Sensitisation to peach allergen Pru p 7 is associated with severe clinical symptoms in a Spanish population.

BACKGROUND: Pru p 7 has been reported as a major allergen in peach allergy, associated with severe clinical symptoms and related to IgE sensitisation to cypress pollen. The main objective of this study was to prospectively evaluate the frequency of sensitisation to Pru p 7 and its clinical relevance amongst pediatric patients with peach allergy in Madrid (Spain). METHODS: Patients with a history of IgE-mediated symptoms (oral allergy syndrome, urticaria/angioedema, rhinoconjunctivitis/asthma, gastrointestinal symptoms, or anaphylaxis) occurring within 2 h after peach intake or contact were prospectively recruited from February 2020 to September 2021. Skin tests, sIgE by ImmunoCAP® (Pru p 1, Pru p 3, Pru p 4, Pru p 7, and Cupressus arizonica) and oral food challenge (OFC) were performed. The study was approved by the local Ethics Committee (PI-4513). RESULTS: Ninety-two patients were included (53.3% male); median age, 10 (IQR 6.0-14.75) years. Seventy-four (80.4%) patients had a reaction after ingestion of fresh peach (25.0% from peel, 23.9% from pulp, and 44.6% from both). Fifteen (16.3%) patients were sensitised to Pru p 7. Upper airway symptoms, anaphylaxis, and grade 2 reactions were statistically more frequent in patients sensitised to Pru p 7. Seven (7.9%) patients presented with exercise as a cofactor, four of whom were sensitised to Pru p 7 (p = .001). Patients sensitised to Pru p 7 were significantly more likely to have a positive OFC result than patients who were not (p = .008). Four patients who reacted to peach at OFC were sensitised to Pru p 7. Specific IgE against Cupressus arizonica pollen was positive in 25 (62.5%) patients. CONCLUSIONS: Pru p 7 sensitisation was observed in 16.3% of our population and was related to severe reactions, upper airway symptoms, anaphylaxis, and the presence of an eliciting cofactor.

Respiratory syncytial virus outbreak during the COVID-19 pandemic. How has it changed? / Epidemia de virus respiratorio sincitial durante la pandemia de COVID-19. ¿Cómo ha cambiado?

Introduction: The epidemiology of respiratory syncytial virus (RSV) infection has changed during the COVID-19 pandemic. Our objectives were to describe the RSV epidemic in 2021 and compare it with the previous years to the pandemic. Methods: Retrospective study performed in Madrid (Spain) in a large pediatric hospital comparing the epidemiology and clinical data of RSV admissions during 2021 and the two previous seasons. Results: 899 children were admitted for RSV infection during the study period. During 2021, the outbreak peaked in June and the last cases were identified in July. Previous seasons were detected in autumn-winter. The number of admissions in 2021 was significantly lower than in previous seasons. There were no differences between seasons regarding age, sex or disease severity. Conclusion: RSV hospitalizations during 2021 in Spain moved to summer with no cases in autumn and winter 2020–2021. Unlike other countries, clinical data were similar between epidemics.(AU)

Introducción: La epidemiología de la infección por virus respiratorio sincitial (VRS) ha cambiado durante la pandemia de COVID-19. Nuestros objetivos fueron describir la epidemia de VRS en 2021 y compararla con las de los años previos a la pandemia. Métodos: Estudio retrospectivo realizado en Madrid (España), en un hospital pediátrico terciario, que compara los datos epidemiológicos y clínicos de los ingresos por VRS durante 2021 y las 2 temporadas anteriores. Resultados: Ingresaron 899 niños por infección por VRS en el período de estudio. Durante 2021, el brote alcanzó su punto máximo en junio y los últimos casos se identificaron en julio. En las temporadas anteriores se detectaron en otoño-invierno. El número de hospitalizaciones en 2021 fue significativamente menor que en temporadas anteriores. No hubo diferencias entre temporadas en cuanto a edad, sexo o gravedad de la enfermedad. Conclusión: Las hospitalizaciones por VRS durante 2021 en España se trasladaron a verano, sin casos en otoño e invierno 2020-2021. A diferencia de otros países, los datos clínicos fueron similares entre epidemias.(AU)

Respiratory syncytial virus outbreak during the COVID-19 pandemic. How has it changed?

