Study reveals impact of centuries of human activity in American tropics

 The devastating effects of human activity on wildlife in the American tropics over the last 500 years are revealed in a new study published today.

More than half of the species in local 'assemblages' -- sets of co-existing species -- of medium and large mammals living in the Neotropics of Meso and South America have died out since the region was first colonised by Europeans in the 1500s.

Researchers at the University of East Anglia (UEA), in the UK, and University of São Paulo (USP), Brazil, found that human activity such as habitat change and overhunting is largely responsible for the overwhelming loss, or 'defaunation', in mammal diversity across Latin America.

The study, published in the journal Scientific Reports, compared all animal inventories at over 1000 Neotropical study sites published over the past 30 years with baseline data going back to the Colonial era.

The findings draw on a compilation of 1,029 separate mammal assemblages -- typically a few kilometres apart from each other -- spanning approximately 10,700 km and 85° of latitude across 23 countries, from Mexico to Argentina and Chile.

They reveal that the dominant cause of local species extinction and assemblage downsizing -- the reduction in body size within each assemblage -- is a direct result of habitat changes such as farming, logging and fires, and aggravated by the chronic process of overhunting.

Dr Juliano André Bogoni, a postdoctoral researcher sponsored by the São Paulo Research Foundation and working at UEA's School of Environmental Sciences, led the study with Prof Carlos Peres, also of UEA, and Prof Katia Ferraz from USP.

Dr Bogoni said: "Our findings can be used to inform international conservation policies to prevent further erosion of, or restore, native biodiversity. Further conservation efforts should be mobilized to prevent the most faunally-intact biomes, such as Amazonia and the Pantanal wetlands, from following in the footsteps of 'empty ecosystems' that are now typical of historically degraded areas such as the Brazilian Atlantic Forest and the Caatinga.

"This includes effective implementation and law enforcement in existing protected areas, and curbing political pressures to either downgrade or downsize these areas. Greater investment should be allocated to more effective control of illegal hunting, particularly commercial hunting, deforestation, and anthropogenic fires, as well as ensure that fully implemented protected areas are working."

Prof Peres said: "Sound resource management should be sensitive to the socioeconomic context, while recruiting rather than antagonizing potential local alliances who can effectively fill the institutional void in low-governance regions.

"Hominins and other mammals have co-existed since the earliest Paleolithic hunters wielding stone tools some three million years ago. Over this long timescale biodiversity losses have only recently accelerated to breakneck speeds since the industrial revolution.

"Let us make sure that this relentless wave of local extinctions is rapidly decelerated, or else the prospects for Neotropical mammals and other vertebrates will look increasingly bleak."

The team looked at 165 species and analysed local losses in more than 1000 sets of medium to large-bodied mammal species that had been surveyed across the Neotropics.

On average more than 56 per cent of the local wildlife within mammal assemblages across the Neotropics were wiped out, with ungulates lowland tapir and white-lipped peccary comprising the most losses. The extent of defaunation was widespread, but increasingly affecting relatively intact major biomes that are rapidly succumbing to encroaching deforestation frontiers.

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Big answers from tiny particles

 A team of scientists led by Kanazawa University proposed a new mathematical framework to understand the properties of the fundamental particles called neutrinos. This work may help cosmologists make progress on the apparent paradox of the existence of matter in the Universe.

The Standard Model of particle physics that outlines the basic constituents of matter and the forces that act between them has seen remarkable experimental success, culminating in the discovery of the last predicted particle, the Higgs boson, in 2012. However, the Standard Model does not resolve some of the long-standing issues in cosmology, such as the identity of "dark matter" that we know must be there but we cannot see, and why there is so much matter in the Universe compared with antimatter. Many scientists believe that the ghost-like particles called neutrinos may be an important part of the answer.

