Checklist of monogeneans from Egyptian marine fishes, including some newly collected species.

A checklist of 113 monogenean species parasitizing marine fishes (60 species) from different localities in Egypt is provided. The list is supplemented by eight newly collected monogenean species from Red Sea fishes, off Safaga and El-Quseir. Five of these species are new Egyptian records: Calydiscoides euzeti Justine, 2007, Calydiscoides rohdei Oliver, 1984, Lethrinitrema austrosinense (Li & Chen, 2005) Sun, Li & Yang, 2014, Pseudohaliotrema sphincteroporus Yamaguti, 1953, and Pentatres sphyraenae Euzet & Razarihelisoa, 1959. Furthermore, Lutjanus ehrenbergii (Peters), Lethrinus nebulosus (Forsskål), Lethrinus mahsena (Forsskål), Siganus stellatus (Forsskål), and Sphyraena flavicauda Rüppell represent new host records. The current study also lists nine monogenean species from the Gulf of Aqaba for which the coordinates of the sampling localities were not clearly defined, but which could also belong to the Egyptian fauna as the gulf is part of the Red Sea basin. Dactylogyrus aegyptiacus Ramadan, 1983 is transferred to Ecnomotrema Kritsky, 2023 as E. aegyptiacum (Ramadan, 1983) n. comb. Entobdella aegyptiacus Amer, 1990, Polylabroides aegyptiacus Mahmoud & Shaheed 1998, Gotocotyla sigani Abdel Aal, Ghattas & Badawy, 2001, Neohexostoma epinepheli Abdel Aal, Ghattas & Badawy, 2001, Neothoracocotyle commersoni Abdel Aal, Ghattas & Badawy, 2001, Acleotrema maculatum Morsy, El Fayoumi & Fahmy, 2014, Diplectanum harid Morsy, El Fayoumi, Al Shahawy & Fahmy, 2014, and Pseudorhabdosynochus chlorostigma Morsy, El Fayoumi, Al Shahawy & Fahmy, 2014, are considered species inquirendae. Paranaella diplodae Bayoumy, Abd El-Hady & Hassanain, 2007 is considered incertae sedis. Allencotyla lutini El-Dien, 1995 and Lamellodiscus diplodicus Bayoumy, 2003 are regarded as nomina nuda.

Evolutionary morphology of haptoral anchors in monogenoids (Dactylogyridae) of marine catfish (Siluriformes: Ariidae) from the Atlantic coast of South America.

Exploring the phylogenetic signal of morphological traits using geometric morphometry represents a powerful approach to assess the relative weights of convergence and shared evolutionary history in shaping species' forms. We evaluated the phylogenetic signal in shape and size of ventral and dorsal haptoral anchors of 10 species of monogenoids (Hamatopeduncularia, Chauhanellus and Susanlimocotyle) occurring in marine catfish (Siluriformes: Ariidae) from the Atlantic coast of South America. The phylogenetic relationships among these species were mapped onto the morphospaces of shape and size of dorsal and ventral anchors. Two different tests (squared change-parsimony and Kmult) were applied to establish whether the spatial positions in the phylomorphospace were influenced by phylogenetic relationships. A significant phylogenetic signal was found between anchor form and parasite phylogeny. Allometric effects on anchor shape were non-significant. Phylogenetically distant species on the same host differed markedly in anchor morphology, suggesting little influence of host species on anchor form. A significantly higher level of shape variation among ventral anchors was also found, suggesting that the evolutionary forces shaping ventral anchor morphology may operate with differing intensities or exhibit distinct mechanisms compared to their dorsal counterparts. Our results suggest that phylogenetic relationships were a key driver of changes in shape (but not size) of anchors of monogenoids of South American ariids. However, it seems that the emergence of the digitiform haptor in Hamatopenducularia and in some species of Chauhanellus played an important role in the reduction in anchor size and may cause secondary losses of anchors in other groups of monogenoids.

The origin and speciation of orchids.

