Showing papers in "Proceedings of the National Academy of Sciences of the United States of America in 2021"

Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences

Abstract: In the field of artificial intelligence, a combination of scale in data and model capacity enabled by unsupervised learning has led to major advances in representation learning and statistical generation In the life sciences, the anticipated growth of sequencing promises unprecedented data on natural sequence diversity Protein language modeling at the scale of evolution is a logical step toward predictive and generative artificial intelligence for biology To this end, we use unsupervised learning to train a deep contextual language model on 86 billion amino acids across 250 million protein sequences spanning evolutionary diversity The resulting model contains information about biological properties in its representations The representations are learned from sequence data alone The learned representation space has a multiscale organization reflecting structure from the level of biochemical properties of amino acids to remote homology of proteins Information about secondary and tertiary structure is encoded in the representations and can be identified by linear projections Representation learning produces features that generalize across a range of applications, enabling state-of-the-art supervised prediction of mutational effect and secondary structure and improving state-of-the-art features for long-range contact prediction

An evidence review of face masks against COVID-19.

Abstract: The science around the use of masks by the public to impede COVID-19 transmission is advancing rapidly. In this narrative review, we develop an analytical framework to examine mask usage, synthesizing the relevant literature to inform multiple areas: population impact, transmission characteristics, source control, wearer protection, sociological considerations, and implementation considerations. A primary route of transmission of COVID-19 is via respiratory particles, and it is known to be transmissible from presymptomatic, paucisymptomatic, and asymptomatic individuals. Reducing disease spread requires two things: limiting contacts of infected individuals via physical distancing and other measures and reducing the transmission probability per contact. The preponderance of evidence indicates that mask wearing reduces transmissibility per contact by reducing transmission of infected respiratory particles in both laboratory and clinical contexts. Public mask wearing is most effective at reducing spread of the virus when compliance is high. Given the current shortages of medical masks, we recommend the adoption of public cloth mask wearing, as an effective form of source control, in conjunction with existing hygiene, distancing, and contact tracing strategies. Because many respiratory particles become smaller due to evaporation, we recommend increasing focus on a previously overlooked aspect of mask usage: mask wearing by infectious people ("source control") with benefits at the population level, rather than only mask wearing by susceptible people, such as health care workers, with focus on individual outcomes. We recommend that public officials and governments strongly encourage the use of widespread face masks in public, including the use of appropriate regulation.

Insect decline in the Anthropocene: Death by a thousand cuts

Abstract: Nature is under siege. In the last 10,000 y the human population has grown from 1 million to 7.8 billion. Much of Earth’s arable lands are already in agriculture (1), millions of acres of tropical forest are cleared each year (2, 3), atmospheric CO2 levels are at their highest concentrations in more than 3 million y (4), and climates are erratically and steadily changing from pole to pole, triggering unprecedented droughts, fires, and floods across continents. Indeed, most biologists agree that the world has entered its sixth mass extinction event, the first since the end of the Cretaceous Period 66 million y ago, when more than 80% of all species, including the nonavian dinosaurs, perished. Ongoing losses have been clearly demonstrated for better-studied groups of organisms. Terrestrial vertebrate population sizes and ranges have contracted by one-third, and many mammals have experienced range declines of at least 80% over the last century (5). A 2019 assessment suggests that half of all amphibians are imperiled (2.5% of which have recently gone extinct) (6). Bird numbers across North America have fallen by 2.9 billion since 1970 (7). Prospects for the world’s coral reefs, beyond the middle of this century, could scarcely be more dire (8). A 2020 United Nations report estimated that more than a million species are in danger of extinction over the next few decades (9), but also see the more bridled assessments in refs. 10 and 11. Although a flurry of reports has drawn attention to declines in insect abundance, biomass, species richness, and range sizes (e.g., refs. 12⇓⇓⇓⇓⇓–18; for reviews see refs. 19 and 20), whether the rates of declines for insects are on par with or exceed those for other groups remains unknown. There are still too … [↵][1]1To whom correspondence may be addressed. Email: david.wagner{at}uconn.edu. [1]: #xref-corresp-1-1

Learning loss due to school closures during the COVID-19 pandemic.

