An observation-based, reduced-form model for oxidation in the remote marine troposphere.

The hydroxyl radical (OH) fuels atmospheric chemical cycling as the main sink for methane and a driver of the formation and loss of many air pollutants, but direct OH observations are sparse. We develop and evaluate an observation-based proxy for short-term, spatial variations in OH (ProxyOH) in the remote marine troposphere using comprehensive measurements from the NASA Atmospheric Tomography (ATom) airborne campaign. ProxyOH is a reduced form of the OH steady-state equation representing the dominant OH production and loss pathways in the remote marine troposphere, according to box model simulations of OH constrained with ATom observations. ProxyOH comprises only eight variables that are generally observed by routine ground- or satellite-based instruments. ProxyOH scales linearly with in situ [OH] spatial variations along the ATom flight tracks (median r2 = 0.90, interquartile range = 0.80 to 0.94 across 2-km altitude by 20° latitudinal regions). We deconstruct spatial variations in ProxyOH as a first-order approximation of the sensitivity of OH variations to individual terms. Two terms modulate within-region ProxyOH variations-water vapor (H2O) and, to a lesser extent, nitric oxide (NO). This implies that a limited set of observations could offer an avenue for observation-based mapping of OH spatial variations over much of the remote marine troposphere. Both H2O and NO are expected to change with climate, while NO also varies strongly with human activities. We also illustrate the utility of ProxyOH as a process-based approach for evaluating intermodel differences in remote marine tropospheric OH.

Large contribution of biomass burning emissions to ozone throughout the global remote troposphere.

Ozone is the third most important anthropogenic greenhouse gas after carbon dioxide and methane but has a larger uncertainty in its radiative forcing, in part because of uncertainty in the source characteristics of ozone precursors, nitrogen oxides, and volatile organic carbon that directly affect ozone formation chemistry. Tropospheric ozone also negatively affects human and ecosystem health. Biomass burning (BB) and urban emissions are significant but uncertain sources of ozone precursors. Here, we report global-scale, in situ airborne measurements of ozone and precursor source tracers from the NASA Atmospheric Tomography mission. Measurements from the remote troposphere showed that tropospheric ozone is regularly enhanced above background in polluted air masses in all regions of the globe. Ozone enhancements in air with high BB and urban emission tracers (2.1 to 23.8 ppbv [parts per billion by volume]) were generally similar to those in BB-influenced air (2.2 to 21.0 ppbv) but larger than those in urban-influenced air (-7.7 to 6.9 ppbv). Ozone attributed to BB was 2 to 10 times higher than that from urban sources in the Southern Hemisphere and the tropical Atlantic and roughly equal to that from urban sources in the Northern Hemisphere and the tropical Pacific. Three independent global chemical transport models systematically underpredict the observed influence of BB on tropospheric ozone. Potential reasons include uncertainties in modeled BB injection heights and emission inventories, export efficiency of BB emissions to the free troposphere, and chemical mechanisms of ozone production in smoke. Accurately accounting for intermittent but large and widespread BB emissions is required to understand the global tropospheric ozone burden.

Large uncertainties in global hydroxyl projections tied to fate of reactive nitrogen and carbon.

The hydroxyl radical (OH) sets the oxidative capacity of the atmosphere and, thus, profoundly affects the removal rate of pollutants and reactive greenhouse gases. While observationally derived constraints exist for global annual mean present-day OH abundances and interannual variability, OH estimates for past and future periods rely primarily on global atmospheric chemistry models. These models disagree ± 30% in mean OH and in its changes from the preindustrial to late 21st century, even when forced with identical anthropogenic emissions. A simple steady-state relationship that accounts for ozone photolysis frequencies, water vapor, and the ratio of reactive nitrogen to carbon emissions explains temporal variability within most models, but not intermodel differences. Here, we show that departure from the expected relationship reflects the treatment of reactive oxidized nitrogen species (NO y ) and the fraction of emitted carbon that reacts within each chemical mechanism, which remain poorly known due to a lack of observational data. Our findings imply a need for additional observational constraints on NO y partitioning and lifetime, especially in the remote free troposphere, as well as the fate of carbon-containing reaction intermediates to test models, thereby reducing uncertainties in projections of OH and, hence, lifetimes of pollutants and greenhouse gases.

