Molecular epidemiology of SARS-CoV-2: a regional to global perspective

Background After a year of the global SARS-CoV-2 pandemic, a highly dynamic genetic diversity is surfacing. Among nearly 1000 reported virus lineages, dominant lineages such as B.1.1.7 or B.1.351 attract media attention with questions regarding vaccine efficiency and transmission potential. In response to the pandemic, the Jena University Hospital began sequencing SARS-CoV-2 samples in Thuringia in early 2020.Methods Viral RNA was sequenced in tiled amplicons using Nanopore sequencing. Subsequently, bioinformatic workflows were used to process the generated data. As a genomic background, 9,642 representative SARS-CoV-2 genomes (1,917 of German origin) were extracted from more than 300.000 genomes.Results In a comprehensive bioinformatics analysis, we have set Thuringian isolates in the German, European and global context. In Thuringia, a largely rural German region without an international airport and a population density below the German average, we discovered many of the common “EU lineages”. German samples are scattered across eight major clades, and Thuringian samples occupy four of them.Conclusion The rapid emergence and spread of novel variants are of great concern as these lineages could transmit more efficiently, evade current vaccine efforts or undermine diagnostic test accuracy. To anticipate and mitigate these threats, a continuous molecular surveillance is essential.Key messagesBioinformatics analysis of 1,917, 4,251, and 3,474 SARS-CoV-2 genomes from Germany, the EU (except Germany), and non-EU, respectively, subsampled from more than 300,000 public genomes and placed in the context of Thuringian sequencesConstant antigenic drift for SARS-CoV-2 and no clear pattern or clustering is visible in Thuringia based on the current number of samplesCurrently over 100 described lineages are identified in Germany and only a subset (9) are detected in Thuringia so far, most likely due to genetic undersamplingFrom a national perspective, it is likely that high-frequency lineages, which are currently spreading throughout Europe, will eventually also reach ThuringiaSystematic and dense molecular surveillance via whole-genome sequencing is needed to detect concerning new lineages early, limit spread and adjust vaccines if necessaryCompeting Interest StatementThe authors have declared no competing interest.Funding StatementThe work is funded by the German Ministry of Education and Research (BMBF), grant number 01KX2021, and the Thuringian Region Government, grant number TZUZI82094.Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:not applicableAll necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesAll data is available on GISAID.Introduction Methods - Nanopore sequencing and genome reconstruction - Time tree creation Results - Most highly prevalent SARS-CoV-2 lineages in Germany detected in Thuringia - Genetic divergence and current lineage distribution Discussio

Importance and controls of anaerobic ammonium oxidation influenced by riverbed geology

Rivers are an important global sink for excess bioavailable nitrogen: they convert approximately 40% of terrestrial N runoff per year (∼47 Tg) to biologically unavailable N 2 gas and return it to the atmosphere. At present, riverine N 2 production is conceptualized and modelled as denitrification. Anaerobic ammonium oxidation, known as anammox, is an alternative pathway of N 2 production important in marine environments, but its contribution to riverine N 2 production is not well understood. Here we use in situ and laboratory measurements of anammox activity using 15 N tracers and molecular analyses of microbial communities to evaluate anammox in clay-, sand-and chalk-dominated river beds in the Hampshire Avon catchment, UK during summer 2013. Abundance of the hzo gene, which encodes an enzyme central to anammox metabolism, varied across the contrasting geologies. Anammox rates were similar across geologies but contributed different proportions of N 2 production because of variation in denitrification rates. In spite of requiring anoxic conditions, anammox, most likely coupled to partial nitrification, contributed up to 58% of in situ N 2 production in oxic, permeable riverbeds. In contrast, denitrification dominated in low-permeability clay-bed rivers, where anammox contributes roughly 7% to the production of N 2 gas. We conclude that anammox can represent an important nitrogen loss pathway in permeable river sediments