Neutrinos, which hardly interact with other matter, are created by nuclear reactions such as those that power our sun, and trillions of them pass through your body every second. Experiments have shown that, while not massless, neutrinos are much lighter than other particles. This has led physicists to hypothesize that neutrinos get their mass from a different process compared with other particles, called the "Seesaw mechanism."

Now, a research team led by Kanazawa University has developed a new theory to explain the unusual properties of neutrinos.

"We used the seesaw mechanisms with five- or seven-dimensional operators to describe the interaction of a neutrino with two lepton particles and two force-carrying W bosons," explains Mayumi Aoki.

Leptons are a class of elementary particles that include neutrinos, electrons, and so on. Solving these equations showed violations of the Standard Model's prediction that the number of leptons is always conserved.

"To move beyond the Standard Model, we have to explain why lepton conservation is sometimes violated, albeit to a very small degree," says Aoki. "A tiny imbalance of one part in a trillion may explain the why all matter didn't get annihilated by antimatter after the Big Bang."

"Our work explains the origin of the neutrino mass and also provides predictions directly testable by the Large Hadron Collider," says Aoki. The very light masses of neutrinos might hold the key to solving the big questions that have challenged humanity for millennia.

From Science Daily

New study explores if flirting is real and shows it can work

 "She was totally flirting with you," my friend told me after the hosts left our table.

"No, she wasn't. She was just being polite," said another friend.

Misunderstandings about flirting can potentially result in awkwardness or even accusations of sexual harassment. How can we figure out what other people mean when they smile at us? Is there a unique, identifiable facial expression representing flirting -- and if there is, what does it convey, and how effective is it?

Although flirting is mentioned a lot in the general media, and examples are everywhere, there is relatively little scientific work on the topic of flirting, its underlying mechanisms and function.

Now, a new paper by researchers based at the University of Kansas has been published in the Journal of Sex Research examining if flirting has a particular facial cue effectively used by women to indicate interest in a man.

"There are very few scientific articles out there that have systematically studied this well-known phenomenon," said Omri Gillath, professor of psychology at KU, who co-wrote the paper. "None of these studies have identified the flirting facial expression and tested its effects."

Gillath's collaborators were lead author Parnia Haj-Mohamadi, a doctoral student in psychology at KU, and Erika Rosenberg of the University of California-Davis.

The researchers found internal states -- such as being romantically or sexually interested in someone -- can be conveyed to others nonverbally through facial expression.

In other words -- flirting works.

"Across our six studies, we found most men were able to recognize a certain female facial expression as representing flirting," Gillath said. "It has a unique morphology, and it's different from expressions that have similar features -- for example, smiling -- but aren't identified by men as flirting expression."

In the studies, women -- some professional actresses and some volunteers from the community -- were asked either to spontaneously pose a flirting expression (similar to what they'd use at a bar to get attention from a potential mate) or to follow instructions based on existing anthropological literature for what researchers define as flirting.

The team found some women are more effective than others in effectively conveying a flirtatious facial cue, while some men are better at recognizing this cue. Beyond these individual differences, a few expressions were identified by most (if not all) men as flirting.

The researchers used the Facial Action Coding System (FACS) to classify the morphology of highly recognized flirtatious facial expressions. The coding showed the most effective flirting cues include a head turned to one side and tilted down slightly, a slight smile, and eyes turned forward toward the implied target.

After identifying these most recognized expressions of flirting, the researchers used them in experimental studies.

"Our findings support the role of flirtatious expression in communication and mating initiation," Gillath said. "For the first time, not only were we able to isolate and identify the expressions that represent flirting, but we were also able to reveal their function -- to activate associations related with relationships and sex."

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New dopamine sensors could help unlock the mysteries of brain chemistry

 In 2018, Lin Tian and her team at UC Davis Health developed dLight1, a single fluorescent protein-based biosensor. This family of highly specific sensors detects dopamine, a hormone released by neurons to send signals to other nerve cells. When combined with advanced microscopy, dLight1 provides high resolution, real-time imaging of the spatial and temporal release of dopamine in live animals.

