Soil compaction is a major disturbance associated with logging, but we lack a fundamental understanding of how this affects the soil microbiome. We assessed the structural resistance and resilience ...of the microbiome using a high-throughput pyrosequencing approach in differently compacted soils at two forest sites and correlated these findings with changes in soil physical properties and functions. Alterations in soil porosity after compaction strongly limited the air and water conductivity. Compaction significantly reduced abundance, increased diversity, and persistently altered the structure of the microbiota. Fungi were less resistant and resilient than bacteria; clayey soils were less resistant and resilient than sandy soils. The strongest effects were observed in soils with unfavorable moisture conditions, where air and water conductivities dropped well below 10% of their initial value. Maximum impact was observed around 6-12 months after compaction, and microbial communities showed resilience in lightly but not in severely compacted soils 4 years post disturbance. Bacteria capable of anaerobic respiration, including sulfate, sulfur, and metal reducers of the Proteobacteria and Firmicutes, were significantly associated with compacted soils. Compaction detrimentally affected ectomycorrhizal species, whereas saprobic and parasitic fungi proportionally increased in compacted soils. Structural shifts in the microbiota were accompanied by significant changes in soil processes, resulting in reduced carbon dioxide, and increased methane and nitrous oxide emissions from compacted soils. This study demonstrates that physical soil disturbance during logging induces profound and long-lasting changes in the soil microbiome and associated soil functions, raising awareness regarding sustainable management of economically driven logging operations.
Since entering the human population, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2; the causative agent of Coronavirus Disease 2019 COVID-19) has spread worldwide, causing >100 million ...infections and >2 million deaths. While large-scale sequencing efforts have identified numerous genetic variants in SARS-CoV-2 during its circulation, it remains largely unclear whether many of these changes impact adaptation, replication, or transmission of the virus. Here, we characterized 14 different low-passage replication-competent human SARS-CoV-2 isolates representing all major European clades observed during the first pandemic wave in early 2020. By integrating viral sequencing data from patient material, virus stocks, and passaging experiments, together with kinetic virus replication data from nonhuman Vero-CCL81 cells and primary differentiated human bronchial epithelial cells (BEpCs), we observed several SARS-CoV-2 features that associate with distinct phenotypes. Notably, naturally occurring variants in Orf3a (Q57H) and nsp2 (T85I) were associated with poor replication in Vero-CCL81 cells but not in BEpCs, while SARS-CoV-2 isolates expressing the Spike D614G variant generally exhibited enhanced replication abilities in BEpCs. Strikingly, low-passage Vero-derived stock preparation of 3 SARS-CoV-2 isolates selected for substitutions at positions 5/6 of E and were highly attenuated in BEpCs, revealing a key cell-specific function to this region. Rare isolate-specific deletions were also observed in the Spike furin cleavage site during Vero-CCL81 passage, but these were rapidly selected against in BEpCs, underscoring the importance of this site for SARS-CoV-2 replication in primary human cells. Overall, our study uncovers sequence features in SARS-CoV-2 variants that determine cell-specific replication and highlights the need to monitor SARS-CoV-2 stocks carefully when phenotyping newly emerging variants or potential variants of concern.
•Biotic dependencies of river biota were implemented into a distribution model.•T. thymallus will suffer from habitat loss under climate change.•Habitat loss of T. thymallus was attenuated by A. ...auricollis occurrence.•Distribution loss was strongly related to climate change intensity.
Climate change will impact the riverine environment of aquatic organisms. However, most studies focus solely on environmental characteristics to evaluate future distribution shifts. Here, we analyse current and future distribution of the freshwater fish species Thymallus thymallus in relation to the caddisfly Allogamus auricollis. Current and future distributions of the two species were evaluated by a consensus model approach integrating seven different distribution model techniques and testing the effect of considering biotic dependence. Predictions for future distributions were calculated on the basis of the most recent representative concentration pathways (RCPs) of the IPCC for the period of the 2050s. Habitat loss and gain, distribution congruence and altitudinal shift between the two species were quantified on the basis of a full river network. The model considering biotic dependence identified the caddisfly as important variable for the distributions of European grayling, mitigating the drastic effects of climate change. Habitat loss of the grayling was attenuated by considering the distribution of the caddisfly in the distribution modelling. Strong temperature increases as well as run-off decreases led to largest habitat loss of both species (up to 70%). Our combined approach highlighted that the consideration of biotic dependencies in climate change studies improves the understanding for potential future changes of distribution patterns.
Species' differences in cellular factors limit avian influenza A virus (IAV) zoonoses and human pandemics. The IAV polymerase, vPol, harbors evolutionary sites to overcome restriction and determines ...virulence. Here, we establish host ANP32A as a critical driver of selection, and identify host-specific ANP32A splicing landscapes that predict viral evolution. We find that avian species differentially express three ANP32A isoforms diverging in a vPol-promoting insert. ANP32As with shorter inserts interact poorly with vPol, are compromised in supporting avian-like IAV replication, and drive selection of mammalian-adaptive vPol sequences with distinct kinetics. By integrating selection data with multi-species ANP32A splice variant profiling, we develop a mathematical model to predict avian species potentially driving (swallow, magpie) or maintaining (goose, swan) mammalian-adaptive vPol signatures. Supporting these predictions, surveillance data confirm enrichment of several mammalian-adaptive vPol substitutions in magpie IAVs. Profiling host ANP32A splicing could enhance surveillance and eradication efforts against IAVs with pandemic potential.
