The Role of Neutralizing Antibodies in HIV-1 infection

Human immunodeficiency virus type 1 is a major cause of morbidity and mortality worldwide and there is urgent demand for a protective vaccine. A major goal of vaccine development is the elicitation of antibodies capable of neutralizing diverse strains. In order to achieve this goal it is necessary to understand the dynamic relationship between neutralizing antibodies (NAbs) and HIV-1, in vivo. In humans, HIV-1 rapidly escapes from NAbs, confirming that humoral responses inhibit virus replication. However, neutralizing responses are commonly detected in viraemic patients and the clinical impact of NAbs on HIV-1 control is unclear. To investigate this further, viral load (VL) and NAb activity were assessed longitudinally in patients enrolled into a clinical trial of short-course antiretroviral therapy (ART), administered in early infection. The aims of this study were two-fold: i) to understand the importance of VL in the control of NAb responses and ii) to assess whether NAbs contribute to durable control of VL set-point. A high-throughput pseudovirus neutralization assay was developed, using automated counting procedures to quantify infected TZM-bl reporter cells. The assay was used to assess NAb responses with autologous viruses derived from 22 patients. Seven patients with low VL set-points (<104 RNA copies/ml) failed to develop neutralizing responses throughout the 48-144 week follow-up period. In contrast, the remaining patients developed progressively-increasing neutralizing plasma titres (IC50) that correlated with the extent and timing of VL rebound after cessation of ART. This suggests that the production of NAbs depends on the duration and extent of viraemia in early infection. Viral load was poorly predictive of neutralizing responses against heterologous isolates assayed in 38 patients, suggesting that other factors are important in the production of antibodies with cross-neutralizing activity. Depletion of specific immunological compartments can yield crucial information as to their functional importance in vivo. We took advantage of a unique opportunity to investigate the role of NAbs and the consequences of their depletion in an HIV-1 infected human. Three years after cessation of short-course ART, the patient was treated for pre-existing low-grade lymphoplasmacytic lymphoma by antibodymediated depletion of CD20+ B cells using rituximab. This treatment was followed by a 1.7 log10 rise in HIV-1 VL which spontaneously reversed. Autologous NAb responses decreased as viraemia flared, and recovered as VL was controlled. Antibodies were found to target the CD4 binding site (CD4bs), as shown by competitive-binding assays. Sequence analysis revealed diversification through generation of new variants as NAbs decreased, with subsequent selection of NAb-resistant mutants at sites consistent with the binding data. These data suggest that B cell function contributed to long-term control of VL in this individual and that NAbs may be more important in controlling HIV-1 infection than previously suspected

A Rare Case of Squamous Cell Carcinoma of the Bladder Presenting as a Metastatic Right Ventricular Mass

A 74-year-old woman presented with bilateral lower extremity swelling, worsening dyspnea on exertion, and mild hemoptysis. An echocardiogram at time of admission showed a mass in the right ventricle. The pathology of a sample obtained via transvenous biopsy was consistent with squamous cell carcinoma; no primary source could initially be identified. Severe thrombocytopenia, likely consumptive, precluded surgical intervention, so the patient underwent palliative radiation. Unfortunately, she developed fatal respiratory failure. Upon autopsy, the bladder was found to contain polyps of invasive squamous cell carcinoma, similar in morphology to the tumor mass in the heart. Her lungs contained multiple tumor emboli at different stages, which was likely the final cause of her death. Squamous cell carcinoma metastases to the endocardium are extremely rare and without defined treatment. Surgery can improve prognosis in those with primary tumors that are benign or without metastases. In those with symptomatic metastatic tumors, palliative debulking can done although generally will not improve prognosis. It is currently unknown whether radiation improves survival. In this case, irradiation did destroy a portion of the tumor as the final pathology showed extensive necrosis of the tumor; unfortunately, it did not change her symptoms and did not change the final outcome

Overcoming the barriers to implementing urban road user charging schemes

Urban road user charging offers the potential to achieve significant improvements in urban transport, but is notoriously difficult to implement. Cities need guidance on the range of factors to be considered in planning and implementing such schemes. This paper summarises the results of a 3 year programme which has collated evidence on the issues of most concern to cities. A state of the art report has provided evidence on 14 themes, ranging from objectives and design to implementation and evaluation. A set of 16 case studies has reviewed experience in design and implementation across Europe. The paper summarises their findings, provides references to more detailed information, presents the resulting policy recommendations to European, national and local government, and outlines the areas in which further research is needed

Long-Term Irrigation Affects the Dynamics and Activity of the Wheat Rhizosphere Microbiome