INTRODUCTION: The epidemiology of respiratory syncytial virus (RSV) infection has changed during the COVID-19 pandemic. Our objectives were to describe the RSV epidemic in 2021 and compare it with the previous years to the pandemic. METHODS: Retrospective study performed in Madrid (Spain) in a large pediatric hospital comparing the epidemiology and clinical data of RSV admissions during 2021 and the two previous seasons. RESULTS: 899 children were admitted for RSV infection during the study period. During 2021, the outbreak peaked in June and the last cases were identified in July. Previous seasons were detected in autumn-winter. The number of admissions in 2021 was significantly lower than in previous seasons. There were no differences between seasons regarding age, sex or disease severity. CONCLUSION: RSV hospitalizations during 2021 in Spain moved to summer with no cases in autumn and winter 2020-2021. Unlike other countries, clinical data were similar between epidemics.

Respiratory syncytial virus outbreak during the COVID-19 pandemic. How has it changed?

Introduction: The epidemiology of respiratory syncytial virus (RSV) infection has changed during the COVID-19 pandemic. Our objectives were to describe the RSV epidemic in 2021 and compare it with the previous years to the pandemic. Methods: Retrospective study performed in Madrid (Spain) in a large pediatric hospital comparing the epidemiology and clinical data of RSV admissions during 2021 and the two previous seasons. Results: 899 children were admitted for RSV infection during the study period. During 2021, the outbreak peaked in June and the last cases were identified in July. Previous seasons were detected in autumn-winter. The number of admissions in 2021 was significantly lower than in previous seasons. There were no differences between seasons regarding age, sex or disease severity. Conclusion: RSV hospitalizations during 2021 in Spain moved to summer with no cases in autumn and winter 2020-2021. Unlike other countries, clinical data were similar between epidemics.

Introducción: La epidemiología de la infección por virus respiratorio sincitial (VRS) ha cambiado durante la pandemia de COVID-19. Nuestros objetivos fueron describir la epidemia de VRS en 2021 y compararla con las de los años previos a la pandemia. Métodos: Estudio retrospectivo realizado en Madrid (España), en un hospital pediátrico terciario, que compara los datos epidemiológicos y clínicos de los ingresos por VRS durante 2021 y las 2 temporadas anteriores. Resultados: Ingresaron 899 niños por infección por VRS en el período de estudio. Durante 2021, el brote alcanzó su punto máximo en junio y los últimos casos se identificaron en julio. En las temporadas anteriores se detectaron en otoño-invierno. El número de hospitalizaciones en 2021 fue significativamente menor que en temporadas anteriores. No hubo diferencias entre temporadas en cuanto a edad, sexo o gravedad de la enfermedad. Conclusión: Las hospitalizaciones por VRS durante 2021 en España se trasladaron a verano, sin casos en otoño e invierno 2020-2021. A diferencia de otros países, los datos clínicos fueron similares entre epidemias.

First wave of the COVID-19 pandemic in Madrid: handling the unexpected in a tertiary hospital.

Introduction: The COVID-19 pandemic was declared on March 11th, 2020. By the end of January, the first imported cases were detected in Spain and, by March, the number of cases was growing exponentially, causing the implementation of a national lockdown. Madrid has been one of the most affected regions in terms of both cases and deaths. The aim of this study is to describe the epidemic curve and the epidemiological features and outcomes of COVID-19 patients hospitalized in La Paz University Hospital, a tertiary hospital located in Madrid. Methods: We included confirmed and probable COVID-19 cases admitted to our centre from February 26th to June 1st, 2020. We studied trends in hospitalization and ICU admissions using joinpoint regression analysis. Results: A sample of 2970 patients was obtained. Median age was 70 years old (IQR 55-82) and 54.8% of them were male. ICU admission rate was 8.7% with a mortality rate of 45.7%. Global CFR was 21.8%. Median time from symptom onset to death was 14 days (IQR 9-22). Conclusions: We detected an admissions peak on March 21st followed by a descending trend, matching national and regional data. Age and sex distribution were comparable to further series nationally and in western countries.

Metagenomic analysis reveals differences in the co-occurrence and abundance of viral species in SARS-CoV-2 patients with different severity of disease.