Orchids constitute one of the most spectacular radiations of flowering plants. However, their origin, spread across the globe, and hotspots of speciation remain uncertain due to the lack of an up-to-date phylogeographic analysis. We present a new Orchidaceae phylogeny based on combined high-throughput and Sanger sequencing data, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and c. 7% (1921) of the 29 524 accepted species, and use it to infer geographic range evolution, diversity, and speciation patterns by adding curated geographical distributions from the World Checklist of Vascular Plants. The orchids' most recent common ancestor is inferred to have lived in Late Cretaceous Laurasia. The modern range of Apostasioideae, which comprises two genera with 16 species from India to northern Australia, is interpreted as relictual, similar to that of numerous other groups that went extinct at higher latitudes following the global climate cooling during the Oligocene. Despite their ancient origin, modern orchid species diversity mainly originated over the last 5 Ma, with the highest speciation rates in Panama and Costa Rica. These results alter our understanding of the geographic origin of orchids, previously proposed as Australian, and pinpoint Central America as a region of recent, explosive speciation.

Characteristics of endemic human coronavirus infections during times of COVID-19 pandemic.

INTRODUCTION: After the implementation of mitigation strategies during the COVID-19 pandemic, the incidence of respiratory viruses, including human coronaviruses (HCoV), experienced a significant decrease. The aim of this study is to characterize the epidemiology and clinical aspects of HCoV infections in ambulatory adults during COVID-19 pandemic times. METHODS: descriptive, prospective, longitudinal study performed in a private hospital in La Plata, Buenos Aires, Argentina between November 2020 and October 2022; 458 outpatient adults with upper respiratory tract infections (URTI) were studied undergoing clinical and microbiological follow-up. RESULTS: 44 (9.6%) subjects were positive by multiplex PCR for HCoV. 14 of them for 229E (31.8%), 13 for OC43 (29.5%), 11 for HKU-1 (25.1%) and 6 for NL63 (13.6%). A repeated PCR was positive for the same HCoV in 19 (57%) of 33 patients on day 3-5. No hospitalizations or deaths were reported. DISCUSSION: Endemic HCoV caused a significant proportion of URTI among outpatient adults during COVID-19-related restrictions times. An alternating pattern of circulation between alfa-HCoV and beta-HCoV was observed.

Introducción: Tras la implementación de estrategias de mitigación durante la pandemia de COVID-19, la incidencia de virus respiratorios, incluyendo los coronavirus humanos (HCoV), disminuyó significativamente. El objetivo de este estudio es caracterizar la epidemiología y los aspectos clínicos de las infecciones por HCoV en adultos ambulatorios durante la pandemia de COVID-19. Métodos: estudio descriptivo, prospectivo, longitudinal, realizado en un hospital privado de La Plata, Buenos Aires, Argentina, entre noviembre de 2020 y octubre de 2022. Se estudiaron 458 pacientes adultos ambulatorios con infecciones del tracto respiratorio superior (ITRS) bajo seguimiento clínico y microbiológico. Resultados: 44 (9.6%) sujetos fueron positivos por PCR multiplex para HCoV. Se detectaron 14 229E (31.8%), 13 OC43 (29.5%), 11 HKU-1 (25.1%) y 6 NL63 (13.6%). Una segunda PCR fue positiva para el mismo HCoV en 19 (57 %) de 33 pacientes en los días 3-5. No se reportaron hospitalizaciones ni muertes. Discusión: los HCoV endémicos causaron una proporción significativa de ITRS entre pacientes adultos ambulatorios durante los tiempos de restricciones relacionados con COVID-19. Se observó un patrón alternante de circulación entre alfa-HCoV y beta-HCoV.

Characteristics of endemic human Coronavirus infections during times of COVID-19 pandemic / Características de las infecciones causadas por Corona virus humanos endémicos durante la pandemia COVID-19

Abstract Introduction : After the implementation of mitigation strategies during the COVID-19 pandemic, the incidence of respiratory viruses, including human coronaviruses (HCoV), experienced a significant decrease. The aim of this study is to characterize the epidemiology and clinical aspects of HCoV infections in ambulatory adults during COVID-19 pandemic times. Methods : descriptive, prospective, longitudinal study performed in a private hospital in La Plata, Buenos Aires, Argentina between November 2020 and October 2022; 458 outpatient adults with upper respiratory tract infections (URTI) were studied undergoing clinical and microbiological follow-up. Results : 44 (9.6%) subjects were positive by multiplex PCR for HCoV. 14 of them for 229E (31.8%), 13 for OC43 (29.5%), 11 for HKU-1 (25.1%) and 6 for NL63 (13.6%). A repeated PCR was positive for the same HCoV in 19 (57%) of 33 patients on day 3-5. No hospitalizations or deaths were reported. Discussion : Endemic HCoV caused a significant pro portion of URTI among outpatient adults during COVID- 19-related restrictions times. An alternating pattern of circulation between alfa-HCoV and beta-HCoV was observed.