Recently, Tian and her team succeeded in expanding the color spectrum of the dLight1 sensor. In an article published Sept. 7 in Nature Methods, they introduced two new spectral variants of dLight1: the yellow YdLight1 and the red RdLight1.

"The new sensors will help researchers to detect and monitor different information processing activities in the brain," said Lin Tian, associate professor of biochemistry and molecular medicine and the lead author on the study. "With the different colors, we will be able to see multiple neurochemical release and neural activities at the same time."

The RdLight1 permits the simultaneous assessment of dopamine, pre- or post-synaptic neuronal activity and the glutamate release in specific types of cells and neuronal projections in animals. Its increased light penetration and imaging depth provide enhanced dopamine signal quality. This allows researchers to optically dissect dopamine's release and model its effects on neural circuits.

As a neurotransmitter, dopamine plays an important role in movement, attention, learning and the brain's pleasure and reward system.

"These exciting new tools opened a new door to developing color-shifted neurochemical indicators. Together with other tools, they have great potential to unlock the mysteries of brain chemistry in health and disease," Tian said. "The knowledge we gain from these sensors will facilitate the development of safer next-generation therapies to neuropsychiatric disorders such as depression, anxiety, schizophrenia and addiction."

From Science Daily

New treatments for deadly lung disease could be revealed by 3D modeling

 A 3D bioengineered model of lung tissue built by University of Michigan researchers is poking holes in decades worth of flat, Petri dish observations into how the deadly disease pulmonary fibrosis progresses.

The causes of pulmonary fibrosis are not fully understood, but the condition is marked by scar tissue that forms inside the lungs. That scar tissue stiffens the walls of the lungs' air sacs, called alveoli, or, at advanced stages, can completely fill the alveolar spaces. Both scenarios make breathing difficult and decrease the amount of oxygen entering the bloodstream. Often the condition is irreversible, eventually causing lung failure and death.

Some clinicians are concerned that critically ill COVID-19 patients may develop a form of pulmonary fibrosis after a long stay in the ICU.

Researchers are searching for better treatments. While they've managed to find some drugs that relieve symptoms or slow the progression in practice, they haven't been able to reliably replicate those results in today's 2D lab models. So they don't understand how or why those drugs are working, and they can't always predict which compounds will make a difference. The new research from U-M takes a step in that direction, and it starkly demonstrates how prior approaches have been ineffective.

The team showed that in some 2D models, drugs that are already known to be effective in treatment do not produce test results that show efficacy. Their 3D tissue engineered model of fibrotic lung tissue, however, shows that those drugs work.

Before their tests on drugs, they first performed studies to understand how tissue stiffness drives the appearance of myofibroblasts -- cells that correlate with the progression of scarring.

"Even in cells from the same patient, we saw different outcomes," said Daniel Matera, a doctoral candidate and research team member. "When we introduced stiffness into the 2D testing environment, it activated myofibroblasts, essentially creating scar tissue. When we introduced that same kind of stiffness into our 3D testing environment, it prevented or slowed the activation of myofibroblasts, stopping or slowing the creation of scar tissue."

With the majority of pulmonary fibrosis research relying on 2D testing, he said, many have believed the high lung stiffness in patients is what should be targeted by treatments. U-M's research indicates that targeting stiffness alone may not hinder disease progression in patients, even if it works in a Petri dish.

To find effective treatments, researchers first screen libraries of pharmaceutical compounds. Today, they typically do that on cells cultured on flat plastic or hydrogel surfaces, but these settings often do a poor job of recreating what happens in the human body.

Brendon Baker, assistant professor in the U-M Department of Biomedical Engineering, and his team took a tissue engineering approach. They reconstructed 3D lung interstitium, or connective tissue, the home of fibroblasts and location where fibrosis begins. Their goal was to understand how mechanical cues from lung tissue affect fibroblast behavior and disease progression.