Abstract: Suspension of face-to-face instruction in schools during the COVID-19 pandemic has led to concerns about consequences for students' learning. So far, data to study this question have been limited. Here we evaluate the effect of school closures on primary school performance using exceptionally rich data from The Netherlands (n ≈ 350,000). We use the fact that national examinations took place before and after lockdown and compare progress during this period to the same period in the 3 previous years. The Netherlands underwent only a relatively short lockdown (8 wk) and features an equitable system of school funding and the world's highest rate of broadband access. Still, our results reveal a learning loss of about 3 percentile points or 0.08 standard deviations. The effect is equivalent to one-fifth of a school year, the same period that schools remained closed. Losses are up to 60% larger among students from less-educated homes, confirming worries about the uneven toll of the pandemic on children and families. Investigating mechanisms, we find that most of the effect reflects the cumulative impact of knowledge learned rather than transitory influences on the day of testing. Results remain robust when balancing on the estimated propensity of treatment and using maximum-entropy weights or with fixed-effects specifications that compare students within the same school and family. The findings imply that students made little or no progress while learning from home and suggest losses even larger in countries with weaker infrastructure or longer school closures.

The echo chamber effect on social media

Abstract: Social media may limit the exposure to diverse perspectives and favor the formation of groups of like-minded users framing and reinforcing a shared narrative, that is, echo chambers. However, the interaction paradigms among users and feed algorithms greatly vary across social media platforms. This paper explores the key differences between the main social media platforms and how they are likely to influence information spreading and echo chambers’ formation. We perform a comparative analysis of more than 100 million pieces of content concerning several controversial topics (e.g., gun control, vaccination, abortion) from Gab, Facebook, Reddit, and Twitter. We quantify echo chambers over social media by two main ingredients: 1) homophily in the interaction networks and 2) bias in the information diffusion toward like-minded peers. Our results show that the aggregation of users in homophilic clusters dominate online interactions on Facebook and Twitter. We conclude the paper by directly comparing news consumption on Facebook and Reddit, finding higher segregation on Facebook.

Lifestyle and mental health disruptions during COVID-19.

Abstract: Using a longitudinal dataset linking biometric and survey data from several cohorts of young adults before and during the COVID-19 pandemic ([Formula: see text]), we document large disruptions to physical activity, sleep, time use, and mental health. At the onset of the pandemic, average steps decline from 10,000 to 4,600 steps per day, sleep increases by 25 to 30 min per night, time spent socializing declines by over half to less than 30 min, and screen time more than doubles to over 5 h per day. Over the course of the pandemic from March to July 2020 the proportion of participants at risk for clinical depression ranges from 46% to 61%, up to a 90% increase in depression rates compared to the same population just prior to the pandemic. Our analyses suggest that disruption to physical activity is a leading risk factor for depression during the pandemic. However, restoration of those habits through a short-term intervention does not meaningfully improve mental well-being.

Reductions in 2020 US life expectancy due to COVID-19 and the disproportionate impact on the Black and Latino populations.

Abstract: COVID-19 has resulted in a staggering death toll in the United States: over 215,000 by mid-October 2020, according to the Centers for Disease Control and Prevention. Black and Latino Americans have experienced a disproportionate burden of COVID-19 morbidity and mortality, reflecting persistent structural inequalities that increase risk of exposure to COVID-19 and mortality risk for those infected. We estimate life expectancy at birth and at age 65 y for 2020, for the total US population and by race and ethnicity, using four scenarios of deaths-one in which the COVID-19 pandemic had not occurred and three including COVID-19 mortality projections produced by the Institute for Health Metrics and Evaluation. Our medium estimate indicates a reduction in US life expectancy at birth of 1.13 y to 77.48 y, lower than any year since 2003. We also project a 0.87-y reduction in life expectancy at age 65 y. The Black and Latino populations are estimated to experience declines in life expectancy at birth of 2.10 and 3.05 y, respectively, both of which are several times the 0.68-y reduction for Whites. These projections imply an increase of nearly 40% in the Black-White life expectancy gap, from 3.6 y to over 5 y, thereby eliminating progress made in reducing this differential since 2006. Latinos, who have consistently experienced lower mortality than Whites (a phenomenon known as the Latino or Hispanic paradox), would see their more than 3-y survival advantage reduced to less than 1 y.

Asymptomatic SARS-CoV-2 infection: A systematic review and meta-analysis.

