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It does not take into account the differing protection offered by various covid vaccines, natural immunity, the impact of population density on transmission or covid treatment options for immunocompromised people. Estimating the number of immunocompromised people is itself hard: the model the data was based on includes only a few conditions. Others, like severe type-1 diabetes or rheumatoid arthritis, were absent. Nor is everyone with such conditions immunocompromised. But the study still offers insight into where to look for future variants—and where to focus efforts on increasing the supply and take-up of vaccines.

The Swahili Coast is a narrow strip of land that stretches some 2,000 miles along the Eastern African seaboard — from modern-day Mozambique, Comoros and Madagascar in the south, to Somalia in the north

In its medieval heyday, the region was home to hundreds of port towns, each ruled independently, but with a common religion (Islam), language (Kiswahili) and culture.

Many towns grew immensely wealthy thanks to a vibrant trading network with merchants who sailed across the Indian Ocean on the monsoon winds. Middle Eastern pottery, Asian cloths 0c 0c and other luxury goods came in. African gold, ivory and timber 0c 0c went out — along with a steady flow of enslaved people, who were shipped off and sold across the Arabian Peninsula and Persian Gulf. (Slave trading later took place between the Swahili coast and Europe as well.)

A unique cosmopolitan society emerged that blended African customs and beliefs with those of the foreign traders, some of whom stuck around and assimilated.

Islam, for example, arrived from the Middle East and became an integral part of the Swahili social fabric, but with coral-stone mosques built and decorated in a local, East African style

Or consider the Kiswahili language, which is Bantu in origin but borrows heavily from Indian and Middle Eastern tongues

The arrival of Europeans, beginning around 1500, followed by Omani sailors some 200 years later, changed the character of the region

over the past 40 years, archaeologists, linguists and historians have come to see Swahili society as predominantly homegrown — with outside elements adopted over time that had only a marginal impact.

That African-centric version of Swahili roots never sat well with the Swahili people themselves, though

They generally preferred their own origin story, one in which princes from present-day Iran (then known as Persia) sailed across the Indian Ocean, married local women and enmeshed themselves into East African society. Depending on the narrative source, that story dates to around 850 or 1000 — the same period during which genetic mixing was underway, according to the DNA analysis.

“It’s remarkably spot on,” said Mark Horton, an archaeologist at the Royal Agricultural University of England

“This oral tradition was always maligned,”

“Now, with this DNA study, we see there was some truth to it.”

The ancient DNA study is the largest of its kind from Africa, involving 135 skeletons dating to late-medieval and early-modern times, 80 of which have yielded analyzable DNA.

To figure out where these people came from, the researchers compared genetic signatures from the dug-up bones with cheek swabs or saliva samples taken from modern-day individuals living in Africa, the Middle East and around the world.

The burial-site DNA traced back to two primary sources: Africans and present-day Iranians. Smaller contributions came from South Asians and Arabs as well, with foreign DNA representing about half of the skeletons’ genealogy

“It’s surprising that the genetic signature is so strong

Gene sequences from tiny power factories inside the cell, known as mitochondria, were overwhelmingly African in origin. Since children inherit these bits of DNA only from their mothers, the researchers inferred that the maternal forbearers of the Swahili people were mostly of African descent.

By comparison, the Y chromosome, passed from father to son, was chock-full of Asian DNA that the researchers found was common in modern-day Iran. So, a large fraction of Swahili ancestry presumably came from Persian men

Dr. Reich initially assumed that conquering men settled the region by force, displacing the local males in the process. “My hypothesis was that this was a genetic signature of inequality and exploitation,”

hat turned out to be a “naïve expectation,” Dr. Reich said, because “it didn’t take into account the cultural context in this particular case.”

In East Africa, Persian customs never came to dominate. Instead, most foreign influences — language, architecture, fashion, arts — were incorporated into a way of life that remained predominantly African in character, with social strictures, kinship systems and agricultural practices that reflected Indigenous traditions.

