Happy holidays; religion (obviously) moving into plagues today, what else?

Happy holidays; religion (obviously) moving into plagues today, what else?

Happy holidays; religion (obviously) moving into plagues today, what else? But first, Omicron data aside, the 2 most interesting datapoints for me last week were Biogen cutting the price of Aduhelm by 50% and the U.S. population grew by just 0.1% in the year ended July 1, 2021, "the lowest rate since the nation's founding," per Census Bureau population estimates just released. The year 2021 is the first time since 1937 that the U.S. population grew by fewer than one million people, featuring the lowest numeric growth since at least 1900, when the Census Bureau began annual population estimates. Apart from the last few years, when population growth slowed to historically low levels, the slowest rate of growth in the 20th century was from 1918-1919 amid the influenza pandemic and World War I:

Slower population growth has been a trend in the United States for several years, the result of decreasing fertility and net international migration, combined with increasing mortality due to an aging population. In other words, since the mid-2010’s, births and net international migration have been declining at the same time deaths have been increasing. The collective impact of these trends is slower population growth. This trend has been amplified by the COVID-19 pandemic, resulting in a historically slow population increase in 2021:


It’s interesting that one of the most fervent US anti-vaxxing groups has been the religious right, excuse the pun:


Apart from the obvious changes, the pandemic has released all sorts of cultural toxins into the bloodstream of society, infecting the body politic and likely causing lasting and even irreparable damage. One of these is the empowerment of the conspiracy movement, always extant of course but never as activated and dangerous as it is now. It’s manifested itself especially severely in the anti-vaccine campaign, a phenomenon that damages public health, causes civil unrest and, in some parts of the world, leads to direct violence. A curious, though perhaps not completely surprising, element in the movement is conservative Christianity, which remains an extremely powerful force in the US, in particular. Specifically, the reactionary wings of the Roman Catholic and evangelical churches, comprised of the very people who largely voted for Donald Trump and will – if given the morbidly likely chance – do so again. He, naturally, inflamed matters by stating that some US states had closed places of worship to stop the spread of Covid, while allowing “liquor stores and abortion clinics” to stay open.

It’s important to get this right. Most faith communities – including Christianity, Islam and Judaism – closed their places of worship without being asked and have reopened gradually and carefully. They have no objections to vaccines and even actively support them. While there are objections among some orthodox Jewish communities, Israel has been at the forefront of mass vaccination. So why the militant opposition among right-wing Christians, who can surely hold on to their ultra-conservatism while accepting the efficacy of modern medicine?

But they don’t. A recent poll by the US Public Religion Research Institute found that less than half of white evangelicals said they would agree to be vaccinated. Nor is the problem confined to the US. In late 2020 in Canada, Derek Sloan – an Adventist and then a Conservative MP – sponsored a parliamentary petition arguing incorrectly that, “Bypassing proper safety protocols means Covid-19 vaccination is effectively human experimentation.” It received over 40,000 signatures.

Throughout North America, and in parts of Europe, there are churches, often large and wealthy, that have rejected vaccines and even social distancing and masks. Tony Spell is a minister at the Life Tabernacle Church in Baton Rouge, Louisiana, who ignored state law by conducting church gatherings. “We’re anti-mask, anti-social distancing, and anti-vaccine,” he said. Rick Wiles, a particularly odious homophobic and racist broadcaster who pastors a church in Florida, condemned vaccinations as part of a “mass death campaign”, even when he, his wife and daughter-in-law were infected. “This was a full-frontal hit from Hell,” he wrote. “Because Jesus Christ lives in us, we shall live too. Thanks to Jesus Christ, I survived the CCP [Chinese Communist Party] Covid genocide on the American people.”

The list goes on. Arrests have been made, the police have closed churches, physical resistance has taken place, and as the pandemic continues the situation is becoming increasingly polarised and volatile. More established and moderate evangelical churches and leaders, while far from progressive, are more accepting of vaccinations. But they often fight a losing battle. Their problem is how Christian nationalism has eaten its way into their churches, which means a profound fear and hatred of government – seen as either a political opponent or, believe it or not, a vehicle of Satan. As absurd as this might sound, it’s a belief that runs deep. Barack Obama, Hillary Clinton and others have been described as the Antichrist – and the Antichrist is to be opposed by force.

This idea of the great opponent of God has always existed within Christianity but its personification in political figures has become common in recent years. Fuelled by a series of successful end-times books and internet posts, various hate figures – invariably US Democrats – have been identified as the ultimate enemy of religion. The possible consequences, even beyond the pandemic, are terrifying.

Covid, continues the theory, may well be a hoax. If not, it was manufactured as a means to control the population, reduce it, and then allow mass vaccinations to take place. These vaccines apparently allow the state to monitor us, prevent us from procreating, and also stamp us with “the mark of the beast”. The latter is a reference to the Book of Revelation, where the Antichrist – yes, him again – is supposed to seduce Christians into marking their bodies. It’s a grotesque and literalist misreading of a complex, allegorical and poetic ancient text, linked to obsessions with Armageddon and eschatology.

