quarantine

What Happened To The Flu And Other Respiratory Diseases?

A NYC based travel blogger who travels a lot used to get a respiratory infection whenever she flew. That stopped when the airline mask mandates went into effect. The mandates, of course, were designed to hinder the spread of the CoV-2 virus that causes COVID, but it makes sense that if masks and other physical (that is, non-medical) mandates worked to mitigate COVID, then we would see a decrease in other contagious respiratory diseases after the mandates were, well…mandated.

We did.

The mandates worked, despite persistent claims of some to the contrary. This particular blog subject was stimulated by a radio talk show where a couple of nonscientist talking heads announced that there was no scientific proof that the masks or other mandates prevented disease. I previously posted in these pages evidence that masks, in particular, do indeed work to retard the spread of disease (see here, here, here, and here). In this post, I present further data on how the mandates significantly reduced the incidence of other infectious respiratory diseases around the world. If the measures can reduce flu, then you can bet that they also reduced COVID-19.

Note, however, that this is not necessarily an endorsement for returning to the measures. Your humble scribe didn’t much like his glasses fogging up, or having to make two trips from the car to the store because he forgot his mask. But, let’s argue the issue based on its merits and not from false premises based on incorrect claims.

After South Korea implemented various hygiene and social distancing measures in response to COVID, they saw the 2019-20 flu season end an astounding 12 weeks earlier than the previous year. Epidemiological surveillance data bolstered by clinical diagnostic testing showed that infection from several different pathogenic respiratory viruses (including adenovirus, bocavirus, metapneumovirus, rhinovirus, flu, parainfluenza, and respiratory syncytial virus) dropped to nearly 0% just five weeks into 2020!

In the United States, the incidence of infection by influenza, respiratory adenovirus, rhinovirus, enterovirus, RSV, non-COVID coronaviruses, metapneumovirus, and parainfluenza viruses all decreased in March 2020, soon after implementation of mandates. Similar results were seen in Japan.

More dramatically, since pandemic mitigation measures were put in place, there has been a 99% global reduction of infections from both influenza types A and B compared to prior years. In particular, one of two flu B substrains has not been isolated in the world since August 2021 suggesting that this variant is now extinct. The overall genetic diversity of influenza viruses has also dramatically diminished indicating that other flu sub-types (or clades) have disappeared around the world since the pandemic mandates were put in place.

And this reduction of respiratory infectious disease does not only hold for those caused by viruses. Another study looked at surveillance data from 26 countries across 6 continents for several bacterial diseases caused by Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis, which are typically transmitted via respiratory droplets. Numbers of weekly cases in 2020 were compared with corresponding data for 2018 and 2019. Data for disease due to Streptococcus agalactiae, a non-respiratory pathogen, were also collected from nine laboratories for comparison. All countries experienced a significant and sustained reduction in respiratory bacterial diseases in early 2020 (Jan 1 to May 31), coinciding with the introduction of non-medical COVID containment measures in each country. By contrast, the incidence of disease due to S agalactiae (which is not transmitted by the respiratory route) did not differ significantly from the 2 previous years.

Clearly, the mandates significantly reduced the incidence of respiratory infections by non-COVID viruses and bacteria. They worked. So, why did we still have COVID infections after the mandates went into place? The mandates reduced, not eliminated these diseases, so infections still happened. Since we did not have historical COVID infection data from previous years to compare with, the effects of the current mandates on the incidence of COVID are not as clear cut as they are with other diseases for which we do have historical data for comparison. But, as I wrote before (see above), it is clear that places in the US and around the world that used masks and other protective measures saw reduced incidence of COVID compared to similar places that did not.

Bottom line: The studies mentioned here regarding non-COVID infectious diseases fully support data previously posted in these pages that the mandates, including masks, are effective non-medical tools for controlling infectious respiratory diseases.

Don’t let anyone tell you differently.


Lions And Tigers And…Deer? Oh My!