The Inland Pacific Northwest (IPNW) encompasses 1. 6 million cropland hectares and is a major wheat-producing area in the western United States. The climate throughout the region is semi-arid, making the availability of water a significant challenge for IPNW agriculture. Much attention has been given to uncovering the effects of water stress on the physiology of wheat and the dynamics of its soilborne diseases. In contrast, the impact of soil moisture on the establishment and activity of microbial communities in the rhizosphere of dryland wheat remains poorly understood. We addressed this gap by conducting a three-year field study involving wheat grown in adjacent irrigated and dryland (rainfed) plots established in Lind, Washington State. We used deep amplicon sequencing of the V4 region of the 16S rRNA to characterize the responses of the wheat rhizosphere microbiome to overhead irrigation. We also characterized the population dynamics and activity of indigenous Phz+ rhizobacteria that produce the antibiotic phenazine-1-carboxylic acid (PCA) and contribute to the natural suppression of soilborne pathogens of wheat. Results of the study revealed that irrigation affected the Phz+ rhizobacteria adversely, which was evident from the significantly reduced plant colonization frequency, population size and levels of PCA in the field. The observed differences between irrigated and dryland plots were reproducible and amplified over the course of the study, thus identifying soil moisture as a critical abiotic factor that influences the dynamics, and activity of indigenous Phz+ communities. The three seasons of irrigation had a slight effect on the overall diversity within the rhizosphere microbiome but led to significant differences in the relative abundances of specific OTUs. In particular, irrigation differentially affected multiple groups of Bacteroidetes and Proteobacteria, including taxa with known plant growth-promoting activity. Analysis of environmental variables revealed that the separation between irrigated and dryland treatments was due to changes in the water potential (Ψm) and pH. In contrast, the temporal changes in the composition of the rhizosphere microbiome correlated with temperature and precipitation. In summary, our long-term study provides insights into how the availability of water in a semi-arid agroecosystem shapes the belowground wheat microbiome

Phylogenetic analysis consistent with a clinical history of sexual transmission of HIV-1 from a single donor reveals transmission of highly distinct variants

BACKGROUND To combat the pandemic of human immunodeficiency virus 1 (HIV-1), a successful vaccine will need to cope with the variability of transmissible viruses. Human hosts infected with HIV-1 potentially harbour many viral variants but very little is known about viruses that are likely to be transmitted, or even if there are viral characteristics that predict enhanced transmission in vivo. We show for the first time that genetic divergence consistent with a single transmission event in vivo can represent several years of pre-transmission evolution. RESULTS We describe a highly unusual case consistent with a single donor transmitting highly related but distinct HIV-1 variants to two individuals on the same evening. We confirm that the clustering of viral genetic sequences, present within each recipient, is consistent with the history of a single donor across the viral env, gag and pol genes by maximum likelihood and bayesian Markov Chain Monte Carlo based phylogenetic analyses. Based on an uncorrelated, lognormal relaxed clock of env gene evolution calibrated with other datasets, the time since the most recent common ancestor is estimated as 2.86 years prior to transmission (95% confidence interval 1.28 to 4.54 years). CONCLUSION Our results show that an effective design for a preventative vaccine will need to anticipate extensive HIV-1 diversity within an individual donor as well as diversity at the population level

Long-Term Irrigation Affects the Dynamics and Activity of the Wheat Rhizosphere Microbiome

The Inland Pacific Northwest (IPNW) encompasses 1. 6 million cropland hectares and is a major wheat-producing area in the western United States. The climate throughout the region is semi-arid, making the availability of water a significant challenge for IPNW agriculture. Much attention has been given to uncovering the effects of water stress on the physiology of wheat and the dynamics of its soilborne diseases. In contrast, the impact of soil moisture on the establishment and activity of microbial communities in the rhizosphere of dryland wheat remains poorly understood. We addressed this gap by conducting a three-year field study involving wheat grown in adjacent irrigated and dryland (rainfed) plots established in Lind, Washington State. We used deep amplicon sequencing of the V4 region of the 16S rRNA to characterize the responses of the wheat rhizosphere microbiome to overhead irrigation. We also characterized the population dynamics and activity of indigenous Phz+ rhizobacteria that produce the antibiotic phenazine-1-carboxylic acid (PCA) and contribute to the natural suppression of soilborne pathogens of wheat. Results of the study revealed that irrigation affected the Phz+ rhizobacteria adversely, which was evident from the significantly reduced plant colonization frequency, population size and levels of PCA in the field. The observed differences between irrigated and dryland plots were reproducible and amplified over the course of the study, thus identifying soil moisture as a critical abiotic factor that influences the dynamics, and activity of indigenous Phz+ communities. The three seasons of irrigation had a slight effect on the overall diversity within the rhizosphere microbiome but led to significant differences in the relative abundances of specific OTUs. In particular, irrigation differentially affected multiple groups of Bacteroidetes and Proteobacteria, including taxa with known plant growth-promoting activity. Analysis of environmental variables revealed that the separation between irrigated and dryland treatments was due to changes in the water potential (Ψm) and pH. In contrast, the temporal changes in the composition of the rhizosphere microbiome correlated with temperature and precipitation. In summary, our long-term study provides insights into how the availability of water in a semi-arid agroecosystem shapes the belowground wheat microbiome

