Impact of weather types on UK ambient particulate matter concentrations

Each year more than 29,000 premature deaths in the UK are linked to long term-exposure to ambient particulate matter (PM) with a diameter less than 2.5 μm (PM2.5). Many studies have focused on the long-term impacts of exposure to PM, but short-term increases in pollution can also exacerbate health effects, leading to deaths brought forward within exposed populations. This study investigates the impact of different atmospheric circulation patterns on UK PM2.5 concentrations and the relative contribution of local and transboundary pollutants to variations in PM2.5 concentrations. Daily mean PM2.5 observations from 42 UK background sites indicate that easterly, south-easterly and southerly wind directions and anticyclonic circulation patterns enhance background concentrations of PM2.5 at all UK sites by up to 12 μg m-3. Results from back trajectory analysis and the European Monitoring and Evaluation Programme for UK model (EMEP4UK) show this is due to the transboundary transport of pollutants from continental Europe. While back trajectories indicate under easterly, south-easterly and southerly flow 25–50% of the total accumulated primary PM2.5 emissions originate outside of the UK, with a very polluted footprint (0.25–0.35 μg m-2). Anticyclonic conditions, which occur frequently (21%), also lead to increases in PM2.5 concentrations (UK multi-annual mean 14.7 μg m-3). EMEP4UK results indicate this is likely due the build-up of local emissions due to slack winds. Under westerly and north-westerly flow 15–30% of the total accumulated primary PM2.5 emissions originate outside of the UK, and are much less polluted (0.1 μg m-2) with model results indicating transport of clean maritime air masses from the Atlantic. Results indicate that both wind-direction and stability under anticyclonic conditions are important in controlling ambient PM2.5 concentrations across the UK. There is also a strong dependence of high PM2.5 Daily Air Quality Index (DAQI) values on easterly, south-easterly and southerly wind-directions, with >70% of occurrences of observed 48–71+ μg m-3 concentrations occurring under these wind directions. While north-westerly and cyclonic conditions reduce PM2.5 concentrations at all sites by up to 8 μg m-3. PM2.5 DAQI values are also lowest under these conditions, with >80% of 0–11 μg m-3 concentrations and >50% of 12–23 μg m-3 concentrations observed during westerly, north-westerly and northerly wind directions. Indicating that these conditions are likely to be associated with a reduction in the potential health effects from exposure to ambient levels of PM2.5

Assessing costs of Indonesian fires and the benefits of restoring peatland

Deforestation and drainage has made Indonesian peatlands susceptible to burning. Large fires occur regularly, destroying agricultural crops and forest, emitting large amounts of CO2 and air pollutants, resulting in adverse health effects. In order to reduce fire, the Indonesian government has committed to restore 2.49 Mha of degraded peatland, with an estimated cost of US$3.2-7 billion. Here we combine fire emissions and land cover data to estimate the 2015 fires, the largest in recent years, resulted in economic losses totalling US$28 billion, whilst the six largest fire events between 2004 and 2015 caused a total of US$93.9 billion in economic losses. We estimate that if restoration had already been completed, the area burned in 2015 would have been reduced by 6$8.4 billion for 2004–2015, making it a cost-effective strategy for reducing the impacts of peatland fires to the environment, climate and human health

Cross-reactive memory T cells associate with protection against SARS-CoV-2 infection in COVID-19 contacts

Cross-reactive immune responses to SARS-CoV-2 have been observed in pre-pandemic cohorts and proposed to contribute to host protection. Here we assess 52 COVID-19 household contacts to capture immune responses at the earliest timepoints after SARS-CoV-2 exposure. Using a dual cytokine FLISpot assay on peripheral blood mononuclear cells, we enumerate the frequency of T cells specific for spike, nucleocapsid, membrane, envelope and ORF1 SARS-CoV-2 epitopes that cross-react with human endemic coronaviruses. We observe higher frequencies of cross-reactive (p=0.0139), and nucleocapsid-specific (p=0.0355) IL-2-secreting memory T cells in contacts who remained PCR-negative despite exposure (n=26), when compared with those who convert to PCR-positive (n=26); no significant difference in the frequency of responses to spike is observed, hinting at a limited protective function of spike-cross-reactive T cells. Our results are thus consistent with pre-existing non-spike cross-reactive memory T cells protecting SARS-CoV-2-naïve contacts from infection, thereby supporting the inclusion of non-spike antigens in second-generation vaccines