First it was bats and humans, then domestic cats and dogs, farmed mink, and big zoo cats; now gorillas, hippos, and wild deer that have been infected by the SARS-CoV-2 (CoV-2 for short) virus. Many of these animals have become ill and several have died of COVID-19, most recently three snow leopards in South Dakota and Nebraska zoos. This is quite a wanton virus.

Of course, before CoV-2 and COVID-19 were known to the world, we knew that bats, humans and a few other animals, notably civets and even camels, were ready hosts of several different strains of “‘rona” viruses. We also knew that domesticated animals are also susceptible to their own coronavirus diseases—in fact veterinary coronavirus vaccines have been in use for years. Humans are known hosts for several coronaviruses, including those that cause the common cold, as well as the viruses that cause SARS, MERS, and now COVID-19. And we know that humans often catch these germs from bats and other intermediate hosts as diverse as civets and camels. After we genetically identified CoV-2 and were able to follow its spread, we quickly noticed that domestic pets also could be infected. This was closely followed with news that seven big cats at the Bronx zoo had become infected, and that mink farms across Europe were hotbeds for CoV-2 spread between humans and the animals and back. In fact, mink farms became such a hotbed of CoV-2 zoonotic spread that a couple of European countries completely shut down mink farming and culled all their animals. Several US states have also sharply curtailed mink farming. PETA probably applauds.

More recently two snow leopards at the Lincoln, NE children’s zoo and one in a zoo in South Dakota died from COVID. The Lincoln zoo also had two infected Sumatran tigers who recovered after being treated with steroids and antibiotics to prevent secondary infections and pneumonia. How the animals were infected is uncertain, but the most likely scenario is that they caught the virus from a caretaker. The problem is, none of the caretakers tested positive for the virus. Bats? Something else?

Since April 2020, when a tiger tested positive at the Bronx Zoo, dozens of other animals in zoos around the world have caught COVID. This month, the Denver Zoo reported the first coronavirus cases in hyenas, and the St. Louis Zoo found eight positive cases among its big cats, including two snow leopards. Abroad, the virus has killed a lion in India and two tiger cubs in Pakistan. Big cats seem especially susceptible since three other snow leopards at the Louisville Zoo were infected last December, and another snow leopard tested positive at the San Diego Zoo in July. The virus doesn’t just infect our fuzzy friends either; two hippos, named Imani and Hermien, at a zoo in Antwerp recently tested positive for COVID-19. Zoo keepers were first alerted to a potential problem when they noticed that the colossi had “runny noses.”  One reckons that a runny nose for a hippo is a big deal. One also wonders who gets to dab that nasal maw in order to test for the virus.

In fact, zoo and domestic animal infections have become so prevalent that an animal COVID vaccine developed by Zoetis, a NJ-based veterinary pharma company and former Pfizer subsidiary, has been authorized by the USDA for experimental use. The Cincinnati Zoo, for one, has vaccinated  80 animals, from giraffes to apes, against COVID.

Deer too. Oh my! It is one thing for zoo animals to acquire COVID—their captivity makes it easy to limit their interaction with other animals and humans to prevent spread of contagions, and they seldom complain that their rights are being infringed when they are quarantined. However, COVID in wild animals is a different story, as we have seen with bats and how easily they transmit the virus to humans. Scientists now have evidence that CoV-2 also readily propagates in white-tailed deer. In fact, the virus is already widespread in cervids across the US, which likely has significant implications for the long-term course of this pandemic.