BACKGROUND: SARS-CoV-2 infections have a wide spectrum of clinical manifestations whose causes are not completely understood. Some human conditions predispose to severe outcome, like old age or the presence of comorbidities, but many other facets, including coinfections with other viruses, remain poorly characterized. METHODS: In this study, the eukaryotic fraction of the respiratory virome of 120 COVID-19 patients was characterized through whole metagenomic sequencing. RESULTS: Genetic material from respiratory viruses was detected in 25% of all samples, whereas human viruses other than SARS-CoV-2 were found in 80% of them. Samples from hospitalized and deceased patients presented a higher prevalence of different viruses when compared to ambulatory individuals. Small circular DNA viruses from the Anneloviridae (Torque teno midi virus 8, TTV-like mini virus 19 and 26) and Cycloviridae families (Human associated cyclovirus 10), Human betaherpesvirus 6, were found to be significantly more abundant in samples from deceased and hospitalized patients compared to samples from ambulatory individuals. Similarly, Rotavirus A, Measles morbillivirus and Alphapapilomavirus 10 were significantly more prevalent in deceased patients compared to hospitalized and ambulatory individuals. CONCLUSIONS: Results show the suitability of using metagenomics to characterize a broader peripheric virological landscape of the eukaryotic virome in SARS-CoV-2 infected patients with distinct disease outcomes. Identified prevalent viruses in hospitalized and deceased patients may prove important for the targeted exploration of coinfections that may impact prognosis.

Analysis of the genomic diversity of human papillomavirus type 31 in cervical samples reveals the presence of novel sublineages in clade C.

Human papillomavirus 31 (HPV31) is the fourth most frequent high-risk HPV (HR-HPV) genotype identified in cervical cancer (CC) worldwide and in Mexico. It has been recently classified into three lineages (A, B, and C) and eight sublineages (A1, A2, B1, B2, and C1 - C4). Here, we report the complete genomic sequences of 14 HPV31 isolates from cervical samples, and these were compared with viral genome sequences from the GenBank database for phylogenetic and genetic distance analysis. The formation of two novel clades within the C lineage (proposed as C5 and C6) was observed, with a well-defined variant-specific mutational pattern. The smallest average pairwise distance was 0.71% for lineages A and B, 0.94% for lineages A and C, and 1.01% for lineages B and C, and between sublineages, these values were 0.21% for clade A, 0.29% for clade B, and 0.24% for clade C. The isolates were grouped into the sublineages A1, B2, C1-C3, and C6. This is the first report on the whole-genome diversity of HPV31 in Mexico.

The use of readily available laboratory tests for the identification of the emerging yeast Candida auris in Mexico.

Identification of the emerging multidrug-resistant yeast Candida auris is challenging. Here, we describe the role of the Mexico national reference laboratory Instituto de Diagnóstico y Referencia Epidemiológicos Dr. Manuel Martínez Báez (InDRE) and the Mexican national laboratory network in the identification of C. auris. Reference identification of six suspected isolates was done based on phenotypic and molecular laboratory methods, including growth in special media, evaluation of isolate micromorphology, and species-specific PCR and pan-fungal PCR and sequencing. The four C. auris isolates identified were able to grow on modified Sabouraud agar with 10% NaCl incubated at 42 °C. With one exception, isolates of C. auris were spherical to ovoid yeast-like cells and blastoconidia, with no hyphae or pseudohyphae on cornmeal agar. C. auris isolates were resistant to fluconazole. Species-specific and pan-fungal PCR confirmed isolates as C. auris. Sequence analysis revealed the presence of two different C. auris clades in Mexico, clade I (South Asia) and clade IV (South America).

Psychological impact of the COVID-19 pandemic on primary care workers: a cross-sectional study.