“Swahili was an absorbing society,” said Adria LaViolette, an archaeologist at the University of Virginia who has worked on the East African coast for over 35 years. Even as the Persians who arrived influenced the culture, “they became Swahili,”

One major caveat to the study: Nearly all the bones and teeth came from ornamental tombs that were located near grand mosques, sites where only the upper class would have been laid to rest.

the results might not be representative of the general populace.

Protocols for disinterring, sampling and reburying human remains were established in consultation with local religious leaders and community stakeholders. Under Islamic law, exhumations are permitted if they serve a public interest, including that of determining ancestry,

[Science fiction’s influence]…leaves us facing a future we were all warned about, courtesy of dystopian novels mistaken for instruction manuals…[T]he billionaires behind the steering wheel have mistaken cautionary tales and entertainments for a road map, and we’re trapped in the passenger seat.

t even then it would be hard to argue exogeneity, since censorship is a response to society’s values as well as a potential cause of them.

Stross is alleging that the billionaires are getting Gernsback and Campbell’s intentions exactly right. His problem is simply that Gernsback and Campbell were kind of right-wing, at least by modern standards, and he’s worried that their sci-fi acted as propaganda for right-wing ideas.

The question of whether literature has a political effect is an empirical one — and it’s a very difficult empirical one. It’s extremely hard to test the hypothesis that literature exerts a diffuse influence on the values and preconceptions of the citizenry

I think Stross really doesn’t come up with any credible examples of billionaires mistaking cautionary tales for road maps. Instead, most of his article focuses on a very different critique — the idea that sci-fi authors inculcate rich technologists with bad values and bad visions of what the future ought to look like:

I agree that the internet and cell phones have had an ambiguous overall impact on human welfare. If modern technology does have a Torment Nexus, it’s the mobile-social nexus that keeps us riveted to highly artificial, attenuated parasocial interactions for every waking hour of our day. But these technologies are still very young, and it remains to be seen whether the ways in which we use them will get better or worse over time.

There are very few technologies — if any — whose impact we can project into the far future at the moment of their inception. So unless you think our species should just refuse to create any new technology at all, you have to accept that each one is going to be a bit of a gamble.

As for weapons of war, those are clearly bad in terms of their direct effects on the people on the receiving end. But it’s possible that more powerful weapons — such as the atomic bomb — serve to deter more deaths than they cause

yes, AI is risky, but the need to manage and limit risk is a far cry from the litany of negative assumptions and extrapolations that often gets flung in the technology’s directio

I think the main problem with Harper’s argument is simply techno-pessimism. So far, technology’s effects on humanity have been mostly good, lifting us up from the muck of desperate poverty and enabling the creation of a healthier, more peaceful, more humane world. Any serious discussion of the effects of innovation on society must acknowledge that. We might have hit an inflection point where it all goes downhill from here, and future technologies become the Torment Nexuses that we’ve successfully avoided in the past. But it’s very premature to assume we’ve hit that point.

I understand that the 2020s are an exhausted age, in which we’re still reeling from the social ructions of the 2010s. I understand that in such a weary and fearful condition, it’s natural to want to slow the march of technological progress as a proxy for slowing the headlong rush of social progress

And I also understand how easy it is to get negatively polarized against billionaires, and any technologies that billionaires invent, and any literature that billionaires like to read.

But at a time when we’re creating vaccines against cancer and abundant clean energy and any number of other life-improving and productivity-boosting marvels, it’s a little strange to think that technology is ruining the world

The dystopian elements of modern life are mostly just prosaic, old things — political demagogues, sclerotic industries, social divisions, monopoly power, environmental damage, school bullies, crime, opiates, and so on

In fact, the news from Wall Street lately has mostly been about retreat from climate goals, rather than recommitment. Banks and asset managers are withdrawing from international climate alliances and chafing at their rules. Regional banks are stepping up lending to fossil fuel producers. Sustainable investment funds have sustained crippling outflows, and many have collapsed.