Resumen Introducción : Tras la implementación de estrate gias de mitigación durante la pandemia de COVID-19, la incidencia de virus respiratorios, incluyendo los coronavirus humanos (HCoV), disminuyó significati vamente. El objetivo de este estudio es caracterizar la epidemiología y los aspectos clínicos de las infecciones por HCoV en adultos ambulatorios durante la pandemia de COVID-19. Métodos : estudio descriptivo, prospectivo, longitudi nal, realizado en un hospital privado de La Plata, Buenos Aires, Argentina, entre noviembre de 2020 y octubre de 2022. Se estudiaron 458 pacientes adultos ambulatorios con infecciones del tracto respiratorio superior (ITRS) bajo seguimiento clínico y microbiológico. Resultados : 44 (9.6%) sujetos fueron positivos por PCR multiplex para HCoV. Se detectaron 14 229E (31.8%), 13 OC43 (29.5%), 11 HKU-1 (25.1%) y 6 NL63 (13.6%). Una segunda PCR fue positiva para el mismo HCoV en 19 (57 %) de 33 pacientes en los días 3-5. No se reportaron hospitalizaciones ni muertes. Discusión : los HCoV endémicos causaron una pro porción significativa de ITRS entre pacientes adultos ambulatorios durante los tiempos de restricciones rela cionados con COVID-19. Se observó un patrón alternante de circulación entre alfa-HCoV y beta-HCoV.

Impacto de la movilidad poblacional en el comportamiento de virus respiratorios durante la pandemia COVID-19 / Impact of population mobility on the behavior of respira tory viruses during the COVID-19 pandemic

Resumen Introducción : Durante la pandemia de SARS-CoV-2 en Argentina se implementaron intervenciones no farma cológicas que produjeron cambios en la movilidad de la población. El objetivo de este estudio fue relacionar los porcentajes de positividad y la diversidad viral con la movi lidad poblacional durante parte del período de restricciones. Métodos : Estudio retrospectivo analítico realizado en el Instituto Médico Platense durante los años 2020 a 2022 que incluyó 458 pacientes a los que se les tomó un hisopado nasofaríngeo para la búsqueda de patóge nos respiratorios por PCR multiplex. Se analizaron los cambios en la movilidad de la población utilizando los "Informes de Movilidad Local", herramienta desarrollada por Google, cuyos datos son de público acceso. Resultados : La movilidad poblacional se correlacionó significativamente con el porcentaje de positividad de las muestras (p = <0.01; R2 = 0.89) y la diversidad viral (p = 0.04; R2 = 0.78). Discusión : Las intervenciones no farmacológicas destinadas a limitar la propagación del SARS-CoV-2 tuvieron efecto en la circulación de otros virus respi ratorios, hallándose mayor porcentaje de positividad y diversidad a medida que las mismas disminuyeron su grado de restricción.

Abstract Introduction : During the SARS-CoV-2 pandemic, Ar gentina population suffered from significant changes in population mobility due to non-pharmaceutical interventions. The aim of this study was to describe the impact of the mobility restrictions to the rates of positivity and diversity among different respiratory viruses. Methods : Retrospective analytical study per formed at Instituto Médico Platense in La Plata that included 458 patients with nasopharyngeal swab to search for respiratory pathogens by multiplex PCR. Changes in mobility were studied using "Community Mobility Reports", data set developed by Google and publicly available. Results : Community mobility had significant cor relation with the percentages of viral test positiv ity (p = < 0.01; R2=0.89) and viral diversity (p = 0.04; R2 = 0.78). Discussion : Non-pharmaceutical interventions estab lished to contain SARS-CoV-2 spread had a significant impact in the circulation patterns of other respiratory viruses.

[Impact of population mobility on the behavior of respiratory viruses during the COVID-19 pandemic]. / Impacto de la movilidad poblacional en el comportamiento de virus respiratorios durante la pandemia COVID-19.