"Recreating the 3D fibrous structure of the lung interstitium allowed us to confirm effective drugs that wouldn't be identified as hits in traditional screening settings," Baker said.

At the center of the pulmonary fibrosis mystery is the fibroblast, a cell found in the lung interstitium that is crucial to healing but, paradoxically, can also drive disease progression. When activated, after an injury or when disease is present, they become myofibroblasts. Regulated properly, they play an important role in wound healing, but when misregulated, they can drive chronic disease. In the case of pulmonary fibrosis, they cause the stiffening of lung tissue that hampers breathing.

"Our lung tissue model looks and behaves similarly to what we have observed when imaging real lung tissue," Baker said. "Patient cells within our model can actively stiffen, degrade or remodel their own environment just like they do in disease."

 Read more at Science Daily

Dams exacerbate the consequences of climate change on river fish

 A potential response of river fish to environmental changes is to colonize new habitats. But what happens when dams and weirs restrict their movement? And are native and alien species similarly affected? Researchers from the Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB) and the Spanish University of Girona (UdG) have addressed these questions in a recent study.

River ecosystems are frequently fragmented by dams and weirs. As a result, native fish are often restricted in their movement along the river course and are unable to colonize new habitats. Thus, barriers impede native species from adjusting their distributions in response to the effects of climate change such as changes in water temperature and quality.

On the other hand, river fragmentation might also limit the further spread of invasive alien species. Using the Ebro River in Spain as an example, the research team has investigated how habitats of native and alien fish species change under different climate scenarios and how dams mediate habitat accessibility.

"The Ebro River is particularly vulnerable and threatened by climate change and species invasions. In addition, the Ebro River is fragmented by over 300 dams and many smaller barriers, which makes it even worse for the native fish species," said Emili García-Berthou, Professor at the University of Girona and co-author of the study.

By applying a spatial modelling framework, the authors showed that losses of native species and gains of alien species and consequentially most pronounced biodiversity changes are particularly expected in the lower and mid reaches of larger Ebro River tributaries. According to their results, the majority of species are projected to shift their range in upstream direction with alien species such as eastern mosquitofish, wels catfish and common carp showing especially large habitat gains.

"The Ebro River system is home to several endemic species that exclusively occur on the Iberian Peninsula. These species are particularly imperilled by barriers that limit movements in response to climate change. Whether dams can effectively prevent the spread of alien species is questionable. In fact, the establishment of alien fishes is often facilitated by the changed flow and habitat conditions that result from damming rivers," said IGB researcher Johannes Radinger, lead author of the study.

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A warm Jupiter orbiting a cool star

 A planet observed crossing in front of, or transiting, a low-mass star has been determined to be about the size of Jupiter. While hundreds of Jupiter-sized planets have been discovered orbiting larger sun-like stars, it is rare to see these planets orbiting low-mass host stars and the discovery could help astronomers to better understand how these giant planets form.

"This is only the fifth Jupiter-sized planet transiting a low-mass star that has been observed and the first with such a long orbital period, which makes this discovery really exciting," said Caleb Cañas, lead author of the paper and a Ph.D. student at Penn State and NASA Earth and Space Science Fellow.

Originally detected by NASA's Transiting Exoplanet Survey Satellite (TESS) spacecraft, astronomers characterized the planet's mass, radius, and its orbital period using the Habitable-zone Planet Finder (HPF), an astronomical spectrograph built by a Penn State team and installed on the 10m Hobby-Eberly Telescope at McDonald Observatory in Texas. A paper describing the research appears in the September 2020 issue of the Astronomical Journal and is publicly accessible on arXiv.

"A transiting Jupiter-sized planet is amenable to further observations to see how well the orbit is aligned with the spin-axis of the host star and to constrain how it could have formed," said Cañas. "Furthermore, the low mass of the host star and the long orbital period result in a Jupiter with a moderate temperature compared to similar planets detected with NASA's Kepler space telescope."