In some cases, it’s a classic prisoner’s dilemma: If firms collectively shift to cleaner energy, a cooler climate benefits everyone more in the future

in the short term, each firm has an individual incentive to cash in on fossil fuels, making the transition much harder to achieve.

when it comes to avoiding climate damage to their own operations, the financial industry is genuinely struggling to comprehend what a warming future will mean.

A global compact of financial institutions made commitments worth $130 trillion to try to bring down emissions, confident that governments would create a regulatory and financial infrastructure to make those investments profitable. And in 2022, the Inflation Reduction Act passed.

What about the risk that climate change poses to the financial industry’s own investments, through more powerful hurricanes, heat waves that knock out power grids, wildfires that wipe out towns?

“If we think about what is going to be the best way to tilt your portfolios in the direction to benefit, it’s really difficult to do,”

“These will probably be great investments over 20 years, but when we’re judged over one to three years, it’s a little more challenging for us.”

Some firms cater to institutional clients, like public employee pension funds, that want combating climate change to be part of their investment strategy and are willing to take a short-term hit. But they aren’t a majority

And over the past couple of years, many banks and asset managers have shrunk from anything with a climate label for fear of losing business from states that frown on such concerns.

On top of that, the war in Ukraine scrambled the financial case for backing a rapid energy transition. Artificial intelligence and the movement toward greater electrification are adding demand for power, and renewables haven’t kept up

All of that is about the relative appeal of investments that would slow climate change

If you bought some of the largest solar-energy exchange-traded funds in early 2023, you would have lost about 20 percent of your money, while the rest of the stock market soared.

There is evidence that banks and investors price in some physical risk, but also that much of it still lurks, unheeded.

“I’m very, very worried about this, because insurance markets are this opaque weak link,” Dr. Sastry said. “There are parallels to some of the complex linkages that happened in 2008, where there is a weak and unregulated market that spills over to the banking system.”

Regulators worry that failing to understand those ripple effects could not just put a single bank in trouble but even become a contagion that would undermine the financial system.

But while the European Central Bank has made climate risk a consideration in its policy and oversight, the Federal Reserve has resisted taking a more active role, despite indications that extreme weather is feeding inflation and that high interest rates are slowing the transition to clean energy.

“The argument has been, ‘Unless we can convincingly show it’s part of our mandate, Congress should deal with it, it’s none of our business,’”

a much nearer-term uncertainty looms: the outcome of the U.S. election, which could determine whether further action is taken to address climate concerns or existing efforts are rolled back. An aggressive climate strategy might not fare as well during a second Trump administration, so it may seem wise to wait and see how it shakes out.

big companies are hesitating on climate-sensitive investments as November approaches, but says that “two things are misguided and quite dangerous about that hypothesis.”

One: States like California are establishing stricter rules for carbon-related financial disclosures and may step it up further if Republicans win

And two: Europe is phasing in a “carbon border adjustment mechanism,” which will punish polluting companies that want to do business there.

at the moment, even European financial institutions feel pressure from the United States, which — while providing some of the most generous subsidies so far for renewable-energy investment — has not imposed a price on carbon.

The global insurance company Allianz has set out a plan to align its investments in a way that would prevent warming above 1.5 degrees Celsius by the end of the century, if everyone else did the same. But it’s difficult to steer a portfolio to climate-friendly assets while other funds take on polluting companies and reap short-term profits for impatient clients.

“This is the main challenge for an asset manager, to really bring the customer along,” said Markus Zimmer, an Allianz economist. Asset managers don’t have sufficient tools on their own to move money out of polluting investments and into clean ones, if they want to stay in business,

“Of course it helps if the financial industry is somehow ambitious, but you cannot really substitute the lack of actions by policymakers,”

According to new research, the benefit is greater when decarbonization occurs faster, because the risks of extreme damage mount as time goes on. But without a uniform set of rules, someone is bound to scoop up the immediate profits, disadvantaging those that don’t — and the longer-term outcome is adverse for all.

