Genome-to-genome analysis highlights the effect of the human innate and adaptive immune systems on the hepatitis C virus

Outcomes of hepatitis C virus (HCV) infection and treatment depend on viral and host genetic factors. Here we use human genome-wide genotyping arrays and new whole-genome HCV viral sequencing technologies to perform a systematic genome-to-genome study of 542 individuals who were chronically infected with HCV, predominantly genotype 3. We show that both alleles of genes encoding human leukocyte antigen molecules and genes encoding components of the interferon lambda innate immune system drive viral polymorphism. Additionally, we show that IFNL4 genotypes determine HCV viral load through a mechanism dependent on a specific amino acid residue in the HCV NS5A protein. These findings highlight the interplay between the innate immune system and the viral genome in HCV control

Utility of a buccal swab point-of-care test for the IFNL4 genotype in the era of direct acting antivirals for hepatitis C virus.

BACKGROUND: The CC genotype of the IFNL4 gene is known to be associated with increased Hepatitis C (HCV) cure rates with interferon-based therapy and may contribute to cure with direct acting antivirals. The Genedrive® IFNL4 is a CE marked Point of Care (PoC) molecular diagnostic test, designed for in vitro diagnostic use to provide rapid, real-time detection of IFNL4 genotype status for SNP rs12979860. METHODS: 120 Participants were consented to a substudy comparing IFNL4 genotyping results from a buccal swab analysed on the Genedrive® platform with results generated using the Affymetix UK Biobank array considered to be the gold standard. RESULTS: Buccal swabs were taken from 120 participants for PoC IFNL4 testing and a whole blood sample for genetic sequencing. Whole blood genotyping vs. buccal swab PoC testing identified 40 (33%), 65 (54%), and 15 (13%) had CC, CT and TT IFNL4 genotype respectively. The Buccal swab PoC identified 38 (32%) CC, 64 (53%) CT and 18 (15%) TT IFNL4 genotype respectively. The sensitivity and specificity of the buccal swab test to detect CC vs non-CC was 90% (95% CI 76-97%) and 98% (95% CI 91-100%) respectively. CONCLUSIONS: The buccal swab test was better at correctly identifying non-CC genotypes than CC genotypes. The high specificity of the Genedrive® assay prevents CT/TT genotypes being mistaken for CC, and could avoid patients being identified as potentially 'good responders' to interferon-based therapy

Microbotanical residues for the study of early hominin tools

More than 2 million years ago in East Africa, the earliest hominin stone tools evolved amidst changes in resource base, with pounding technology playing a key role in this adaptive process. Olduvai Gorge (now Oldupai) is a famed locality that remains paramount for the study of human evolution, also yielding some of the oldest battering tools in the world. However, direct evidence of the resources processed with these technologies is lacking entirely. One way to obtain this evidence is through the analysis of surviving residues. Yet, linking residues with past processing activities is not simple. In the case of plant exploitation, this link can only be established by assessing site-based reference collections inclusive of both anthropogenic and natural residues as a necessary first step and comparative starting point. In this paper, we assess microbotanical remains from rock clasts sourced at the same quarry utilized by Oldowan hominins at Oldupai Gorge. We mapped this signal and analysed it quantitatively to classify its spatial distribution objectively, extracting proxies for taxonomic identification and further comparison with freestanding soils. In addition, we used blanks to manufacture pounding tools for blind, controlled replication of plant processing. We discovered that stone blanks are in fact environmental reservoirs in which plant remains are trapped by lithobionts, preserved as hardened accretions. Tool use, on the other hand, creates residue clusters; however, their spatial distribution can be discriminated from purely natural assemblages by the georeferencing of residues and statistical analysis of resulting patterns. To conclude, we provide a protocol for best practice and a workflow that has the advantage of overcoming environmental noise, reducing the risk of false positive, delivering a firm understanding of residues as polygenic mixtures, a reliable use of controls, and most importantly, a stronger link between microbotanical remains and stone tool use. © 2022. The Author(s).Materials and methods Results - Blanks as environmental reservoirs - Utilization creates residue clusters - Anthropogenic residue distribution - Of lichen habitability, proxy palimpsests, and hardened accretions - A protocol to study plant residue from Oldowan pounding tool

Interferon lambda 4 impacts the genetic diversity of hepatitis C virus

Hepatitis C virus (HCV) is a highly variable pathogen that frequently establishes chronic infection. This genetic variability is affected by the adaptive immune response but the contribution of other host factors is unclear. Here, we examined the role played by interferon lambda-4 (IFN-λ4) on HCV diversity; IFN-λ4 plays a crucial role in spontaneous clearance or establishment of chronicity following acute infection. We performed viral genome-wide association studies using human and viral data from 485 patients of white ancestry infected with HCV genotype 3a. We demonstrate that combinations of host genetic variants, which determine IFN-λ4 protein production and activity, influence amino acid variation across the viral polyprotein - not restricted to specific viral proteins or HLA restricted epitopes - and modulate viral load. We also observed an association with viral di-nucleotide proportions. These results support a direct role for IFN-λ4 in exerting selective pressure across the viral genome, possibly by a novel mechanism

Global monitoring of volcanic SO2 degassing with unprecedented resolution from TROPOMI onboard Sentinel-5 Precursor

