clusters of outbreaks are likely to arise in the US and that hospitals, businesses, and schools should begin preparing for social distancing. The US has 57 confirmed COVID-19 cases, 40 of whom are connected to the Diamond Princess cruise ship. While there are no signs of sustained transmission in the US, the warning is based on the rising infections in Iran, Korea and Italy.

New Orleans goes ahead with its Mardi Gras parade and celebration.

Feb 28 and 29: Fauci changes his tune and acknowledges that “It could be really bad,” but also adds, “I don’t think it’s gonna be, because I think we’d be able to do the kind of mitigation (sic). It could be mild.” And, “Right now…there is no need to change anything that you’re doing on a day-by-day basis. Right now the risk is still low, but this could change….I mean this could be a major outbreak.”

March 1: The first confirmed COVID-19 case appears in NYC. More cases rapidly appear in following days and viral sequence analyses traces the source of the virus back to China but via Europe. The travel ban from China seems to have worked, but viral entry from Europe was not expected.

March 8: The entire country of Italy goes into complete lockdown.

March 10: Fauci again advises that “…the risk is relatively low,” but also cknowledges that “there are parts of the country right now that are having community spread in which the risk there is clearly a bit more than that.” He cautions, “…we should like the country to realize that as a nation, we can’t be doing the kinds of things we were doing a few months ago.”

A choir practice in Skagit County Washington is attended by 61 people, including one who had developed a “cold” three days prior. In the days following the 2.5 hour practice, 52 COVID-19 cases occur (an infection rate of 87%). Three are hospitalized and two die from the disease.

March 11: WHO declares a pandemic.

Trump bans all travel from 26 European countries.

March 12: Biden rejects all travel bans saying that viruses do not respect borders.

March 13: Trump declares a national emergency.

March 16: Trump urges Americans to avoid restaurants, bars, unnecessary travel, and groups of more than 10 people.

States begin ordering “shelter in place” restrictions.

March 18: Trump signs the Defense Protection Act that allows the military to provide States with PPE and ventilators from the US strategic reserves. He also announces that the US Navy hospital ships, Comfort and Mercy, will be deployed to the East and West Coasts in case hospitals are overwhelmed by COVID-19 cases.

March 23: NYC confirms 21,000 COVID-19 cases making it the epicenter of the US outbreak.

March 31: More than 1/3 of the world population is under some form of lockdown.

April 3: For the first time, Biden supports travel bans to slow spread of CoV-2.

Summary: No one knew we were facing a once-in-a-generation pandemic. The important question is: “Why did it take so long for the health professionals around the world to recognize the extent of the threat and advise the world to act more forcefully? The answer partly is because this virus did not behave as expected based on recent experience with SARS, MERS, avian flu, swine flu, Zika and Ebola outbreaks. Those viruses did not come with “stealth” vectors, or asymptomatic virus spreaders, which led to much faster and unexpected transmission of Cov-2. Also, the constellation of COVID-19 symptoms were confusing and not as straightforward as, say Ebola, where it is unambiguous how the virus affects people. Finally, this range of often unrelated symptoms associated with COVID-19 is further confounded by the long-lasting adverse health sequelae in many patients that are rare in most other viral infections.

In other words, health professionals had a very steep learning curve with this virus that they did not have with other significant pathogens we have encountered in recent decades.  The professionals had to learn on the fly and are still learning. This timeline reflects that learning curve and shows how professional opinions changed over a matter of weeks, or even days, as new information emerged.

This will happen again.

Note on sources: This timeline was assembled from numerous sources including the Washington Post, The Wall Street Journal, The New York Times, The Guardian, Summit News, CNN online, Real Clear Politics, Yahoo News, Business Insider, Forbes, Wikipedia, ABC News, and several medical journals.


Texas Replaces NYC As The New Hotspot

A 30-year old man who attended a COVID party in San Antonio has died from the disease. Before he died, he told doctors that he thought the virus was a hoax and intended to prove it with the party. He reportedly concluded, “I made a mistake.” Bexar County, where San Antonio is has about 19-20,000 confirmed COVID cases and is seeing about 1000 new cases a day. Most cases are in people aged 20-39.

Elsewhere, in Harris County Texas, Houston hospitals are full and ICUs are overwhelmed requiring COVID patients to wait in ERs for a bed. Because of this, Houston hospitals are also increasingly diverting ambulances to other regional hospitals, which also affects non-COVID patients, such as those with cardiovascular emergencies. There has been a spike in at-home deaths from cardiac arrest in the county, which could be directly from COVID disease or from delayed medical attention to non-COVID patients.

During an eight-day period in late June and early July, Houston’s 12 busiest emergency departments hit a maximum capacity three times, in contrast to zero times in the same period a year earlier. And when a hospital does have beds available, they sometimes do not have the staff to manage those patients, due to COVID-related absences.

On June 24, several hospital executives affiliated with the Texas Medical Center — a sprawling medical campus that’s home to most of Houston’s major hospital systems — issued a warning that COVID-19 hospitalizations were growing at an “alarming rate” and could soon put an unsustainable strain on hospital resources. They were right.

