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In recent years, an increasing number of outbreaks of Dengue, Chikungunya and Zika viruses have been reported in Asia and the Americas. Monitoring virus genotype diversity is crucial to understand the emergence and spread of outbreaks, both aspects that are vital to develop effective prevention and treatment strategies. Hence, we developed an efficient method to classify virus sequences with respect to their species and sub-species (i.e. serotype and/or genotype). This tool provides an easy-to-use software implementation of this new method and was validated on a large dataset assessing the classification performance with respect to whole-genome sequences and partial-genome sequences. Available online: http://krisp.org.za/tools.php.

Dengue virus and its four serotypes (DENV-1 to DENV-4) infect 390 million people and are implicated in at least 25,000 deaths annually, with the largest disease burden in tropical and subtropical regions. We investigated the spatial dynamics of DENV-1, DENV-2 and DENV-3 in Brazil by applying a statistical framework to complete genome sequences. For all three serotypes, we estimated that the introduction of new lineages occurred within 7 to 10-year intervals. New lineages were most likely to be imported from the Caribbean region to the North and Northeast regions of Brazil, and then to disperse at a rate of approximately 0.5 km/day. Joint statistical analysis of evolutionary, epidemiological and ecological data indicates that aerial transportation of humans and/or vector mosquitoes, rather than Aedes aegypti infestation rates or geographical distances, determine dengue virus spread in Brazil.

Editorial summary The World Health Organization has declared Zika virus an international public health emergency. Knowledge of Zika virus genomic epidemiology is currently limited due to challenges in obtaining and processing samples for sequencing. The ZiBRA project is a United Kingdom–Brazil collaboration that aims to improve this situation using new sequencing technologies.

Tillage intensity affects soil structure in many ways but the magnitude and type (+/−) of change depends on site-specific (e.g., soil type) and experimental details (crop rotation, study length, sampling depth, etc.). This meta-analysis examines published effects of chisel plowing (CP), no-tillage (NT) and perennial cropping systems (PER) relative to moldboard plowing (MP) on three soil structure indicators: wet aggregate stability (AS), bulk density (BD) and soil penetration resistance (PR). The data represents four depth increments (from 0 to >40-cm) in 295 studies from throughout the continental U.S. Overall, converting from MP to CP did not affect those soil structure indicators but reducing tillage intensity from MP to NT increased AS in the surface (<15-cm) and slightly decreased BD and PR below 25-cm. The largest positive effect of NT on AS was observed within Inceptisols and Entisols after a minimum of three years. Compared to MP, NT had a minimal effect on soil compaction indicators (BD and PR) but as expected, converting from MP to PER systems improved soil structure at all soil depths (0 to >40-cm). Among those three soil structure indicators, AS was the most sensitive to management practices; thus, it should be used as a physical indicator for overall soil health assessment. In addition, based on this national meta-analysis, we conclude that reducing tillage intensity improves soil structure, thus offering producers assurance those practices are feasible for crop production and that they will also help sustain soil resources.

This multiplex PCR enrichment protocol enables sequencing of Zika and other viral genomes of low abundance from clinical samples using the Illumina platform, or the portable MinION sequencer, facilitating direct application in field situations. Genome sequencing has become a powerful tool for studying emerging infectious diseases; however, genome sequencing directly from clinical samples (i.e., without isolation and culture) remains challenging for viruses such as Zika, for which metagenomic sequencing methods may generate insufficient numbers of viral reads. Here we present a protocol for generating coding-sequence-complete genomes, comprising an online primer design tool, a novel multiplex PCR enrichment protocol, optimized library preparation methods for the portable MinION sequencer (Oxford Nanopore Technologies) and the Illumina range of instruments, and a bioinformatics pipeline for generating consensus sequences. The MinION protocol does not require an Internet connection for analysis, making it suitable for field applications with limited connectivity. Our method relies on multiplex PCR for targeted enrichment of viral genomes from samples containing as few as 50 genome copies per reaction. Viral consensus sequences can be achieved in 1–2 d by starting with clinical samples and following a simple laboratory workflow. This method has been successfully used by several groups studying Zika virus evolution and is facilitating an understanding of the spread of the virus in the Americas. The protocol can be used to sequence other viral genomes using the online Primal Scheme primer designer software. It is suitable for sequencing either RNA or DNA viruses in the field during outbreaks or as an inexpensive, convenient method for use in the lab.

This report describes and characterizes three novel RNA viruses isolated from dead birds collected during West Nile virus surveillance in Harris County, TX, USA (the Houston metropolitan area). The novel viruses are identified as members of the families Nyamaviridae, Orthomyxoviridae, and Peribunyaviridae and have been designated as San Jacinto virus, Mason Creek virus, and Buffalo Bayou virus, respectively. Their potential public health and/or veterinary importance are still unknown.