INTRODUCTION: During the SARS-CoV-2 pandemic, Argentina population suffered from significant changes in population mobility due to non-pharmaceutical interventions. The aim of this study was to describe the impact of the mobility restrictions to the rates of positivity and diversity among different respiratory viruses. METHODS: Retrospective analytical study performed at Instituto Médico Platense in La Plata that included 458 patients with nasopharyngeal swab to search for respiratory pathogens by multiplex PCR. Changes in mobility were studied using "Community Mobility Reports", data set developed by Google and publicly available. RESULTS: Community mobility had significant correlation with the percentages of viral test positivity (p = < 0.01; R2=0.89) and viral diversity (p = 0.04; R2 = 0.78). DISCUSSION: Non-pharmaceutical interventions established to contain SARS-CoV-2 spread had a significant impact in the circulation patterns of other respiratory viruses.

Introducción: Durante la pandemia de SARS-CoV-2 en Argentina se implementaron intervenciones no farmacológicas que produjeron cambios en la movilidad de la población. El objetivo de este estudio fue relacionar los porcentajes de positividad y la diversidad viral con la movilidad poblacional durante parte del período de restricciones. Métodos: Estudio retrospectivo analítico realizado en el Instituto Médico Platense durante los años 2020 a 2022 que incluyó 458 pacientes a los que se les tomó un hisopado nasofaríngeo para la búsqueda de patógenos respiratorios por PCR multiplex. Se analizaron los cambios en la movilidad de la población utilizando los "Informes de Movilidad Local", herramienta desarrollada por Google, cuyos datos son de público acceso. Resultados: La movilidad poblacional se correlacionó significativamente con el porcentaje de positividad de las muestras (p = <0.01; R2 = 0.89) y la diversidad viral (p = 0.04; R2 = 0.78). Discusión: Las intervenciones no farmacológicas destinadas a limitar la propagación del SARS-CoV-2 tuvieron efecto en la circulación de otros virus respiratorios, hallándose mayor porcentaje de positividad y diversidad a medida que las mismas disminuyeron su grado de restricción.

Validation of a Reduced Set of High-Performance Triggers for Identifying Patient Safety Incidents with Harm in Primary Care: TriggerPrim Project.

OBJECTIVE: The aim of the study was to construct and validate a reduced set of high-performance triggers for identifying adverse events (AEs) via electronic medical records (EMRs) review in primary care (PC). METHODS: This was a cross-sectional descriptive study for validating a diagnostic test. The study included all 262 PC centers of Madrid region (Spain). Patients were older than 18 years who attended their PC center over the last quarter of 2018. The randomized sample was n = 1797. Main measurements were as follows: ( a ) presence of each of 19 specific computer-identified triggers in the EMR and ( b ) occurrence of an AE. To collect data, EMR review was conducted by 3 doctor-nurse teams. Triggers with statistically significant odds ratios for identifying AEs were selected for the final set after adjusting for age and sex using logistic regression. RESULTS: The sensitivity (SS) and specificity (SP) for the selected triggers were: ≥3 appointments in a week at the PC center (SS = 32.3% [95% confidence interval {CI}, 22.8%-41.8%]; SP = 92.8% [95% CI, 91.6%-94.0%]); hospital admission (SS = 19.4% [95% CI, 11.4%-27.4%]; SP = 97.2% [95% CI, 96.4%-98.0%]); hospital emergency department visit (SS = 31.2% [95% CI, 21.8%-40.6%]; SP = 90.8% [95% CI, 89.4%-92.2%]); major opioids prescription (SS = 2.2% [95% CI, 0.0%-5.2%]; SP = 99.8% [95% CI, 99.6%-100%]); and chronic benzodiazepine treatment in patients 75 years or older (SS = 14.0% [95% CI, 6.9%-21.1%]; SP = 95.5% [95% CI, 94.5%-96.5%]).The following values were obtained in the validation of this trigger set (the occurrence of at least one of these triggers in the EMR): SS = 60.2% (95% CI, 50.2%-70.1%), SP = 80.8% (95% CI, 78.8%-82.6%), positive predictive value = 14.6% (95% CI, 11.0%-18.1%), negative predictive value = 97.4% (95% CI, 96.5%-98.2%), positive likelihood ratio = 3.13 (95% CI, 2.3-4.2), and negative likelihood ratio = 0.49 (95% CI, 0.3-0.7). CONCLUSIONS: The set containing the 5 selected triggers almost triples the efficiency of EMR review in detecting AEs. This suggests that this set is easily implementable and of great utility in risk-management practice.