Dr. Shi’s group was fascinated by how coronaviruses jump from species to species. To find viruses, they took samples from bats and other animals, as well as from sick people living near animals carrying these viruses or associated with the wildlife trade. Much of this work was conducted in partnership with the EcoHealth Alliance, a U.S.-based scientific organization that, since 2002, has been awarded over $80 million in federal funding to research the risks of emerging infectious diseases.

Their research showed that the viruses most similar to SARS‑CoV‑2, the virus that caused the pandemic, circulate in bats that live roughly 1,000 miles away from Wuhan. Scientists from Dr. Shi’s team traveled repeatedly to Yunnan province to collect these viruses and had expanded their search to Southeast Asia. Bats in other parts of China have not been found to carry viruses that are as closely related to SARS-CoV-2.

When the Covid-19 outbreak was detected, Dr. Shi initially wondered if the novel coronavirus had come from her laboratory, saying she had never expected such an outbreak to occur in Wuhan.

The SARS‑CoV‑2 virus is exceptionally contagious and can jump from species to species like wildfire. Yet it left no known trace of infection at its source or anywhere along what would have been a thousand-mile journey before emerging in Wuhan.

The year before the outbreak, the Wuhan institute, working with U.S. partners, had proposed creating viruses with SARS‑CoV‑2’s defining feature

The laboratory pursued risky research that resulted in viruses becoming more infectious: Coronaviruses were grown from samples from infected animals and genetically reconstructed and recombined to create new viruses unknown in nature. These new viruses were passed through cells from bats, pigs, primates and humans and were used to infect civets and humanized mice (mice modified with human genes). In essence, this process forced these viruses to adapt to new host species, and the viruses with mutations that allowed them to thrive emerged as victors.

Worse still, as the pandemic raged, their American collaborators failed to publicly reveal the existence of the Defuse proposal. The president of EcoHealth, Peter Daszak, recently admitted to Congress that he doesn’t know about virus samples collected by the Wuhan institute after 2015 and never asked the lab’s scientists if they had started the work described in Defuse.

By 2019, Dr. Shi’s group had published a database describing more than 22,000 collected wildlife samples. But external access was shut off in the fall of 2019, and the database was not shared with American collaborators even after the pandemic started, when such a rich virus collection would have been most useful in tracking the origin of SARS‑CoV‑2. It remains unclear whether the Wuhan institute possessed a precursor of the pandemic virus.

In 2021, The Intercept published a leaked 2018 grant proposal for a research project named Defuse, which had been written as a collaboration between EcoHealth, the Wuhan institute and Ralph Baric at the University of North Carolina, who had been on the cutting edge of coronavirus research for years. The proposal described plans to create viruses strikingly similar to SARS‑CoV‑2.

Coronaviruses bear their name because their surface is studded with protein spikes, like a spiky crown, which they use to enter animal cells. The Defuse project proposed to search for and create SARS-like viruses carrying spikes with a unique feature: a furin cleavage site — the same feature that enhances SARS‑CoV‑2’s infectiousness in humans, making it capable of causing a pandemic. Defuse was never funded by the United States.

owever, in his testimony on Monday, Dr. Fauci explained that the Wuhan institute would not need to rely on U.S. funding to pursue research independently.

While it’s possible that the furin cleavage site could have evolved naturally (as seen in some distantly related coronaviruses), out of the hundreds of SARS-like viruses cataloged by scientists, SARS‑CoV‑2 is the only one known to possess a furin cleavage site in its spike. And the genetic data suggest that the virus had only recently gained the furin cleavage site before it started the pandemic.

Ultimately, a never-before-seen SARS-like virus with a newly introduced furin cleavage site, matching the description in the Wuhan institute’s Defuse proposal, caused an outbreak in Wuhan less than two years after the proposal was drafted.

When the Wuhan scientists published their seminal paper about Covid-19 as the pandemic roared to life in 2020, they did not mention the virus’s furin cleavage site — a feature they should have been on the lookout for, according to their own grant proposal, and a feature quickly recognized by other scientists.

