NS3 Variability in Hepatitis C Virus Genotype 1A Isolates from Liver Tissue and Serum Samples of Treatment-Naïve Patients with Chronic Hepatitis C.

Background: Hepatitis C virus (HCV) NS3 resistance-associated substitutions (RASs) reduce HCV susceptibility to protease inhibitors. Little is known about NS3 RASs in viral isolates from the liver of chronic hepatitis C (CHC) patients infected with HCV genotype-1a (G1a). Aim: The objective of this work was to study NS3 variability in isolates from the serum and liver of HCV-G1a-infected patients naïve to direct-acting antivirals (DAAs). Methods: NS3 variability of HCV-G1a isolates from the serum and liver of 11 naïve CHC patients, and from sera of an additional 20 naïve CHC patients, was investigated by next-generation sequencing. Results: At a cutoff of 1%, NS3 RASs were detected in all the samples examined. At a cutoff of 15%, they were found in 54.5% (6/11) and 27.3% (3/11) of the paired liver and serum samples, respectively, and in 22.5% (7/31) of the overall serum samples examined. Twenty-six out of thirty-one (84%) patients showed NS3 variants with multiple RASs. Phylogenetic analysis showed that NS3 sequences clustered within 2 clades, with 10/31 (32.2%) patients infected by clade I, 15/31 (48.8%) by clade II, and 6/31 (19.3%) by both clades. Conclusions: Though the number of patients examined was limited, NS3 variants with RASs appear to be major components of both intrahepatic and circulating viral quasispecies populations in DAA-naïve patients

A global observational analysis to understand changes in air quality during exceptionally low anthropogenic emission conditions

This global study, which has been coordinated by the World Meteorological Organization Global Atmospheric Watch (WMO/GAW) programme, aims to understand the behaviour of key air pollutant species during the COVID-19 pandemic period of exceptionally low emissions across the globe. We investigated the effects of the differences in both emissions and regional and local meteorology in 2020 compared with the period 2015-2019. By adopting a globally consistent approach, this comprehensive observational analysis focuses on changes in air quality in and around cities across the globe for the following air pollutants PM2.5, PM10, PMC (coarse fraction of PM), NO2, SO2, NOx, CO, O-3 and the total gaseous oxidant (O-X = NO2 + O-3) during the pre-lockdown, partial lockdown, full lockdown and two relaxation periods spanning from January to September 2020. The analysis is based on in situ ground-based air quality observations at over 540 traffic, background and rural stations, from 63 cities and covering 25 countries over seven geographical regions of the world. Anomalies in the air pollutant concentrations (increases or decreases during 2020 periods compared to equivalent 2015-2019 periods) were calculated and the possible effects of meteorological conditions were analysed by computing anomalies from ERA5 reanalyses and local observations for these periods. We observed a positive correlation between the reductions in NO2 and NOx concentrations and peoples' mobility for most cities. A correlation between PMC and mobility changes was also seen for some Asian and South American cities. A clear signal was not observed for other pollutants, suggesting that sources besides vehicular emissions also substantially contributed to the change in air quality. As a global and regional overview of the changes in ambient concentrations of key air quality species, we observed decreases of up to about 70% in mean NO2 and between 30% and 40% in mean PM2.5 concentrations over 2020 full lockdown compared to the same period in 2015-2019. However, PM2.5 exhibited complex signals, even within the same region, with increases in some Spanish cities, attributed mainly to the long-range transport of African dust and/or biomass burning (corroborated with the analysis of NO2/CO ratio). Some Chinese cities showed similar increases in PM2.5 during the lockdown periods, but in this case, it was likely due to secondary PM formation. Changes in O-3 concentrations were highly heterogeneous, with no overall change or small increases (as in the case of Europe), and positive anomalies of 25% and 30% in East Asia and South America, respectively, with Colombia showing the largest positive anomaly of similar to 70%. The SO2 anomalies were negative for 2020 compared to 2015-2019 (between similar to 25 to 60%) for all regions. For CO, negative anomalies were observed for all regions with the largest decrease for South America of up to similar to 40%. The NO2/CO ratio indicated that specific sites (such as those in Spanish cities) were affected by biomass burning plumes, which outweighed the NO2 decrease due to the general reduction in mobility (ratio of similar to 60%). Analysis of the total oxidant (OX = NO2 + O-3) showed that primary NO2 emissions at urban locations were greater than the O-3 production, whereas at background sites, O-X was mostly driven by the regional contributions rather than local NO2 and O-3 concentrations. The present study clearly highlights the importance of meteorology and episodic contributions (e.g., from dust, domestic, agricultural biomass burning and crop fertilizing) when analysing air quality in and around cities even during large emissions reductions. There is still the need to better understand how the chemical responses of secondary pollutants to emission change under complex meteorological conditions, along with climate change and socio-economic drivers may affect future air quality. The implications for regional and global policies are also significant, as our study clearly indicates that PM2.5 concentrations would not likely meet the World Health Organization guidelines in many parts of the world, despite the drastic reductions in mobility. Consequently, revisions of air quality regulation (e.g., the Gothenburg Protocol) with more ambitious targets that are specific to the different regions of the world may well be required.Peer reviewe