Is primary care a patient-safe setting? Prevalence, severity, nature, and causes of adverse events: numerous and mostly avoidable.

Knowing the frequency and characteristics of adverse events (AEs) is key to implementing actions that can prevent their occurrence. However, reporting systems are insufficient for this purpose and epidemiological studies are also required. Currently, the reviewing of clinical records is the gold standard method for knowing the frequency and characteristics of AEs. Research on AEs in a primary care setting has been limited and primarily focuses on specific types of events (medication errors, etc.) or patients. Large studies that search for any kind of AE in all patients are scarce. This study aimed to estimate the prevalence of AEs in the primary care setting and their characteristics. SETTING: all 262 primary health-care centres in the Madrid region (Spain) during the last quarter of 2018. DESIGN: cross-sectional descriptive study. Eligible population: subjects over 18 years of age who attended medical consultation over the last year (N = 2 743 719); a randomized sample stratified by age. MAIN OUTCOMES: age, sex, occurrence of an AE, number of consultations in the study period, avoidability, severity, place of occurrence, type of event, and contributory factors. The clinical records were reviewed by three teams, each composed of one doctor and one nurse trained and with expertise in patient safety. The SPSS software package (version 26) was used for the statistical analyses. The evaluators reviewed 1797 clinical records. The prevalence of AEs over the study period was 5.0% [95% confidence interval (CI): 4.0%‒6.0%], with higher values in women (5.7%; 95% CI: 4.6%‒6.8%;P = 0.10) and patients over 75 years of age (10.3%; 95% CI: 8.9%‒11.7%; P < 0.001). The overall occurrence per hundred consultations was estimated to be 1.58% (95% CI: 1.28%‒1.94%). Of the detected AEs, 71.3% (95% CI: 62.1%‒80.5%) were avoidable. Additionally, 60.6% (95% CI: 50.7%‒70.5%) were categorized as mild, 31.9% (95% CI: 22.4%‒41.4%) as moderate, and 7.4% (95% CI: 2.1%‒12.7%) as severe. Primary care was the occurrence setting in 76.6% (95% CI: 68.0%‒85.2%) of cases. The overall incidence of AEs related to medication was 53.2% (95% CI: 50.9%‒55.5%). The most frequent types of AEs were prescription errors (28.7%; 95% CI: 19.5%‒37.9%), followed by drug administration errors by patients (17.0%; 95% CI: 9.4%‒24.6%), and clinical assessment errors (11.7%; 95% CI: 5.2%‒18.2%). The most common contributory factors were those related to the patient (80.6%; 95% CI: 71.1%‒90.1%) and tasks (59.7%; 95% CI: 48.0%‒71.4%). A high prevalence of AEs (1 in 66 consultations) was observed, which was slightly higher than that reported in similar studies. About 3 out of 4 such events were considered to be avoidable and 1 out of 13 was severe. Prescription errors, drug administration errors by patients, and clinical assessment errors were the most frequent types of AEs. Graphical Abstract.

Rtapas: An R Package to Assess Cophylogenetic Signal between Two Evolutionary Histories.

Cophylogeny represents a framework to understand how ecological and evolutionary process influence lineage diversification. The recently developed algorithm Random Tanglegram Partitions provides a directly interpretable statistic to quantify the strength of cophylogenetic signal and incorporates phylogenetic uncertainty into its estimation, and maps onto a tanglegram the contribution to cophylogenetic signal of individual host-symbiont associations. We introduce Rtapas, an R package to perform Random Tanglegram Partitions. Rtapas applies a given global-fit method to random partial tanglegrams of a fixed size to identify the associations, terminals, and internal nodes that maximize phylogenetic congruence. This new package extends the original implementation with a new algorithm that examines the contribution to phylogenetic incongruence of each host-symbiont association and adds ParaFit, a method designed to test for topological congruence between two phylogenies, to the list of global-fit methods than can be applied. Rtapas facilitates and speeds up cophylogenetic analysis, as it can handle large phylogenies (100+ terminals) in affordable computational time as illustrated with two real-world examples. Rtapas can particularly cater for the need for causal inference in cophylogeny in two domains: (i) Analysis of complex and intricate host-symbiont evolutionary histories and (ii) assessment of topological (in)congruence between phylogenies produced with different DNA markers and specifically identify subsets of loci for phylogenetic analysis that are most likely to reflect gene-tree evolutionary histories. [Cophylogeny; cophylogenetic signal; gene tree incongruence; phylogenetic congruence; phylogenomics.].