The host star, TOI-1899, is a low-mass (M dwarf) star about 419 light years away from Earth. The planet, TOI-1899 b, is two-thirds the mass of Jupiter, ten percent larger in radius than Jupiter, and is 0.16 astronomical units (AU) -- a measure defined as the distance between the Earth and the sun -- from its host star such that a full year on TOI-1899 takes only 29 Earth days. For comparison, the four other transiting Jupiter-size planets around comparable stars complete their orbits in less than 4 days.

The planet was detected by TESS using the transit method, which searches for stars showing periodic dips in their brightness as a telltale sign of an orbiting object crossing in front of the star and blocking a portion of its light. The signal was later confirmed as a planet using precision observations from the HPF spectrograph that measure the planet's mass by analyzing how it causes its host start to the wobble.

From a formation and orbital evolution perspective, there is not a clear dividing line between warm Jupiters and the large planets even closer to their host stars, the more commonly discovered hot Jupiters.

"Warm Jupiters like TOI-1899 b orbit surprisingly close to their star," said Rebekah Dawson, assistant professor of astronomy and astrophysics at Penn State and an author of the paper. "Even though the planet's orbital period is long compared to many other giant planets detected and characterized through the transit method, it still places the giant planet much closer to its star than we'd expect from classical formation theories. Detailed characterization of their physical and orbital properties, system architecture, and host stars -- as the HPF team has done for TOI-1899 b -- allow us test theories for how giant planets can form or be displaced so close to their star."

The Habitable-zone Planet Finder was delivered to the 10m Hobby Eberly Telescope at McDonald Observatory in late 2017, and started full science operations in late 2018. HPF is designed to detect and characterize planets in the Habitable-zone -- the region around the star where a planet could sustain liquid water on its surface -- around nearby M-dwarf stars, but is also capable of making sensitive measurements for planets outside the habitable zone.

"This warm Jupiter is a compelling target for atmospheric characterization with upcoming missions like the James Webb Space Telescope," said Suvrath Mahadevan, professor of astronomy and astrophysics at Penn State, the principal investigator of the HPF spectrograph, and an author of the paper. "HPF was critical in helping us to confirm this, but detecting a second transit is important to very precisely pin down its period."

Read more at Science Daily

Possible marker of life spotted on venus

 

Planet Venus

An international team of astronomers today announced the discovery of a rare molecule -- phosphine -- in the clouds of Venus. On Earth, this gas is only made industrially or by microbes that thrive in oxygen-free environments. Astronomers have speculated for decades that high clouds on Venus could offer a home for microbes -- floating free of the scorching surface but needing to tolerate very high acidity. The detection of phosphine could point to such extra-terrestrial 'aerial' life.

"When we got the first hints of phosphine in Venus's spectrum, it was a shock!," says team leader Jane Greaves of Cardiff University in the UK, who first spotted signs of phosphine in observations from the James Clerk Maxwell Telescope (JCMT), operated by the East Asian Observatory, in Hawai'i. Confirming their discovery required using 45 antennas of the Atacama Large Millimeter/submillimeter Array (ALMA) in Chile, a more sensitive telescope in which the European Southern Observatory (ESO) is a partner. Both facilities observed Venus at a wavelength of about 1 millimetre, much longer than the human eye can see -- only telescopes at high altitude can detect it effectively.

The international team, which includes researchers from the UK, US and Japan, estimates that phosphine exists in Venus's clouds at a small concentration, only about twenty molecules in every billion. Following their observations, they ran calculations to see whether these amounts could come from natural non-biological processes on the planet. Some ideas included sunlight, minerals blown upwards from the surface, volcanoes, or lightning, but none of these could make anywhere near enough of it. These non-biological sources were found to make at most one ten thousandth of the amount of phosphine that the telescopes saw.

To create the observed quantity of phosphine (which consists of hydrogen and phosphorus) on Venus, terrestrial organisms would only need to work at about 10% of their maximum productivity, according to the team. Earth bacteria are known to make phosphine: they take up phosphate from minerals or biological material, add hydrogen, and ultimately expel phosphine. Any organisms on Venus will probably be very different to their Earth cousins, but they too could be the source of phosphine in the atmosphere.