At the Wuhan Institute of Virology, a team of scientists had been hunting for SARS-like viruses for over a decade, led by Shi Zhengl

In May, citing failures in EcoHealth’s monitoring of risky experiments conducted at the Wuhan lab, the Biden administration suspended all federal funding for the organization and Dr. Daszak, and initiated proceedings to bar them from receiving future grants. In his testimony on Monday, Dr. Fauci said that he supported the decision to suspend and bar EcoHealth.

Separately, Dr. Baric described the competitive dynamic between his research group and the institute when he told Congress that the Wuhan scientists would probably not have shared their most interesting newly discovered viruses with him. Documents and email correspondence between the institute and Dr. Baric are still being withheld from the public while their release is fiercely contested in litigation.

In the end, American partners very likely knew of only a fraction of the research done in Wuhan. According to U.S. intelligence sources, some of the institute’s virus research was classified or conducted with or on behalf of the Chinese military.

In the congressional hearing on Monday, Dr. Fauci repeatedly acknowledged the lack of visibility into experiments conducted at the Wuhan institute, saying, “None of us can know everything that’s going on in China, or in Wuhan, or what have you. And that’s the reason why — I say today, and I’ve said at the T.I.,” referring to his transcribed interview with the subcommittee, “I keep an open mind as to what the origin is.”

The Wuhan lab pursued this type of work under low biosafety conditions that could not have contained an airborne virus as infectious as SARS‑CoV‑2.

Labs working with live viruses generally operate at one of four biosafety levels (known in ascending order of stringency as BSL-1, 2, 3 and 4) that describe the work practices that are considered sufficiently safe depending on the characteristics of each pathogen. The Wuhan institute’s scientists worked with SARS-like viruses under inappropriately low biosafety conditions.

​​Biosafety levels are not internationally standardized, and some countries use more permissive protocols than others.

In one experiment, Dr. Shi’s group genetically engineered an unexpectedly deadly SARS-like virus (not closely related to SARS‑CoV‑2) that exhibited a 10,000-fold increase in the quantity of virus in the lungs and brains of humanized mice. Wuhan institute scientists handled these live viruses at low biosafety levels, including BSL-2.

Even the much more stringent containment at BSL-3 cannot fully prevent SARS‑CoV‑2 from escaping. Two years into the pandemic, the virus infected a scientist in a BSL-3 laboratory in Taiwan, which was, at the time, a zero-Covid country. The scientist had been vaccinated and was tested only after losing the sense of smell. By then, more than 100 close contacts had been exposed. Human error is a source of exposure even at the highest biosafety levels, and the risks are much greater for scientists working with infectious pathogens at low biosafety.

An early draft of the Defuse proposal stated that the Wuhan lab would do their virus work at BSL-2 to make it “highly cost-effective.” Dr. Baric added a note to the draft highlighting the importance of using BSL-3 to contain SARS-like viruses that could infect human cells, writing that “U.S. researchers will likely freak out.”

Years later, after SARS‑CoV‑2 had killed millions, Dr. Baric wrote to Dr. Daszak: “I have no doubt that they followed state determined rules and did the work under BSL-2. Yes China has the right to set their own policy. You believe this was appropriate containment if you want but don’t expect me to believe it. Moreover, don’t insult my intelligence by trying to feed me this load of BS.”

SARS‑CoV‑2 is a stealthy virus that transmits effectively through the air, causes a range of symptoms similar to those of other common respiratory diseases and can be spread by infected people before symptoms even appear. If the virus had escaped from a BSL-2 laboratory in 2019, the leak most likely would have gone undetected until too late.

One alarming detail — leaked to The Wall Street Journal and confirmed by current and former U.S. government officials — is that scientists on Dr. Shi’s team fell ill with Covid-like symptoms in the fall of 2019. One of the scientists had been named in the Defuse proposal as the person in charge of virus discovery work. The scientists denied having been sick.

The hypothesis that Covid-19 came from an animal at the Huanan Seafood Market in Wuhan is not supported by strong evidence.