Sensitivity of bipartite network analyses to incomplete sampling and taxonomic uncertainty.

Bipartite network analysis is a powerful tool to study the processes structuring interactions in ecological communities. In applying the method, it is assumed that the sampled interactions provide an accurate representation of the actual community. However, acquiring a representative sample may be difficult as not all species are equally abundant or easily identifiable. Two potential sampling issues can compromise the conclusions of bipartite network analyses: failure to capture the full range of interactions (sampling completeness) and use of a taxonomic level higher than species to evaluate the network (taxonomic resolution). We asked how commonly used descriptors of bipartite antagonistic communities (modularity, nestedness, connectance, and specialization [H2 ']) are affected by reduced host sampling completeness, parasite taxonomic resolution, and their crossed effect, as they are likely to co-occur. We used a quantitative niche model to generate weighted bipartite networks that resembled natural host-parasite communities. The descriptors were more sensitive to uncertainty in parasite taxonomic resolution than to host sampling completeness. When only 10% of parasite taxonomic resolution was retained, modularity and specialization decreased by ~76% and ~12%, respectively, and nestedness and connectance increased by ~114% and ~345% respectively. The loss of taxonomic resolution led to a wide range of possible communities, which made it difficult to predict its effects on a given network. With regards to host sampling completeness, standardized nestedness, connectance, and specialization were robust, whereas modularity was sensitive (~30% decrease). The combination of both sampling issues had an additive effect on modularity. In communities with low effort for both sampling issues (50%-10% of sampling completeness and taxonomic resolution), estimators of modularity, and nestedness could not be distinguished from those of random assemblages. Thus, the categorical description of communities with low sampling effort (e.g., if a community is modular or not) should be done with caution. We recommend evaluating both sampling completeness and taxonomic certainty when conducting bipartite network analyses. Care should also be exercised when using nonrobust descriptors (the four descriptors for parasite taxonomic resolution; modularity for host sampling completeness) when sampling issues are likely to affect a dataset.

Diversification processes between monogenoids (Dactylogyridae) and their marine catfish (Siluriformes: Ariidae) from the Atlantic coast of South America.

Due to their high specificity, monogenoids from fish provide an interesting model to study historical associations of hosts and parasites. High agreement between host and parasite phylogeny is often interpreted as evidence of cospeciation. However, cophylogenetic signal may also arise from other, either adaptive or non-adaptive, processes. We applied the recently developed Cophylospace Framework to better understand the evolutionary relationship between monogenoids and marine catfish from the Atlantic coast of South America. The associations between 12 marine catfish and 10 monogenoid species were assessed. Molecular data of host and parasite species were used for phylogenetic reconstruction. We used anchor morphology based on Procrustes coordinates to evaluate whether closely related hosts are associated with morphologically similar parasites. To assess the association between parasite phylogeny and host morphology, we produced a distance matrix based on morphological characters of catfishes. Agreement between phylogenies and between phylogeny and morphology was measured using Procrustes R2 computed with PACo. The parasite phylogeny obtained in this study represents the first complete phylogenetic hypothesis of monogenoids parasitizing ariids from South America. The Cophylospace analysis suggested that phylogenetic and morphological distance of monogenoids contributes similarly to explain the pattern of host­parasite associations, whereas parasite phylogeny is more strongly associated with the morphological traits of the hosts than with host phylogeny. This evidence suggests that cospeciation is not a major force accounting for diversification in the monogenoids studied. Rather host morphological traits seem to be a more important driver, which conforms with evidence from other host‒monogenoid systems.

[Prevention of infections related to health care in primary care. Lessons from the pandemic]. / Prevención de infecciones relacionadas con la asistencia sanitaria en atención primaria. Lecciones de la pandemia.