Microsimulation models incorporating both demand and supply dynamics

There has been rapid growth in interest in real-time transport strategies over the last decade, ranging from automated highway systems and responsive traffic signal control to incident management and driver information systems. The complexity of these strategies, in terms of the spatial and temporal interactions within the transport system, has led to a parallel growth in the application of traffic microsimulation models for the evaluation and design of such measures, as a remedy to the limitations faced by conventional static, macroscopic approaches. However, while this naturally addresses the immediate impacts of the measure, a difficulty that remains is the question of how the secondary impacts, specifically the effect on route and departure time choice of subsequent trips, may be handled in a consistent manner within a microsimulation framework. The paper describes a modelling approach to road network traffic, in which the emphasis is on the integrated microsimulation of individual trip-makers’ decisions and individual vehicle movements across the network. To achieve this it represents directly individual drivers’ choices and experiences as they evolve from day-to-day, combined with a detailed within-day traffic simulation model of the space–time trajectories of individual vehicles according to car-following and lane-changing rules and intersection regulations. It therefore models both day-to-day and within-day variability in both demand and supply conditions, and so, we believe, is particularly suited for the realistic modelling of real-time strategies such as those listed above. The full model specification is given, along with details of its algorithmic implementation. A number of representative numerical applications are presented, including: sensitivity studies of the impact of day-to-day variability; an application to the evaluation of alternative signal control policies; and the evaluation of the introduction of bus-only lanes in a sub-network of Leeds. Our experience demonstrates that this modelling framework is computationally feasible as a method for providing a fully internally consistent, microscopic, dynamic assignment, incorporating both within- and between-day demand and supply dynamic

Full-genome next-generation sequencing of hepatitis C virus to assess the accuracy of genotyping by the commercial assay LiPA and the prevalence of resistance-associated substitutions in a Belgian cohort

Funding Information: This work and KTC were supported by grants from the Fonds voor Wetenschappelijk Onderzoek Vlaanderen (FWO) ( G069214 , G0B2317N , 1S38819N ). LC acknowledges FWO travel grant for a research visit at University of Oxford ( V431117N ). The authors thank the staff in Oxford in their support of the laboratory work and the donation of the probes used for enrichment of HCV. Publisher Copyright: © 2022 Elsevier B.V.Background: Although most currently used regimens for Hepatitis C virus (HCV) infections can be initiated without prior knowledge of genotype and subtype, genotyping is still useful to identify patients who might benefit from a personalized treatment due to resistance to direct-acting antivirals (DAA). Objectives: To assess the utility of full-genome next-generation sequencing (FG-NGS) for HCV genotyping. Study design: 138 HCV plasma samples previously genotyped by VERSANT HCV Genotype Assay (LiPA) were subjected to FG-NGS and phylogenetically genotyped Genome Detective. Consensuses were analysed by HCV-GLUE for resistance-associated substitutions (RASs) and their impact on treatment response was investigated. Results: 102/138 (73.9%) samples were sequenced to a genome coverage and depth of >90% of the HCV open reading frame covered by >100 reads/site. Concordant genotype and subtype results were assigned in 97.1% and 79.4% of samples, respectively. FG-NGS resolved the subtype of 13.7% samples that had ambiguous calls by LiPA and identified one dual infection and one recombinant strain. At least one RAS was found for the HCV genes NS3, NS5A, and NS5B in 2.91%, 36.98% and 27.3% samples, respectively. Irrespective of the observed RAS, all patients responded well to DAA treatment, except for HCV1b-infected patients treated with Zepatier (33.3% failure rate (5/15)). Conclusion: While LiPA and FG-NGS showed overall good concordance, FG-NGS improved specificity for subtypes, recombinant and mixed infections. FG-NGS enabled the detection of RAS, but its predictive value for treatment outcome in DAA-naïve patients remains uncertain. With additional refinements, FG-NGS may be the way forward for HCV genotyping.publishersversionpublishe

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