Discovery and multimerization of cross-reactive single-domain antibodies against SARS-like viruses to enhance potency and address emerging SARS-CoV-2 variants.

Coronaviruses have been the causative agent of three epidemics and pandemics in the past two decades, including the ongoing COVID-19 pandemic. A broadly-neutralizing coronavirus therapeutic is desirable not only to prevent and treat COVID-19, but also to provide protection for high-risk populations against future emergent coronaviruses. As all coronaviruses use spike proteins on the viral surface to enter the host cells, and these spike proteins share sequence and structural homology, we set out to discover cross-reactive biologic agents targeting the spike protein to block viral entry. Through llama immunization campaigns, we have identified single domain antibodies (VHHs) that are cross-reactive against multiple emergent coronaviruses (SARS-CoV, SARS-CoV-2, and MERS). Importantly, a number of these antibodies show sub-nanomolar potency towards all SARS-like viruses including emergent CoV-2 variants. We identified nine distinct epitopes on the spike protein targeted by these VHHs. Further, by engineering VHHs targeting distinct, conserved epitopes into multi-valent formats, we significantly enhanced their neutralization potencies compared to the corresponding VHH cocktails. We believe this approach is ideally suited to address both emerging SARS-CoV-2 variants during the current pandemic as well as potential future pandemics caused by SARS-like coronaviruses.

Global trends in ozone concentration and attributable mortality for urban, peri-urban, and rural areas between 2000 and 2019: a modelling study.

BACKGROUND: Data on long-term trends of ozone exposure and attributable mortality across urban-rural catchment areas worldwide are scarce, especially for low-income and middle-income countries. This study aims to estimate trends in ozone concentrations and attributable mortality for urban-rural catchment areas worldwide. METHODS: In this modelling study, we used a health impact function to estimate ozone concentrations and ozone-attributable chronic respiratory disease mortality for urban areas worldwide, and their surrounding peri-urban, peri-rural, and rural areas. We estimated ozone-attributable respiratory health outcomes using a modified Global Burden of Diseases, Injuries, and Risk Factors 2019 Study approach. We evaluate long-term trends with linear regressions of annual ozone concentrations and ozone-attributable mortality against time in years, and examined the influence of each health impact function input parameter to temporal changes in ozone-attributable disease burden estimates for 12 946 cities worldwide by region, from 2000 to 2019. FINDINGS: Ozone-attributable mortality worldwide increased by 46% from 2000 (290 400 deaths [95% CI 151 800-457 600]) to 2019 (423 100 deaths [95% CI 223 200-659 400]). The fraction of global ozone-attributable mortality occurring in peri-urban areas remained unchanged from 2000 to 2019 (56%), whereas urban areas gained in their share of global ozone-attributable burden (from 35% to 37%; 54 000 more deaths). Across all cities studied, average population-weighted mean ozone concentration increased by 11% (46 parts per billion [ppb] to 51 ppb). The number of cities with concentrations above the WHO peak season ozone standard (60 µg/m3) increased from 11 568 (89%) of 12 946 cities in 2000 to 12 433 (96%) cities in 2019. Percent change in ozone-attributable mortality averaged across 11 032 cities within each region from 2000 to 2019 ranged from -62% in eastern Europe to 350% in tropical Latin America. The contribution of ozone concentrations, population size, and baseline chronic respiratory disease rates to the change in ozone-attributable mortality differed regionally. INTERPRETATION: Ozone exposure is increasing worldwide, contributing to disproportionate ozone mortality in peri-urban areas and increasing ozone exposure and attributable mortality in urban areas worldwide. Reducing ozone precursor emissions in areas affecting urban and peri-urban exposure can yield substantial public health benefits. FUNDING: NASA Health and Air Quality Applied Sciences Team, the National Institute for Occupational Safety and Health, and the NOAA Co-operative Agreement with the Cooperative Institute for Research in Environmental Sciences.

Survey of residential indoor particulate matter measurements 1990-2019.