Abstract: Quantification of asymptomatic infections is fundamental for effective public health responses to the COVID-19 pandemic. Discrepancies regarding the extent of asymptomaticity have arisen from inconsistent terminology as well as conflation of index and secondary cases which biases toward lower asymptomaticity. We searched PubMed, Embase, Web of Science, and World Health Organization Global Research Database on COVID-19 between January 1, 2020 and April 2, 2021 to identify studies that reported silent infections at the time of testing, whether presymptomatic or asymptomatic. Index cases were removed to minimize representational bias that would result in overestimation of symptomaticity. By analyzing over 350 studies, we estimate that the percentage of infections that never developed clinical symptoms, and thus were truly asymptomatic, was 35.1% (95% CI: 30.7 to 39.9%). At the time of testing, 42.8% (95% prediction interval: 5.2 to 91.1%) of cases exhibited no symptoms, a group comprising both asymptomatic and presymptomatic infections. Asymptomaticity was significantly lower among the elderly, at 19.7% (95% CI: 12.7 to 29.4%) compared with children at 46.7% (95% CI: 32.0 to 62.0%). We also found that cases with comorbidities had significantly lower asymptomaticity compared to cases with no underlying medical conditions. Without proactive policies to detect asymptomatic infections, such as rapid contact tracing, prolonged efforts for pandemic control may be needed even in the presence of vaccination.

A guideline to limit indoor airborne transmission of COVID-19.

Abstract: The current revival of the American economy is being predicated on social distancing, specifically the Six-Foot Rule, a guideline that offers little protection from pathogen-bearing aerosol droplets sufficiently small to be continuously mixed through an indoor space. The importance of airborne transmission of COVID-19 is now widely recognized. While tools for risk assessment have recently been developed, no safety guideline has been proposed to protect against it. We here build on models of airborne disease transmission in order to derive an indoor safety guideline that would impose an upper bound on the "cumulative exposure time," the product of the number of occupants and their time in an enclosed space. We demonstrate how this bound depends on the rates of ventilation and air filtration, dimensions of the room, breathing rate, respiratory activity and face mask use of its occupants, and infectiousness of the respiratory aerosols. By synthesizing available data from the best-characterized indoor spreading events with respiratory drop size distributions, we estimate an infectious dose on the order of 10 aerosol-borne virions. The new virus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) is thus inferred to be an order of magnitude more infectious than its forerunner (SARS-CoV), consistent with the pandemic status achieved by COVID-19. Case studies are presented for classrooms and nursing homes, and a spreadsheet and online app are provided to facilitate use of our guideline. Implications for contact tracing and quarantining are considered, and appropriate caveats enumerated. Particular consideration is given to respiratory jets, which may substantially elevate risk when face masks are not worn.

People have shaped most of terrestrial nature for at least 12,000 years

Abstract: Archaeological and paleoecological evidence shows that by 10,000 BCE, all human societies employed varying degrees of ecologically transformative land use practices, including burning, hunting, species propagation, domestication, cultivation, and others that have left long-term legacies across the terrestrial biosphere. Yet, a lingering paradigm among natural scientists, conservationists, and policymakers is that human transformation of terrestrial nature is mostly recent and inherently destructive. Here, we use the most up-to-date, spatially explicit global reconstruction of historical human populations and land use to show that this paradigm is likely wrong. Even 12,000 y ago, nearly three quarters of Earth’s land was inhabited and therefore shaped by human societies, including more than 95% of temperate and 90% of tropical woodlands. Lands now characterized as “natural,” “intact,” and “wild” generally exhibit long histories of use, as do protected areas and Indigenous lands, and current global patterns of vertebrate species richness and key biodiversity areas are more strongly associated with past patterns of land use than with present ones in regional landscapes now characterized as natural. The current biodiversity crisis can seldom be explained by the loss of uninhabited wildlands, resulting instead from the appropriation, colonization, and intensifying use of the biodiverse cultural landscapes long shaped and sustained by prior societies. Recognizing this deep cultural connection with biodiversity will therefore be essential to resolve the crisis.

Machine learning-accelerated computational fluid dynamics.

