Utility of MF-non coding region for measles molecular surveillance during post-elimination phase, Spain, 2017-2020

Background: In countries entering the post-elimination phase for measles, the study of variants by sequencing of 450 nucleotides of the N gene (N450) does not always allow the tracing of chains of transmission. Indeed, between 2017 and 2020, most measles virus sequences belonged to either the MVs/Dublin.IRL/8.16 (B3-Dublin) or the MVs/Gir Somnath.IND/42.16 (D8-Gir Somnath) variants. We evaluated the additional use of a non-coding region (MF-NCR) as a tool to enhance resolution and infer case origin, chains of transmission and characterize outbreaks. Methods: We obtained 115 high-quality MF-NCR sequences from strains collected from Spanish patients infected with either B3-Dublin or D8-Gir Somnath variants between 2017 and 2020, performed epidemiological, phylogenetic and phylodynamic analyses and applied a mathematical model to determine relatedness among identified clades. Results: Applying this model allowed us to identify phylogenetic clades potentially derived from concomitant importations of the virus rather than single chain of transmission, inferred based on only N450 and epidemiology data. In a third outbreak, we found two related clades that corresponded to two chains of transmission. Discussion: Our results show the ability of the proposed method to improve identification of simultaneous importations in the same region which could trigger enhanced contact tracing. Moreover, the identification of further transmission chains indicates that the size of import-related outbreaks was smaller than previously found, supporting the interpretation that endemic measles transmission was absent in Spain between 2017 and 2020. We suggest considering the use of the MF-NCR region in conjunction with the study of N450 variants in future WHO recommendations for measles surveillance.This work was supported by the “Instituto de Salud Carlos III” (PI15CIII/00023, PI19ICIII/0041). AG was funded by CIBER de Epidemiología y Salud Pública (CIBERESP), ISCIII. CJ was funded by the ECDC/EUPHEM fellowship.S

Comparison of circulation patterns of mumps virus in the Netherlands and Spain (2015–2020)

BackgroundMumps is a viral infection mainly characterized by inflammation of the parotid glands. Despite of vaccination programs, infections among fully vaccinated populations were reported. The World Health Organization (WHO) recommends molecular surveillance of mumps based on sequencing of the small hydrophobic (SH) gene. The use of hypervariable non-coding regions (NCR) as additional molecular markers was proposed in multiple studies. Circulation of mumps virus (MuV) genotypes and variants in different European countries were described in the literature. From 2010 to 2020, mumps outbreaks caused by genotype G were described. However, this issue has not been analyzed from a wider geographical perspective. In the present study, sequence data from MuV detected in Spain and in The Netherlands during a period of 5  years (2015- March 2020) were analyzed to gain insights in the spatiotemporal spread of MuV at a larger geographical scale than in previous local studies.MethodsA total of 1,121 SH and 262 NCR between the Matrix and Fusion protein genes (MF-NCR) sequences from both countries were included in this study. Analysis of SH revealed 106 different haplotypes (set of identical sequences).ResultsOf them, seven showing extensive circulation were considered variants. All seven were detected in both countries in coincident temporal periods. A single MF-NCR haplotype was detected in 156 sequences (59.3% of total), and was shared by five of the seven SH variants, as well as three minor MF-NCR haplotypes. All SH variants and MF-NCR haplotypes shared by both countries were detected first in Spain.DiscussionOur results suggest a transmission way from south to north Europe. The higher incidence rate of mumps in Spain in spite of similar immunization coverage in both countries, could be associated with higher risk of MuV exportation. In conclusion, the present study provided novel insights into the circulation of MuV variants and haplotypes beyond the borders of single countries. In fact, the use of MF-NCR molecular tool allowed to reveal MuV transmission flows between The Netherlands and Spain. Similar studies including other (European) countries are needed to provide a broader view of the data presented in this study

Investigating Local Patterns of Mumps Virus Circulation, Using a Combination of Molecular Tools