While the discovery of phosphine in Venus's clouds came as a surprise, the researchers are confident in their detection. "To our great relief, the conditions were good at ALMA for follow-up observations while Venus was at a suitable angle to Earth. Processing the data was tricky, though, as ALMA isn't usually looking for very subtle effects in very bright objects like Venus," says team member Anita Richards of the UK ALMA Regional Centre and the University of Manchester. "In the end, we found that both observatories had seen the same thing -- faint absorption at the right wavelength to be phosphine gas, where the molecules are backlit by the warmer clouds below," adds Greaves, who led the study published today in Nature Astronomy.

Another team member, Clara Sousa Silva of the Massachusetts Institute of Technology in the US, has investigated phosphine as a "biosignature" gas of non-oxygen-using life on planets around other stars, because normal chemistry makes so little of it. She comments: "Finding phosphine on Venus was an unexpected bonus! The discovery raises many questions, such as how any organisms could survive. On Earth, some microbes can cope with up to about 5% of acid in their environment -- but the clouds of Venus are almost entirely made of acid."

The team believes their discovery is significant because they can rule out many alternative ways to make phosphine, but they acknowledge that confirming the presence of "life" needs a lot more work. Although the high clouds of Venus have temperatures up to a pleasant 30 degrees Celsius, they are incredibly acidic -- around 90% sulphuric acid -- posing major issues for any microbes trying to survive there.

ESO astronomer and ALMA European Operations Manager Leonardo Testi, who did not participate in the new study, says: "The non-biological production of phosphine on Venus is excluded by our current understanding of phosphine chemistry in rocky planets' atmospheres. Confirming the existence of life on Venus's atmosphere would be a major breakthrough for astrobiology; thus, it is essential to follow-up on this exciting result with theoretical and observational studies to exclude the possibility that phosphine on rocky planets may also have a chemical origin different than on Earth."

More observations of Venus and of rocky planets outside our Solar System, including with ESO's forthcoming Extremely Large Telescope, may help gather clues on how phosphine can originate on them and contribute to the search for signs of life beyond Earth.

Read more at Science Daily

Carbon-rich exoplanets may be made of diamonds

 As missions like NASA's Hubble Space Telescope, TESS and Kepler continue to provide insights into the properties of exoplanets (planets around other stars), scientists are increasingly able to piece together what these planets look like, what they are made of, and if they could be habitable or even inhabited.

In a new study published recently in The Planetary Science Journal, a team of researchers from Arizona State University (ASU) and the University of Chicago have determined that some carbon-rich exoplanets, given the right circumstances, could be made of diamonds and silica.

"These exoplanets are unlike anything in our solar system," says lead author Harrison Allen-Sutter of ASU's School of Earth and Space Exploration.

Diamond exoplanet formation

When stars and planets are formed, they do so from the same cloud of gas, so their bulk compositions are similar. A star with a lower carbon to oxygen ratio will have planets like Earth, comprised of silicates and oxides with a very small diamond content (Earth's diamond content is about 0.001%).

But exoplanets around stars with a higher carbon to oxygen ratio than our sun are more likely to be carbon-rich. Allen-Sutter and co-authors Emily Garhart, Kurt Leinenweber and Dan Shim of ASU, with Vitali Prakapenka and Eran Greenberg of the University of Chicago, hypothesized that these carbon-rich exoplanets could convert to diamond and silicate, if water (which is abundant in the universe) were present, creating a diamond-rich composition.

Diamond-anvils and X-rays

To test this hypothesis, the research team needed to mimic the interior of carbide exoplanets using high heat and high pressure. To do so, they used high pressure diamond-anvil cells at co-author Shim's Lab for Earth and Planetary Materials.