US COVID-19 Shutdown Demonstrates Importance of Background NO2 in Inferring NOx Emissions From Satellite NO2 Observations.

Satellite nitrogen dioxide (NO2) measurements are used extensively to infer nitrogen oxide emissions and their trends, but interpretation can be complicated by background contributions to the NO2 column sensed from space. We use the step decrease of US anthropogenic emissions from the COVID-19 shutdown to compare the responses of NO2 concentrations observed at surface network sites and from satellites (Ozone Monitoring Instrument [OMI], Tropospheric Ozone Monitoring Instrument [TROPOMI]). After correcting for differences in meteorology, surface NO2 measurements for 2020 show decreases of 20% in March-April and 10% in May-August compared to 2019. The satellites show much weaker responses in March-June and no decrease in July-August, consistent with a large background contribution to the NO2 column. Inspection of the long-term OMI trend over remote US regions shows a rising summertime NO2 background from 2010 to 2019 potentially attributable to wildfires.

GISS-E2.1: Configurations and Climatology.

This paper describes the GISS-E2.1 contribution to the Coupled Model Intercomparison Project, Phase 6 (CMIP6). This model version differs from the predecessor model (GISS-E2) chiefly due to parameterization improvements to the atmospheric and ocean model components, while keeping atmospheric resolution the same. Model skill when compared to modern era climatologies is significantly higher than in previous versions. Additionally, updates in forcings have a material impact on the results. In particular, there have been specific improvements in representations of modes of variability (such as the Madden-Julian Oscillation and other modes in the Pacific) and significant improvements in the simulation of the climate of the Southern Oceans, including sea ice. The effective climate sensitivity to 2 × CO2 is slightly higher than previously at 2.7-3.1°C (depending on version) and is a result of lower CO2 radiative forcing and stronger positive feedbacks.

Isotopic constraint on the twentieth-century increase in tropospheric ozone.

Tropospheric ozone (O3) is a key component of air pollution and an important anthropogenic greenhouse gas1. During the twentieth century, the proliferation of the internal combustion engine, rapid industrialization and land-use change led to a global-scale increase in O3 concentrations2,3; however, the magnitude of this increase is uncertain. Atmospheric chemistry models typically predict4-7 an increase in the tropospheric O3 burden of between 25 and 50 per cent since 1900, whereas direct measurements made in the late nineteenth century indicate that surface O3 mixing ratios increased by up to 300 per cent8-10 over that time period. However, the accuracy and diagnostic power of these measurements remains controversial2. Here we use a record of the clumped-isotope composition of molecular oxygen (18O18O in O2) trapped in polar firn and ice from 1590 to 2016 AD, as well as atmospheric chemistry model simulations, to constrain changes in tropospheric O3 concentrations. We find that during the second half of the twentieth century, the proportion of 18O18O in O2 decreased by 0.03 ± 0.02 parts per thousand (95 per cent confidence interval) below its 1590-1958 AD mean, which implies that tropospheric O3 increased by less than 40 per cent during that time. These results corroborate model predictions of global-scale increases in surface pollution and vegetative stress caused by increasing anthropogenic emissions of O3 precursors4,5,11. We also estimate that the radiative forcing of tropospheric O3 since 1850 AD is probably less than +0.4 watts per square metre, consistent with results from recent climate modelling studies12.

Schizont transcriptome variation among clinical isolates and laboratory-adapted clones of the malaria parasite Plasmodium falciparum.