Religion on the good side has been a profound force in human history and, contrary to many assumptions, it remains so today, for better or worse. Even before humans left the cave and gave up hunter-gathering, before settled communities, in one form or another, faith shaped our destinies. Today among other reasons to take these institutions and forces seriously, survey after survey highlights that faith leaders are often the most trusted group among leaders, across many world regions. We have fought over different gods and differ on many core values from the first inklings of civilization. In virtually all, however, from the most primitive to the most sophisticated, the central premise has been the belief in protecting communities of believers, whether from others or from unknown or misunderstood threats. These have been fundamental principles for millennia. Likewise, the most positive human values hold that in considering our roles and actions, we should do unto others as we would have them do unto us. Fast forward to 2020: frictions between different religions and other isms remains intense, predictably so. But Covid-19 is new, both in its qualitative and quantitative aspects. This “new” is coupled with other factors, in particular, ease of transmission of a global virus affecting all corners of the world, science-based technological capability to limit its deadly effects, and an unprecedented ability to instantly communicate everywhere, for good or ill. This is a good document to start with here, on the interaction between vaccines and religion:


Here are some survey results, with most Christians (55%) saying that churches have not made much of a difference in the country’s handling of the coronavirus, with the remainder more likely to say they have helped (28%) rather than harmed (16%). A strong majority of atheists (71%), meanwhile, say that religious organizations have done more harm than good in the country’s response to the pandemic.

Democrats are much more likely than Republicans to say that churches have done more harm than good in the country’s response to the pandemic (39% vs. 9%), as are Americans who attend religious services a few times a year or less compared with those who attend monthly or more often (30% vs. 14%). The US is still a very ‘religious country’: Top of Form

For vaccines, we know there will be individuals who will be difficult to reach, others who will be dubious about the reliability of any public health measure that comes with the backing of scientists, or who basically mistrust their government in whatever form. Still others will resist because their spiritual leaders counsel their congregants not to be vaccinated, invoking traditions, myths, customs, taboos, or other reasons to oppose, however strong the case for efficacy and safety may be. The Vatican has just said the use of Covid-19 vaccines developed using cell lines derived from aborted foetuses is "morally acceptable" in the absence of an alternative jab: "All vaccinations recognised as clinically safe and effective can be used in good conscience with the certain knowledge that the use of such vaccines does not constitute formal co-operation with the abortion from which the cells used in production of the vaccines derive," the Vatican’s Congregation for the Doctrine of the Faith announced in a statement. The text, which was approved by Pope Francis, also said there was “a moral imperative” to ensure that poorer countries were able to access effective vaccines. The doctrinal orthodoxy office said that “vaccination is not, as a rule, a moral obligation” and must be voluntary. But from an ethical point of view, “the morality of vaccination depends not only on the duty to protect one’s own health but also on the duty to pursue the common good,” the office said. The AstraZeneca vaccine is among those developed using cells derived from foetuses aborted decades ago, although no foetal cells will be present in the vaccine itself. It is worth a look at this, which describes the emotional relationship that led to the cells for vaccine production being isolated:


As Pope Francis said “How sad it would be if access to a Covid-19 vaccine was made a priority for the richest. It would be sad if the vaccine became the property of such-and-such nation and not universal for everyone,” That said, religious support is not a given. Individual Dioceses and Bishops can and have differing opinions and have opposed COVID vaccination for various reasons. In the US, Bishop Joseph Brennan, head of the Diocese of Fresno, said in a video: “I won’t be able to take a vaccine, brothers and sisters, and I encourage you not to, if it was developed with material from stem cells that were derived from a baby that was aborted, or material that was cast off from artificial insemination of a human embryo”:


In the case of Islam, the Qur’ān oblige its followers to seek protection from illness, regardless of who is providing that protection. Respected Muslim leaders thus argue that they want a cure, or at least a vaccine, as badly as anyone else. Religious support should therefore be expected. The Prophet Muhammad said: “There is no disease that God has created for which He has not made a cure that is known by some people and unbeknownst to others, except death.” The husband/wife BioNTech team are of Turkish Muslim heritage. Other Islamic leaders, however, have concerns around the safety and permissibility of vaccines that are being developed, and what they say can influence millions. For the 225 million Indonesian Muslims, the supreme authority on religious affairs is the Indonesian Ulama Council or the MUI. When the central MUI issued a fatwa in 2019 that suggested that the measles and rubella vaccine was forbidden, many conservative families across the archipelago refused to vaccinate. A central problem is related to the halal status of the vaccine; in an emergency situation, halal certification in principle should not be an issue. The latest news is that the MUI together with the Indonesian Halal Certification Agency (BPJPH) has just finished a study on the halal status of a possible Covid vaccine and is expected to soon issue a fatwa that will allow (or not) Indonesians to be vaccinated. In other settings (Nigeria, Pakistan), Muslim leaders came to fear that polio vaccination presented dangers though with careful dialogue most doubts were overcome. One turning point came in Nigeria when leaders vaccinated their children in public. Regarding COVID-19 and vaccine prospects, their position is still not confirmed. But, in the UAE, their highest council has recommended use of vaccines even if they contain pork gelatin:


