Ecological fitting is the forerunner to diversification in a plant virus with broad host range.

The evolution and diversification of ssRNA plant viruses are often examined under reductionist conditions that ignore potentially much wider biotic interactions. The host range of a plant virus is central to interactions at higher levels that are organized by both fitness and ecological criteria. Here we employ a strategy to minimize sampling biases across distinct plant communities and combine it with a high-throughput sequencing approach to examine the influence of four habitats on the evolution of Watermelon mosaic virus (WMV). Local, regional and global levels of genetic diversity that correspond to spatial and temporal extents are used to infer haplotype relationships using network and phylogenetic approaches. We find that the incidence and genetic diversity of WMV were structured significantly by host species and habitat type. A single haplotype that infected 11 host species of a total of 24 showed that few constraints on host species use exist in the crop communities. When the evolution of WMV was examined at broader levels of organization, we found variation in genetic diversity and contrasting host use footprints that broadly corresponded to habitat effects. The findings demonstrated that nondeterministic ecological factors structured the genetic diversity of WMV. Habitat-driven constraints underlie host use preferences.

Clinical characteristics and outcomes among hospitalised COVID-19 patients across epidemic waves in Spain: An unCoVer analysis.

BACKGROUND AND OBJECTIVES: The COVID-19 pandemic had a significant impact in population health worldwide, and particularly in people with pre-existing chronic diseases. Early risk identification and stratification is essential to reduce the impact of future outbreaks of pandemic potential. This study aimed to comprehensively examine factors associated with COVID-19 mortality across the pandemic waves in Spain. METHODS: A retrospective study analyzed the characteristics of 13,974 patients admitted to Spanish hospitals due to SARS-CoV-2 infection from 2020-01-28 to 2022-12-31. The demographic and clinical features of patients during hospitalization on each pandemic waves were analyzed. MAIN FINDINGS: The findings highlight the heterogeneity of patient characteristics, comorbidities and outcomes, across the waves. The high prevalence of cardiometabolic diseases (53.9%) among COVID-19 patients emphasizes the importance of controlling these risk factors to prevent severe COVID-19 outcomes. CONCLUSIONS: In summary, the study associate hospital mortality with factors such as advanced age and comorbidities. The decline in mortality after the 4th wave indicates potential influences like vaccination, viral adaptation, or improved treatments. Notably, dementia and cancer metastases emerge as critical factors linked to higher mortality, highlighting the importance of addressing these conditions in COVID-19 management and preparing for future challenges.

Impact of the COVID-19 pandemic in mortality due to respiratory diseases: A comparative analysis of 2021 and 2020 vs 2019 in Spain.

INTRODUCTION: We previously reported an increase in respiratory mortality in 2020 in Spain after COVID-19. It is unclear if this rise is sustained in the longer-term. We aimed to determine whether respiratory mortality in 2021 in Spain returned to pre-pandemic levels. MATERIAL AND METHODS: In an observational, large study using official National Institute of Statistics data, we explored deaths due to respiratory diseases, that is, all causes of death by the standard WHO list of diseases of the respiratory system plus COVID-19, tuberculosis and lung cancer. Using the latest available official data of Spain, we analyzed changes in the mortality pattern in Spain from January 2019 to December 2021. We endorsed STROBE guidance for observational research. RESULTS: There were 98,714 deaths due to respiratory diseases in 2021 in Spain, corresponding to 21.9% of all deaths, becoming second in the ranking of causes of death. Respiratory diseases mortality in Spain has not returned to pre-pandemic levels in 2021, still with an increase of 30.3% (95% CI 30.2-30.4) compared to rates in 2019. All respiratory-specific causes of death decreased in 2021, except for lung cancer, that increased in women and decreased in men compared to 2019 (both p<0.05). In a multivariate analysis some established risk factors for respiratory diseases mortality were confirmed, such as male gender and older age; further, an association with reduced mortality in rural Spain was observed, still with a large geographical variability. CONCLUSIONS: The COVID-19 pandemic has had a lasting impact on deaths due to respiratory diseases and certain specific causes of death in 2021, and it has disproportionately affected certain regions.

ABO blood group as a determinant of COVID-19 and Long COVID: An observational, longitudinal, large study.

