The news from China is bad. The lifting of strict COVID-19 regulations in early December -regulations that had been sternly enforced for almost three years, under the country’s so-called “Zero-COVID” policy- has been followed by a great surge of infections. The existence of such a surge was suspected for weeks but denied by Chinese officialdom, who withheld data. Then, on January 14, a spokeswoman from the National Health Commission admitted that the country had suffered almost 60,000 Covid-related deaths since December 8. The virus is belatedly tormenting China the way it tormented northern Italy, New York City, and parts of Brazil back in spring of 2020.

The China surge hit first in urban areas, including Beijing and Shanghai, but also far-flung cities such as Dongguan in the South and Yulin in the North. Hospitals were overwhelmed, medicines (including simple fever reducers such as ibuprofen) became scarce, and many healthcare professionals continued to work despite being infected themselves. Since early January, the disease has begun piling up victims in rural areas well. Small clinics and community health centers are filling with patients to whom they can offer only basic care. The Chinese population remains especially vulnerable because immunity from past infections is very low and full vaccination of elderly people is low also. The three years of “Zero-COVID” were evidently wasted by Chinese authorities, who might have used that delay period to prepare better for the inevitable. But they did not.

So the pandemic is not over. The Covid coronavirus, known as SARS-CoV-2, is not gone. It’s as busy as ever, replicating, mutating, evolving. It will almost certainly remain in the human population forever. And there is no guarantee (despite what some people believe they have heard) that it will evolve into a less harmless form, such as the viruses that cause common colds. That misunderstanding is sometimes supported by an ill-informed adage that passes for wisdom: “A successful parasite does not kill its host.” Wrong. The correct statement would be: “A successful parasite does not kill its host until it has had time to infect another host.” If the coronavirus infects person A, transmits to person B and person C, and from person C onward to others, then it has achieved evolutionary success, whether or not person A dies. Darwinian natural selection, the main mechanism of evolution, does not “see” and does not “care” what happens to infected individuals after they have transmitted a virus.

Amid the continuing turmoil, we need to appreciate that SARS-CoV-2 may remain not just present but deadly, and that we may need to continue vaccinating against it, and fighting it in other ways, for decades.

Where did this virus come from? How did it get into humans? Those questions are also important, because the answers will help guide our efforts to prevent similar viral pandemics in the future. The mystery of the origins of SARS-CoV-2 has been hotly discussed, with mostly scientific experts on one side of the matter and mostly amateur sleuths plus a few journalists on the other. That discussion has been muddled by misinformation, speculation, and accusation, all offered to suggest that the virus somehow leaked from a laboratory. A lab leak is theoretically possible, but there is no positive evidence that it happened. There is much empirical evidence and expert analysis by molecular evolutionary virologists and epidemiologists, on the other hand, suggesting that the virus probably reached humans by natural spillover from a wild animal. That seems to have occurred in or around a certain “wet market” in the city of Wuhan. The animal carrying the virus may have been a raccoon dog or a palm civet or a bamboo rat or one of the other wild creatures, captured live and transported to Wuhan, that were on sale for food in the market. Some evidence even suggests that two distinct chains of human infection began in the market, which might reflect viral transmission from two different animals. The carrier animal (or animals) likely acquired the virus, either in the wild or during transport, from a horseshoe bat. Viruses similar to SARS-CoV-2 have been detected in horseshoe bats in southern China, and also in Thailand and Laos, just across the southern Chinese border.

More evidence is needed, but the process of gathering such evidence and sharing it among scientists has been severely constrained by two factors: the pandemic itself and mutual distrust between the Chinese government and its critics in the West, much exacerbated by this origins controversy.

One more thing is important for everyone to remember: that the trafficking of wild animals for food-bats or raccoon dogs in China, bats or pangolins in Africa, other creatures elsewhere- is not the only disruptive activity that exposes humans to wildlife viruses. The extraction of timber and fossil fuels from richly diverse tropical ecosystems is another. The mining of strategic minerals such as coltan—a material essential for the manufacture of high-tech electronic devices—is still another. Therefore, anyone who owns a smart phone or a laptop computer or a fancy camera, or even a new car, also owns a share of responsibility for the continuing threat of viral spillover.

Eight billion humans presently inhabit this planet, all of us hungry, all of us thirsty, all of us consuming energy and wood and other material resources, in various quantities, as our appetites dictate and our levels of affluence allow. At the other end of the spectrum of sentience lie viruses, these relatively simple creatures, of which Earth harbors many millions of different forms. Among the millions, maybe one or two million kinds of virus reside in nonhuman mammals and birds. I highlight mammals and birds because they are generally the sources of the new viruses that infect people—not just SARS-CoV-2 and the original SARS virus of 2003, but also Ebola virus and Marburg and Lassa and Hendra and Nipah and HIV and many others.