Sadly, many conspiracy theories centre on religion. Much of the scepticism here is purported to date back to recent times. In 2011, the CIA orchestrated a fake Hepatitis B vaccination campaign in the neighbourhood in which it suspected Osama bin Laden was hiding: Abbottabad, Khyber Pakhtunkhwa, Pakistan. The CIA’s goal in cleverly pursuing this drive was to obtain Osama bin Laden’s family DNA samples. It won’t surprise you to know that Dr Afridi who led this is a traitor in Pakistan, while being “hailed as a hero” in the US:


The CIA’s botched fake vaccination drive, which was revealed to Pakistanis in 2011, deepened existing distrust of the polio vaccination campaign among certain Pakistani people. In 2012, a resurgence of polio cases appeared in Peshawar, Karachi, and in the Federally Administered Tribal Areas along Pakistan’s border with Afghanistan, washing away the eradication progress of the early 2000s. Ever since the CIA’s operation, the Taliban and other Islamist militant groups have reinforced growing distrust of vaccines with anti-Western rhetoric and utilized anti-vaccination sentiment as a tool in their anti-Western messaging. Healthcare workers are still killed, labelled as “Western spies”.  Despite an expressed commitment toward limiting vaccine misinformation content online from both the Pakistani government and social platforms, one of the most pernicious outbreaks of vaccine-related misinformation in Pakistan’s history occurred on April 22, 2019, well beyond the Bin Laden issue. On that date, a set of staged videos claiming that children had fallen sick after being administered their polio vaccinations began spreading on social media platforms. The videos were posted as part of a pre-planned conspiracy against the polio eradication campaign. Much of the misinformation posted on platforms on April 22nd has since been deleted, making it difficult to determine where the videos first appeared (videos currently still exist on Twitter and Facebook). On April 22nd, the videos spread across social platforms, registering at least 24,444 interactions on Twitter within the first 24 hours of being posted. Local news media channels that picked up the story only amplified the rumours. Below is a screenshot from 1 video that gained a great degree of traction on social platforms and within professional media coverage. In the video, while standing in the Hayatabad Medical Complex, Nazar Muhammad, a private school teacher and resident of Peshawar warns viewers that children had begun falling sick after being administered expired polio vaccinations. He then clearly instructs the children surrounding him to fall asleep:

I could go on with countless (really) other videos in which he tells reporters in front of a Peshawar hospital that some children had died after being vaccinated. However much junk this is, the spread of misinformation about the polio vaccine caused mass hysteria in northwest Pakistan. On April 22nd alone, concerned parents brought a total of 25,000 children to the 3 hospitals of Peshawar. On the same day, a mob of 500 people set fire to a health clinic in Peshawar and obviously healthcare workers were killed. Next, others commented that the addition of Vitamin A to the polio vaccine may have contributed to the rise of the rumour. This is because Vitamin A, which was additionally added to polio vaccines to help malnourished children, can cause symptoms of stomach pain and/or nausea. This may have lent validity to the suggestion that the vaccine itself was making children sick. But, due to the outbreak of violence, Pakistan suspended its anti-polio campaign on April 27th:


Historic data on engagements and interactions from January to June 2019 was collected by automatically collecting posts that contained keywords and hashtags related to polio. Crowdtangle was used to collect Facebook, Instagram and Reddit posts, while the Python programming language was used to automatically collect tweets from the Twitter Search API. The sample was based on the CrowdTangle database. In the data analysis, a group focused on calculating keyword frequency spikes over time and analysing top retweeters and posts that gained high interactions:

Total number of tweets containing the hashtag #no_more_polio on each day between April 21st and 25th. What’s interesting about Pakistan’s hashtag usage is that all 4 hashtags most commonly used to spread anti-polio vaccine messages appear to be pro-vaccine in nature. However, hashtags like #no_more_polio actually express resistance to the polio vaccine, not the disease of polio itself. One can look at analyses for Google too:

Also interesting are the 6th and 7th most commonly searched questions related to polio: “Does the polio vaccine have side effects?” and “who invented polio vaccine?” The high frequency of searches of the 7th question in particular demonstrates a lack of understanding among Pakistani citizens about the origin of the polio vaccine. One of the most effective anti-vax strategies is to focus on the immediate effects of a vaccination on a child. Posting images of rashes or a child looking listless or ill utilizes the credibility of personal experience. In this context, reporting on the purported effects on children was common. There were numerous Instagram posts with a screenshot of an article originally uploaded by New York Daily News. The post claims that 230+ children were suffering from nausea following their vaccinations, though that statistic is never mentioned in the article:

Within this particular format of messaging, another prominent theme emerges: amplification of the rumour by professional media. These are typical other tweets:

Many social media posts included images of polio vaccinators being assisted by armed police officers, whose jobs involve ensuring the vaccinators’ safety, especially given that attacks targeting polio vaccinators are common in Pakistan. The posts inaccurately conflate the weapons in the photograph with the idea of government oppression, suggesting, without basis, that polio vaccinators force parents into vaccinating their children:

Since many of the key figures involved in Pakistan’s polio eradication campaign are associated directly and indirectly with Prime Minister Imran Khan’s political party (Pakistan Tehreek-e-Insaf), it is sometimes suggested that the goal of polio eradication has become politicized, being carried out almost exclusively by the prime minister’s party. The Pakistan incident should be seen as a critical event from which platforms, health authorities, and other actors can learn. Understanding what happened in Pakistan in April 2019 could potentially allow us to handle similar situations more effectively in the future, for COVID-19 (good luck with that one).

In Judaism, Rabbi Hershel Schachter, who is a highly respected American Orthodox rabbi: “If a democratic government ultimately legislates that a COVID-19 vaccination is safe for the public or specific populations, people must comply with this ruling. Jews who refuse to abide by government-mandated vaccination endanger all of society.” He then notes that the measles outbreak in Hasidic communities in the United States with low vaccination rates and the subsequent public disgust with ultra-Orthodox Jews illustrates the potential for desecrating God’s name when Jews defy normative practice and legal requirements. Remarkably, some anti-vaccination activists have begun Star of David that Nazis forced Jews to wear, to promote their cause. 

What about religion, lockdowns and the law; on November 25th as Americans were preparing their turkeys for Thanksgiving, the U.S. Supreme Court, by a 5-to-4 vote, undermined states’ ability to control that pandemic. In Roman Catholic Diocese of Brooklyn vs. Cuomo, the Court temporarily enjoined limits on in-person religious worship imposed by New York Governor Andrew Cuomo. Although the injunction will have little effect because the restrictions were no longer in place by the time of the ruling, the decision has the potential to upend public health law during the current pandemic and afterward. Since March 2020, U.S. governors have placed numerous restrictions on public gatherings. Many of these restrictions have been challenged in court as violating a broad array of constitutional rights, including free exercise of religion, freedom of speech, and the right to travel. Initially, most courts rejected these claims, citing the Supreme Court’s 1905 decision in Jacobson vs. Massachusetts, which upheld a Cambridge, Massachusetts, regulation mandating smallpox vaccination during an outbreak. On May 29th 2020, the Supreme Court issued its first Covid-19–related decision in South Bay United Pentecostal Church vs. Newsom. In this case, the Court, by a 5-to-4 vote, declined to block California’s limit on attendance at places of worship. Although the majority did not issue an opinion, Chief Justice John Roberts, in a concurring opinion, emphasized the heavy burden facing litigants who seek emergency relief from the Court. He further noted that the state had imposed similar restrictions on secular gatherings. Quoting Jacobson, he added that the Constitution “principally entrusts ‘[t]he safety and the health of the people’ to the politically accountable officials of the States.” In his dissent, Justice Brett Kavanaugh argued that California’s policy discriminated against religious services by treating them differently from many secular activities.

On July 24th, the Court revisited Covid-19–related restrictions on religious worship in Calvary Chapel Dayton Valley vs. Sisolak. Once again, without an opinion, the Court denied an emergency petition by a 5-to-4 vote. In pointed dissents, Justices Samuel Alito, Neil Gorsuch, and Kavanaugh argued that the Nevada order in question discriminated against religion by treating casinos more favourably than places of worship. Alito also questioned Jacobson’s relevance to free-exercise claims, noting that it was not a First Amendment case. By the time New York’s restrictions came before the Court, its composition had changed. In September 2020, Justice Ruth Bader Ginsburg died. The far more conservative Justice Amy Coney Barrett replaced her. With Barrett’s ascension to the Court, there was a 5-to-4 majority willing to block limits on religious services. The orders at issue in Roman Catholic Diocese limited in-person worship in so-called red zones of Covid-19 transmission to no more than 10 people; only 25 people could attend services in orange zones. Many other activities, such as grocery shopping and education, faced no such caps. After the litigation began, Cuomo revised the designations so that the plaintiffs, the Roman Catholic Diocese of Brooklyn and Agudath Israel of America, could hold services in their facilities at up to 50% of capacity. To Roberts, who dissented from the ruling, this development meant that there was no longer any reason for the Court to intercede, even though he found New York’s orders troubling.