BACKGROUND: An association of ABO blood group and COVID-19 remains controversial. METHODS: Following STROBE guidance for observational research, we explored the distribution of ABO blood group in patients hospitalized for acute COVID-19 and in those with Long COVID. Contingency tables were made and risk factors were explored using crude and adjusted Mantle-Haentzel odds ratios (OR and 95% CI). RESULTS: Up to September 2022, there were a total of 5,832 acute COVID-19 hospitalizations in our hospital, corresponding to 5,503 individual patients, of whom blood group determination was available for 1,513 (27.5%). Their distribution by ABO was: 653 (43.2%) group 0, 690 (45.6%) A, 113 (7.5%) B, and 57 (3.8%) AB, which corresponds to the expected frequencies in the general population. In parallel, of 676 patients with Long COVID, blood group determination was available for 135 (20.0%). Their distribution was: 60 (44.4%) from group 0, 61 (45.2%) A, 9 (6.7%) B, and 5 (3.7%) AB. The distribution of the ABO system of Long COVID patients did not show significant differences with respect to that of the total group (p ≥ 0.843). In a multivariate analysis adjusting for age, sex, ethnicity, and severity of acute COVID-19 infection, subgroups A, AB, and B were not significantly associated with developing Long COVID with an OR of 1.015 [0.669-1.541], 1.327 [0.490-3.594] and 0.965 [0.453-2.058], respectively. The effect of the Rh+ factor was also not significant 1,423 [0.772-2,622] regarding Long COVID. CONCLUSIONS: No association of any ABO blood subgroup with COVID-19 or developing Long COVID was identified.

Trends of COPD in Spain: Changes Between Cross Sectional Surveys 1997, 2007 and 2017.

INTRODUCTION: We aim to describe the changes in prevalence and risk factors associated to chronic obstructive pulmonary disease (COPD) in Spain, comparing three population-based studies conducted in three timepoints. METHODS: We compared participants from IBERPOC conducted in 1997, EPISCAN conducted in 2007 and EPISCAN II in 2017. COPD was defined as a postbronchodilator FEV1/FVC (forced expiratory volume in 1s/forced vital capacity) ratio <0.70, according to GOLD criteria; subsequently, also as the FEV1/FVC below the lower limit of normal (LLN). RESULTS: COPD prevalence in the population between 40 and 69 years decreased from 21.6% (95% CI 20.7%-23.2%) in 1997 to 8.8% (95% CI 8.2%-9.5%) in 2017, a 59.2% decline (p<0.001). In 2007, the prevalence was 7.7% (95% CI 6.8%-8.7%) with an upward trend of 1.1 percentage points in 2017 (p=0.073). Overall COPD prevalence decreased in men and women, although a significant increase was observed in the last decade in females (p<0.05). Current smokers significantly increased in the last decades (25.4% in 1997, 29.1% in 2007 and 23.4% in 2017; p<0.001). Regrettably, COPD underdiagnosis was constantly high, 77.6% in 1997, 78.4% in 2007, and to 78.2% in 2017 (p=0.95), higher in younger ages (40-49 yrs and 50-59 yrs) and also higher in women than in men in all three studies (p<0.05). CONCLUSIONS: We report a significant reduction of 59.2% in the prevalence of COPD in Spain from 1997 to 2017 in subjects aged 40-69 years. Our study highlights the significant underdiagnosis of COPD, particularly sustained in women and younger populations.

Experience With Elexacaftor/Tezacaftor/Ivacaftor in Patients With Cystic Fibrosis and Advanced Disease.