In December 2019, Chinese investigators assumed the outbreak had started at a centrally located market frequented by thousands of visitors daily. This bias in their search for early cases meant that cases unlinked to or located far away from the market would very likely have been missed

To make things worse, the Chinese authorities blocked the reporting of early cases not linked to the market and, claiming biosafety precautions, ordered the destruction of patient samples on January 3, 2020, making it nearly impossible to see the complete picture of the earliest Covid-19 cases. Information about dozens of early cases from November and December 2019 remains inaccessible.

A pair of papers published in Science in 2022 made the best case for SARS‑CoV‑2 having emerged naturally from human-animal contact at the Wuhan market by focusing on a map of the early cases and asserting that the virus had jumped from animals into humans twice at the market in 2019

More recently, the two papers have been countered by other virologists and scientists who convincingly demonstrate that the available market evidence does not distinguish between a human superspreader event and a natural spillover at the market.

Furthermore, the existing genetic and early case data show that all known Covid-19 cases probably stem from a single introduction of SARS‑CoV‑2 into people, and the outbreak at the Wuhan market probably happened after the virus had already been circulating in humans.

Not a single infected animal has ever been confirmed at the market or in its supply chain. Without good evidence that the pandemic started at the Huanan Seafood Market, the fact that the virus emerged in Wuhan points squarely at its unique SARS-like virus laboratory.

With today’s technology, scientists can detect how respiratory viruses — including SARS, MERS and the flu — circulate in animals while making repeated attempts to jump across species. Thankfully, these variants usually fail to transmit well after crossing over to a new species and tend to die off after a small number of infections

investigators have not reported finding any animals infected with SARS‑CoV‑2 that had not been infected by humans. Yet, infected animal sources and other connective pieces of evidence were found for the earlier SARS and MERS outbreaks as quickly as within a few days, despite the less advanced viral forensic technologies of two decades ago.

Even though Wuhan is the home base of virus hunters with world-leading expertise in tracking novel SARS-like viruses, investigators have either failed to collect or report key evidence that would be expected if Covid-19 emerged from the wildlife trade. For example, investigators have not determined that the earliest known cases had exposure to intermediate host animals before falling ill.

No antibody evidence shows that animal traders in Wuhan are regularly exposed to SARS-like viruses, as would be expected in such situations.

In previous outbreaks of coronaviruses, scientists were able to demonstrate natural origin by collecting multiple pieces of evidence linking infected humans to infected animals

In contrast, virologists and other scientists agree that SARS‑CoV‑2 required little to no adaptation to spread rapidly in humans and other animals. The virus appears to have succeeded in causing a pandemic upon its only detected jump into humans.

it was a SARS-like coronavirus with a unique furin cleavage site that emerged in Wuhan, less than two years after scientists, sometimes working under inadequate biosafety conditions, proposed collecting and creating viruses of that same design.

a laboratory accident is the most parsimonious explanation of how the pandemic began.

Given what we now know, investigators should follow their strongest leads and subpoena all exchanges between the Wuhan scientists and their international partners, including unpublished research proposals, manuscripts, data and commercial orders. In particular, exchanges from 2018 and 2019 — the critical two years before the emergence of Covid-19 — are very likely to be illuminating (and require no cooperation from the Chinese government to acquire), yet they remain beyond the public’s view more than four years after the pandemic began.

it is undeniable that U.S. federal funding helped to build an unprecedented collection of SARS-like viruses at the Wuhan institute, as well as contributing to research that enhanced them.

Advocates and funders of the institute’s research, including Dr. Fauci, should cooperate with the investigation to help identify and close the loopholes that allowed such dangerous work to occur. The world must not continue to bear the intolerable risks of research with the potential to cause pandemics.

A successful investigation of the pandemic’s root cause would have the power to break a decades-long scientific impasse on pathogen research safety, determining how governments will spend billions of dollars to prevent future pandemics. A credible investigation would also deter future acts of negligence and deceit by demonstrating that it is indeed possible to be held accountable for causing a viral pandemic

Last but not least, people of all nations need to see their leaders — and especially, their scientists — heading the charge to find out what caused this world-shaking event. Restoring public trust in science and government leadership requires it.