The majority disagreed. In an unsigned per curiam opinion, it held that the plaintiffs’ rights to free exercise were most likely violated because the governor’s orders “single out houses of worship for especially harsh treatment” that was not imposed on stores, factories, and schools. Because of such discrimination, the majority concluded, the orders were subject to strict scrutiny. Hence, they could survive judicial review only if they were “narrowly tailored” to address a “compelling” state interest. Although the Court accepted that controlling Covid-19 was a compelling state interest, it found that the orders were not narrowly tailored because they were tighter than those imposed by other states and because no outbreaks had been associated with the plaintiffs’ houses of worship. The Court added, “Even in a pandemic, the Constitution cannot be put away and forgotten.”

The concurring opinions were more pointed. Gorsuch derided New York and other unnamed states for treating religious worship more harshly than other activities. He also criticized Roberts’s South Bay opinion for relying on Jacobson, which he called a “modest” decision. Gorsuch added, “things never go well” when the Court tries to “stay out of the way in times of crisis.”

In his dissent, Justice Stephen Breyer pointed to epidemiologic evidence that in-person worship may pose a greater risk than shopping and other activities that were less stringently regulated to argue that the Court should defer to state officials. In her dissent, Justice Sonia Sotomayor argued that New York had not discriminated against religious institutions because it treated worship more favourably than many secular activities. She added, “Justices of this Court play a deadly game in second guessing the expert judgment of health officials.”

The injunction ordered by the Court will have little direct effect because the relevant caps on attendance were no longer in place when the ruling was issued. Moreover, the majority appeared open to restrictions that treat religious services identically to comparable secular activities. Nevertheless, the Court’s eagerness to intervene even though New York’s orders were no longer in effect and its failure to consider epidemiologic evidence in determining which activities are comparable to worship will serve as a warning that state orders that impose tighter measures on worship than on some secular activities will face the strictest of scrutiny. Furthermore, the Court’s finding that New York’s restrictions were not narrowly tailored because there was no evidence of viral transmission in the petitioners’ houses of worship and because other states had looser regulations suggests that states will not be able to act before super-spreader events occur or as long as other states take a more lax approach.

This development presents states with a dilemma. In the absence of a national pandemic policy or sufficient stimulus support, many governors have responded to the new surge in Covid-19 cases by imposing fine-tuned restrictions in an attempt to protect health without decimating the economy. Some of these measures have affected religious liberty in troubling ways; others are epidemiologically questionable. For example, Rhode Island has banned all social gatherings in homes while allowing catered events. Unquestionably, courts must ensure that such measures do not serve as a pretext for discriminating against vulnerable people or quashing protected liberties. Nevertheless, the Court’s approach in Roman Catholic Diocese devalues federalism and public health, making it difficult for states to rely on science and craft fine-tuned measures in response to local conditions. Although courts should not abdicate their role during a pandemic, they also should not rush to assume an expertise they lack. Already, the case’s effects have been felt. In December, the Court ordered a lower court to reconsider its rejection of a challenge to a California regulation that affects in-person worship. Beyond the pandemic, Roman Catholic Diocese’s most important legacy may be the dethroning of Jacobson. Gorsuch is correct that Jacobson was not a free-exercise case and does not control such claims. Still, for more than 115 years, Jacobson has been the key precedent supporting vaccine mandates and other public health laws. It has also served as a reminder of the importance of public health evidence and the fact that “real liberty” cannot exist in the absence of reasonable restraints to protect the public’s health. With Jacobson apparently side-lined, the future of many public health laws, including and especially vaccine mandates, appears perilous.

Now plagues. There are now, trapped in Arctic ice, diseases that have not circulated in the air for millions of years — in some cases, since before humans were around to encounter them. Which means our immune systems would have no idea how to fight back when those prehistoric plagues emerge from the ice. The Arctic also stores terrifying bugs from more recent times. In Alaska, already, researchers have discovered remnants of the 1918 flu. They actually extracted it from the cadaver of a frozen woman. that infected as many as 500 million and killed as many as 100 million — about 5% of the world’s population and almost six times as many as had died in the world war for which the pandemic served as a kind of gruesome capstone. As the BBC reported in May, scientists suspect smallpox and the bubonic plague are trapped in Siberian ice, too — an abridged history of devastating human sickness, left out like egg salad in the Arctic sun. Experts caution that many of these organisms won’t actually survive the thaw and point to the fastidious lab conditions under which they have already reanimated several of them - the 32,000 year old "extremophile" bacteria revived in 2005, an 8 million-year-old bug brought back to life in 2007, the 3.5 million-year-old one that a Russian scientist self-injected just out of curiosity - to suggest that those are necessary conditions for the return of such ancient plagues. But already last year, a boy was killed and 20 others infected by anthrax released when retreating permafrost exposed the frozen carcass of a reindeer killed by the bacteria at least 75 years earlier; 2,000 present-day reindeer were infected too, carrying and spreading the disease beyond the tundra.