Abstract: Numerical simulation of fluids plays an essential role in modeling many physical phenomena, such as weather, climate, aerodynamics, and plasma physics. Fluids are well described by the Navier-Stokes equations, but solving these equations at scale remains daunting, limited by the computational cost of resolving the smallest spatiotemporal features. This leads to unfavorable trade-offs between accuracy and tractability. Here we use end-to-end deep learning to improve approximations inside computational fluid dynamics for modeling two-dimensional turbulent flows. For both direct numerical simulation of turbulence and large-eddy simulation, our results are as accurate as baseline solvers with 8 to 10× finer resolution in each spatial dimension, resulting in 40- to 80-fold computational speedups. Our method remains stable during long simulations and generalizes to forcing functions and Reynolds numbers outside of the flows where it is trained, in contrast to black-box machine-learning approaches. Our approach exemplifies how scientific computing can leverage machine learning and hardware accelerators to improve simulations without sacrificing accuracy or generalization.

The ORF8 protein of SARS-CoV-2 mediates immune evasion through down-regulating MHC-Ι.

Abstract: COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a global pandemic and has claimed over 2 million lives worldwide. Although the genetic sequences of SARS-CoV and SARS-CoV-2 have high homology, the clinical and pathological characteristics of COVID-19 differ significantly from those of SARS. How and whether SARS-CoV-2 evades (cellular) immune surveillance requires further elucidation. In this study, we show that SARS-CoV-2 infection leads to major histocompability complex class Ι (MHC-Ι) down-regulation both in vitro and in vivo. The viral protein encoded by open reading frame 8 (ORF8) of SARS-CoV-2, which shares the least homology with SARS-CoV among all viral proteins, directly interacts with MHC-Ι molecules and mediates their down-regulation. In ORF8-expressing cells, MHC-Ι molecules are selectively targeted for lysosomal degradation via autophagy. Thus, SARS-CoV-2-infected cells are much less sensitive to lysis by cytotoxic T lymphocytes. Because ORF8 protein impairs the antigen presentation system, inhibition of ORF8 could be a strategy to improve immune surveillance.

Network medicine framework for identifying drug-repurposing opportunities for COVID-19.

Abstract: The COVID-19 pandemic has highlighted the need to quickly and reliably prioritize clinically approved compounds for their potential effectiveness for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. Here, we deployed algorithms relying on artificial intelligence, network diffusion, and network proximity, tasking each of them to rank 6,340 drugs for their expected efficacy against SARS-CoV-2. To test the predictions, we used as ground truth 918 drugs experimentally screened in VeroE6 cells, as well as the list of drugs in clinical trials that capture the medical community's assessment of drugs with potential COVID-19 efficacy. We find that no single predictive algorithm offers consistently reliable outcomes across all datasets and metrics. This outcome prompted us to develop a multimodal technology that fuses the predictions of all algorithms, finding that a consensus among the different predictive methods consistently exceeds the performance of the best individual pipelines. We screened in human cells the top-ranked drugs, obtaining a 62% success rate, in contrast to the 0.8% hit rate of nonguided screenings. Of the six drugs that reduced viral infection, four could be directly repurposed to treat COVID-19, proposing novel treatments for COVID-19. We also found that 76 of the 77 drugs that successfully reduced viral infection do not bind the proteins targeted by SARS-CoV-2, indicating that these network drugs rely on network-based mechanisms that cannot be identified using docking-based strategies. These advances offer a methodological pathway to identify repurposable drugs for future pathogens and neglected diseases underserved by the costs and extended timeline of de novo drug development.

Agricultural intensification and climate change are rapidly decreasing insect biodiversity.

Abstract: Major declines in insect biomass and diversity, reviewed here, have become obvious and well documented since the end of World War II. Here, we conclude that the spread and intensification of agriculture during the past half century is directly related to these losses. In addition, many areas, including tropical mountains, are suffering serious losses because of climate change as well. Crops currently occupy about 11% of the world's land surface, with active grazing taking place over an additional 30%. The industrialization of agriculture during the second half of the 20th century involved farming on greatly expanded scales, monoculturing, the application of increasing amounts of pesticides and fertilizers, and the elimination of interspersed hedgerows and other wildlife habitat fragments, all practices that are destructive to insect and other biodiversity in and near the fields. Some of the insects that we are destroying, including pollinators and predators of crop pests, are directly beneficial to the crops. In the tropics generally, natural vegetation is being destroyed rapidly and often replaced with export crops such as oil palm and soybeans. To mitigate the effects of the Sixth Mass Extinction event that we have caused and are experiencing now, the following will be necessary: a stable (and almost certainly lower) human population, sustainable levels of consumption, and social justice that empowers the less wealthy people and nations of the world, where the vast majority of us live, will be necessary.