We surveyed literature on measurements of indoor particulate matter in all size fractions, in residential environments free of solid fuel combustion (other than wood for recreation or space heating). Data from worldwide studies from 1990 to 2019 were assembled into the most comprehensive collection to date. Out of 2752 publications retrieved, 538 articles from 433 research projects met inclusion criteria and reported unique data, from which more than 2000 unique sets of indoor PM measurements were collected. Distributions of mean concentrations were compiled, weighted by study size. Long-term trends, the impact of non-smoking, air cleaners, and the influence of outdoor PM were also evaluated. Similar patterns of indoor PM distributions for North America and Europe could reflect similarities in the indoor environments of these regions. Greater observed variability for all regions of Asia may reflect greater heterogeneity in indoor conditions, but also low numbers of studies for some regions. Indoor PM concentrations of all size fractions were mostly stable over the survey period, with the exception of observed declines in PM2.5 in European and North American studies, and in PM10 in North America. While outdoor concentrations were correlated with indoor concentrations across studies, indoor concentrations had higher variability, illustrating a limitation of using outdoor measurements to approximate indoor PM exposures.

Assessing the association between fine particulate matter (PM2.5) constituents and cardiovascular diseases in a mega-city of Pakistan.

Concerning PM2.5 concentrations, rapid industrialization, along with increase in cardiovascular disease (CVD) were recorded in Pakistan, especially in urban areas. The degree to which air pollution contributes to the increase in the burden of CVD in Pakistan has not been assessed due to lack of data. This study aims to describe the characteristics of PM2.5 constituents and investigate the impact of individual PM2.5 constituent on cardiovascular morbidity in Karachi, a mega city in Pakistan. Daily levels of twenty-one constituents of PM2.5 were analyzed using samples collected at two sites from fall 2008 to summer 2009 in Karachi. Hospital admission and emergency room visits due to CVD were collected from two large hospitals. Negative Binominal Regression was used to estimate associations between pollutants and the risk of CVD. All PM2.5 constituents were assessed in single-pollutant models and selected constituents were assessed in multi-pollutant models adjusting for PM2.5 mass and gaseous pollutants. The most common CVD subtypes among our participants were ischemic heart disease, hypertension, heart failure, and cardiomyopathy. Extremely high levels of PM2.5 constituents from fossil-fuels combustion and industrial emissions were observed, with notable peaks in winter. The most consistent associations were found between exposure to nickel (5-14% increase per interquartile range) and cardiovascular hospital admissions. Suggestive evidence was also observed for associations between cardiovascular hospital admissions and Al, Fe, Ti, and nitrate. Our findings suggested that PM2.5 generated from fossil-fuels combustion and road dust resuspension were associated with the increased risk of CVD in Pakistan.

The fitness landscapes of cis-acting binding sites in different promoter and environmental contexts.

The biophysical nature of the interaction between a transcription factor and its target sequences in vitro is sufficiently well understood to allow for the effects of DNA sequence alterations on affinity to be predicted. But even in relatively simple in vivo systems, the complexities of promoter organization and activity have made it difficult to predict how altering specific interactions between a transcription factor and DNA will affect promoter output. To better understand this, we measured the relative fitness of nearly all Escherichia coli sigma(70) -35 binding sites in different promoter and environmental contexts by competing four randomized -35 promoter libraries controlling the expression of the tetracycline resistance gene (tet)against each other in increasing concentrations of drug. We sequenced populations after competition to determine the relative enrichment of each -35 sequence. We observed a consistent relationship between the frequency of recovery of each -35 binding site and its predicted affinity for sigma(70) that varied depending on the sequence context of the promoter and drug concentration. Overall the relative fitness of each promoter could be predicted by a simple thermodynamic model of transcriptional regulation, in which the rate of transcriptional initiation (and hence fitness) is dependent upon the overall stability of the initiation complex, which in turn is dependent upon the energetic contributions of all sites within the complex. As implied by this model, a decrease in the free energy of association at one site could be compensated for by an increase in the binding energy at another to produce a similar output. Furthermore, these data show that a large and continuous range of transcriptional outputs can be accessed by merely changing the -35, suggesting that evolved or engineered mutations at this site could allow for subtle and precise control over gene expression.