INTRODUCTION: Elexacaftor/tezacaftor/ivacaftor (ETI) was used through the early access programme in Spain from December 2019 in cystic fibrosis (CF) patients with homozygous or heterozygous F508del mutation with advanced lung disease. METHODOLOGY: Multicentre, ambispective, observational, study in which 114 patients in follow-up in 16 national CF units were recruited. Clinical data, functional tests, nutritional parameters, quality of life questionnaires, microbiological isolates, number of exacerbations, antibiotic treatments and side effects were collected. The study also compared patients with homozygous and heterozygous F508del mutations. RESULTS: Of the 114 patients, 85 (74.6%) were heterozygous for F508del mutation, and the mean age was 32.2±9.96 years. After 30 months of treatment, lung function measured by FEV1% showed improvement from 37.5 to 48.6 (p<0.001), BMI increased from 20.5 to 22.3 (p<0.001), and all isolated microorganisms decreased significantly. The total number of exacerbations was also significantly reduced from 3.9 (±2.9) to 0.9 (±1.1) (p<0.001). All items in the CFQ-R questionnaire showed improvement, except for the digestive domain. Oxygen therapy use decreased by 40%, and only 20% of patients referred for lung transplantation remained on the active transplant list. ETI was well-tolerated, with only 4 patients discontinuing treatment due to hypertransaminemia. CONCLUSIONS: ETI decreases the number of exacerbations, increases lung function and nutritional parameters, decrease in all isolated microorganisms, for 30 months of treatment. There is an improvement in the CFQ-R questionnaire score except for the digestive item. It is a safe and well-tolerated drug.

The Emergence of COVID-19 as a Cause of Death in 2020 and its Effect on Mortality by Diseases of the Respiratory System in Spain: Trends and Their Determinants Compared to 2019.

OBJECTIVE: To analyze the causes of death by diseases of the respiratory system in Spain in 2020, with special interest in COVID-19; also its trends and determinants, and compare them with 2019. MATERIAL AND METHODS: Retrospective cohort study. The coding of all those causes of death by diseases of the respiratory system were regrouped. A descriptive analysis of all deaths and by gender, age, and the 17 Autonomous Communities (CC.AA.) was performed. Also, odds ratios of death in crude and multivariate analysis by logistic regression were estimated. RESULTS: In Spain in 2020, 60,358 deaths were attributed to "COVID-19 virus identified" and another 14,481 to "COVID-19 virus not identified (suspicious)". Regrouping the specific causes of death, in 2020 the diseases of the respiratory system caused a total of 139,880 deaths, which corresponds to 28.3% of all deaths in Spain. Compared to 2019, an increase of 68.5% was observed. By gender, deaths by diseases of the respiratory system were higher in men (32.0%) than in women (24.6%), although in specific causes the percentage was higher in women with suspected COVID-19, asthma, respiratory insufficiency and other diseases of the respiratory system. Finally, the variables associated with death from COVID-19 in the multivariate analysis were being male, increasing age (maximum at 80 years), completed studies up to secondary level, employed, and single or widowed marital status, although with a marked variation by CC.AA. CONCLUSIONS: In Spain in 2020, COVID-19 produced a large increase (68.5%) in deaths by diseases of the respiratory system compared to the previous year.

The Emergence of COVID-19 as a Cause of Death in 2020 and its Effect on Mortality by Diseases of the Respiratory System in Spain: Trends and Their Determinants Compared to 2019.

Objective: To analyze the causes of death by diseases of the respiratory system in Spain in 2020, with special interest in COVID-19; also its trends and determinants, and compare them with 2019. Material and methods: Retrospective cohort study. The coding of all those causes of death by diseases of the respiratory system were regrouped. A descriptive analysis of all deaths and by gender, age, and the 17 Autonomous Communities (CC.AA.) was performed. Also, odds ratios of death in crude and multivariate analysis by logistic regression were estimated. Results: In Spain in 2020, 60,358 deaths were attributed to "COVID-19 virus identified" and another 14,481 to "COVID-19 virus not identified (suspicious)". Regrouping the specific causes of death, in 2020 the diseases of the respiratory system caused a total of 139,880 deaths, which corresponds to 28.3% of all deaths in Spain. Compared to 2019, an increase of 68.5% was observed. By gender, deaths by diseases of the respiratory system were higher in men (32.0%) than in women (24.6%), although in specific causes the percentage was higher in women with suspected COVID-19, asthma, respiratory insufficiency and other diseases of the respiratory system. Finally, the variables associated with death from COVID-19 in the multivariate analysis were being male, increasing age (maximum at 80 years), completed studies up to secondary level, employed, and single or widowed marital status, although with a marked variation by CC.AA. Conclusions: In Spain in 2020, COVID-19 produced a large increase (68.5%) in deaths by diseases of the respiratory system compared to the previous year.