Impacts of the COVID-19 pandemic on rural America.

Abstract: Despite considerable social scientific attention to the impacts of the COVID-19 pandemic on urbanized areas, very little research has examined its impact on rural populations. Yet rural communities-which make up tens of millions of people from diverse backgrounds in the United States-are among the nation's most vulnerable populations and may be less resilient to the effects of such a large-scale exogenous shock. We address this critical knowledge gap with data from a new survey designed to assess the impacts of the pandemic on health-related and economic dimensions of rural well-being in the North American West. Notably, we find that the effects of the COVID-19 pandemic on rural populations have been severe, with significant negative impacts on unemployment, overall life satisfaction, mental health, and economic outlook. Further, we find that these impacts have been generally consistent across age, ethnicity, education, and sex. We discuss how these findings constitute the beginning of a much larger interdisciplinary COVID-19 research effort that integrates rural areas and pushes beyond the predominant focus on cities and nation-states.

Pandemic precarity: COVID-19 is exposing and exacerbating inequalities in the American heartland.

Abstract: Crises lay bare the social fault lines of society In the United States, race, gender, age, and education have affected vulnerability to COVID-19 infection Yet, consequences likely extend far beyond morbidity and mortality Temporarily closing the economy sent shock waves through communities, raising the possibility that social inequities, preexisting and current, have weakened economic resiliency and reinforced disadvantage, especially among groups most devastated by the Great Recession We address pandemic precarity, or risk for material and financial insecurity, in Indiana, where manufacturing loss is high, metro areas ranked among the hardest hit by the Great Recession nationally, and health indicators stand in the bottom quintile Using longitudinal data (n = 994) from the Person to Person Health Interview Study, fielded in 2019-2020 and again during Indiana's initial stay-at-home order, we provide a representative, probability-based assessment of adverse economic outcomes of the pandemic Survey-weighted multivariate regressions, controlling for preexisting inequality, find Black adults over 3 times as likely as Whites to report food insecurity, being laid off, or being unemployed Residents without a college degree are twice as likely to report food insecurity (compared to some college), while those not completing high school (compared to bachelor's degree) are 4 times as likely to do so Younger adults and women were also more likely to report economic hardships Together, the results support contentions of a Matthew Effect, where pandemic precarity disproportionately affects historically disadvantaged groups, widening inequality Strategically deployed relief efforts and longer-term policy reforms are needed to challenge the perennial and unequal impact of disasters

SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma.

Abstract: To investigate the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the immune population, we coincupi bated the authentic virus with a highly neutralizing plasma from a COVID-19 convalescent patient. The plasma fully neutralized the virus for seven passages, but, after 45 d, the deletion of F140 in the spike N-terminal domain (NTD) N3 loop led to partial breakthrough. At day 73, an E484K substitution in the receptor-binding domain (RBD) occurred, followed, at day 80, by an insertion in the NTD N5 loop containing a new glycan sequon, which generated a variant completely resistant to plasma neutralization. Computational modeling predicts that the deletion and insertion in loops N3 and N5 prevent binding of neutralizing antibodies. The recent emergence in the United Kingdom, South Africa, Brazil, and Japan of natural variants with similar changes suggests that SARS-CoV-2 has the potential to escape an effective immune response and that vaccines and antibodies able to control emerging variants should be developed.

Plastic waste release caused by COVID-19 and its fate in the global ocean.

Abstract: The COVID-19 pandemic has led to an increased demand for single-use plastics that intensifies pressure on an already out-of-control global plastic waste problem. While it is suspected to be large, the magnitude and fate of this pandemic-associated mismanaged plastic waste are unknown. Here, we use our MITgcm ocean plastic model to quantify the impact of the pandemic on plastic discharge. We show that 8.4 ± 1.4 million tons of pandemic-associated plastic waste have been generated from 193 countries as of August 23, 2021, with 25.9 ± 3.8 thousand tons released into the global ocean representing 1.5 ± 0.2% of the global total riverine plastic discharge. The model projects that the spatial distribution of the discharge changes rapidly in the global ocean within 3 y, with a significant portion of plastic debris landing on the beach and seabed later and a circumpolar plastic accumulation zone will be formed in the Arctic. We find hospital waste represents the bulk of the global discharge (73%), and most of the global discharge is from Asia (72%), which calls for better management of medical waste in developing countries.