In September of last year, genetic analysis of the gene that encodes the ACE2 protein (i.e., the viral receptors expressed on many cells in the body) in many different animal species suggested that CoV-2 could easily infect deer (and several other animals too). A survey of white-tailed deer in the Northeast and Midwest found that 40% had antibodies against the CoV-2 virus, indicating prior exposure. Between April and December 2020, veterinarians at Penn State found active CoV-2 infections in ~30% of deer tested across Iowa. Then during the winter COVID surge in humans from Nov. 23, 2020, to Jan. 10 of this year, ~80% of the tested deer were infected. The prevalence of the virus in deer was 50 to 100 times greater than in Iowa residents at the time (and the deer reportedly did not wear face masks). The study, published about two months ago, indicates that white-tailed deer have become a permanent reservoir for CoV-2. While it is not fully understood how the virus entered the deer population, genetic sequence analysis of nearly 100 viral samples found that the variants circulating in deer matched the variants circulating in people. This suggests that deer caught the virus from people multiple times in Iowa alone. How that happens is not known since people usually do not have close contact with live deer. More concerning is whether viral variants arising in deer readily pass back to people.

Bottom line. Clearly, a lot of different animal species can catch Cov-2 and spread it. It is clear that people can spread coronaviruses to pets and other animals, but the FDA says that the reverse, animal-to-human virus transmission, is not common. But, it clearly happens as we have seen with this pandemic, and with many other viruses that cause SARS, MERS, AIDS, Ebola, flu, etc., that spread from animals to humans. The prevalence of CoV-2 infection in so many species of mammals, especially in animals that have close contact with humans, suggests that several animal species, not just bats, can serve as permanent reservoirs for the virus and the jump to humans is something that can happen over and over. This is not unprecedented. It is what we see with influenza, which is carried back and forth between the Northern and Southern hemispheres with migratory birds, in which different flu viruses shuffle their genomes to create the new strains of flu for which we have to vaccinate against each year. This animal reservoir for flu makes it next to impossible to eliminate influenza, and similar animal hosts for CoV-2 likely would make it nigh impossible to eliminate COVID too. I raised this specter some months ago in these pages when reporting that pet dogs and cats can carry the virus. Our furry friends represent a viral reservoir that is in even closer contact with people than bats, deer, and fortunately, hippos and leopards.

We also have to be worried about the CoV-2 virus mutating in the different animal species that harbor and spread it. We know that happens in bats, which makes it almost certain that new strains of the virus will arise in deer and dogs too. We have already seen this on mink farms in the Netherlands and Poland. Farmworkers passed the virus to captive animals where it spread, mutated, and then spilled back into humans. In fact, zoonotic transmission from animals to humans probably happens thousands of times a year. Researchers from the EcoHealth Alliance and from Duke-NUS Medical School in Singapore, estimate that each year many people are newly infected with SARS-related coronaviruses. Many may get sick, but there are many reasons why most of these infections never grow into noticeable outbreaks (for example see my earlier blog post about unusual respiratory infection clusters in China and Los Angeles just before COVID). The researchers also created a detailed map of Asian habitats of 23 bat species known to harbor SARS-related coronaviruses then overlaid it with data on where humans live to create a map of potential infection hot spots. They found that close to 500 million people live in areas where bat-to-human transfer is likely, and this risk is highest in southern China, Vietnam, Cambodia, and Indonesia. Other surveys done before COVID-19 showed that many people in Southeast Asia harbor antibodies against other SARS-related coronaviruses. Blending these data with data on how often people encounter bats and how long antibodies remain in the blood, the researchers calculated that ~400,000 undetected human infections with these viruses occur each year across the region.

That is just for bat-to-human transfer in Southern Asia. It now looks like we will have to also concern ourselves with zoonotic coronavirus transfer from Buddy and Bambi too.

For this reason, researchers are working to develop a universal coronavirus vaccine that will be effective against most viral strains and variants. I will write about this soon. Stay tuned.

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The History Of Vaccine Mandates In The US

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As employers and the President are pushing vaccine mandates because too many have refused them, voices are crying out for their perceived rights saying “my body my choice.” They do not like their bosses or the government telling them to get vaccinated. This is a clash between individual rights and public health measures designed to save lives and to protect the larger community. Who gets to make the key decisions? How far can the government and employers go? Do individual rights trump community safety?