Objetivo: Analizar las causas de muerte por enfermedades del aparato respiratorio en España durante el año 2020, con especial interés en COVID-19; también sus tendencias y determinantes, y compararlas con el año 2019. Material y métodos: Estudio de cohortes retrospectivo. Se reagrupó la codificación de todas aquellas causas de muerte por enfermedades del aparato respiratorio. Se realizó un análisis descriptivo de todas las defunciones por sexo, edad en las 17 Comunidades Autónomas (CC. AA.). Además, se estimaron las odds ratios de muerte en análisis crudo y multivariado por regresión logística. Resultados: En España en el año 2020 se atribuyeron 60.358 muertes a «COVID-19 virus identificado¼ y otras 14.481 a «COVID-19 virus no identificado (sospechoso)¼. Reagrupando las causas específicas de muerte, en el año 2020 las enfermedades del aparato respiratorio provocaron un total de 139.880 muertes, lo que corresponde al 28,3% de todas las muertes en España. En comparación con el año 2019, se observó un aumento del 68,5%. Por género, las defunciones por enfermedades del aparato respiratorio fueron mayores en los varones (32,0%) que en las mujeres (24,6%), aunque en causas específicas el porcentaje fue mayor en mujeres en COVID-19 sospechosa, asma, insuficiencia respiratoria y otras enfermedades del aparato respiratorio. Finalmente, las variables asociadas a la muerte por COVID-19 en el análisis multivariante fueron el género masculino, el aumento de la edad (máximo a los 80 años), estudios completados hasta secundaria y el estado civil soltero o viudo, aunque con una marcada variación por CC. AA. Conclusiones: En España en el año 2020 la COVID-19 produjo un gran incremento (68,5%) de muertes por enfermedades del aparato respiratorio en comparación con el año anterior.

Prevalence of Chronic Obstructive Pulmonary Disease in an Urban Area. Changes in COPD Ten Years on.

Purpose: The prevalence of Chronic obstructive pulmonary disease (COPD) in Spain has been evaluated in the last ten years by EPISCAN in 2007 and EPISCAN II in 2017. This study describes changes in the prevalence of COPD in an urban region of Spain in the last 10 years, its risk factors and underdiagnosis. Patients and Methods: Participants from the Autonomous Community of Madrid (Spain) were selected from both studies up to the age of 80 years. A descriptive analysis of their sociodemographic and clinical characteristics, as well as by gender, was conducted. COPD was defined by a post-bronchodilator ratio <0.70. Results: The prevalence of COPD in the Autonomous Community of Madrid increased non-significantly from 11.0% (95% CI: 8.9-13.5%) to 12.1% (95% CI: 9.6-15.1, p=0.612). However, the prevalence by gender showed an increase in women (5.6% to 14.7%, p<0.001) and a decrease in men (17.6% to 9.8%, p=0.08). Underdiagnosis was reduced from 81.0% to 67.9% (p=0.006), although with greater underdiagnosis in women (86.4% in EPISCAN and 100% in EPISCAN II). Smoking was higher in men than in women in EPISCAN (31.2% vs 23.0%, p<0.01) but with no differences by gender in EPISCAN II (25.5% men vs 26.0% women, p=0.146). Age, smoking, low BMI, and a sedentary lifestyle were consistently associated with COPD. Conclusion: In 10 years in Madrid, there have been no changes in the global prevalence of COPD, but there have been important changes in women, with an increase in its prevalence, smoking habit and underdiagnosis.

Metagenomics show high spatiotemporal virus diversity and ecological compartmentalisation: Virus infections of melon, Cucumis melo, crops, and adjacent wild communities.

The emergence of viral diseases results from novel transmission dynamics between wild and crop plant communities. The bias of studies towards pathogenic viruses of crops has distracted from knowledge of non-antagonistic symbioses in wild plants. Here, we implemented a high-throughput approach to compare the viromes of melon (Cucumis melo) and wild plants of crop (Crop) and adjacent boundaries (Edge). Each of the 41-plant species examined was infected by at least one virus. The interactions of 104 virus operational taxonomic units (OTUs) with these hosts occurred largely within ecological compartments of either Crop or Edge, with Edge having traits of a reservoir community. Local scale patterns of infection were characterised by the positive correlation between plant and virus richness at each site, the tendency for increased specialist host use through seasons, and specialist host use by OTUs observed only in Crop, characterised local-scale patterns of infection. In this study of systematically sampled viromes of a crop and adjacent wild communities, most hosts showed no disease symptoms, suggesting non-antagonistic symbioses are common. The coexistence of viruses within species-rich ecological compartments of agro-systems might promote the evolution of a diversity of virus strategies for survival and transmission. These communities, including those suspected as reservoirs, are subject to sporadic changes in assemblages, and so too are the conditions that favour the emergence of disease.