Structure of SARS-CoV-2 ORF8, a rapidly evolving immune evasion protein.

Abstract: The molecular basis for the severity and rapid spread of the COVID-19 disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is largely unknown. ORF8 is a rapidly evolving accessory protein that has been proposed to interfere with immune responses. The crystal structure of SARS-CoV-2 ORF8 was determined at 2.04-A resolution by X-ray crystallography. The structure reveals a ∼60-residue core similar to SARS-CoV-2 ORF7a, with the addition of two dimerization interfaces unique to SARS-CoV-2 ORF8. A covalent disulfide-linked dimer is formed through an N-terminal sequence specific to SARS-CoV-2, while a separate noncovalent interface is formed by another SARS-CoV-2-specific sequence, 73YIDI76 Together, the presence of these interfaces shows how SARS-CoV-2 ORF8 can form unique large-scale assemblies not possible for SARS-CoV, potentially mediating unique immune suppression and evasion activities.

Insects and recent climate change

Abstract: Insects have diversified through more than 450 million y of Earth's changeable climate, yet rapidly shifting patterns of temperature and precipitation now pose novel challenges as they combine with decades of other anthropogenic stressors including the conversion and degradation of land. Here, we consider how insects are responding to recent climate change while summarizing the literature on long-term monitoring of insect populations in the context of climatic fluctuations. Results to date suggest that climate change impacts on insects have the potential to be considerable, even when compared with changes in land use. The importance of climate is illustrated with a case study from the butterflies of Northern California, where we find that population declines have been severe in high-elevation areas removed from the most immediate effects of habitat loss. These results shed light on the complexity of montane-adapted insects responding to changing abiotic conditions. We also consider methodological issues that would improve syntheses of results across long-term insect datasets and highlight directions for future empirical work.

Quantifying asymptomatic infection and transmission of COVID-19 in New York City using observed cases, serology, and testing capacity.

Abstract: The contributions of asymptomatic infections to herd immunity and community transmission are key to the resurgence and control of COVID-19, but are difficult to estimate using current models that ignore changes in testing capacity. Using a model that incorporates daily testing information fit to the case and serology data from New York City, we show that the proportion of symptomatic cases is low, ranging from 13 to 18%, and that the reproductive number may be larger than often assumed. Asymptomatic infections contribute substantially to herd immunity, and to community transmission together with presymptomatic ones. If asymptomatic infections transmit at similar rates as symptomatic ones, the overall reproductive number across all classes is larger than often assumed, with estimates ranging from 3.2 to 4.4. If they transmit poorly, then symptomatic cases have a larger reproductive number ranging from 3.9 to 8.1. Even in this regime, presymptomatic and asymptomatic cases together comprise at least 50% of the force of infection at the outbreak peak. We find no regimes in which all infection subpopulations have reproductive numbers lower than three. These findings elucidate the uncertainty that current case and serology data cannot resolve, despite consideration of different model structures. They also emphasize how temporal data on testing can reduce and better define this uncertainty, as we move forward through longer surveillance and second epidemic waves. Complementary information is required to determine the transmissibility of asymptomatic cases, which we discuss. Regardless, current assumptions about the basic reproductive number of severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) should be reconsidered.

Constraining the atmospheric limb of the plastic cycle.

Abstract: Plastic pollution is one of the most pressing environmental and social issues of the 21st century. Recent work has highlighted the atmosphere’s role in transporting microplastics to remote locations [S. Allen et al., Nat. Geosci. 12, 339 (2019) and J. Brahney, M. Hallerud, E. Heim, M. Hahnenberger, S. Sukumaran, Science 368, 1257–1260 (2020)]. Here, we use in situ observations of microplastic deposition combined with an atmospheric transport model and optimal estimation techniques to test hypotheses of the most likely sources of atmospheric plastic. Results suggest that atmospheric microplastics in the western United States are primarily derived from secondary re-emission sources including roads (84%), the ocean (11%), and agricultural soil dust (5%). Using our best estimate of plastic sources and modeled transport pathways, most continents were net importers of plastics from the marine environment, underscoring the cumulative role of legacy pollution in the atmospheric burden of plastic. This effort uses high-resolution spatial and temporal deposition data along with several hypothesized emission sources to constrain atmospheric plastic. Akin to global biogeochemical cycles, plastics now spiral around the globe with distinct atmospheric, oceanic, cryospheric, and terrestrial residence times. Though advancements have been made in the manufacture of biodegradable polymers, our data suggest that extant nonbiodegradable polymers will continue to cycle through the earth’s systems. Due to limited observations and understanding of the source processes, there remain large uncertainties in the transport, deposition, and source attribution of microplastics. Thus, we prioritize future research directions for understanding the plastic cycle.