With our voracious consumption, our disruption of diverse ecosystems, our devastation of natural landscapes all over the globe, we humans continue driving the most vulnerable of our fellow creatures toward extinction: the western chimpanzee, the eastern lowland gorilla, the tiger, the slender-billed curlew, the sociable lapwing, Hill’s horseshoe bat, and too many others to name, each serving as host to its own viruses. Many of those viruses are malleable opportunists. Evolution allows them to change, rather quickly, and compels them to survive. As the planet gets smaller and emptier, their best remaining opportunity will be to infect us.

That’s a grim and ironic sort of justice, and we should do all possible not to earn it.

L'articolo Ecological disruption and pandemic threats proviene da InsideOver.

This article appeared first on “The New York Times” as an op-ed. Inside Overs strongly thanks The New York Times and Professor Quamenn for giving the opportunity of publishing it.

The Covid-19 pandemic has been a lesson in speed — the speed at which a novel virus among humans can spread, the speed at which it can rack up fatalities and cripple economies, the speed at which vaccines can be designed and produced, the speed at which misinformation can undermine public health. Amid all that rapidity is a different kind of speed, which drives the rest, like an engine spinning the cars on a nauseating carnival ride: the speed of viral evolution.

The coronavirus, like many other viruses of its ilk (RNA viruses with highly changeable genomes), evolves fast. It has adapted quickly to us. Now arises the crucial question of whether humans and human ingenuity can adapt faster.

Unless the answer is yes, we face a long, doleful future of continued suffering. Some experts reckon the toll of endemic Covid might be somewhere from 100,000 to 250,000 deaths every year, just in the United States. Millions of lives depend on whether human science, human governance and human wisdom can outpace the ingenuity of SARS-CoV-2, a relatively simple but enterprising agent consisting of four structural proteins plus an RNA genome.

Charles Darwin said the mechanisms of evolution never move quickly, but Darwin didn’t know about viruses. “That natural selection will always act with extreme slowness, I fully admit,” he wrote in “On the Origin of Species,” published in 1859. The first virus discovered, tobacco mosaic virus, didn’t come to scientific attention until decades later. As evolutionary theory developed from Darwin’s work and throughout much of the 20th century, it drew mostly on evidence from fields such as paleontology, biogeography, embryology and comparative anatomy — visible patterns that can reveal slow changes over long stretches of time. Those data are generally far less useful for measuring evolution when it happens fast.

But we have a new form of evidence for evolution: the sequencing and comparison of genomes. Whiz-bang machines do the sequencing — reading out the genetic code, letter by letter — and powerful computers help do the comparing, and it’s all much faster and cheaper.

Scientists can now track changes, mutation by mutation, in the DNA or the RNA that encodes each creature’s genetic instructions, watching and measuring as some of those mutations, the few that just happen to be useful, spread through a population. They can assemble a portrait in motion of even the fastest-evolving creatures, such as bacteria and viruses. When the bacteria or viruses happen to be pathogens that can infect humans, this discipline is called genomic epidemiology.

Among the pioneers of genomic epidemiology is Sharon Peacock, a professor of public health and microbiology at the University of Cambridge as well as the executive director of the Covid-19 Genomics UK Consortium. It’s a group of public health agencies and research institutions founded in April 2020 to sequence and analyze genomes of the new coronavirus. At this point, the contribution by labs in Britain accounts for almost 2.8 million of the globally reported SARS-CoV-2 sequences, about 23 percent of the world’s total.

Dr. Peacock and those who helped her establish and fund this effort recognized early that genomic information could be crucial to the pandemic response. But just gathering sequences and making them available to other scientists is not enough. That’s genomics without epidemiology — the application of population-level knowledge to public health.

“If you’re talking about speed,” Dr. Peacock told me recently, “the key thing is to think of the whole pipeline from start to finish.” What she meant by “pipeline” is a chain of physical steps (such as sampling a patient), laboratory processes (such as extracting viral genetic material and sequencing that virus’s genome) and analysis (interpreting the differences between one genome and another). They yield insights that can inform both clinical treatment of individuals and protection of the populace.

Hardware tools are important to such work. Software is also crucial. During the first year of the Covid-19 pandemic, a young graduate student named Áine O’Toole, along with other members of Andrew Rambaut’s lab at the University of Edinburgh, developed a tool called PANGOLIN (Phylogenetic Assignment of Named Global Outbreak Lineages). It became one of the go-to systems for placing new genomes on the SARS-CoV-2 family tree, assigning them rational if unmemorable labels (such as B.1.1.7), and contextualizing new variants of the virus when they emerged.