BACKGROUND: Malaria parasites are genetically polymorphic and phenotypically plastic. In studying transcriptome variation among parasites from different infections, it is challenging to overcome potentially confounding technical and biological variation between samples. We investigate variation in the major human parasite Plasmodium falciparum, generating RNA-seq data on multiple independent replicate sample preparations of merozoite-containing intra-erythrocytic schizonts from a panel of clinical isolates and from long-term laboratory-adapted clones, with a goal of robustly identifying differentially expressed genes. RESULTS: Analysis of biological sample replicates shows that increased numbers improve the true discovery rate of differentially expressed genes, and that six independent replicates of each parasite line allowed identification of most differences that could be detected with larger numbers. For highly expressed genes, focusing on the top quartile at schizont stages, there was more power to detect differences. Comparing cultured clinical isolates and laboratory-adapted clones, genes more highly expressed in the laboratory-adapted clones include those encoding an AP2 transcription factor (PF3D7_0420300), a ubiquitin-binding protein and two putative methyl transferases. In contrast, higher expression in clinical isolates was seen for the merozoite surface protein gene dblmsp2, proposed to be a marker of schizonts forming merozoites committed to sexual differentiation. Variable expression was extremely strongly, but not exclusively, associated with genes known to be targeted by Heterochromatin Protein 1. Clinical isolates show variable expression of several known merozoite invasion ligands, as well as other genes for which new RT-qPCR assays validate the quantitation and allow characterisation in samples with more limited material. Expression levels of these genes vary among schizont preparations of different clinical isolates in the first ex vivo cycle in patient erythrocytes, but mean levels are similar to those in continuously cultured clinical isolates. CONCLUSIONS: Analysis of multiple biological sample replicates greatly improves identification of genes variably expressed between different cultured parasite lines. Clinical isolates recently established in culture show differences from long-term adapted clones in transcript levels of particular genes, and are suitable for analyses requiring biological replicates to understand parasite phenotypes and variable expression likely to be relevant in nature.

Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development.

Parasites infect hosts in widely varying environments, encountering diverse challenges for adaptation. To identify malaria parasite genes under locally divergent selection across a large endemic region with a wide spectrum of transmission intensity, genome sequences were obtained from 284 clinical Plasmodium falciparum infections from four newly sampled locations in Senegal, The Gambia, Mali and Guinea. Combining these with previous data from seven other sites in West Africa enabled a multi-population analysis to identify discrete loci under varying local selection. A genome-wide scan showed the most exceptional geographical divergence to be at the early gametocyte gene locus gdv1 which is essential for parasite sexual development and transmission. We identified a major structural dimorphism with alternative 1.5 kb and 1.0 kb sequence deletions at different positions of the 3'-intergenic region, in tight linkage disequilibrium with the most highly differentiated single nucleotide polymorphism, one of the alleles being very frequent in Senegal and The Gambia but rare in the other locations. Long non-coding RNA transcripts were previously shown to include the entire antisense of the gdv1 coding sequence and the portion of the intergenic region with allelic deletions, suggesting adaptive regulation of parasite sexual development and transmission in response to local conditions.

Multiplication rate variation in the human malaria parasite Plasmodium falciparum.

It is important to understand intrinsic variation in asexual blood stage multiplication rates of the most virulent human malaria parasite, Plasmodium falciparum. Here, multiplication rates of long-term laboratory adapted parasite clones and new clinical isolates were measured, using a newly standardised assay of growth from low starting density in replicate parallel cultures with erythrocytes from multiple different donors, across multiple cycles. Multiplication rates of long-term established clones were between 7.6 and 10.5 fold per 48 hours, with clone Dd2 having a higher rate than others (clones 3D7, HB3 and D10). Parasite clone-specific growth was then analysed in co-culture assays with all possible heterologous pairwise combinations. This showed that co-culture of different parasites did not affect their replication rates, indicating that there were no suppressive interactions operating between parasites. Multiplication rates of eleven new clinical isolates were measured after a few weeks of culture, and showed a spectrum of replication rates between 2.3 and 6.0 fold per 48 hours, the entire range being lower than for the long-term laboratory adapted clones. Multiplication rate estimates remained stable over time for several isolates tested repeatedly up to three months after culture initiation, indicating considerable persistence of this important trait variation.

Filling the gap: Using fishers' knowledge to map the extent and intensity of fishing activity.