Mumps is a vaccine-preventable disease caused by the mumps virus (MuV). However, MuV has re-emerged in many countries with high vaccine coverage. The World Health Organization (WHO) recommends molecular surveillance based on sequencing of the small hydrophobic (SH) gene. Additionally, the combined use of SH and non-coding regions (NCR) has been described in different studies, proving to be a useful complement marker to discriminate general patterns of circulation at national and international levels. The aim of this work is to test local-level usefulness of the combination of SH and MF-NCR sequencing in tracing hidden transmission clusters and chains during the last epidemic wave (2015-2020) in Spain. A database with 903 cases from the Autonomous Community of Madrid was generated by the integration of microbiological and epidemiological data. Of these, 453 representative cases were genotyped. Eight different SH variants and thirty-four SH haplotypes were detected. Local MuV circulation showed the same temporal pattern previously described at a national level. Only two of the thirteen previously identified outbreaks were caused by more than one variant/haplotype. Geographical representation of SH variants allowed the identification of several previously undetected clusters, which were analysed phylogenetically by the combination of SH and MF-NCR, in a total of 90 cases. MF-NCR was not able to improve the discrimination of geographical clusters based on SH sequencing, showing limited resolution for outbreak investigations.A.M.G. was funded by CIBER de Epidemiología y Salud Pública (CIBERESP), ISCIII. This work was supported by the “Instituto de Salud Carlos III” (PI15CIII/00023 and PI19ICIII/0041).S

Genomic Analysis of West Nile Virus Lineage 1 Detected in Mosquitoes during the 2020–2021 Outbreaks in Andalusia, Spain

Emerging infectious diseases are one of the most important global health challenges because of their impact on human and animal health. The vector-borne West Nile virus (WNV) is transmitted between birds by mosquitos, but it can also infect humans and horses causing disease. The local circulation of WNV in Spain has been known for decades, and since 2010, there have been regular outbreaks in horses, although only six cases were reported in humans until 2019. In 2020, Spain experienced a major outbreak with 77 human cases, which was followed by 6 additional cases in 2021, most of them in the Andalusian region (southern Spain). This study aimed to characterize the genomes of the WNV circulating in wild-trapped mosquitoes during 2020 and 2021 in Andalusia. We sequenced the WNV consensus genome from two mosquito pools and carried out the phylogenetic analyses. We also compared the obtained genomes with those sequenced from human samples obtained during the outbreak and the genomes obtained previously in Spain from birds (2007 and 2017), mosquitoes (2008) and horses (2010) to better understand the eco-epidemiology of WNV in Spain. As expected, the WNV genomes recovered from mosquito pools in 2020 were closely related to those recovered from humans of the same outbreak. In addition, the strain of WNV circulating in 2021 was highly related to the WNV strain that caused the 2020 outbreak, suggesting that WNV is overwintering in the area. Consequently, future outbreaks of the same strain may occur in in the future.This research was funded by the Research State Agency projects PGC2018-095704-B-I00 and PID2020-118921RJ-I00Instituto de Salud Carlos III Project PI19CIII_00014European Commission—NextGenerationEU (Regulation EU 2020/2094), through CSIC’s Global Health Platform (PTI Salud Global+)