I think we probably don't have to worry very much about ancient diseases from millions of years ago. Animal diseases can't trivially become contagious among humans. Sometimes an animal disease jumps from beast to man, like COVID or HIV, but these are rare and epochal events. Usually they happen when the disease is very common in some population of animals that lives very close to humans for a long time. It’s not “one guy digs up a reindeer and then boom”.

If a plague is so ancient that it's from before humans evolved, it's probably not that dangerous. In theory, it could be dangerous for whatever animal it originally evolved for - a rabbit plague infecting rabbits, or an elephant plague infecting elephants. And then maybe after many rabbits are infected, some human might eat an infected rabbit and get unlucky, and the plague might mutate to affect humans. But I don't think this is any more likely than any of the zillion plagues that already infect rabbits jumping to humans, and nobody is worrying about those.

The story about anthrax is a distraction. The fact that someone got anthrax from a corpse frozen in permafrost is irrelevant; there is anthrax now, and you could get it from a perfectly fresh corpse or living animal if you wanted. It's adapted to animals and it can't spread from person to person. Just because you got an irrelevant-to-humans modern animal disease when you dug up a modern animal, doesn't mean you're going to get a dangerous-to-humans disease from an ancient animals.

But I'm more concerned about recent human plagues coming back. Not bubonic plague; that one is another distraction. The reason we don't get more Black Deaths isn't because yersinia pestis died off or mellowed out. It's because we have good sanitation and pest control.

And doctors whose knowledge of medicine doesn't begin and end with "look like a creepy bird" But the 1918 Spanish flu has, as far as I know, legitimately died out. Lots of people like saying that in a sense it's still with us. This NEJM paper points out that it's the ancestor of all existing flu strains. But most of these flu strains are less infectious than it was. This didn't make sense to me the first, second, or third time I asked about it: why would a flu evolve into an inferior flu? Sure, it might evolve into a less deadly flu because it's perfectly happy being more infectious but less deadly:


But I think the Spanish flu was also especially infectious; so why would it evolve away from that? One possible answer is "because by 1919, everyone had immunity to the 1918 flu, so it evolved away from it - and now nobody has immunity, but it lost the original blueprint." The 1918 flu was a really optimal point in fluspace, but during all of history up until 1918, the flu's evolutionary hill-climbing algorithm didn't manage to find that point, and since flu has no memory it's not going to be any easier for it to find it the second time, after it evolved away from it. So plausibly, existing flus are strictly worse at their job than Spanish flu was, and digging up an intact copy of the latter would be really bad.

And then there's smallpox. No mystery why smallpox died out: we killed it. But then we stopped vaccinating people against it, and now if it comes back it would be really bad:


This actually raises a broader question: how worried should we be about getting smallpox from corpses and artifacts in general? Should we freak out every time we dig up an Egyptian mummy? This study does our freaking out for us: they catalogue several incidents of archaeological or incidental excavation of smallpox-infected corpses, including, yes, the mummy of Pharaoh Rameses:


Chinese writings from 1122 bce contain references to smallpox-like disease, and it has been hypothesized that smallpox caused the death of Ramses V in Egypt in ≈1157 BCE because poxvirus-like lesions were seen on the mummy. The most recent epidemics of smallpox occurred through the 1900s, and the last naturally occurring case of smallpox was seen in Somalia in 1977. Historical tissue specimens and artifacts yield useful information about the history of and vaccination against smallpox. However, the absolute viability of poxviruses in well-preserved samples has not been determined. Thus, it is not known what risks these artifacts might pose to persons who come into contact with them.

An anecdote from eighteenth century England describes an outbreak of smallpox believed, at the time, to be caused by exposure to a long-buried corpse. The grave of a person with smallpox who died 30 years earlier was unearthed in the process of preparing a second grave nearby, and several of the funeral attendees became ill with smallpox. Whether these grieving attendees contracted smallpox from the graveside or from another ill person in the community, a likely occurrence during an outbreak, is unknown. However, occupationally derived smallpox infections beset mortuary workers and those who had close contact with bodies of deceased patients with smallpox. In these cases, the disease was likely contracted by contact with virus in or on the corpse or on contaminated clothing or linens. These infections may have occurred because of exposure to a recently deceased patient with smallpox, but a question remains with us now: can live virus be maintained in well-preserved ancient corpses and mummies?

An early examination of evidence for variola virus was conducted on a piece of skin from a male mummy housed at the Cairo Museum of Antiquities. The mummy had vesicular cutaneous lesions distributed in a pattern characteristic of smallpox. A portion of skin processed for light microscopy did not show definitive pathologic characteristics of smallpox. However, these ancient tissues were not ideally preserved for histological examination. The discovery of lesions present in a typical distribution on the mummified body of Ramses V implicated smallpox as the young pharaoh’s cause of death and shed new light on ancient Egyptian history, as well as that of variola virus. Centuries after his death, skin taken from the shroud of the mummy of Ramses V showed some viral particles and had faint immunologic reactivity; however, the sampling method was noted to have potentially been flawed and no live virus or viral DNA was isolated or amplified from specimens. Human DNA was also not detected in these specimens. Thus, although there is no laboratory data to firmly support a postmortem diagnosis, the visual appearance was suggestive of a variola infection before his death.