Knowledge of the extent and intensity of fishing activities is critical to inform management in relation to fishing impacts on marine conservation features. Such information can also provide insight into the potential socio-economic impacts of closures (or other restrictions) of fishing grounds that could occur through the future designation of Marine Conservation Zones (MCZs). We assessed the accuracy and validity of fishing effort data (spatial extent and relative effort) obtained from Fishers' Local Knowledge (LK) data compared to that derived from Vessel Monitoring System (VMS) data for a high-value shellfish fishery, the king scallop (Pecten maximus L.) dredge fishery in the English Channel. The spatial distribution of fishing effort from LK significantly correlated with VMS data and the correlation increased with increasing grid cell resolution. Using a larger grid cell size for data aggregation increases the estimation of the total area of seabed impacted by the fishery. In the absence of historical VMS data for vessels ≤15 m LOA (Length Overall), LK data for the inshore fleet provided important insights into the relative effort of the inshore (<6 NM from land) king scallop fishing fleet in the English Channel. The LK data provided a good representation of the spatial extent of inshore fishing activity, whereas representation of the offshore fishery was more precautionary in terms of defining total impact. Significantly, the data highlighted frequently fished areas of particular importance to the inshore fleet. In the absence of independent sources of geospatial information, the use of LK can inform the development of marine planning in relation to both sustainable fishing and conservation objectives, and has application in both developed and developing countries where VMS technology is not utilised in fisheries management.

Isotopic evidence of multiple controls on atmospheric oxidants over climate transitions.

The abundance of tropospheric oxidants, such as ozone (O3) and hydroxyl (OH) and peroxy radicals (HO2 + RO2), determines the lifetimes of reduced trace gases such as methane and the production of particulate matter important for climate and human health. The response of tropospheric oxidants to climate change is poorly constrained owing to large uncertainties in the degree to which processes that influence oxidants may change with climate and owing to a lack of palaeo-records with which to constrain levels of atmospheric oxidants during past climate transitions. At present, it is thought that temperature-dependent emissions of tropospheric O3 precursors and water vapour abundance determine the climate response of oxidants, resulting in lower tropospheric O3 in cold climates while HOx (= OH + HO2 + RO2) remains relatively buffered. Here we report observations of oxygen-17 excess of nitrate (a proxy for the relative abundance of atmospheric O3 and HOx) from a Greenland ice core over the most recent glacial-interglacial cycle and for two Dansgaard-Oeschger events. We find that tropospheric oxidants are sensitive to climate change with an increase in the O3/HOx ratio in cold climates, the opposite of current expectations. We hypothesize that the observed increase in O3/HOx in cold climates is driven by enhanced stratosphere-to-troposphere transport of O3, and that reactive halogen chemistry is also enhanced in cold climates. Reactive halogens influence the oxidative capacity of the troposphere directly as oxidants themselves and indirectly via their influence on O3 and HOx. The strength of stratosphere-to-troposphere transport is largely controlled by the Brewer-Dobson circulation, which may be enhanced in colder climates owing to a stronger meridional gradient of sea surface temperatures, with implications for the response of tropospheric oxidants and stratospheric thermal and mass balance. These two processes may represent important, yet relatively unexplored, climate feedback mechanisms during major climate transitions.

Evaluating a Space-Based Indicator of Surface Ozone-NO x -VOC Sensitivity Over Midlatitude Source Regions and Application to Decadal Trends.