On Sept. 9, Biden announced the most sweeping vaccine requirements in American history, ordering that businesses with 100 or more employees ensure that all their workers are either vaccinated or get tested weekly for the coronavirus. The new rules also require vaccinations for federal workers and for federal contractors, as well as for workers at healthcare facilities that receive funding from Medicare and Medicaid. This will affect about 100 million people.

The authority for these government mandates, claims Biden, is a 1970 federal statute that gives the Secretary of Labor authority to issue a six month Emergency Temporary Standard (ETS) to protect workers from “grave danger from exposure to substances or agents determined to be toxic or physically harmful.” His move has triggered a political and legal battle, with many Republican governors vowing to fight the mandates in court. The mandates raise several new questions regarding this vague statute: Is a virus a “…toxic or physically harmful substance?” Does COVID-19 present a “grave danger?” Has the executive branch exceeded its authority in offering a solution to a problem previously reserved to the states? Do these mandates violate the 14th Amendment by depriving workers of their personal liberties? It is important to note that Biden’s mandates do not actually make vaccines compulsory: The government may levy a fine or forbid a child from attending school, but no American will be forced to get an unwanted jab. This has not always been the case.

There are historical precedents for vaccine mandates and even for forced vaccination.

In February 1991, five Philadelphia children died from measles, a disease that was mostly eradicated in the US, due to vaccination. Measles once sickened millions of kids, each year hospitalizing ~50,000 and killing close to 500 before a successful vaccine was developed in 1963. After that, cases dropped dramatically as all states mandated measles shots for school children. Vaccine hesitancy and resistance were rare because people saw the tangible success of the measles vaccine.

But, in Philadelphia that winter of 1991, the serious cases of measles came from a single source, a church cult that rejected “…all means of healing apart from God’s way.” Church members took no medicines, owned no thermometers, and saw no doctors. Rejecting all birth control, they raised large families in close quarters, a recipe for the measles epidemic, which they cooked. Trying to contain the threat to the rest of the city, officials worked through the courts to gain access to the homes of the congregants and received the authority to vaccinate the children against the wishes of their parents. In this public health emergency, defending the parents’ anti-vax actions was close to impossible. Even the ACLU took a pass.

Vaccine mandates even appeared during the Revolutionary War. George Washington mandated that all his troops be immunized against smallpox, even against their will. He described smallpox to Virginia’s Governor Patrick Henry as “more destructive to an Army in a Natural Way, than the Enemy’s Sword.” As I wrote earlier in these pages, smallpox had doomed the Colonial Army’s assault on Quebec in 1775, and it threatened Washington’s main force. Washington’s mandate proved a brilliant gambit and smallpox largely disappeared from the ranks. Some historians point to the mandate as a major factor in winning the war against the Brits.

During that war, smallpox vaccination entailed a primitive vaccination procedure known as variolation. That involved opening a lesion from an infected person and scraping its contents into the arm of a recipient. It was effective, but the vaccinated person became quite ill for a couple of weeks, and about 3% of them died from the pox. Later, in 1796, the English scientist Edward Jenner discovered a much safer method of immunization using cowpox, a virus similar to smallpox that did not cause significant disease in people. But the new smallpox vaccine got a mixed reception in the US as some resisted it for reasons of personal safety based on the variolation experience. They rationalized, “what good could possibly come from polluting the body with dangerous foreign matter?” Or, “Why challenge the plans of the Creator?” Still, Jenner’s vaccine was a clear improvement over variolation and drove a steady decline in smallpox outbreaks throughout the 19th century. States began passing laws mandating smallpox vaccinations for school children, and some forcibly vaccinated prisoners, paupers, and orphans.