The health system failed to guarantee the safety of both professionals and citizens who came to the centers at the beginning of the pandemic. The lack of materials and guidelines for the prevention of infections caused in Spain the worst catastrophe in the history of patient safety and occupational health in healthcare. It also happened in other countries but Spain had the highest rates of infected health workers in the world. It was a largely avoidable event. We review what measures have been taken to prevent infections in primary care centers, such as hand hygiene, masks and personal protection material or the maintenance of social distance, among others. We update the recommendations and raise the perspectives in a situation that requires flexibility and adaptability to maintain quality and safe care.

[Primary care organization in pandemic times]. / Organización de la Atención Primaria en tiempos de pandemia.

The COVID-19 pandemic has forced the adoption of drastic changes in primary care, modifying the organization and work dynamics previously established. From one day to the next, professionals had to adapt to the new situation to be able to attend cases and contacts tracing, to avoid contagion and to maintain attention to other health problems. At the beginning of the pandemic, professionals had to establish new practices and care circuits in primary care in an improvised way, due to lack of updated guidelines, without adequate means of protection, evaluating their risks and benefits on the fly. We present the main organizational changes in the first level of care and describe, from the point of view of patient safety and the consequences for patients and professionals of the priority care for COVID-19. Finally, we consider how to incorporate the knowledge acquired during the pandemic, analyzing the advantages and disadvantages of the adopted measures to maintain as much as possible a safe, accessible and quality primary care.

Hundreds of nuclear and plastid loci yield novel insights into orchid relationships.

PREMISE: The inference of evolutionary relationships in the species-rich family Orchidaceae has hitherto relied heavily on plastid DNA sequences and limited taxon sampling. Previous studies have provided a robust plastid phylogenetic framework, which was used to classify orchids and investigate the drivers of orchid diversification. However, the extent to which phylogenetic inference based on the plastid genome is congruent with the nuclear genome has been only poorly assessed. METHODS: We inferred higher-level phylogenetic relationships of orchids based on likelihood and ASTRAL analyses of 294 low-copy nuclear genes sequenced using the Angiosperms353 universal probe set for 75 species (representing 69 genera, 16 tribes, 24 subtribes) and a concatenated analysis of 78 plastid genes for 264 species (117 genera, 18 tribes, 28 subtribes). We compared phylogenetic informativeness and support for the nuclear and plastid phylogenetic hypotheses. RESULTS: Phylogenetic inference using nuclear data sets provides well-supported orchid relationships that are highly congruent between analyses. Comparisons of nuclear gene trees and a plastid supermatrix tree showed that the trees are mostly congruent, but revealed instances of strongly supported phylogenetic incongruence in both shallow and deep time. The phylogenetic informativeness of individual Angiosperms353 genes is in general better than that of most plastid genes. CONCLUSIONS: Our study provides the first robust nuclear phylogenomic framework for Orchidaceae and an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely thoroughly documented: nuclear and plastid phylogenetic trees can contain strongly supported discordances, and this incongruence must be reconciled prior to interpretation in evolutionary studies, such as taxonomy, biogeography, and character evolution.

Next-generation cophylogeny: unravelling eco-evolutionary processes.

A fundamental question in evolutionary biology is how microevolutionary processes translate into species diversification. Cophylogeny provides an appropriate framework to address this for symbiotic associations, but historically has been primarily limited to unveiling patterns. We argue that it is essential to integrate advances from ecology and evolutionary biology into cophylogeny, to gain greater mechanistic insights and transform cophylogeny into a platform to advance understanding of interspecific interactions and diversification more widely. We discuss key directions, such as incorporating trait reconstruction and considering multiple scales of network organization, and highlight recent developments for implementation. A new quantitative framework is proposed to allow integration of relevant information, such as quantitative traits and assessment of the contribution of individual mechanisms to cophylogenetic patterns.

Assembly rules of helminth parasite communities in grey mullets: combining components of diversity.