It was Dr. Rambaut, Dr. O’Toole and their lab colleagues who helped spot and track the first major variant, now called Alpha, when it appeared in southeastern England, moving toward London, in autumn of 2020. One year later, scientists in South Africa and Botswana, sequencing samples from travelers, detected another rising variant, named Omicron.

Such quick detection of variants is enormously valuable, but only if the data are transformed promptly into clear, actionable guidance. “We still have the important gaps in getting it into the clinic,” Dr. Peacock said. These gaps include making it easy for public health and medical personnel not trained in sequencing to use the data and the willingness of health care providers like hospitals to finance such work. “At the moment, the majority of sequencing beyond Covid-19 is funded by public health agencies and research funding,” she said.

That hasn’t changed since 2014, when Pardis Sabeti, a computational geneticist at Harvard University, led a team of genomic scientists responding to the horrific Ebola virus outbreak in West Africa. They sequenced 99 genomes of the virus, sampled from patients at a hospital in Sierra Leone. Comparing sequences revealed that all those cases most likely resulted from human-to-human transmission, rather than from spillovers from a wildlife host.

The West Africa outbreak ended after more than 28,000 Ebola cases and 11,000 deaths, by which point genomic epidemiology had proved its value by revealing how the virus was spreading. With Covid-19, there have been 589 million known cases and more than six million deaths so far. The new discipline is scarcely able to keep up, let alone get ahead of the virus. Sarah Cobey, an evolutionary biologist at the University of Chicago who works at the juncture of immunology, viral evolution and epidemiology, sees “gaping holes” in the genetic surveillance of Covid-19.

“Even though we do have lots and lots of sequences, they are disproportionally from a few locations,” Dr. Cobey told me. During the first year of the pandemic, Britain, New Zealand, Australia and Iceland were among the countries that sequenced a high share of cases. The Netherlands and the Democratic Republic of Congo were also notable for prompt sequencing. As the pandemic progressed, scientists in South Africa mounted an important sequencing effort (as reflected in the detection first of the Beta variant, then of the Omicron), and coverage improved also in Canada and Scandinavia. Other parts of the world remain “blind spots,” Dr. Cobey said.

The sad but not surprising fact is that high-income countries sequenced 16 times as many coronavirus genomes as a proportion of cases as low- and middle-income countries. Money is a limiting factor, but not just money. “I think the fundamental problem is really lack of scientific leadership to coordinate this kind of data gathering,” Dr. Cobey said. Few countries have had their Sharon Peacock or political leadership to heed and support the scientific leaders.

The world needs that leadership, broadening and paying for sequencing surveillance of this coronavirus and its changes, everywhere the virus goes. But we need much more, as Dr. Cobey and Dr. Peacock and other scientists warn.

We need ambitious seroprevalence studies (screening of blood samples for evidence of past infection) that will help scientists learn how many undetected infections have occurred. What’s the real case total in each country and around the world? We need farsighted and well-funded research on vaccine platforms that can be quickly adapted for use against whole classes of newly emerged pathogens, not just hurried efforts to create a booster for the latest variant. We need a universal coronavirus vaccine and a universal influenza vaccine, although neither — given the formidable capacity of those viruses to evolve — may be achievable.

More simply, we need temperature-stable and needle-free vaccines that can reduce the problems of vaccine refusal in high-income countries and vaccine unavailability in low-income countries that are hot. We need better antiviral drugs, even for rare but dangerous viruses (such as Nipah virus), entailing development efforts that may never be profitable for pharmaceutical companies.

Even more simply, as Dr. Cobey noted, we need investments toward much better ventilation and air filtration in our public buildings, reducing the spread of the coronavirus and other airborne pathogens. That’s not scientifically exciting, she conceded; it’s just important and cost-effective.

The evolutionary journey of this coronavirus has been grim and awesome. Arguably, the measured transformations of SARS-CoV-2 over the past 31 months, from the original strain to the subvariants of Omicron, provide one of the most precise pictures of swift evolution at a global scale in the wild — that is, not in beakers and flasks, not in laboratories, but in us. Evolution deniers, take note.

All of us should take note. We have 12 million snapshots of this thing in motion — which is enough, at the standard cinema projection rate of 24 frames per second, to make a movie of SARS-CoV-2 evolution 138 hours long. But because evolutionary biology is a descriptive science, not a predictive one, we still don’t know how the story might end. Probably it doesn’t end at all. And the genomic epidemiologists, as smart as they are, can’t save us from what’s still coming. We have to save ourselves.

L'articolo We Are Still in a Race Against the Coronavirus proviene da InsideOver.