In 1905, the issue of vaccine mandates reached the Supreme Court in the seminal case of Jacobson v. Massachusetts. Henning Jacobson, a Lutheran pastor in Cambridge had defied a city ordinance requiring smallpox vaccinations during an outbreak. He refused to pay a $5 fine so he was arrested. Jacobson posited that “healthy and law-abiding” people like himself (even though he was disobeying the law at the time) posed a minimal danger to the community. He argued that even if his refusal to be vaccinated led to him spreading the smallpox virus, the only victims would be others “who failed or refused to be vaccinated.” In other words, he reasoned that it would be ok to not get the vax because the vaxed would be safe, but wholly ignored the rights to safety of those who were not vaxed. 

It is an argument that is repeated today about the CoV-2 vax. Using modern science that was not available in the early 20th century, experts have repeatedly refuted this argument, explaining that many people who want the vax cannot be fully vaccinated because they are immunocompromised, or allergic to the vaccine’s contents, or do not have access to the vaccine. Also, we now know that the more RNA viruses, like the coronavirus, are allowed to spread, the greater the chance more deadly variants can appear. Jacobson’s contention that the decision to vaccinate solely belongs to the individual, not to the state, employers, or to medical authorities remains a central tenant of today's anti-vaxers.

The Supreme Court disagreed with Jacobson. The majority opinion, written by Justice John Marshall Harlan, asserted that “the liberty secured by the Constitution does not import an absolute right in each person to be at all times, and in all circumstances, wholly freed from restraint.” Rather, he argued, the Constitution rests upon “the fundamental principle of the social compact…that all shall be governed by certain laws for the protection, safety, prosperity and happiness of the people, and not for the profit, honor or private interests of any one man, family or class of men.” Jacobson had not only broken the law, the court suggested he also had violated the principle upon which a well-ordered society depends. We are not wholly independent the court ruled. The greater good of the community can trump individual rights.

Using Jacobson as precedent, the Supreme Court in 1922, upheld a local ordinance in San Antonio requiring proof of smallpox vaccination for people entering “public schools or other places of education.”  

Later, during World War II, the US military made vaccines mandatory for a host of diseases, such as typhoid, yellow fever and tetanus, and it still mandates certain vaccines for troops in certain deployments. Soon after the war very successful vaccines were developed against several childhood diseases like polio, measles, mumps and chickenpox. Guided by the Supreme Court’s ruling in Jacobson, all 50 states put laws on the books mandating many of these vaccinations for school children. Even today, many school districts and colleges mandate certain vaccines for students and staff. Hospitals, too, often mandate certain vaccines for their staff. Until lately, vaccine mandates have not generated much angst and anger.

Why is this? Perhaps vaccines have done their job too well: Many of them have erased the tragic evidence of why they were needed in the first place. The world no longer deals with small pox, thanks to the vaccine. Almost no one in this country has seen someone ravaged by polio, or a child hospitalized with measles, or who lost his hearing due to chicken pox, all thanks to vaccines. Yet, now with COVID-19, anti-vaccine anxieties have found their way into the political mainstream, especially among conservatives. An estimated 80 million American adults remain unvaccinated against COVID and represent potential factories for producing the next deadly coronavirus variant, which is very preventable.

As I have addressed before in these pages, many factors fuel resistance to the life-saving shots, including doubts about their quick development and their possible long-term effects. But a growing distrust of professional expertise, including medical science, has also played a role, which is unwarranted. Who are you going to believe, a medical scientist like me with nothing to gain in the debate (except the safety of my friends, family, and self), or someone who read a web post from folks who are selling nostrums they claim will protect you, like Dr. Steve Hotze, or from one of America’s Frontline Doctors whose web site claimed that gynecological problems were caused by having sex with demons? Do you jump on the side of those who tout that their individual freedoms have been abridged, but who do not consider the freedoms from disease of the greater community, and whom the courts already have decided against?

Almost 300 years ago, Benjamin Franklin struggled over whether to have his sons variolated against smallpox. In his “Autobiography,” he worried that well-meaning people were tragically misjudging the calculus between the risks and benefits of the procedure, as he had once done, with a tragic result. He wrote, “In 1736, I lost one of my sons, a fine boy of four years old, by the smallpox….I long regretted bitterly and still regret that I had not given it to him by inoculation. This I mention for the sake of the parents who omit that operation, on the supposition that they should never forgive themselves if a child died under it; my example showing that the regret may be the same either way, and that, therefore, the safer should be chosen.”