Impact of the SARS-CoV-2 Virus Pandemic on Patients with Bronchiectasis: A Multicenter Study.

BACKGROUND: Infection by SARS-CoV-2 has unquestionably had an impact on the health of patients with chronic respiratory airway diseases, such as COPD and asthma, but little information is available about its impact on patients with bronchiectasis. The objective of the present study was to analyze the effect of the SARS-CoV-2 pandemic on the state of health, characteristics, and clinical severity (including the number and severity of exacerbations) of patients with non-cystic fibrosis bronchiectasis. METHODS: This study was multicenter, observational, and ambispective (with data collected before and during the SARS-CoV-2 pandemic), and included 150 patients diagnosed with non-cystic fibrosis bronchiectasis. RESULTS: A significant drop was observed in the number and severity of the exacerbations (57% in all exacerbations and 50% in severe exacerbations) in the E-FACED and BSI multidimensional scores, in the pandemic, compared with the pre-pandemic period. There was also a drop in the percentage of sputum samples positive for pathogenic microorganisms in general (from 58% to 44.7%) and, more specifically, Pseudomonas aeruginosa (from 23.3% to 13.3%) and Haemophilus influenzae (from 21.3% to 14%). CONCLUSIONS: During the SARS-CoV-2 period, a significant reduction was observed in the exacerbations, severity, and isolations of pathogenic microorganisms in patients with bronchiectasis.

Longitudinal Study of Therapeutic Adherence in a Cystic Fibrosis Unit: Identifying Potential Factors Associated with Medication Possession Ratio.

Cystic fibrosis (CF) is a genetic and multisystemic disease that requires a high therapeutic demand for its control. The aim of this study was to assess therapeutic adherence (TA) to different treatments to study possible clinical consequences and clinical factors influencing adherence. This is an ambispective observational study of 57 patients aged over 18 years with a diagnosis of CF. The assessment of TA was calculated using the Medication Possession Ratio (MPR) index. These data were related to exacerbations and the rate of decline in FEV1 percentage. Compliance was good for all CFTR modulators, azithromycin, aztreonam, and tobramycin in solution for inhalation. The patients with the best compliance were older; they had exacerbations and the greatest deterioration in lung function during this period. The three variables with the highest importance for the compliance of the generated Random Forest (RF) models were age, FEV1%, and use of Ivacaftor/Tezacaftor. This is one of the few studies to assess adherence to CFTR modulators and symptomatic treatment longitudinally. CF patient therapy is expensive, and the assessment of variables with the highest importance for a high MPR, helped by new Machine learning tools, can contribute to defining new efficient TA strategies with higher benefits.

Structuring of plant communities across agricultural landscape mosaics: the importance of connectivity and the scale of effect.

BACKGROUND: Plant communities of fragmented agricultural landscapes, are subject to patch isolation and scale-dependent effects. Variation in configuration, composition, and distance from one another affect biological processes of disturbance, productivity, and the movement ecology of species. However, connectivity and spatial structuring among these diverse communities are rarely considered together in the investigation of biological processes. Spatially optimised predictor variables that are based on informed measures of connectivity among communities, offer a solution to untangling multiple processes that drive biodiversity. RESULTS: To address the gap between theory and practice, a novel spatial optimisation method that incorporates hypotheses of community connectivity, was used to estimate the scale of effect of biotic and abiotic factors that distinguish plant communities. We tested: (1) whether different hypotheses of connectivity among sites was important to measuring diversity and environmental variation among plant communities; and (2) whether spatially optimised variables of species relative abundance and the abiotic environment among communities were consistent with diversity parameters in distinguishing four habitat types; namely Crop, Edge, Oak, and Wasteland. The global estimates of spatial autocorrelation, which did not consider environmental variation among sites, indicated significant positive autocorrelation under four hypotheses of landscape connectivity. The spatially optimised approach indicated significant positive and negative autocorrelation of species relative abundance at fine and broad scales, which depended on the measure of connectivity and environmental variation among sites. CONCLUSIONS: These findings showed that variation in community diversity parameters does not necessarily correspond to underlying spatial structuring of species relative abundance. The technique used to generate spatially-optimised predictors is extendible to incorporate multiple variables of interest along with a priori hypotheses of landscape connectivity. Spatially-optimised variables with appropriate definitions of connectivity might be better than diversity parameters in explaining functional differences among communities.