First, they immersed silicon carbide in water and compressed the sample between diamonds to a very high pressure. Then, to monitor the reaction between silicon carbide and water, they conducted laser heating at the Argonne National Laboratory in Illinois, taking X-ray measurements while the laser heated the sample at high pressures.

As they predicted, with high heat and pressure, the silicon carbide reacted with water and turned into diamonds and silica.

Habitability and inhabitability

So far, we have not found life on other planets, but the search continues. Planetary scientists and astrobiologists are using sophisticated instruments in space and on Earth to find planets with the right properties and the right location around their stars where life could exist.

For carbon-rich planets that are the focus of this study, however, they likely do not have the properties needed for life.

While Earth is geologically active (an indicator habitability), the results of this study show that carbon-rich planets are too hard to be geologically active and this lack of geologic activity may make atmospheric composition uninhabitable. Atmospheres are critical for life as it provides us with air to breathe, protection from the harsh environment of space, and even pressure to allow for liquid water.

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How coronavirus took hold in North America and in Europe

 

Global spread of coronavirus, concept illustration

A new study combines evolutionary genomics from coronavirus samples with computer-simulated epidemics and detailed travel records to reconstruct the spread of coronavirus across the world in unprecedented detail.

Published in the journal Science, the results suggest an extended period of missed opportunity when intensive testing and contact tracing might have prevented SARS-CoV-2 from becoming established in North America and Europe.

The paper also challenges suggestions that linked the earliest known cases of COVID-19 on each continent in January to outbreaks detected weeks later, and provides valuable insights that could inform public health response and help with anticipating and preventing future outbreaks of COVID-19 and other zoonotic diseases.

"Our aspiration was to develop and apply powerful new technology to conduct a definitive analysis of how the pandemic unfolded in space and time, across the globe," said University of Arizona researcher Michael Worobey, who led an interdisciplinary team of scientists from 13 research institutions in the U.S., Belgium, Canada and the U.K. "Before, there were lots of possibilities floating around in a mish-mash of science, social media and an unprecedented number of preprint publications still awaiting peer review."

The team based their analysis on results from viral genome sequencing efforts, which began immediately after the virus was identified. These efforts quickly grew into a worldwide effort unprecedented in scale and pace and have yielded tens of thousands of genome sequences, publicly available in databases.

Contrary to widespread narratives, the first documented arrivals of infected individuals traveling from China to the U.S. and Europe did not snowball into continental outbreaks, the researchers found.

Instead, swift and decisive measures aimed at tracing and containing those initial incursions of the virus were successful and should serve as model responses directing future actions and policies by governments and public health agencies, the study's authors conclude.

How the Virus Arrived in the U.S. and Europe

A Chinese national flying into Seattle from Wuhan, China on Jan. 15 became the first patient in the U.S. shown to be infected with the novel coronavirus and the first to have a SARS-CoV-2 genome sequenced. This patient was designated 'WA1.' It was not until six weeks later that several additional cases were detected in Washington state.

"And while all that time goes past, everyone is in the dark and wondering, 'What's happening?'" Worobey said. "We hope we're OK, we hope there are no other cases, and then it becomes clear, from a remarkable community viral sampling program in Seattle, that there are more cases in Washington and they are genetically very similar to WA1's virus."

Worobey and his collaborators tested the prevailing hypothesis suggesting that patient WA1 had established a transmission cluster that went undetected for six weeks. Although the genomes sampled in February and March share similarities with WA1, they are different enough that the idea of WA1 establishing the ensuing outbreak is very unlikely, they determined. The researchers' findings indicate that the jump from China to the U.S. likely occurred on or around Feb. 1 instead.

The results also puts to rest speculation that this outbreak, the earliest substantial transmission cluster in the U.S., may have been initiated indirectly by dispersal of the virus from China to British Columbia, Canada, just north of Washington State, and then spread from Canada to the U.S. Multiple SARS-CoV-2 genomes published by the British Columbia Center for Disease Control appeared to be ancestral to the viral variants sampled in Washington State, strongly suggesting a Canadian origin of the U.S. epidemic. However, the present study revealed sequencing errors in those genomes, thus ruling out this scenario.