The mortality rate from COVID is decreasing, but the number of people getting very ill is increasing. That is likely because the virus is running rampant in younger people who flaunt social isolation. What they don’t realize is that many infected young people will have long lasting health problems as previously reported in these pages.

It is noteworthy that Texas was one of the first states to open back up.


‘Superspreading’ Drives Most COVID-19 Spread

  • On March 10, a choir practice in Skagit County Washington was attended by 61 people, including one who had developed a “cold” three days prior to the practice. In the days following the 2.5 hour practice, 52 COVID-19 cases occurred (an infection rate of 87%). Three were hospitalized and two died from the disease.
  • A couple of weeks before that choir practice, a Boston biotechnology company held a two-day leadership conference for about 175 of its world-wide executives. Apparently, someone was unknowingly infected and it spread to participants who took it back to their homes. At least 99 people from the meeting alone came down with COVID-19.
  • About the same time, a funeral in Albany, GA was attended by >100 people. The virus was in attendance as well leading to a huge outbreak that spread into surrounding rural areas causing one of the nation’s largest local outbreaks of COVID-19.
  • In Arkansas, an infected pastor passed the virus to more than 30 Sunday church attendees, three of whom died.

Epidemiology:

Somewhere between 10-20% of infected people are likely responsible for 80% of COVID-19 cases as recently described in Scientific American and reported in a study published in the Proceedings of the National Academy of Sciences. These “superspreaders” are typically asymptomatic and under the age of 60 according to investigators at Emory University’s Rollins School of Public Health.

Epidemiologists who study infectious diseases refer to the R0, or “R naught,” value, which is a mathematical description of the reproduction number of an infectious disease. Seasonal flu has an R0 of about 2, meaning that each infected person, on average, will spread the virus to two more people. The R0 for Cov-2 is about 4, meaning it is twice as infectious as the flu. For comparison, the R0 for measles, the most infectious virus we know, is 12-18. For the SARS pandemic in 2003, the early R0 was about 2.75 but soon was brought down to <1 due to isolation strategies.

In addition to R0, scientists use a value called the dispersion factor (k), which describes how much a disease clusters. The lower k is, the more the transmission clusters, or comes from a small number of people. A 2005 Nature paper estimated that SARS had a k of 0.16. The estimated k for MERS, which emerged in 2012, is about 0.25. In the Spanish flu pandemic of 1918, in contrast, the value was about one, indicating that clusters played much less of a role in spreading the Spanish flu than it did in spreading the SARS and MERS coronaviruses.

Current estimates of k for CoV-2 vary. In January, researchers at the University of Bern concluded that k for COVID-19 is somewhat higher than for SARS and MERS. In a recent preprint, it was estimated that k for COVID-19 is as low as 0.1, which means that probably about 10% of cases lead to 80% of the spread.

Superspreading:

According to the CDC, super spreading is caused, in part, by individuals known as “superemitters,” who release more aerosol particles during speech than do their peers. Some people shed far more virus, and for a longer period of time, than others, perhaps because of differences in their immune system or the distribution of virus receptors and virus in their body.

Yet, other factors play a role in creating superspreader events. These are physical factors including crowd size, close contact, closed environment, and ventilation. Japanese researchers found that CoV-2 transmission was 18 times greater in a closed vs open-air space. Unsurprisingly, London researchers also found that the largest clusters of outbreaks were in indoor spaces like nursing homes, churches, schools, shopping areas, dormitories, prisons and ships.

It makes sense that an important factor in creating a superspreader event is the number of people involved. If a group of five friends meet, the chance of a superspreader event is much less than if 500 met. Plus, the chance of having an infectious person in the group is much reduced in the group of five vs 500. Hence, it makes sense to limit the size of gatherings in attempt to limit superspreader events.

Time also plays a key role in the virus spread. Various groups consider 10-15 minutes contact with an infected person to be the magic limit. This might help explain why grocery store cashiers, who only interact with customers for a couple of minutes, have not been hard hit with the virus, while meat-packing employees who work long shifts side-by-side, have been hard hit in some places.

Bottom line:

Reducing superspreading events by avoiding the “three C’s,” Closed spaces with poor ventilation, Crowded spaces, and Close contact settings, have a dramatic effect at reducing the R0 of the virus, which, in turn, limits its morbidity and mortality. That is what the quarantine efforts have attempted to do. Certain countries around the world (S Korea and China for example) that have been very quick to identify and strictly control local outbreaks have been successful in reducing superspreading events. But, their strict measures are anathema to the psyche of the US. We prefer to deal more with the disease than the draconian restriction of our freedoms.

Other research reported in these pages has shown that liberal use of face masks can also reduce the R0 value to <1, which is the bench mark for stopping an infectious disease. Could liberal use of face masks be the happy medium for the US? Could it be a way to avoid draconian social and life restrictions while limiting the spread of the virus until we have an effective vaccine?

I believe so.