Use of the inverse abundance approach to identify the sources of NO and N2O release from Spanish forest soils under oxic and hypoxic conditions

Forest soils exhibit a variety of complex biochemical nitrogen (N) reactions in which nitric oxide (NO) and nitrous oxide (N2O) can be produced by coexisting processes that respond differently to the same environmental conditions. In general, two biochemical processes, (i) the oxidation of ammonia (nitrification) and (ii) the reduction of nitrate (denitrification), are known as the major sources of nitrogen oxides. Few reports indicated that a direct oxidation of soil organic N compounds (Norg) to NO and N2O may also be significant in soils. A triplet 15N tracer experiment (TTE) combined with an inverse abundance approach (IAA) was applied to quantify NO and N2O formation in soil related to different but simultaneously utilized soil N sources (ammonium, nitrate, and Norg). In addition, the impact of oxic and hypoxic conditions (21 and 2% v/v O2, respectively) on total soil NO/N2O release and source composition was studied. Experiments were conducted with soil samples from 5 different Basque forest stands (mature beech, young beech, mature pine, young pine, and new pine plantation). The release rates of NO and N2O were higher in the soil samples from beech stands than in the samples from pine stands. The change from oxic to hypoxic conditions increased the NO release rate 2- to 14-fold and the N2O release rate 3.6- to 25-fold. The study suggests that, under oxic conditions, N2O formation based on Norg appears to be the dominant pathway of soil N2O production (48–76% to total N2O release). Under hypoxic conditions, the relative contribution of Norg significantly decreased, whereas its absolute contribution increased concomitantly. Denitrification was the dominant process of soil N2O release under hypoxic conditions and served as the major pathway of soil NO release under both oxic and hypoxic conditions (40 and 60% of total soil NO release, respectively). We conclude that the individual contribution of different soil N pools to the total soil N gas release and the impact of environmental parameters (e.g., O2 availability) are site-specific. Nonetheless, further research is required to elucidate the impact of forest stands on soil NO and N2O production, particularly N2O formation directly based on Norg transformation.This work was supported by the Ministry of Science and Innovation of Spain (HD2008-0065 and SUM2006-00017-C03-00), K-Egokitzen-Etortek 2010–2012, GV IT-526-10 and DAAD (German Academic Exchange Service).Ministry of Science and Innovation of SpainK-Egokitzen-EtortekGerman Academic Exchange ServicePeer reviewe

Blunt duodenal rupture: a 6-year statewide experience.

OBJECTIVES: To characterize the incidence, presentation, diagnostic features, injury pattern, and mortality of blunt duodenal rupture. METHODS: The records of 103,864 patients entered into a state-wide trauma registry during a 6-year period were screened for the diagnosis of blunt duodenal injury. The hospital records of all patients meeting diagnostic criteria of blunt duodenal rupture from 28 trauma centers were reviewed. RESULTS: Blunt duodenal injury was identified in 206 (0.2%) patients. Thirty (14.5%) of these had full-thickness rupture of the duodenum. Of these 30 patients, 21 had been involved in motor vehicle crashes. Twenty-five presented with either abdominal pain, tenderness, or guarding on physical examination. Diagnostic peritoneal lavage was performed on 12 patients. Three patients were found to have isolated rupture of the duodenum. Computerized tomography was the primary diagnostic investigation in eighteen cases. Extravasation of contrast was noted in only two cases. Four studies were interpreted as normal. The second portion of the duodenum was most commonly injured, and there was a high incidence of associated intra-abdominal injuries. Seven patients underwent operation \u3e12 hours after admission. Twenty-six patients survived to hospital discharge. Two deaths were caused by duodenal injury-related sepsis. CONCLUSION: Blunt rupture of the duodenum is rare. Most blunt duodenal injuries do not result in full-thickness injury. The majority of patients with duodenal rupture presented with either a history or a physical examination suggestive of intra-abdominal injury. Computerized tomography results were often negative or nonspecific. Delay in diagnosis of duodenal rupture remains common but does not appear to affect mortality. Overall mortality was lower than previously reported