Over the last four decades, space-based nadir observations of sulfur dioxide (SO2 ) proved to be a key data source for assessing the environmental impacts of volcanic emissions, for monitoring volcanic activity and early signs of eruptions, and ultimately mitigating related hazards on local populations and aviation. Despite its importance, a detailed picture of global SO 2 daily degassing is difficult to produce, notably for lower-tropospheric plumes, due largely to the limited spatial resolution and coverage or lack of sensitivity and selectivity to SO2 of current (and previous) nadir sensors. We report here the first volcanic SO2 measurements from the hyperspectral TROPOspheric Monitoring Instrument (TROPOMI) launched in October 2017 onboard the ESA’s Sentinel-5 Precursor platform. Using the operational processing algorithm, we explore the benefit of improved spatial resolution to the monitoring of global volcanic degassing. We find that TROPOMI surpasses any space nadir sensor in its ability to detect weak degassing signals and captures day-to-day changes in SO2 emissions. The detection limit of TROPOMI to SO2 emissions is a factor of 4 better than the heritage Aura/Ozone Monitoring Instrument (OMI). Here we show that TROPOMI SO2 daily observations carry a wealth of information on volcanic activity. Provided with adequate wind speed data, temporally resolved SO2 fluxes can be obtained at hourly time steps or shorter. We anticipate that TROPOMI SO2 data will help to monitor global volcanic daily degassing and better understand volcanic processes and impacts

Viral genome wide association study identifies novel hepatitis C virus polymorphisms associated with sofosbuvir treatment failure

Persistent hepatitis C virus (HCV) infection is a major cause of chronic liver disease, worldwide. With the development of direct-acting antivirals, treatment of chronically infected patients has become highly effective, although a subset of patients responds less well to therapy. Sofosbuvir is a common component of current de novo or salvage combination therapies, that targets the HCV NS5B polymerase. We use pre-treatment whole-genome sequences of HCV from 507 patients infected with HCV subtype 3a and treated with sofosbuvir containing regimens to detect viral polymorphisms associated with response to treatment. We find three common polymorphisms in non-targeted HCV NS2 and NS3 proteins are associated with reduced treatment response. These polymorphisms are enriched in post-treatment HCV sequences of patients unresponsive to treatment. They are also associated with lower reductions in viral load in the first week of therapy. Using in vitro short-term dose-response assays, these polymorphisms do not cause any reduction in sofosbuvir potency, suggesting an indirect mechanism of action in decreasing sofosbuvir efficacy. The identification of polymorphisms in NS2 and NS3 proteins associated with poor treatment outcomes emphasises the value of systematic genome-wide analyses of viruses in uncovering clinically relevant polymorphisms that impact treatment

Rethinking use-wear analysis and experimentation as applied to the study of past hominin tool use

In prehistoric human populations, technologies played a fundamental role in the acquisition of different resources and are represented in the main daily living activities, such as with bone, wooden, and stone-tipped spears for hunting, and chipped-stone tools for butchering. Considering that paleoanthropologists and archeologists are focused on the study of different processes involved in the evolution of human behavior, investigating how hominins acted in the past through the study of evidence on archeological artifacts is crucial. Thus, investigat ing tool use is of major importance for a comprehensive understanding of all processes that characterize human choices of raw materials, techniques, and tool types. Many functional assumptions of tool use have been based on tool design and morphology according to archeologists’ interpretations and ethnographic observations. Such assumptions are used as baselines when inferring human behavior and have driven an improvement in the methods and techniques employed in functional studies over the past few decades. Here, while arguing that use-wear analysis is a key discipline to assess past hominin tool use and to interpret the organization and variability of artifact types in the archeological record, we aim to review and discuss the current state-of-the-art methods, protocols, and their limitations. In doing so, our discussion focuses on three main topics: (1) the need for fundamental improvements by adopting established methods and techniques from similar research fields, (2) the need to implement and combine different levels of experimentation, and (3) the crucial need to establish standards and protocols in order to improve data quality, standard ization, repeatability, and reproducibility. By adopting this perspective, we believe that studies will increase the reliability and applicability of use-wear methods on tool function. The need for a holistic approach that combines not only use-wear traces but also tool technology, design, curation, durability, and efficiency is also debated and revised. Such a revision is a crucial step if archeologists want to build major inferences on human decision making behavior and biocultural evolution processes.info:eu-repo/semantics/publishedVersio

Fusion of hyperspectral and lidar data using morphological attribute profiles

In this paper we investigate the application of Morphological Attribute Profiles to both hyperspectral and LiDAR data to fuse spectral, spatial and elevation data for classification purposes. While hyperspectral data provides a wealth of spectral information, multi-return LiDAR data provides geometrical information on the elevation and the structure of the objects on the ground as well as a measure of their laser cross section. Therefore, hyperspectral and LiDAR data are complementary information sources and potentially their joint analysis can improve classification accuracies. Morphological Profiles (MPs) and Morphological Attribute Profiles (MAPs) have been successfully used as tools to combine spectral and spatial information for classification of remote sensing data. MPs and MAPs can also be used with the LiDAR data to reduce the irregularities in the LiDAR measurements which are inherent with the sampling strategy used in the acquisition process. Experiments carried out on hyperspectral and LiDAR data acquired on a urban area of the city of Trento (Italy) point out the effectiveness of MAPs for the classification process