Organisms aggregate in ecological communities. It has been widely debated whether these associations are explained by deterministic or, in contrast, random processes. The answer may vary, depending on the level of an organisational scale (α, ß and γ) and the facet of diversity considered: taxonomic, functional and phylogenetic. Diversity at the level of a sampling unit (i.e. host individual) is the α diversity; ß diversity represents the extent of dissimilarity in diversity among sampling units (within a level of an organisational scale, ß1; between levels of an organisational scale, ß2); and the total diversity of a system is γ diversity. Thus, the combination of facets and levels of a scale may be useful to disentangle the mechanisms driving the composition of a parasite community. Using helminth parasite taxonomic, functional, and a proxy for phylogenetic diversity of three species of grey mullets (Teleostei: Mugilidae) from the Mediterranean Sea, we show that random and deterministic processes of different nature explain the assemblage of parasite communities. The parasite community at a host individual (α) was invariably a random subset of the total diversity in the community for the three facets of diversity. At the ß1 level, taxonomic diversity was lower than expected by chance, whereas functional diversity and the proxy for phylogenetic diversity were random. At the ß2 level, diversity patterns suggested environmental filtering of the parasite assemblage: species, trait, and phylogenetic compositions of parasite communities seemed to depend primarily on the species of host, but also on the locality and season. Our study shows that parasite communities are not totally understood if any of the components (i.e. facets and levels) of diversity is neglected.

Host age predicts parasite occurrence, richness, and nested infracommunities in a pilot whale-helminth network.

Ecological data on marine mammal parasites represent an excellent opportunity to expand our understanding of host-parasite systems. In this study, we used a dataset of intestinal helminth parasites on 167 long-finned pilot whales Globicephala melas (Traill, 1809) from seven localities in the Faroe Islands to evaluate the extent to which the host's age and sex influence the occurrence, richness, and nested pattern of helminth parasites and the importance of individual hosts to the helminth community. We found positive effects of age on both the occurrence and richness of helminths. Older host individuals showed an ordered accumulation of parasites, as evidenced by the nested pattern in their composition. Males had a higher occurrence of parasites than females, but the richness of helminths did not differ between sexes. Our findings suggest that differences in host-parasite interactions in long-finned pilot whales result mainly from age-structured variations in biological and behavioral characteristics.

Random Tanglegram Partitions (Random TaPas): An Alexandrian Approach to the Cophylogenetic Gordian Knot.

Symbiosis is a key driver of evolutionary novelty and ecological diversity, but our understanding of how macroevolutionary processes originate extant symbiotic associations is still very incomplete. Cophylogenetic tools are used to assess the congruence between the phylogenies of two groups of organisms related by extant associations. If phylogenetic congruence is higher than expected by chance, we conclude that there is cophylogenetic signal in the system under study. However, how to quantify cophylogenetic signal is still an open issue. We present a novel approach, Random Tanglegram Partitions (Random TaPas) that applies a given global-fit method to random partial tanglegrams of a fixed size to identify the associations, terminals, and nodes that maximize phylogenetic congruence. By means of simulations, we show that the output value produced is inversely proportional to the number and proportion of cospeciation events employed to build simulated tanglegrams. In addition, with time-calibrated trees, Random TaPas can also distinguish cospeciation from pseudocospeciation. Random TaPas can handle large tanglegrams in affordable computational time and incorporates phylogenetic uncertainty in the analyses. We demonstrate its application with two real examples: passerine birds and their feather mites, and orchids and bee pollinators. In both systems, Random TaPas revealed low cophylogenetic signal, but mapping its variation onto the tanglegram pointed to two different coevolutionary processes. We suggest that the recursive partitioning of the tanglegram buffers the effect of phylogenetic nonindependence occurring in current global-fit methods and therefore Random TaPas is more reliable than regular global-fit methods to identify host-symbiont associations that contribute most to cophylogenetic signal. Random TaPas can be implemented in the public-domain statistical software R with scripts provided herein. A User's Guide is also available at GitHub.[Codiversification; coevolution; cophylogenetic signal; Symbiosis.].

Towards a Unified Functional Trait Framework for Parasites.

Trait-based research holds high potential to unveil ecological and evolutionary processes. Functional traits are fitness-related characteristics of individuals, which are measured at individual level and defined without using information external to the individual. Despite the usefulness of the functional approach to understand the performance of individuals in ecosystems, and parasitism being the most common life-history strategy on Earth, studies based on functional traits of parasites are still scarce. Since the choice of functional traits is a critical step for any study, we propose a core list of seven functional traits of metazoan parasites, related to three universal challenges faced by organisms (dispersal, establishment, and persistence), and give guidelines to define appropriate functional traits in future parasite community studies.