Determining effective strategies for mitigating surface ozone (O3) pollution requires knowledge of the relative ambient concentrations of its precursors, NO x , and VOCs. The space-based tropospheric column ratio of formaldehyde to NO2 (FNR) has been used as an indicator to identify NO x -limited versus NO x -saturated O3 formation regimes. Quantitative use of this indicator ratio is subject to three major uncertainties: (1) the split between NO x -limited and NO x -saturated conditions may shift in space and time, (2) the ratio of the vertically integrated column may not represent the near-surface environment, and (3) satellite products contain errors. We use the GEOS-Chem global chemical transport model to evaluate the quantitative utility of FNR observed from the Ozone Monitoring Instrument over three northern midlatitude source regions. We find that FNR in the model surface layer is a robust predictor of the simulated near-surface O3 production regime. Extending this surface-based predictor to a column-based FNR requires accounting for differences in the HCHO and NO2 vertical profiles. We compare four combinations of two OMI HCHO and NO2 retrievals with modeled FNR. The spatial and temporal correlations between the modeled and satellite-derived FNR vary with the choice of NO2 product, while the mean offset depends on the choice of HCHO product. Space-based FNR indicates that the spring transition to NO x -limited regimes has shifted at least a month earlier over major cities (e.g., New York, London, and Seoul) between 2005 and 2015. This increase in NO x sensitivity implies that NO x emission controls will improve O3 air quality more now than it would have a decade ago.

Regional variation in bycatches associated with king scallop (Pecten maximus L.) dredge fisheries.

The biomass and composition of bycatch from king scallop dredge fisheries was assessed and compared between the English Channel, Cardigan Bay in Wales and around the Isle of Man. Bycatch composition varied significantly at localised, and broad, geographic scales. The mean proportion of scallop dredge bycatch biomass in the English Channel was 19% of total catch biomass. The proportion of bycatch was lower in Cardigan Bay (15%) but notably higher around the Isle of Man (53%). The proportion of individual bycatch species in dredge catches were low, therefore scallop dredging is unlikely to cause a substantial increase the population mortality of individual commercially fished species beyond that caused by the target fisheries for those species, or bycatches of other fisheries. The amount and mortality of organisms left on the seabed in the dredge path was not quantified in this study but should also be considered in management of the fishery. The discard rate of finfish and shellfish of commercial value from the king scallop dredge fishery in the English Channel was between 18 and 100%, with a higher rate of discarding occurring in the eastern English Channel compared to the west. The clear regional differences in bycatch composition and variation in the quantity of discards mean that an area by area approach to managing bycatch species is required in relation to the king scallop dredge fishery.

Quantification of the indirect effects of scallop dredge fisheries on a brown crab fishery.

This study aimed to describe the characteristics of the by-catch of Cancer pagurus in king scallop dredges in the Isle of Man, and to determine the damage, immediate mortality and estimated mortality during fishing seasons associated with scallop dredges. Based on dredge surveys, spatial and seasonal variations were observed, with the highest number of crabs found off the west coast of the Isle of Man in the autumn when berried females crabs were most frequently caught. In general, female crabs comprised 84% of the catch. The damage levels of crabs was high with 45% of crabs recorded as crushed or dead or with severe damage, whilst 24% of crabs exhibited missing limbs. Estimates of the potential mortality associated with scallop dredging led to a lower and upper estimate of possible crab by-catch mortality of 15t and 24t respectively which represented 3.0-4.8% of the commercial landings of brown crab for the Isle of Man. Heaviest mortalities of crabs occurred in autumn to the west of the Isle of Man when female berried crabs move offshore into deeper water. The use of a temporary and spatially restricted scallop dredging closure could provide a simple solution to mitigate additional crab mortality in the event that scallop dredging increased beyond current levels in the future.

Microsatellite genotyping and genome-wide single nucleotide polymorphism-based indices of Plasmodium falciparum diversity within clinical infections.