Instead, the new study implicates a direct-from-China source of the U.S. outbreak, right around the time the U.S. administration implemented a travel ban for travelers from China in early February. The nationality of the "index case" of the U.S. outbreak cannot be known for certain because tens of thousands of U.S. citizens and visa holders traveled from China to the U.S. even after the ban took effect.

A similar scenario marks the first known introduction of coronavirus into Europe. On Jan. 20, an employee of an automotive supply company in Bavaria, Germany, flew in for a business meeting from Shanghai, China, unknowingly carrying the virus, ultimately leading to infection of 16 co-workers. In that case, too, an impressive response of rapid testing and isolation prevented the outbreak from spreading any further, the study concludes. Contrary to speculation, this German outbreak was not the source of the outbreak in Northern Italy that eventually spread widely across Europe and eventually to New York City and the rest of the U.S.

The authors also show that this China-to-Italy-US dispersal route ignited transmission clusters on the East Coast slightly later in February than the China-to-US movement of the virus that established the Washington State outbreak. The Washington transmission cluster also predated small clusters of community transmission in February in California, making it the earliest anywhere in North America.

Early Containment Works

The authors say intensive interventions, involving testing, contact tracing, isolation measures and a high degree of compliance of infected individuals, who reported their symptoms to health authorities and self-isolated in a timely manner, helped Germany and the Seattle area contain those outbreaks in January.

"We believe that those measures resulted in a situation where the first sparks could successfully be stamped out, preventing further spread into the community," Worobey said. "What this tells us is that the measures taken in those cases are highly effective and should serve as a blueprint for future responses to emerging diseases that have the potential to escalate into worldwide pandemics."

To reconstruct the pandemic's unfolding, the scientists ran computer programs that carefully simulated the epidemiology and evolution of the virus, in other words, how SARS-CoV-2 spread and mutated over time.

"This allowed us to re-run the tape of how the epidemic unfolded, over and over again, and then check the scenarios that emerge in the simulations against the patterns we see in reality," Worobey said.

"In the Washington case, we can ask, 'What if that patient WA1 who arrived in the U.S. on Jan. 15 really did start that outbreak?' Well, if he did, and you re-run that epidemic over and over and over, and then sample infected patients from that epidemic and evolve the virus in that way, do you get a pattern that looks like what we see in reality? And the answer was no," he said.

"If you seed that early Italian outbreak with the one in Germany, do you see the pattern that you get in the evolutionary data? And the answer, again, is no," he said.

"By re-running the introduction of SARS-CoV-2 into the U.S. and Europe through simulations, we showed that it was very unlikely that the first documented viral introductions into these locales led to productive transmission clusters," said co-author Joel Wertheim of the University of California, San Diego. "Molecular epidemiological analyses are incredibly powerful for revealing transmissions patterns of SARS-CoV-2."

Other methods were then combined with the data from the virtual epidemics, yielding exceptionally detailed and quantitative results.

"Fundamental to this work stands our new tool combining detailed travel history information and phylogenetics, which produces a sort of 'family tree' of how the different genomes of virus sampled from infected individuals are related to each other," said co-author Marc Suchard of the University of California, Los Angeles. "The more accurate evolutionary reconstructions from these tools provide a critical step to understand how SARS-CoV-2 spread globally in such a short time."

"We have to keep in mind that we have studied only short-term evolution of this virus, so it hasn't had much time to accumulate many mutations," said co-author Philippe Lemey of the University of Leuven, Belgium. "Add to that the uneven sampling of genomes from different parts of the world, and it becomes clear that there are huge benefits to be gained from integrating various sources of information, combining genomic reconstructions with complementary approaches like flight records and the total number of COVID-19 cases in various global regions in January and February."

Read more at Science Daily