BACKGROUNDNeutralizing antibodies are considered a key correlate of protection by current SARS-CoV-2 vaccines. The manner in which human infections respond to therapeutic SARS-CoV-2 antibodies, ...including convalescent plasma therapy, remains to be fully elucidated.METHODSWe conducted a proof-of-principle study of convalescent plasma therapy based on a phase I trial in 30 hospitalized COVID-19 patients with a median interval between onset of symptoms and first transfusion of 9 days (IQR, 7-11.8 days). Comprehensive longitudinal monitoring of the virological, serological, and disease status of recipients allowed deciphering of parameters on which plasma therapy efficacy depends.RESULTSIn this trial, convalescent plasma therapy was safe as evidenced by the absence of transfusion-related adverse events and low mortality (3.3%). Treatment with highly neutralizing plasma was significantly associated with faster virus clearance, as demonstrated by Kaplan-Meier analysis (P = 0.034) and confirmed in a parametric survival model including viral load and comorbidity (adjusted hazard ratio, 3.0; 95% CI, 1.1-8.1; P = 0.026). The onset of endogenous neutralization affected viral clearance, but even after adjustment for their pretransfusion endogenous neutralization status, recipients benefitted from plasma therapy with high neutralizing antibodies (hazard ratio, 3.5; 95% CI, 1.1-11; P = 0.034).CONCLUSIONOur data demonstrate a clear impact of exogenous antibody therapy on the rapid clearance of viremia before and after onset of the endogenous neutralizing response, and point beyond antibody-based interventions to critical laboratory parameters for improved evaluation of current and future SARS-CoV-2 therapies.TRIAL REGISTRATIONClinicalTrials.gov NCT04869072.FUNDINGThis study was funded via an Innovation Pool project by the University Hospital Zurich; the Swiss Red Cross Glückskette Corona Funding; Pandemiefonds of the UZH Foundation; and the Clinical Research Priority Program "Comprehensive Genomic Pathogen Detection" of the University of Zurich.
Next-generation sequencing (NGS) technologies enable new insights into the diversity of virus populations within their hosts. Diversity estimation is currently restricted to single-nucleotide ...variants or to local fragments of no more than a few hundred nucleotides defined by the length of sequence reads. To study complex heterogeneous virus populations comprehensively, novel methods are required that allow for complete reconstruction of the individual viral haplotypes. Here, we show that assembly of whole viral genomes of ∼8600 nucleotides length is feasible from mixtures of heterogeneous HIV-1 strains derived from defined combinations of cloned virus strains and from clinical samples of an HIV-1 superinfected individual. Haplotype reconstruction was achieved using optimized experimental protocols and computational methods for amplification, sequencing and assembly. We comparatively assessed the performance of the three NGS platforms 454 Life Sciences/Roche, Illumina and Pacific Biosciences for this task. Our results prove and delineate the feasibility of NGS-based full-length viral haplotype reconstruction and provide new tools for studying evolution and pathogenesis of viruses.
Of 1,118 patients with COVID-19 at a university hospital in Switzerland during October 2020–June 2021, we found 83 (7.4%) had probable or definite healthcare-associated COVID-19. After in-hospital ...exposure, we estimated secondary attack rate at 23.3%. Transmission was associated with longer contact times and with lower cycle threshold values among index patients.
We report a rare case of Toscana virus infection imported into Switzerland in a 23-year old man who travelled to Imperia (Italy) 10 days before onset of symptoms. Symptoms included both meningitis ...and as well epididymitis. This is only the fourth case of Toscana virus reported in Switzerland.
The patient presented with lymphocytic meningitis and scrotal pain due to epididymitis. Meningitis was initially treated with ceftriaxone. Herpes simplex, tick-borne encephalitis, enterovirus, measles, mumps, rubella and Treponema pallidum were excluded with specific polymerase chain reaction (PCR) or serology. In support of routine diagnostic PCR and serology assays, unbiased viral metagenomic sequencing was performed of cerebrospinal fluid and serum. Toscana virus infection was identified in cerebrospinal fluid and the full coding sequence could be obtained. Specific PCR in cerebrospinal fluid and blood and serology with Immunoglobulin (Ig) M and IgG against Toscana virus confirmed our diagnosis. Neurological symptoms recovered spontaneously after 5 days.
This case of Toscana virus infection highlights the benefits of unbiased metagenomic sequencing to support routine diagnostics in rare or unexpected viral infections. With increasing travel histories of patients, physicians should be aware of imported Toscana virus as the agent for viral meningitis and meningoencephalitis.
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