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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What Is Going On In India?

The situation. India is in the throes of a second major Covid-19 surge that has hit faster and harder than the first wave did. That is often how viral pandemics behave. This catastrophic second wave came after a strict lockdown of the country in early 2020 following the first wave. In January 2021 India’s Prime Minister Modi declared that the lockdown had succeeded and that they had defeated the virus, and he re-opened the country. Until March, India was recording barely 13,000 new COVID-19 cases a day, fewer than Germany or France, and a drop in the bucket for a nation of 1.4 billion people. A few weeks after Modi’s victory declaration, however, daily cases began slowly climbing, then in late March they exploded, becoming a vertical line rather than an upward sloping curve. By mid-April India reported 315,000 new cases in one day, setting a world record. Yesterday (May 5) India set yet another record with 3700 daily deaths, according to the Johns Hopkins University tracker. The case and death rates are still climbing. Today, almost 50% of the world’s new cases come from India, according to the WHO.

India has reported 2,000-4,000 COVID-19 deaths a day for several weeks now. Since the country’s health infrastructure is poor, this likely represents a significant undercount of the mortality. As of April 30, the official total death count was around 200,000. However, the official tallies do not reflect the thousands in poor and rural areas who cannot get medical care and die at home and are not counted. For example, in just one day at one crematorium in Bhopal, workers cremated 110 COVID-19 victims, but the official total death toll for the city was just 10. Experts suspect that the total death toll in India is 1-2 million.

The second wave of the pandemic also has overwhelmed hospitals across India. Securing a hospital bed, even for the critically ill, is nearly impossible. Hospitals put up signs declaring they have no beds, and families in large cities have to search for days to find beds, often hundreds of miles away. Sick people die on the roads outside hospitals and in traffic jams created by ambulances ferrying critically ill patients in search of a bed. There are images of patients gasping for oxygen while waiting to see a doctor.

Because getting admitted to a hospital is so difficult now, patients who are admitted are much sicker than in India’s first wave. The average temperature readings of second wave patients are 2 to 3 degrees higher than they were during the first wave when temperatures averaged 100-101 degrees Fahrenheit. Blood oxygen levels of recently admitted patients run lower than they did last year meaning the patients are more critical and in greater need of oxygen. The patients are also younger this time around, between the ages of 35 and 45, and often without other pre-existing conditions.

Critical healthcare necessities are in short supply in India, from intensive care beds, medicine, oxygen, and ventilators. Delhi hospitals have tweeted messages appealing for oxygen. At one Delhi hospital, 20 critically ill patients died after the hospital’s oxygen delivery was delayed seven hours. Families are often told that they have to provide their own oxygen for hospitalized family members or take them home. In a video post, the director of a hospital said they had 60 patients in need of oxygen with only two hours of supply left.

Help for India has been offered by several countries, including the US, UK, Germany and even from India’s archrival Pakistan, which offered ventilators, oxygen supply kits, digital X-ray machines, PPE, and related items.

Bottom line. This is a snapshot of what things look like in India now, almost a year and a half after the virus first introduced itself to the world. In January, India believed that its strict lockdown measures had defeated the virus. They did not. How the more deadly second wave of the virus and disease appeared, almost overnight, will be the topic of the next blog post. It should concern all of us, because it could also happen here.

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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.


More Than Half CoV-2 Transmission Comes From People Without COVID-19 Symptoms

The Journal of the American Medical Association just reported that 59% of new CoV-2 infections are likely caused by infected people who do not show COVID-19 symptoms. This conclusion is based on the results of a decision analytical model that assessed the spread from pre-symptomatic, never-symptomatic and symptomatic people infected with CoV-2. 35% of viral transmission came from pre-symptomatic people, and 24% from people who never develop symptoms.  