A global observational analysis to understand changes in air quality during exceptionally low anthropogenic emission

This global study, which has been coordinated by the World Meteorological Organization Global Atmospheric Watch (WMO/GAW) programme, aims to understand the behaviour of key air pollutant species during the COVID-19 pandemic period of exceptionally low emissions across the globe. We investigated the effects of the differences in both emissions and regional and local meteorology in 2020 compared with the period 2015–2019. By adopting a globally consistent approach, this comprehensive observational analysis focuses on changes in air quality in and around cities across the globe for the following air pollutants PM2.5, PM10, PMC (coarse fraction of PM), NO2, SO2, NOx, CO, O3 and the total gaseous oxidant (OX = NO2 + O3) during the pre-lockdown, partial lockdown, full lockdown and two relaxation periods spanning from January to September 2020. The analysis is based on in situ ground-based air quality observations at over 540 traffic, background and rural stations, from 63 cities and covering 25 countries over seven geographical regions of the world. Anomalies in the air pollutant concentrations (increases or decreases during 2020 periods compared to equivalent 2015–2019 periods) were calculated and the possible effects of meteorological conditions were analysed by computing anomalies from ERA5 reanalyses and local observations for these periods. We observed a positive correlation between the reductions in NO2 and NOx concentrations and peoples’ mobility for most cities. A correlation between PMC and mobility changes was also seen for some Asian and South American cities. A clear signal was not observed for other pollutants, suggesting that sources besides vehicular emissions also substantially contributed to the change in air quality. As a global and regional overview of the changes in ambient concentrations of key air quality species, we observed decreases of up to about 70% in mean NO2 and between 30% and 40% in mean PM2.5 concentrations over 2020 full lockdown compared to the same period in 2015–2019. However, PM2.5 exhibited complex signals, even within the same region, with increases in some Spanish cities, attributed mainly to the long-range transport of African dust and/or biomass burning (corroborated with the analysis of NO2/CO ratio). Some Chinese cities showed similar increases in PM2.5 during the lockdown periods, but in this case, it was likely due to secondary PM formation. Changes in O3 concentrations were highly heterogeneous, with no overall change or small increases (as in the case of Europe), and positive anomalies of 25% and 30% in East Asia and South America, respectively, with Colombia showing the largest positive anomaly of ~70%. The SO2 anomalies were negative for 2020 compared to 2015–2019 (between ~25 to 60%) for all regions. For CO, negative anomalies were observed for all regions with the largest decrease for South America of up to ~40%. The NO2/CO ratio indicated that specific sites (such as those in Spanish cities) were affected by biomass burning plumes, which outweighed the NO2 decrease due to the general reduction in mobility (ratio of ~60%). Analysis of the total oxidant (OX = NO2 + O3) showed that primary NO2 emissions at urban locations were greater than the O3 production, whereas at background sites, OX was mostly driven by the regional contributions rather than local NO2 and O3 concentrations. The present study clearly highlights the importance of meteorology and episodic contributions (e.g., from dust, domestic, agricultural biomass burning and crop fertilizing) when analysing air quality in and around cities even during large emissions reductions. There is still the need to better understand how the chemical responses of secondary pollutants to emission change under complex meteorological conditions, along with climate change and socio-economic drivers may affect future air quality. The implications for regional and global policies are also significant, as our study clearly indicates that PM2.5 concentrations would not likely meet the World Health Organization guidelines in many parts of the world, despite the drastic reductions in mobility. Consequently, revisions of air quality regulation (e.g., the Gothenburg Protocol) with more ambitious targets that are specific to the different regions of the world may well be required.Peer reviewedFinal Published versio