Epidemiological and virological surveillance of mumps, Spain 2005-2022

Artículo[ES]Introducción: La parotiditis es una enfermedad frecuente, que sigue causando brotes incluso en poblaciones bien vacunadas. El objetivo de este estudio ha sido describir el patrón epidemiológico de la enfermedad y la calidad de la vigilancia de la parotiditis en España. Método: Fuentes: casos notificados a Red Nacional de Vigilancia Epidemiológica (RENAVE) entre 2005-2022 y resultados del programa de vigilancia microbiológica de parotiditis (PVMP) del Centro Nacional de Microbiología (CNM) entre 2016-2021. Se analizaron los casos por año, comunidad autónoma, sexo, edad, tipo de caso, vacunación e investigación de laboratorio. Se calcularon tasas anuales y de periodo. Del PVMP se analizaron muestras y determinaciones realizadas. Se analizó la cumplimentación de variables y la integración de la información de laboratorio en los casos notificados. Resultados: Se describen tres ondas epidémicas: 2005-2009, 2010-2014 y 2015-2020. La incidencia fue mínima en 2021 recuperándose ligeramente en 2022. La parotiditis afectó fundamentalmente a adolescentes y adultos jóvenes. El 32% de todos los casos estaban vacunados con dos dosis. Solo El 48% de los casos sospechosos investigados se confirmaron La saliva presentó la mayor tasa de positividad de PCR. La cumplimentación es adecuada para variables sociodemográficas, baja para la vacunación y muy baja para la gravedad. La información de laboratorio obtenida en el CNM en general no se notifica a RENAVE. Conclusiones: la parotiditis es una enfermedad frecuente que se debe monitorizar. Toda la información generada en actividades de vigilancia debe integrarse en un mismo sistema que sirva para la acción en salud pública. [EN] Introduction: mumps is a common disease, which continues to cause outbreaks even in well-vaccinat-ed vaccinated populations. The objective is to describe the surveillance of mumps in Spain. We present the analysis of cases reported to RENAVE (National epidemiological surveillance network) between 2005 and 2022 and the results of the mumps microbiological surveillance programme (PVMP) of the CNM (National Center of Microbiology) between 2016 and 2021. The completion of the variables and the integration of laboratory information in the reported cases are analysed.Method: Sources: cases reported to RENAVE and cases and samples from the CNM’s PVMP. Cases are analysed by year, autonomous community, sex and age, type of case, vaccination and laboratory data. Annual and period rates are calculated. Samples and determinations are analysed for PVMP.Results: Three epidemic waves are described: 2005-2009, 2010-2014 and 2015-2020. Incidence was minimal in 2021, recovering slightly in 2022. Mumps mainly affects adolescents and young adults. 32% of cases are vaccinated with two doses. Only 48% of investigated cases are confirmed. Saliva has the best PCR positivity rate. Completion is adequate for sociodemographic variables, low for vaccination and very low for severity. Information on laboratory studies performed in CNM is generally, not re-ported to RENAVE.Conclusions: Mumps is a common disease that should be monitored. All information generated in surveillance activities should be integrated into a single system devoted for public health action.N

CartoCell, a high-content pipeline for 3D image analysis, unveils cell morphology patterns in epithelia

Decades of research have not yet fully explained the mechanisms of epithelial self-organization and 3D packing. Single-cell analysis of large 3D epithelial libraries is crucial for understanding the assembly and function of whole tissues. Combining 3D epithelial imaging with advanced deep-learning segmentation methods is essential for enabling this high-content analysis. We introduce CartoCell, a deep-learning-based pipeline that uses small datasets to generate accurate labels for hundreds of whole 3D epithelial cysts. Our method detects the realistic morphology of epithelial cells and their contacts in the 3D structure of the tissue. CartoCell enables the quantification of geometric and packing features at the cellular level. Our single-cell cartography approach then maps the distribution of these features on 2D plots and 3D surface maps, revealing cell morphology patterns in epithelial cysts. Additionally, we show that CartoCell can be adapted to other types of epithelial tissues.This work is supported by the project PID2019-103900GB-I00 funded by MCIN/AEI /10.13039/501100011033 and Programa Operativo FEDER Andalucía 2014–2020 (US-1380953) to L.M.E. Work by L.M.E. and J.A.A.-S.R. has been funded by the Junta de Andalucía (Consejerı´a de economı´a, conocimiento, empresas y Universidad) grant PY18-631 co-funded by FEDER funds. A.T. has been funded by a ‘‘Contrato predoctoral PIF’’ from Universidad de Sevilla. C.G.-V. has been funded by a ‘‘Contrato predoctoral para la formacio´ n de doctores’’ BES-2017-082306. G.B. was supported by a Comunidad de Madrid contract (CAM) and by an FPI grant from MINECO (BES-2022-077789). F.M.-B. was supported by MICINN (PID2020-120367GB-I00) and Fundacio´ n Ramo´ n Areces (CIVP18A3904). P.G.-G. has been funded by Margarita Salas Fellowship – NextGenerationEU. C.H.F.-E. has been funded by Marı´a Zambrano Fellowship – NextGenerationEU. I.A.-C. would like to acknowledge that his work has been partially supported by the University of the Basque Country UPV/EHU grant GIU19/027 and by grant PID2021-126701OB-I00, funded by MCIN/AEI/10.13039/501100011033 and by ‘‘ERDF A way of making Europe." L.M.E. also wants to thank PIE-202120E047 – Conexiones-Life network for networking and input

CartoCell, a high-content pipeline for 3D image analysis, unveils cell morphology patterns in epithelia