There have been 2 examples of corpses exhumed from crypts during archeologic excavations in the twentieth century. In both examples, the corpses had what were described as typical variola lesions, and the bodies had been contained in cool, dark environments. No live virus, viral DNA, or human DNA remained within these corpses. However, a corpse from sixteenth century Italy showed immunologic electron microscopy results that were consistent with those expected for orthopoxvirus infection. An archeologic excavation of a known Native American grave site (1640–1650) in Ontario, Canada, recovered bones from an adult male. The bones had visual scarring and an appearance consistent with osteomyelitis variolosa, a disease manifestation of smallpox in the bones and joints. On the basis of extensive document review and bone analysis, the investigators determined that the person likely had smallpox before 1639 and survived the infection with long-term osteomyelitis variolosa.

Two corpses with questionable lesions and that had been contained within permafrost in Siberia have been unearthed: one was unearthed naturally during flooding, and the other during an archeologic excavation. Dating of the corpses to the late seventeenth or early eighteenth century matched with written accounts of smallpox epidemics in the local communities for one of the sites, but no live virus was obtained from these remains. The more recent archeologically excavated corpse was sampled as soon as graves and mummified remains were exposed to the surface. The corpse yielded DNA closely related to more recent variola virus specimens. This finding provided further insight into the strain of variola that was circulating in northeastern Siberia during the late seventeenth or early eighteenth centuries.

There are 2 accounts of remains with suspicious lesions that were accidently unearthed during construction at a burial site. In 2000, mummified remains were discovered at a construction site in Kentucky. No live virus or viral DNA was isolated from these remains. More recently in 2011, the remains of a woman buried in an iron coffin were uncovered during construction at a known African-American cemetery in New York, New York. Preservation of the body was remarkable because of the airtight environment provided by the iron coffin. The presence on the body of lesions with the characteristic deep-seated, umbilicated appearance and in a centrifugal distribution of smallpox lesions immediately prompted concern for unearthed smallpox. No live virus or viral DNA was isolated from or visualized in any of multiple specimens taken from the body and evaluated by cell culture, molecular methods, or immunohistochemical stains. Human DNA was isolated from a tooth pulp specimen. Thus, the results do not conclusively verify the hypothesis of smallpox as the cause of death. However, visual inspection cast little doubt on this hypothesis:

Mummified remains of a woman buried in an iron coffin, New York, New York, USA, mid-1800s.

Some accounts from the eighteenth century report that material used in variolation (often scab material) was stored for ≤8 years before successful use. Thus, long-term storage and subsequent use of variola virus from preserved specimens have long been recognized. However, during the era of eradication, 45 scab specimens were collected from variolators and tested 9 months after collection; live virus was not isolated from any of the specimens. Nevertheless, stored crusts have caused immediate concern for potential exposures and their discovery has caused immediate exposure mitigation and testing.

In the past 10 years, suspected variola crusts have been discovered in the United States on 3 occasions. In Virginia, a crust labeled as a smallpox scab was on display at a museum and was accompanied by a letter describing its origin (panel A below). The letter and crust were sent from 1 family member to another in Virginia in 1876, and the correspondence stated that the crusts came from the arm of an infant and were to be used to vaccinate others. No live virus was isolated from this crust. However, non-variola orthopoxvirus DNA and human DNA were successfully extracted. This rare letter and scab are evidence to support arm-to-arm vaccination in the United States around the same time that it was also performed in Great Britain:

Recovered crusts. A) Lesion crust material from Virginia, USA, photographed after gamma irradiation. B) Lesion crust material from an envelope contained within a book, New Mexico, USA, nineteenth century. C) Lesion crust material from a jar on display in a museum, Arkansas.

A second incident of suspected smallpox scabs on display at a local museum occurred in Arkansas (panel B). These relics were donated by the family of a physician who practiced in Arkansas during 1871–1926. In 1905, there was a large smallpox outbreak in Arkansas. No live variola virus, viral DNA, or human DNA were isolated from the specimens. The crusts were affixed to blocks of wood with a dense resin, and the resin may have been inhibitory to the PCR or DNA stability. The origins and species of these specimens will continue to remain a mystery.

In 2003, a librarian in New Mexico opened a book and an envelope containing lesion crusts fell out of the book (panel C). The envelope was labeled “scabs from vaccination of W.B. Yarrington’s children,” and the book was dated 1888. Similar to the relic from Virginia, no live virus was isolated from this material, but non-variola orthopoxvirus DNA was isolated. In this instance, human DNA was not amplified. The question of precisely what virus was used in vaccination in the United States in the nineteenth century is intriguing from the perspective of historical significance and the evolution of orthopoxviruses.