SARS-CoV-2 exposure in wild white-tailed deer ( Odocoileus virginianus ).

Abstract: Widespread human SARS-CoV-2 infections combined with human-wildlife interactions create the potential for reverse zoonosis from humans to wildlife. We targeted white-tailed deer (Odocoileus virginianus) for serosurveillance based on evidence these deer have angiotensin-converting enzyme 2 receptors with high affinity for SARS-CoV-2, are permissive to infection, exhibit sustained viral shedding, can transmit to conspecifics, exhibit social behavior, and can be abundant near urban centers. We evaluated 624 prepandemic and postpandemic serum samples from wild deer from four US states for SARS-CoV-2 exposure. Antibodies were detected in 152 samples (40%) from 2021 using a surrogate virus neutralization test. A subset of samples tested with a SARS-CoV-2 virus neutralization test showed high concordance between tests. These data suggest white-tailed deer in the populations assessed have been exposed to SARS-CoV-2.

Ongoing global and regional adaptive evolution of SARS-CoV-2.

Abstract: Understanding the trends in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution is paramount to control the COVID-19 pandemic. We analyzed more than 300,000 high-quality genome sequences of SARS-CoV-2 variants available as of January 2021. The results show that the ongoing evolution of SARS-CoV-2 during the pandemic is characterized primarily by purifying selection, but a small set of sites appear to evolve under positive selection. The receptor-binding domain of the spike protein and the region of the nucleocapsid protein associated with nuclear localization signals (NLS) are enriched with positively selected amino acid replacements. These replacements form a strongly connected network of apparent epistatic interactions and are signatures of major partitions in the SARS-CoV-2 phylogeny. Virus diversity within each geographic region has been steadily growing for the entirety of the pandemic, but analysis of the phylogenetic distances between pairs of regions reveals four distinct periods based on global partitioning of the tree and the emergence of key mutations. The initial period of rapid diversification into region-specific phylogenies that ended in February 2020 was followed by a major extinction event and global homogenization concomitant with the spread of D614G in the spike protein, ending in March 2020. The NLS-associated variants across multiple partitions rose to global prominence in March to July, during a period of stasis in terms of interregional diversity. Finally, beginning in July 2020, multiple mutations, some of which have since been demonstrated to enable antibody evasion, began to emerge associated with ongoing regional diversification, which might be indicative of speciation.

The persistent threat of emerging plant disease pandemics to global food security

Abstract: Plant disease outbreaks are increasing and threaten food security for the vulnerable in many areas of the world. Now a global human pandemic is threatening the health of millions on our planet. A stable, nutritious food supply will be needed to lift people out of poverty and improve health outcomes. Plant diseases, both endemic and recently emerging, are spreading and exacerbated by climate change, transmission with global food trade networks, pathogen spillover, and evolution of new pathogen lineages. In order to tackle these grand challenges, a new set of tools that include disease surveillance and improved detection technologies including pathogen sensors and predictive modeling and data analytics are needed to prevent future outbreaks. Herein, we describe an integrated research agenda that could help mitigate future plant disease pandemics.

Collectivism predicts mask use during COVID-19.

Abstract: Since its outbreak, COVID-19 has impacted world regions differentially. Whereas some regions still record tens of thousands of new infections daily, other regions have contained the virus. What explains these striking regional differences? We advance a cultural psychological perspective on mask usage, a precautionary measure vital for curbing the pandemic. Four large-scale studies provide evidence that collectivism (versus individualism) positively predicts mask usage-both within the United States and across the world. Analyzing a dataset of all 3,141 counties of the 50 US states (based on 248,941 individuals), Study 1a revealed that mask usage was higher in more collectivistic US states. Study 1b replicated this finding in another dataset of 16,737 individuals in the 50 US states. Analyzing a dataset of 367,109 individuals in 29 countries, Study 2 revealed that mask usage was higher in more collectivistic countries. Study 3 replicated this finding in a dataset of 277,219 Facebook users in 67 countries. The link between collectivism and mask usage was robust to a host of control variables, including cultural tightness-looseness, political affiliation, demographics, population density, socioeconomic indicators, universal health coverage, government response stringency, and time. Our research suggests that culture fundamentally shapes how people respond to crises like the COVID-19 pandemic. Understanding cultural differences not only provides insight into the current pandemic, but also helps the world prepare for future crises.