A global observational analysis to understand changes in air quality during exceptionally low anthropogenic emission conditions

This global study, which has been coordinated by the World Meteorological Organization Global Atmospheric Watch (WMO/GAW) programme, aims to understand the behaviour of key air pollutant species during the COVID-19 pandemic period of exceptionally low emissions across the globe. We investigated the effects of the differences in both emissions and regional and local meteorology in 2020 compared with the period 2015–2019. By adopting a globally consistent approach, this comprehensive observational analysis focuses on changes in air quality in and around cities across the globe for the following air pollutants PM2.5, PM10, PMC (coarse fraction of PM), NO2, SO2, NOx, CO, O3 and the total gaseous oxidant (OX = NO2 + O3) during the pre-lockdown, partial lockdown, full lockdown and two relaxation periods spanning from January to September 2020. The analysis is based on in situ ground-based air quality observations at over 540 traffic, background and rural stations, from 63 cities and covering 25 countries over seven geographical regions of the world. Anomalies in the air pollutant concentrations (increases or decreases during 2020 periods compared to equivalent 2015–2019 periods) were calculated and the possible effects of meteorological conditions were analysed by computing anomalies from ERA5 reanalyses and local observations for these periods. We observed a positive correlation between the reductions in NO2 and NOx concentrations and peoples’ mobility for most cities. A correlation between PMC and mobility changes was also seen for some Asian and South American cities. A clear signal was not observed for other pollutants, suggesting that sources besides vehicular emissions also substantially contributed to the change in air quality. As a global and regional overview of the changes in ambient concentrations of key air quality species, we observed decreases of up to about 70% in mean NO2 and between 30% and 40% in mean PM2.5 concentrations over 2020 full lockdown compared to the same period in 2015–2019. However, PM2.5 exhibited complex signals, even within the same region, with increases in some Spanish cities, attributed mainly to the long-range transport of African dust and/or biomass burning (corroborated with the analysis of NO2/CO ratio). Some Chinese cities showed similar increases in PM2.5 during the lockdown periods, but in this case, it was likely due to secondary PM formation. Changes in O3 concentrations were highly heterogeneous, with no overall change or small increases (as in the case of Europe), and positive anomalies of 25% and 30% in East Asia and South America, respectively, with Colombia showing the largest positive anomaly of ~70%. The SO2 anomalies were negative for 2020 compared to 2015–2019 (between ~25 to 60%) for all regions. For CO, negative anomalies were observed for all regions with the largest decrease for South America of up to ~40%. The NO2/CO ratio indicated that specific sites (such as those in Spanish cities) were affected by biomass burning plumes, which outweighed the NO2 decrease due to the general reduction in mobility (ratio of ~60%). Analysis of the total oxidant (OX = NO2 + O3) showed that primary NO2 emissions at urban locations were greater than the O3 production, whereas at background sites, OX was mostly driven by the regional contributions rather than local NO2 and O3 concentrations. The present study clearly highlights the importance of meteorology and episodic contributions (e.g., from dust, domestic, agricultural biomass burning and crop fertilizing) when analysing air quality in and around cities even during large emissions reductions. There is still the need to better understand how the chemical responses of secondary pollutants to emission change under complex meteorological conditions, along with climate change and socio-economic drivers may affect future air quality. The implications for regional and global policies are also significant, as our study clearly indicates that PM2.5 concentrations would not likely meet the World Health Organization guidelines in many parts of the world, despite the drastic reductions in mobility. Consequently, revisions of air quality regulation (e.g., the Gothenburg Protocol) with more ambitious targets that are specific to the different regions of the world may well be required.World Meteorological Organization Global Atmospheric Watch programme is gratefully acknowledged for initiating and coordinating this study and for supporting this publication. We acknowledge the following projects for supporting the analysis contained in this article: Air Pollution and Human Health for an Indian Megacity project PROMOTE funded by UK NERC and the Indian MOES, Grant reference number NE/P016391/1; Regarding project funding from the European Commission, the sole responsibility of this publication lies with the authors. The European Commission is not responsible for any use that may be made of the information contained therein. This project has received funding from the European Commission’s Horizon 2020 research and innovation program under grant