Historical specimens come to the attention of public health authorities when there is a perception that they may constitute a potential risk to those who are handling or may have handled the artifacts. This concern extends to specific groups of persons who might work routinely with historical specimens, including archaeologists and museum archivists, as well as those who may stumble upon these specimens on an irregular basis, such as construction workers or the general public. Although live variola virus has never been isolated from historical tissues, this finding does not eliminate the possibility of live variola virus resurfacing from well-preserved tissue material. Moreover, variola virus has been absent for >30 years, and there is an increasingly large population of susceptible persons who have never been vaccinated against smallpox.

The discovery of a series of corpses and mummies with suspected smallpox lesions in the late 1970s and 1980s sparked a series of commentaries over the risks to archaeologists and anthropologists and the potential need for vaccination of workers. This proposition has been hotly debated, and opponents have argued that live variola virus has never been isolated from archeologic specimens and that live virus vaccination carries its own risks. This debate underscores the lack of firm scientific evidence to enable an informed assessment of risk to those who come into contact with artifacts and relics potentially contaminated with variola virus. The inability to exclude the possibility of risk led to the vaccination of 3 archaeologists who handled a corpse with suspect lesions in London in 1985. Current recommendations from the Advisory Committee on Immunisation Practices do not specifically address vaccination for those who work with antiquities, including corpses and tissue material. Although routine vaccination is not recommended, prudent preparation and recognition of potential smallpox relics is advised for those who work with potentially contaminated tissues and corpses.

Archival specimens offer opportunities to delve into the past and capture a glimpse of the history of an eradicated disease. There are no published reports of residual live microbes found in archeologic relics. Furthermore, on the basis of experiences in the past several decades, risks for transmission of live organisms from such relics would seem to be non-existent; nevertheless, archeologic specimens should be handled with caution. Each situation should be approached independently and with vigilance and attention.

So, I think there's strong evidence that smallpox can't survive on relics in normal conditions. But what about frozen in permafrost? Experiments from back when smallpox walked the earth suggested it could survive a decade or more if you preserved it carefully. There's some evidence that flu viruses can survive freezing and thawing. And this story mentions a bunch of scientists who tried to search for Spanish flu and smallpox in permafrosted bodies. They didn’t find any live viruses, but there were able to recover a few shreds of useful DNA:


The good news is that these viruses probably can't be generically "released". If some dead body with smallpox starts thawing, it's not like the smallpox virus has been freed from its prison, genie-style, and can travel upon the air currents until it finds an unsuspecting host. You really have to be out there licking corpses.

I think if something goes wrong, the third most likely vector will be curious Siberians who see a corpse half-hidden in the ice and go investigate. The second most likely vector will be archaeologists. And the most likely vector, by far, will be scientists investigating to see whether something could go wrong.

Present-day stocks of variola virus are maintained at 2 WHO reference laboratories: the CDC (Atlanta, GA, USA) and the State Research Center of Virology and Biotechnology (VECTOR) (Koltsovo, Russia). There is concern that if variola virus is present outside these 2 laboratories, its accidental or intentional release could cause illness in a population increasingly composed of unvaccinated persons. Anecdotal reports and formal scientific evidence have not ruled out the possibility that the virus may survive prolonged periods in preserved skin and tissue material, such as those that might be on display in museums, or in unearthed human remains. For example, permafrost is an environment that closely mirrors laboratory freezer storage of live virus, and the maintenance of viable smallpox virus in human remains found in such an environment has been debated. Environmental contamination with potentially live variola virus recovered from historical relics could threaten our confidence that the disease has been eradicated. In addition to immediate public health concern about such relics, there is much to be gained from investigation of artifacts in terms of scientific and historical interests.

Finally today, the scale of the international efforts to sequence SARS-CoV-2 genomes is unprecedented: nearly 2 million genomes have been sequenced in the first 18 months of the pandemic. Early availability of genomes allowed rapid characterisation of the virus, thus kickstarting many highly successful vaccine development programmes. Worldwide genomic resources have provided a good understanding of the pandemic, supported close monitoring of the emergence of viral genomic diversity and pinpointed those sites to prioritise for functional characterisation. Continued genomic surveillance of global viral populations will be crucial to inform the timing of vaccine updates so as to pre-empt the spread of immune escape lineages. While genome sequencing has provided us with an exceptionally powerful tool to monitor the evolution of SARS-CoV-2, there is room for further improvements in particular in the form of less heterogeneous global surveillance and tools to rapidly identify concerning viral lineages.




Emerging hot spots in the US. The x-axis is growth rate of new cases compared to last week, the y-axis is the new case per hundred, and z is the latitude. Each state is colour coded by vaccination rate:


Justin Stebbing

Managing Director

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