The changing risk and burden of wildfire in the United States.

Abstract: Recent dramatic and deadly increases in global wildfire activity have increased attention on the causes of wildfires, their consequences, and how risk from wildfire might be mitigated. Here we bring together data on the changing risk and societal burden of wildfire in the United States. We estimate that nearly 50 million homes are currently in the wildland–urban interface in the United States, a number increasing by 1 million houses every 3 y. To illustrate how changes in wildfire activity might affect air pollution and related health outcomes, and how these linkages might guide future science and policy, we develop a statistical model that relates satellite-based fire and smoke data to information from pollution monitoring stations. Using the model, we estimate that wildfires have accounted for up to 25% of PM2.5 (particulate matter with diameter

The inflated significance of neutral genetic diversity in conservation genetics

Abstract: The current rate of species extinction is rapidly approaching unprecedented highs, and life on Earth presently faces a sixth mass extinction event driven by anthropogenic activity, climate change, and ecological collapse. The field of conservation genetics aims at preserving species by using their levels of genetic diversity, usually measured as neutral genome-wide diversity, as a barometer for evaluating population health and extinction risk. A fundamental assumption is that higher levels of genetic diversity lead to an increase in fitness and long-term survival of a species. Here, we argue against the perceived importance of neutral genetic diversity for the conservation of wild populations and species. We demonstrate that no simple general relationship exists between neutral genetic diversity and the risk of species extinction. Instead, a better understanding of the properties of functional genetic diversity, demographic history, and ecological relationships is necessary for developing and implementing effective conservation genetic strategies.

Modeling SARS-CoV-2 viral kinetics and association with mortality in hospitalized patients from the French COVID cohort.

Abstract: The characterization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral kinetics in hospitalized patients and its association with mortality is unknown We analyzed death and nasopharyngeal viral kinetics in 655 hospitalized patients from the prospective French COVID cohort The model predicted a median peak viral load that coincided with symptom onset Patients with age ≥65 y had a smaller loss rate of infected cells, leading to a delayed median time to viral clearance occurring 16 d after symptom onset as compared to 13 d in younger patients (P 20) Using a joint model, viral dynamics after hospital admission was an independent predictor of mortality (HR = 131, P < 10-3) Finally, we used our model to simulate the effects of effective pharmacological interventions on time to viral clearance and mortality A treatment able to reduce viral production by 90% upon hospital admission would shorten the time to viral clearance by 20 and 29 d in patients of age <65 y and ≥65 y, respectively Assuming that the association between viral dynamics and mortality would remain similar to that observed in our population, this could translate into a reduction of mortality from 19 to 14% in patients of age ≥65 y with risk factors Our results show that viral dynamics is associated with mortality in hospitalized patients Strategies aiming to reduce viral load could have an effect on mortality rate in this population

Historic Yangtze flooding of 2020 tied to extreme Indian Ocean conditions.

Abstract: Heavy monsoon rainfall ravaged a large swath of East Asia in summer 2020. Severe flooding of the Yangtze River displaced millions of residents in the midst of a historic public health crisis. This extreme rainy season was not anticipated from El Nino conditions. Using observations and model experiments, we show that the record strong Indian Ocean Dipole event in 2019 is an important contributor to the extreme Yangtze flooding of 2020. This Indian Ocean mode and a weak El Nino in the Pacific excite downwelling oceanic Rossby waves that propagate slowly westward south of the equator. At a mooring in the Southwest Indian Ocean, the thermocline deepens by a record 70 m in late 2019. The deepened thermocline helps sustain the Indian Ocean warming through the 2020 summer. The Indian Ocean warming forces an anomalous anticyclone in the lower troposphere over the Indo-Northwest Pacific region and intensifies the upper-level westerly jet over East Asia, leading to heavy summer rainfall in the Yangtze Basin. These coupled ocean-atmosphere processes beyond the equatorial Pacific provide predictability. Indeed, dynamic models initialized with observed ocean state predicted the heavy summer rainfall in the Yangtze Basin as early as April 2020.