BACKGROUND: In regions where malaria is endemic, individuals are often infected with multiple distinct parasite genotypes, a situation that may impact on evolution of parasite virulence and drug resistance. Most approaches to studying genotypic diversity have involved analysis of a modest number of polymorphic loci, although whole genome sequencing enables a broader characterisation of samples. METHODS: PCR-based microsatellite typing of a panel of ten loci was performed on Plasmodium falciparum in 95 clinical isolates from a highly endemic area in the Republic of Guinea, to characterize within-isolate genetic diversity. Separately, single nucleotide polymorphism (SNP) data from genome-wide short-read sequences of the same samples were used to derive within-isolate fixation indices (F ws), an inverse measure of diversity within each isolate compared to overall local genetic diversity. The latter indices were compared with the microsatellite results, and also with indices derived by randomly sampling modest numbers of SNPs. RESULTS: As expected, the number of microsatellite loci with more than one allele in each isolate was highly significantly inversely correlated with the genome-wide F ws fixation index (r = -0.88, P < 0.001). However, the microsatellite analysis revealed that most isolates contained mixed genotypes, even those that had no detectable genome sequence heterogeneity. Random sampling of different numbers of SNPs showed that an F ws index derived from ten or more SNPs with minor allele frequencies of >10 % had high correlation (r > 0.90) with the index derived using all SNPs. CONCLUSIONS: Different types of data give highly correlated indices of within-infection diversity, although PCR-based analysis detects low-level minority genotypes not apparent in bulk sequence analysis. When whole-genome data are not obtainable, quantitative assay of ten or more SNPs can yield a reasonably accurate estimate of the within-infection fixation index (F ws).

Studying abroad: Exploring factors influencing nursing students' decisions to apply for clinical placements in international settings.

BACKGROUND: For over 15 years the College of Nursing at the University of Saskatchewan has facilitated study abroad clinical placements in a number of countries to enhance student learning. Nursing students often find their study abroad experience to be a defining moment in their educational program, and in their personal and professional growth. OBJECTIVES: The main objective of this research was to explore factors influencing nursing students' decisions to study abroad. DESIGN: A descriptive longitudinal design study was conducted using an online survey. SETTINGS: The Study Abroad Survey was distributed to all undergraduate and graduate nursing students, in all years of all programs, at all sites of the College of Nursing, University of Saskatchewan in Saskatchewan, Canada. PARTICIPANTS: A total of 1058 nursing students registered in the 2013-2014 academic year were surveyed. METHODS: The data were collected using an online survey administered by Campus Labs™ (2014). RESULTS: Students indicated that their interest in study abroad international experiences was high (84%), with many perceived benefits, but barriers to participation were also high for these students. Financial barriers topped the list (71%), followed by family responsibilities (30%) and job obligations (23%). CONCLUSION: The research highlights the factors behind student decision making related to international placements, and provides the basis for improvements to the College of Nursing's International Study Abroad Program (ISAP). Previous travel and international service learning, resulting in increased perceived value of a study abroad experience may prove to be the more significant factor influencing decision making, rather than financial barrier.

Genome-wide analysis of selection on the malaria parasite Plasmodium falciparum in West African populations of differing infection endemicity.

Locally varying selection on pathogens may be due to differences in drug pressure, host immunity, transmission opportunities between hosts, or the intensity of between-genotype competition within hosts. Highly recombining populations of the human malaria parasite Plasmodium falciparum throughout West Africa are closely related, as gene flow is relatively unrestricted in this endemic region, but markedly varying ecology and transmission intensity should cause distinct local selective pressures. Genome-wide analysis of sequence variation was undertaken on a sample of 100 P. falciparum clinical isolates from a highly endemic region of the Republic of Guinea where transmission occurs for most of each year and compared with data from 52 clinical isolates from a previously sampled population from The Gambia, where there is relatively limited seasonal malaria transmission. Paired-end short-read sequences were mapped against the 3D7 P. falciparum reference genome sequence, and data on 136,144 single nucleotide polymorphisms (SNPs) were obtained. Within-population analyses identifying loci showing evidence of recent positive directional selection and balancing selection confirm that antimalarial drugs and host immunity have been major selective agents. Many of the signatures of recent directional selection reflected by standardized integrated haplotype scores were population specific, including differences at drug resistance loci due to historically different antimalarial use between the countries. In contrast, both populations showed a similar set of loci likely to be under balancing selection as indicated by very high Tajima's D values, including a significant overrepresentation of genes expressed at the merozoite stage that invades erythrocytes and several previously validated targets of acquired immunity. Between-population FST analysis identified exceptional differentiation of allele frequencies at a small number of loci, most markedly for five SNPs covering a 15-kb region within and flanking the gdv1 gene that regulates the early stages of gametocyte development, which is likely related to the extreme differences in mosquito vector abundance and seasonality that determine the transmission opportunities for the sexual stage of the parasite.