agreement No 874990 (EMERGE project). European Regional Development Fund (project MOBTT42) under the Mobilitas Pluss programme; Estonian Research Council (project PRG714); Estonian Research Infrastructures Roadmap project Estonian Environmental Observatory (KKOBS, project 2014-2020.4.01.20-0281). European network for observing our changing planet project (ERAPLANET, grant agreement no. 689443) under the European Union’s Horizon 2020 research and innovation program, Estonian Ministry of Sciences projects (grant nos. P180021, P180274), and the Estonian Research Infrastructures Roadmap project Estonian Environmental Observatory (3.2.0304.11-0395). Eastern Mediterranean and Middle East—Climate and Atmosphere Research (EMME-CARE) project, which has received funding from the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement no. 856612) and the Government of Cyprus. INAR acknowledges support by the Russian government (grant number 14.W03.31.0002), the Ministry of Science and Higher Education of the Russian Federation (agreement 14.W0331.0006), and the Russian Ministry of Education and Science (14.W03.31.0008). We are grateful to to the following agencies for providing access to data used in our analysis: A.M. Obukhov Institute of Atmospheric Physics Russian Academy of Sciences; Agenzia Regionale per la Protezione dell’Ambiente della Campania (ARPAC); Air Quality and Climate Change, Parks and Environment (MetroVancouver, Government of British Columbia); Air Quality Monitoring & Reporting, Nova Scotia Environment (Government of Nova Scotia); Air Quality Monitoring Network (SIMAT) and Emission Inventory, Mexico City Environment Secretariat (SEDEMA); Airparif (owner & provider of the Paris air pollution data); ARPA Lazio, Italy; ARPA Lombardia, Italy; Association Agr´e´ee de Surveillance de la Qualit´e de l’Air en ˆIle-de- France AIRPARIF / Atmo-France; Bavarian Environment Agency, Germany; Berlin Senatsverwaltung für Umwelt, Verkehr und Klimaschutz, Germany; California Air Resources Board; Central Pollution Control Board (CPCB), India; CETESB: Companhia Ambiental do Estado de S˜ao Paulo, Brazil. China National Environmental Monitoring Centre; Chandigarh Pollution Control Committee (CPCC), India. DCMR Rijnmond Environmental Service, the Netherlands. Department of Labour Inspection, Cyprus; Department of Natural Resources Management and Environmental Protection of Moscow. Environment and Climate Change Canada; Environmental Monitoring and Science Division Alberta Environment and Parks (Government of Alberta); Environmental Protection Authority Victoria (Melbourne, Victoria, Australia); Estonian Environmental Research Centre (EERC); Estonian University of Life Sciences, SMEAR Estonia; European Regional Development Fund (project MOBTT42) under the Mobilitas Pluss programme; Finnish Meteorological Institute; Helsinki Region Environmental Services Authority; Haryana Pollution Control Board (HSPCB), IndiaLondon Air Quality Network (LAQN) and the Automatic Urban and Rural Network (AURN) supported by the Department of Environment, Food and Rural Affairs, UK Government; Madrid Municipality; Met Office Integrated Data Archive System (MIDAS); Meteorological Service of Canada; Minist`ere de l’Environnement et de la Lutte contre les changements climatiques (Gouvernement du Qu´ebec); Ministry of Environment and Energy, Greece; Ministry of the Environment (Chile) and National Weather Service (DMC); Moscow State Budgetary Environmental Institution MOSECOMONITORING. Municipal Department of the Environment SMAC, Brazil; Municipality of Madrid public open data service; National institute of environmental research, Korea; National Meteorology and Hydrology Service (SENAMHI), Peru; New York State Department of Environmental Conservation; NSW Department of Planning, Industry and Environment; Ontario Ministry of the Environment, Conservation and Parks, Canada; Public Health Service of Amsterdam (GGD), the Netherlands. Punjab Pollution Control Board (PPCB), India. R´eseau de surveillance de la qualit´e de l’air (RSQA) (Montr´eal); Rosgydromet. Mosecomonitoring, Institute of Atmospheric Physics, Russia; Russian Foundation for Basic Research (project 20–05–00254) SAFAR-IITM-MoES, India; S˜ao Paulo State Environmental Protection Agency, CETESB; Secretaria de Ambiente, DMQ, Ecuador; Secretaría Distrital de Ambiente, Bogot´a, Colombia. Secretaria Municipal de Meio Ambiente Rio de Janeiro; Mexico City Atmospheric Monitoring System (SIMAT); Mexico City Secretariat of Environment, Secretaría del Medio Ambiente (SEDEMA); SLB-analys, Sweden; SMEAR Estonia station and Estonian University of Life Sciences (EULS); SMEAR stations data and Finnish Center of Excellence; South African Weather Service and Department of Environment, Forestry and Fisheries through SAAQIS; Spanish Ministry for the Ecological Transition and the Demographic Challenge (MITECO); University of Helsinki, Finland; University of Tartu, Tahkuse air monitoring station; Weather Station of the Institute of Astronomy, Geophysics and Atmospheric Science of the University of S˜ao Paulo; West Bengal Pollution Control Board (WBPCB).http://www.elsevier.com/locate/envintam2023Geography, Geoinformatics and Meteorolog