Soil organic carbon (SOC) influences several soil functions, making it one of the most important soil health indicators. Its quantity is determined by anthropogenic and inherent factors that must be understood to improve SOC management and interpretation. Topsoil (≤15 cm) SOC response to tillage depth and intensity, cover crops, stover removal, manure addition, and various cropping systems was assessed using 7610 observations from eight U.S. regions. Overall, including cover crops, reducing tillage depth and intensity increased SOC. The positive effects of cover crops were more noticeable in South Central, Northwest, and Midwest regions. Removing high rates (>65%) of crop residue decreased SOC in Midwestern and Southeastern soils. Depending on region, applying manure increased SOC by 21 to 41%, compared to non-manured soils. Diversified cropping systems (e.g., those utilizing small mixed vegetables, perennials, or dairy-based systems) had the highest topsoil SOC content, while more intensive annual row crops and large-scale single vegetable production systems, had the lowest. Among inherent factors, SOC increased as precipitation increased, but decreased as mean annual temperature increased. Texture influenced SOC, showing higher values in fine-texture than coarse-texture soils. Finally, this assessment confirmed that SOC can be a sensitive soil health indicator for evaluating conservation practices.

In February 2019, following the annual taxon ratification vote, the order Bunyavirales was amended by creation of two new families, four new subfamilies, 11 new genera and 77 new species, merging of two species, and deletion of one species. This article presents the updated taxonomy of the order Bunyavirales now accepted by the International Committee on Taxonomy of Viruses (ICTV).

Plant available water content or matric potential, particle size (texture), aeration, and penetration resistance are soil physical properties that influence soil structure, bulk density, aggregation, and several metabolic plant processes. Collectively they influence productivity and sustainability of agricultural practices, primarily through their impact on root development and growth. To simplify use of these parameters for assessing soil physical condition, the least limiting water range (LLWR) was developed as an integrated, comprehensive soil physical quality indicator. Our objective was to use the LLWR to evaluate corn (Zea mays L.) seedling root growth in soils with clay, sandy clay loam, or sand texture. Overall, root growth was affected by soil water content, aeration, and penetration resistance. Upper and lower LLWR boundaries were defined by a minimum air‐filled porosity and maximum soil penetration resistance for water contents between field capacity and permanent wilting point. Herein, the LLWR was calculated using a range of minimum air‐filled porosity (0.117–0.146 m3 m−3), field capacity (–2.2 to –5.3 kPa), and permanent wilting point or matric potential values (–461 to –6,516 kPa), and a restrictive penetration resistance value of 1.6 MPa as boundaries. The LLWR was sensitive to soil texture, decreasing from fine to coarse soils. The highest and lowest relative root growth measurements fell inside and outside the LLWR boundaries, proving that this index can successfully predict the optimum soil physical conditions for seedlings root growth and can therefore be used as a sensitive soil physical quality. Core Ideas Soil strength, aeration, and water content can interactively affect plant root growth. At water content close to saturation, root growth is limited by low oxygen availability. In dry soils, root growth is limited by low water availability and/or mechanical impedance. The least‐limiting water range index integrates soil water, aeration, and soil strength effects. Least‐limiting water range successfully predicted optimum soil physical conditions for root growth.

Maize (Zea mays L.) stover can be harvested for multiple uses or left in the field to sustain soil organic carbon (SOC), cycle essential plant nutrients, and protect soil health. This 13‐yr field study quantified effects of no (0 Mg ha–1 yr–1), low (1.0–1.4 Mg ha–1 yr–1), moderate (3.5–4.0 Mg ha–1 yr–1), or high rates (4.7–5.4 Mg ha–1 yr–1) of stover harvest from either continuous maize or maize–soybean [Glycine max (L.) Merr.] rotation on grain yield, plant nutrient concentrations, and multiple soil properties at two sites in Iowa. Stover harvest increased plant macro‐ and micro‐nutrient removal, but did not affect average grain yields of either crops. Soil inorganic carbon (IC), SOC, bulk density, pH, and cation exchange capacity (CEC) showed no significant differences due to stover harvest. Plant tissue and soil‐test nutrient concentration effects were also minor and site‐specific. Stover harvest significantly (p < .05) decreased exchangeable K and Ca concentrations by 8.3–23.8% and 0.3–22.5% but overall soil health indicator effects were minimal. Overall, based on crop yields, plant nutrient and soil‐test concentrations, soil health indicators, and carbon sequestration estimates, maize stover harvest can be sustainable provided: (a) grain yields consistently exceed 11 Mg ha–1, (b) stover removal does not exceed 40% of the aboveground biomass (i.e., 3.5–4.0 Mg ha–1 yr–1), and (c) plant nutrients (especially K) are closely monitored. Core Ideas Thirteen‐year maize stover harvest effects on crop yield, nutrients, and soil health were quantified. Stover harvest increased plant nutrient removal, but crop grain yields were not affected. There was no effect on soil organic carbon, soil inorganic carbon, pH, bulk density, or cation exchange capacity. If maize stover is going to be harvested, it is essential to closely monitor soil‐test K. With good soil management, crop residue harvest can be sustainable.