Decades of research have not yet fully explained the mechanisms of epithelial self-organization and 3D packing. Single-cell analysis of large 3D epithelial libraries is crucial for understanding the assembly and function of whole tissues. Combining 3D epithelial imaging with advanced deep-learning segmentation methods is essential for enabling this high-content analysis. We introduce CartoCell, a deep-learning-based pipeline that uses small datasets to generate accurate labels for hundreds of whole 3D epithelial cysts. Our method detects the realistic morphology of epithelial cells and their contacts in the 3D structure of the tissue. CartoCell enables the quantification of geometric and packing features at the cellular level. Our single-cell cartography approach then maps the distribution of these features on 2D plots and 3D surface maps, revealing cell morphology patterns in epithelial cysts. Additionally, we show that CartoCell can be adapted to other types of epithelial tissues

Microplastics and Their Effect in Horticultural Crops: Food Safety and Plant Stress

The presence of micro and nanoplastics in the food chain constitutes an emergent multifactorial food safety and physiological stress problem, which must be approached with a strategic perspective since it affects public health when consuming products that have this pollutant, such as fish and crustaceans, fruits, and vegetables. In this review, the authors present the results by scientists from different disciplines who are dedicated to discovering their chemical constitution and origin, the contents of these microparticles in edible plants, the contamination of water-irrigated soils, the mechanisms that concentrate microplastics in these soils, methods to determine them, contamination of freshwater sources of cities, and the negative effect of nano and microplastics on various food products and their detrimental impact on the environment. Recent findings of plant uptake mechanisms complement this, but more research is needed

Modulation of GABAA receptors and of GABAergic synapses by the natural alkaloid gelsemine

The Gelsemium elegans plant preparations have shown beneficial activity against common diseases, including chronic pain and anxiety. Nevertheless, their clinical uses are limited by their toxicity. Gelsemine, one of the most abundant alkaloids in the Gelsemium plants, have replicated these therapeutic and toxic actions in experimental behavioral models. However, the molecular targets underlying these biological effects remain unclear. The behavioral activity profile of gelsemine suggests the involvement of GABAA receptors (GABAARs), which are the main biological targets of benzodiazepines (BDZs), a group of drugs with anxiolytic, hypnotic, and analgesic properties. Here, we aim to define the modulation of GABAARs by gelsemine, with a special focus on the subtypes involved in the BDZ actions. The gelsemine actions were determined by electrophysiological recordings of recombinant GABAARs expressed in HEK293 cells, and of native receptors in cortical neurons. Gelsemine inhibited the agonist-evoked currents of recombinant and native receptors. The functional inhibition was not associated with the BDZ binding site. We determined in addition that gelsemine diminished the frequency of GABAergic synaptic events, likely through a presynaptic modulation. Our findings establish gelsemine as a negative modulator of GABAARs and of GABAergic synaptic function. These pharmacological features discard direct anxiolytic or analgesic actions of gelsemine through GABAARs but support a role of GABAARs on the alkaloid induced toxicity. On the other hand, the presynaptic effects of the alkaloid provide an additional mechanism to explain their beneficial effects. Collectively, our results contribute novel information to improve understanding of gelsemine actions in the mammalian nervous system

Supplemental information CartoCell, a high-content pipeline for 3D image analysis, unveils cell morphology patterns in epithelia

Document S1. Figures S1–S6 Table S1. Extracted features from 353 curated cysts (104 cysts at 4 days, 103 cysts at 7 days, 116 cysts at 10 days), related to Figure 2 Table S2. Hyperparameter search space for our proposed 3D ResU-Net, related to Figure 1 Table S3. Performance evaluation of our pipeline (CartoCell) on images of different epithelial tissues and comparison with other state-of-the-art segmentation methods, using the evaluation metrics described in STAR Methods, related to Figure 1 Table S4. Relative error between features extracted using automatically segmented cysts and manually curated cysts (STAR Methods), related to Figure 1 Table S5. Cyst morphology and scutoid location statistics, related to Figure 2 Table S6. Comparison of morphology and packing features of normoxic and hypoxic MDCK cysts, related to Figure 2 Table S7. Classification of the developmental stages of Drosophila egg chambers employed, related to Figure 3 Document S2. Article plus supplemental informationPeer reviewe