This means that until the vaccines are widely disseminated, identifying and isolating people with COVID-19 will be much less effective at controlling the spread of the virus than previously thought. Effective control of the disease still requires social isolation measures such as wearing face masks indoors, distancing from others, hand hygiene, and limiting indoor contact with other people.


New Coronavirus Mutation Enhances Spread

The Wall Street Journal reports that countries across Europe and beyond are banning travel from the UK in order to stem a more-infectious strain of Covid-19 that has been found in the London area. The new strain was first reported last Monday, and on Saturday, England announced that it is imposing fresh lockdowns in London and surrounding areas, which also include a ban on households mixing at Christmas. Similar restrictions have been taken across Europe with Italy announcing a complete lock down across the country. Germany and the Netherlands imposed lockdowns through Christmas, and Austria said Friday that nonessential businesses will be closed starting Dec. 26. However, it also appears that the new strain has popped up in Denmark and South Africa. Holland reported one case with the new virus variant.

Scientists believe the new strain of the coronavirus could be as much as 70% more transmissible than previous strains, but there is no evidence at this time that it is any more deadly or more resistant to the vaccines.

It seems that the virus mutated to change the spike protein on the surface of the virus, increasing the protein’s ability to cling to and chauffeur the virus into human cells. These changes allow the mutation, known as N501Y, to spread faster than other versions of the virus. Early analysis suggests the variant first occurred in September either in London—where it was identified on Sept. 21—or in the nearby county of Kent, where it was found on Sept. 20. That might explain why quarantine restrictions that have been effective elsewhere in England have not been effective in Kent. By mid-November, 28% of cases in London were attributable to the new variant. In the week starting Dec. 9, it was responsible for 62% of cases in the capital. In other words, this variant is winning the infection race against all other CoV-2 strains out there. As of December 19, there has been no evidence of the new strain in the US.

Viruses mutate all the time, but coronaviruses do so less than, say, the flu virus. Mutations happen when rare, random errors are made while cells copy millions of viral genomes. Most mutations are innocuous, but sometimes these accidental changes alter the behavior of the virus. Scientists have identified 23 genetic changes in the genome of the new variant, an unusually large number, some of which are associated with small changes in the proteins the virus makes, which, therefore, can change viral behavior. Those include changes in areas known to be associated with how the virus binds and enters cells, which probably explains why it spreads more quickly. While efforts, including quarantine measures and the new vaccines, are designed to drop the infection rate of the virus, or the R0 number, these mutations threaten to work against those efforts and increase the virus R0 value.

Two main questions are now being investigated: Is the new variant more likely to cause increased morbidity and/or mortality, and is it more likely to avoid the body’s immune responses, including those encouraged by vaccines? The provisional answers to those questions are no and no, but the research continues, so these conclusions are preliminary. We will see.

The new variant isn’t the first time a more-transmissible CoV-2 strain has emerged. As reported in these pages last summer, scientists in July described a viral variant that displaced an older strain of coronavirus to become the dominant strain in the global pandemic. Experiments showed that the variant replicated more quickly in tissue culture, but appeared to be just as susceptible to antibodies that targeted the earlier strain, and was not associated with more severe illness.

The bottom line is that as viruses replicate in cells, spread, and replicate some more, they acquire small mutations in their genome. It is like playing the lottery, an occasional mutation will be the “winner” and the ability to spread and even cause new diseases can arise. Like the lottery, the more you play the greater the chance of a winner. This is why calls for “natural herd immunity” by letting people get infected are really bad ideas--they are gambling that while spreading through a population, the virus does not become even more virulent. This also is why health professionals recommend quarantine measures to limit the reproduction-spread-more reproduction of the virus until we have vaccines that effectively block the reproduction and spread and mutation of the virus.

Otherwise, we are just playing the virus lottery.

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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.