Experience With Elexacaftor/Tezacaftor/Ivacaftor in Patients With Cystic Fibrosis and Advanced Disease

Introduction: Elexacaftor/tezacaftor/ivacaftor (ETI) was used through the early access programme in Spain from December 2019 in cystic fibrosis (CF) patients with homozygous or heterozygous F508del mutation with advanced lung disease. Methodology: Multicentre, ambispective, observational, study in which 114 patients in follow-up in 16 national CF units were recruited. Clinical data, functional tests, nutritional parameters, quality of life questionnaires, microbiological isolates, number of exacerbations, antibiotic treatments and side effects were collected. The study also compared patients with homozygous and heterozygous F508del mutations. Results: Of the 114 patients, 85 (74.6%) were heterozygous for F508del mutation, and the mean age was 32.2±9.96 years. After 30 months of treatment, lung function measured by FEV1% showed improvement from 37.5 to 48.6 (p<0.001), BMI increased from 20.5 to 22.3 (p<0.001), and all isolated microorganisms decreased significantly. The total number of exacerbations was also significantly reduced from 3.9 (±2.9) to 0.9 (±1.1) (p<0.001). All items in the CFQ-R questionnaire showed improvement, except for the digestive domain. Oxygen therapy use decreased by 40%, and only 20% of patients referred for lung transplantation remained on the active transplant list. ETI was well-tolerated, with only 4 patients discontinuing treatment due to hypertransaminemia. Conclusions: ETI decreases the number of exacerbations, increases lung function and nutritional parameters, decrease in all isolated microorganisms, for 30 months of treatment. There is an improvement in the CFQ-R questionnaire score except for the digestive item. It is a safe and well-tolerated drug. (AU)

Trends of COPD in Spain: Changes Between Cross Sectional Surveys 1997, 2007 and 2017

Introduction: We aim to describe the changes in prevalence and risk factors associated to chronic obstructive pulmonary disease (COPD) in Spain, comparing three population-based studies conducted in three timepoints. Methods: We compared participants from IBERPOC conducted in 1997, EPISCAN conducted in 2007 and EPISCAN II in 2017. COPD was defined as a postbronchodilator FEV1/FVC (forced expiratory volume in 1s/forced vital capacity) ratio <0.70, according to GOLD criteria; subsequently, also as the FEV1/FVC below the lower limit of normal (LLN). Results: COPD prevalence in the population between 40 and 69 years decreased from 21.6% (95% CI 20.7%–23.2%) in 1997 to 8.8% (95% CI 8.2%–9.5%) in 2017, a 59.2% decline (p<0.001). In 2007, the prevalence was 7.7% (95% CI 6.8%–8.7%) with an upward trend of 1.1 percentage points in 2017 (p=0.073). Overall COPD prevalence decreased in men and women, although a significant increase was observed in the last decade in females (p<0.05). Current smokers significantly increased in the last decades (25.4% in 1997, 29.1% in 2007 and 23.4% in 2017; p<0.001). Regrettably, COPD underdiagnosis was constantly high, 77.6% in 1997, 78.4% in 2007, and to 78.2% in 2017 (p=0.95), higher in younger ages (40–49 yrs and 50–59 yrs) and also higher in women than in men in all three studies (p<0.05). Conclusions: We report a significant reduction of 59.2% in the prevalence of COPD in Spain from 1997 to 2017 in subjects aged 40–69 years. Our study highlights the significant underdiagnosis of COPD, particularly sustained in women and younger populations. (AU)

Real Life With Tezacaftor and Ivacaftor in Adult Patients With Cystic Fibrosis: Spanish Multicenter Study

No disponible