Environmental drivers of small scale spatial variation in the reproductive schedule of a commercially important bivalve mollusc.

Understanding variability in reproductive schedules is essential to the management of recruitment limited fisheries such as that of Pecten maximus. Small scale (<5 km) variation in gonad condition and the onset of spawning of P. maximus were found among commercial scallop grounds in Isle of Man waters. Environmental and fishing drivers of these spatial patterns were investigated using a generalised additive model. Rate of change in temperature over the month prior to sampling was identified as the short term driver of gonad weight associated with the autumn spawning event. Long term drivers were average annual chlorophyll a concentration, scallop density, stratification index and shell size. The model explained 42.8% of deviance in gonad weight. Within site variation in gonad condition was high, indicating a "bet hedging" reproductive strategy which may decrease the chance of fertilisation especially at low densities. Therefore, areas protected from fishing, where scallop densities can increase may help buffer against reproductive failure. An increase in shell length from 100 mm to 110 mm equated to an increase of approximately 20% in gonad weight. Protecting scallops from fishing mortality until 110 mm (age four) compared to 100 mm (age three) may lead to an overall increase in lifetime reproductive output by a factor of 3.4.

Detection of capripoxvirus DNA using a novel loop-mediated isothermal amplification assay.

BACKGROUND: Sheep poxvirus (SPPV), Goat poxvirus (GTPV) and Lumpy skin disease virus (LSDV) are the most serious poxviruses of ruminants. They are double stranded DNA viruses of the genus Capripoxvirus, (subfamily Chordopoxvirinae) within the family Poxviridae. The aim of this study was to develop a Loop-mediated isothermal AMPlification (LAMP) assay for the detection of Capripoxvirus (CaPV) DNA. RESULTS: A single LAMP assay targeting a conserved region of the CaPV P32 gene was selected from 3 pilot LAMP assays and optimised by adding loop primers to accelerate the reaction time. This LAMP assay successfully detected DNA prepared from representative CaPV isolates (SPPV, GTPV and LSDV), and did not cross-react with DNA extracted from other mammalian poxviruses. The analytical sensitivity of the LAMP assay was determined to be at least 163 DNA copies/µl which is equivalent to the performance reported for diagnostic real-time PCR currently used for the detection of CaPV. LAMP reactions were monitored with an intercalating dye using a real-time PCR machine, or by agarose-gel electrophoresis. Furthermore, dual labelled LAMP products (generated using internal LAMP primers that were conjugated with either biotin or fluorescein) could be readily visualised using a lateral-flow device. CONCLUSIONS: This study provides a simple and rapid approach to detect CaPV DNA that may have utility for use in the field, or in non-specialised laboratories where expensive equipment is not available.

Development and evaluation of multiplex RT-LAMP assays for rapid and sensitive detection of foot-and-mouth disease virus.

This paper describes the evaluation of four novel real-time multiplex reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for rapid and sensitive diagnosis of foot-and-mouth disease (FMD). In order to overcome the genetic diversity of FMD viruses (FMDV), these multiplex RT-LAMP assay pairs were established by combining four newly designed primer sets with two primer sets that had been previously published. Using a real-time turbidimeter to detect amplification products and a panel of 300 samples collected throughout the world over a 78-year period, the performance of the multiplex RT-LAMP assays was compared with a FMDV-specific real-time RT-PCR assay. The most successful of the four multiplex RT-LAMP assays achieved a diagnostic sensitivity and specificity of 98.0% and 98.1%, and did not falsely detect FMDV in known negatives or samples containing swine vesicular disease virus, vesicular stomatitis virus or vesicular exanthema of swine virus. Furthermore, the analytical sensitivity of this multiplex RT-LAMP assay was at least as good as the individual component RT-LAMP tests. This is the first report of the development of a multiplex RT-LAMP to accommodate the high sequence variability encountered in RNA virus genomes and these results support the use of RT-LAMP as a cost-effective tool for simple diagnosis of FMD.