Large air quality and human health impacts due to Amazon forest and vegetation fires

Vegetation fires across the tropics emit fine particulate matter (PM2.5) to the atmosphere, degrading regional air quality and impacting human health. Extensive vegetation fires occur regularly across the Amazon basin, but there have been no detailed assessments of the impacts on air quality or human health. We used updated exposure-response relationships and a regional climate-chemistry model, evaluated against a comprehensive set of observational data, to provide the first in-depth assessment of the potential public health benefits due to fire prevention across the Amazon Basin. We focused on 2012, a year with emissions similar to the 11-year average (2008 to 2018). Vegetation fires contributed >80% of simulated dry season mean surface PM2.5 in the western Amazon region particularly in Bolivia and Brazilian states of Rondônia, Acre, and Mato Grosso. We estimate that the prevention of vegetation fires would have averted 16 800 (95UI: 16 300–17 400) premature deaths and 641 000 (95UI: 551 900–741 300) disability adjusted life years (DALYs) across South America, with 26% of the avoided health burden located within the Amazon Basin. The health benefits of fire prevention in the Amazon are comparable to those found in Equatorial Asia

Regulators of yeast endocytosis identified by systematic quantitative analysis

Endocytosis of receptors at the plasma membrane is controlled by a complex mechanism that includes clathrin, adaptors, and actin regulators. Many of these proteins are conserved in yeast yet lack observable mutant phenotypes, which suggests that yeast endocytosis may be subject to different regulatory mechanisms. Here, we have systematically defined genes required for internalization using a quantitative genome-wide screen that monitors localization of the yeast vesicle-associated membrane protein (VAMP)/synaptobrevin homologue Snc1. Genetic interaction mapping was used to place these genes into functional modules containing known and novel endocytic regulators, and cargo selectivity was evaluated by an array-based comparative analysis. We demonstrate that clathrin and the yeast AP180 clathrin adaptor proteins have a cargo-specific role in Snc1 internalization. We additionally identify low dye binding 17 (LDB17) as a novel conserved component of the endocytic machinery. Ldb17 is recruited to cortical actin patches before actin polymerization and regulates normal coat dynamics and actin assembly. Our findings highlight the conserved machinery and reveal novel mechanisms that underlie endocytic internalization

Onset and window of SARS-CoV-2 infectiousness and temporal correlation with symptom onset: a prospective, longitudinal, community cohort study.