Greenhouse gas fluxes (CO2, N2O and CH4) from forest soils in the Basque Country: Comparison of different tree species and growth stages

Forest systems are considered quintessential terrestrial systems for atmospheric CO2 sequestration to mitigate the effect of global warming. Temperate forest soils also present the highest rates of methane uptake among all the natural systems, while may represent a significant source of N2O. Despite of the large area occupied by forest in the Basque Country, no data is yet available regarding greenhouse gas fluxes under these edaphoclimatic conditions. In this manuscript we present a 2-year study which determined the magnitude of CO2, N2O, and CH4 soil gas fluxes in radiata pine, beech and Douglas fir forests using a closed chamber technique. The magnitude of these gas fluxes was additionally compared between different growth stages of radiata pine and beech forest, and the edaphoclimatic parameters that control these gas fluxes in the different forest systems and growth stages were studied. Measured greenhouse gas fluxes were in a low range as already published elsewhere for temperate forest ecosystems. A nitrogen deficit appears to be responsible for these relatively low gas fluxes. Apparently, the different forest species play a key role as controllers responsible for the differences of soil gas-exchange fluxes between the three different forest type systems. The mature pine plantation soil was emitting the most CO2 (1.5 and 2.5 times more than the mature beech and the Douglas fir, respectively), while the Douglas fir forest soil was emitting the most N2O (3 and 17 times more than the mature pine and the mature beech, respectively) and the mature beech forest was the soil type showing the highest CH4 consumption rates (2 and 5.5 times more than the mature pine and the Douglas fir, respectively). The stage of growth and its usual management appear to be important concerning the soil gas-exchange behavior within one forest type. The young beech forest soil emitted 9 times more N2O than the mature, and the new pine and the mature pine plantation soils emitted 2.5 and 2 times more CO2 than the young, respectively. The ground vegetation cover percentage, the organic matter accumulation and the soil porosity seem to be factors which merit a closer look in future studies, as possibly responsible for the differences in gas fluxes among forest types and growth stages. © 2013 Elsevier B.V.This project was funded by the Spanish Government (AGL2009-13339-CO2-01) and by the Basque Government (K-EGOKITZEN ETORTEK 2010-2012 and GV-IT-526-10). Iskander Barrena is the recipient of a predoctoral fellowship from the Department of Education, Universities and Research of the Basque Government.Peer Reviewe

Microbial communities along biogeochemical gradients in a hydrocarbon-contaminated aquifer

Micro-organisms are known to degrade a wide range of toxic substances. How the environment shapes microbial communities in polluted ecosystems and thus influences degradation capabilities is not yet fully understood. In this study, we investigated microbial communities in a highly complex environment: the capillary fringe and subjacent sediments in a hydrocarbon-contaminated aquifer. Sixty sediment sections were analysed using terminal restriction fragment length polymorphism (T-RFLP) fingerprinting, cloning and sequencing of bacterial and archaeal 16S rRNA genes, complemented by chemical analyses of petroleum hydrocarbons, methane, oxygen and alternative terminal electron acceptors. Multivariate statistics revealed concentrations of contaminants and the position of the water table as significant factors shaping the microbial community composition. Micro-organisms with highest T-RFLP abundances were related to sulphate reducers belonging to the genus Desulfosporosinus, fermenting bacteria of the genera Sedimentibacter and Smithella, and aerobic hydrocarbon degraders of the genus Acidovorax. Furthermore, the acetoclastic methanogens Methanosaeta, and hydrogenotrophic methanogens Methanocella and Methanoregula were detected. Whereas sulphate and sulphate reducers prevail at the contamination source, the detection of methane, fermenting bacteria and methanogenic archaea further downstream points towards syntrophic hydrocarbon degradation