Basic data visualization in vintage seismic profiles: indications for the interpretation of the ViDEPI database (offshore Puglia, southern Italy)

The Visibility of Petroleum Exploration Data in Italy (ViDEPI) project represents a freely accessible valuable resource for the research community. However, seismic profiles available from this project present several limitations because information such as the basic shape of the seismic wavelets and the seismic polarity are not available. In this study, using subsurface (i.e., 2D seismic profiles) data related to the Marine Zones B, D and F (offshore Puglia) a review of the basic pulse shape and polarity of seismic wavelets, as well as the shape and polarity of principal reflectors has been addressed. Moreover, borehole data (i.e., lithology and sonic logs) have been used to identify abrupt average velocity changes linked to different lithostratigraphic successions recorded as dominant high-amplitude reflectors

Whole Genome Sequencing and Comparative Genome Analysis of the Halotolerant Deep Sea Black Yeast Hortaea werneckii

Hortaea werneckii, an extreme halotolerant black yeast in the order of Capnodiales, was recently isolated from different stations and depths in the Mediterranean Sea, where it was shown to be the dominant fungal species. In order to explore the genome characteristics of these Mediterranean isolates, we carried out a de-novo sequencing of the genome of one strain isolated at a depth of 3400 m (MC873) and a re-sequencing of one strain taken from a depth of 2500 m (MC848), whose genome was previously sequenced but was highly fragmented. A comparative phylogenomic analysis with other published H. werneckii genomes was also carried out to investigate the evolution of the strains from the deep sea in this environment. A high level of genome completeness was obtained for both genomes, for which genome duplication and an extensive level of heterozygosity (~4.6%) were observed, supporting the recent hypothesis that a genome duplication caused by intraspecific hybridization occurred in most H. werneckii strains. Phylogenetic analyses showed environmental and/or geographical specificity, suggesting a possible evolutionary adaptation of marine H. werneckii strains to the deep sea environment. We release high-quality genome assemblies from marine H. werneckii strains, which provides additional data for further genomics analysis, including niche adaptation, fitness and evolution studies