BACKGROUND: Knowledge of the window of SARS-CoV-2 infectiousness is crucial in developing policies to curb transmission. Mathematical modelling based on scarce empirical evidence and key assumptions has driven isolation and testing policy, but real-world data are needed. We aimed to characterise infectiousness across the full course of infection in a real-world community setting. METHODS: The Assessment of Transmission and Contagiousness of COVID-19 in Contacts (ATACCC) study was a UK prospective, longitudinal, community cohort of contacts of newly diagnosed, PCR-confirmed SARS-CoV-2 index cases. Household and non-household exposed contacts aged 5 years or older were eligible for recruitment if they could provide informed consent and agree to self-swabbing of the upper respiratory tract. The primary objective was to define the window of SARS-CoV-2 infectiousness and its temporal correlation with symptom onset. We quantified viral RNA load by RT-PCR and infectious viral shedding by enumerating cultivable virus daily across the course of infection. Participants completed a daily diary to track the emergence of symptoms. Outcomes were assessed with empirical data and a phenomenological Bayesian hierarchical model. FINDINGS: Between Sept 13, 2020, and March 31, 2021, we enrolled 393 contacts from 327 households (the SARS-CoV-2 pre-alpha and alpha variant waves); and between May 24, 2021, and Oct 28, 2021, we enrolled 345 contacts from 215 households (the delta variant wave). 173 of these 738 contacts were PCR positive for more than one timepoint, 57 of which were at the start of infection and comprised the final study population. The onset and end of infectious viral shedding were captured in 42 cases and the median duration of infectiousness was 5 (IQR 3-7) days. Although 24 (63%) of 38 cases had PCR-detectable virus before symptom onset, only seven (20%) of 35 shed infectious virus presymptomatically. Symptom onset was a median of 3 days before both peak viral RNA and peak infectious viral load (viral RNA IQR 3-5 days, n=38; plaque-forming units IQR 3-6 days, n=35). Notably, 22 (65%) of 34 cases and eight (24%) of 34 cases continued to shed infectious virus 5 days and 7 days post-symptom onset, respectively (survival probabilities 67% and 35%). Correlation of lateral flow device (LFD) results with infectious viral shedding was poor during the viral growth phase (sensitivity 67% [95% CI 59-75]), but high during the decline phase (92% [86-96]). Infectious virus kinetic modelling suggested that the initial rate of viral replication determines the course of infection and infectiousness. INTERPRETATION: Less than a quarter of COVID-19 cases shed infectious virus before symptom onset; under a crude 5-day self-isolation period from symptom onset, two-thirds of cases released into the community would still be infectious, but with reduced infectious viral shedding. Our findings support a role for LFDs to safely accelerate deisolation but not for early diagnosis, unless used daily. These high-resolution, community-based data provide evidence to inform infection control guidance. FUNDING: National Institute for Health and Care Research

Risk factors and vectors for SARS-CoV-2 household transmission: a prospective, longitudinal cohort study

BACKGROUND: Despite circumstantial evidence for aerosol and fomite spread of SARS-CoV-2, empirical data linking either pathway with transmission are scarce. Here we aimed to assess whether the presence of SARS-CoV-2 on frequently-touched surfaces and residents' hands was a predictor of SARS-CoV-2 household transmission. METHODS: In this longitudinal cohort study, during the pre-alpha (September to December, 2020) and alpha (B.1.1.7; December, 2020, to April, 2021) SARS-CoV-2 variant waves, we prospectively recruited contacts from households exposed to newly diagnosed COVID-19 primary cases, in London, UK. To maximally capture transmission events, contacts were recruited regardless of symptom status and serially tested for SARS-CoV-2 infection by RT-PCR on upper respiratory tract (URT) samples and, in a subcohort, by serial serology. Contacts' hands, primary cases' hands, and frequently-touched surface-samples from communal areas were tested for SARS-CoV-2 RNA. SARS-CoV-2 URT isolates from 25 primary case-contact pairs underwent whole-genome sequencing (WGS). FINDINGS: From Aug 1, 2020, until March 31, 2021, 620 contacts of PCR-confirmed SARS-CoV-2-infected primary cases were recruited. 414 household contacts (from 279 households) with available serial URT PCR results were analysed in the full household contacts' cohort, and of those, 134 contacts with available longitudinal serology data and not vaccinated pre-enrolment were analysed in the serology subcohort. Household infection rate was 28·4% (95% CI 20·8-37·5) for pre-alpha-exposed contacts and 51·8% (42·5-61·0) for alpha-exposed contacts (p=0·0047). Primary cases' URT RNA viral load did not correlate with transmission, but was associated with detection of SARS-CoV-2 RNA on their hands (p=0·031). SARS-CoV-2 detected on primary cases' hands, in turn, predicted contacts' risk of infection (adjusted relative risk [aRR]=1·70 [95% CI 1·24-2·31]), as did SARS-CoV-2 RNA presence on household surfaces (aRR=1·66 [1·09-2·55]) and contacts' hands (aRR=2·06 [1·57-2·69]). In six contacts with an initial negative URT PCR result, hand-swab (n=3) and household surface-swab (n=3) PCR positivity preceded URT PCR positivity. WGS corroborated household transmission. INTERPRETATION: Presence of SARS-CoV-2 RNA on primary cases' and contacts' hands and on frequently-touched household surfaces associates with transmission, identifying these as potential vectors for spread in households. FUNDING: National Institute for Health Research Health Protection Research Unit in Respiratory Infections, Medical Research Council