BACKGROUND: The COVID-19 pandemic has had a major impact on the mental health of healthcare workers, yet studies in primary care workers are scarce. AIM: To investigate the prevalence of and associated factors for psychological distress in primary care workers during the first COVID-19 outbreak. DESIGN AND SETTING: This was a multicentre, cross-sectional, web-based survey conducted in primary healthcare workers in Spain, between May and September 2020. METHOD: Healthcare workers were invited to complete a survey to evaluate sociodemographic and work-related characteristics, COVID-19 infection status, exposure to patients with COVID-19, and resilience (using the Connor-Davidson Resilience Scale), in addition to being screened for common mental disorders (depression, anxiety disorders, post-traumatic stress disorder, panic attacks, and substance use disorder). Positive screening for any of these disorders was analysed globally using the term 'any current mental disorder'. RESULTS: A total of 2928 primary care professionals participated in the survey. Of them, 43.7% (95% confidence interval [CI] = 41.9 to 45.4) tested positive for a current mental disorder. Female sex (odds ratio [OR] 1.61, 95% CI = 1.25 to 2.06), having previous mental disorders (OR 2.58, 95% CI = 2.15 to 3.10), greater occupational exposure to patients with COVID-19 (OR 2.63, 95% CI = 1.98 to 3.51), having children or dependents (OR 1.35, 95% CI = 1.04 to 1.76 and OR 1.59, 95% CI = 1.20 to 2.11, respectively), or having an administrative job (OR 2.24, 95% CI = 1.66 to 3.03) were associated with a higher risk of any current mental disorder. Personal resilience was shown to be a protective factor. CONCLUSION: Almost half of primary care workers showed significant psychological distress. Strategies to support the mental health of primary care workers are necessary, including designing psychological support and resilience-building interventions based on risk factors identified.

Genomic Characterization of SARS-CoV-2 Isolated from Patients with Distinct Disease Outcomes in Mexico.

The coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has shown a wide spectrum of clinical manifestations ranging from asymptomatic infections to severe disease and death. Pre-existing medical conditions and age have been mainly linked to the development of severe disease; however, the potential association of viral genetic characteristics with different clinical conditions remains unclear. SARS-CoV-2 variants with increased transmissibility were detected early in the pandemics, and several variants with potential relevance for public health are currently circulating around the world. In this study, we characterized 57 complete SARS-CoV-2 genomes during the exponential growth phase of the early epidemiological curve in Mexico, in April 2020. Patients were categorized under distinct disease severity outcomes: mild disease or ambulatory care, severe disease or hospitalized, and deceased. To reduce bias related to risk factors, the patients were less than 60 years old and with no diagnosed comorbidities A trait-association phylogenomic approach was used to explore genotype-phenotype associations, represented by the co-occurrence of mutations, disease severity outcome categories, and clusters of Mexican sequences. Phylogenetic results revealed a higher genomic diversity compared to the initial viruses detected during the early stage of the local epidemic. We identified a total of 90 single nucleotide variants compared to the Wuhan-Hu-1 genome, including 54 nonsynonymous mutations. We did not find evidence for the co-occurrence of mutations associated with specific disease outcomes. Therefore, in the group of patients studied, disease severity was likely mainly driven by the host genetic background and other demographic factors. IMPORTANCE The genetic association of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) with different clinical conditions remains unclear and needs further investigation. In this study, we characterized 57 complete SARS-CoV-2 genomes from patients in Mexico with distinct disease severity outcomes: mild disease or ambulatory care, severe disease or hospitalized, and deceased. To reduce bias related to risk factors the patients were less than 60 years old and with no diagnosed comorbidities. We did not find evidence for the co-occurrence of mutations associated with specific disease outcomes. Therefore, in the group of patients studied, disease severity was likely mainly driven by the host genetic background and other demographic factors.

Draft genome sequence of first Vibrio diabolicus in Mexico strain InDRE-D1-M1, an emergent threat.

INTRODUCTION: The complete genome of the marine environmental bacterium Vibrio diabolicus isolated from raw shrimp in the city of Guadalajara in the state of Jalisco in Mexico is reported here. METHODOLOGY: Vibrio spp. it was isolated and identified using standard microbiological and molecular techniques. Whole genome sequencing was performed using the Miseq system (Illumina, USA). RESULTS: The Multi Locus Sequence Typing profile of the isolated Vibrio bacteria coincided only with 4 specific loci (atpA, gyrB, pyrH and recA) and with a total coverage of the species belonging to Vibrio spp. Analysis of the complete genome of the Vibrio isolate and other closely related species, using the genomic fingerprints of the Virtual Analysis Method for PHylogenomic fingerprint estimation (VAMPHyRe) software, revealed the clustering of this species among the clade Vibrio diabolicus. The antibiogram revealed that this strain of Vibrio diabolicus is resistant to ampicillin, which is consistent with the bioinformatic finding of the ß-lactamase enzyme that hydrolyzes carbenicillin class A. CONCLUSIONS: This study demonstrated that the environmental marine bacterium Vibrio diabolicus contains carrier genes associated with pathogenicity and ecological function, which could represent a threat to public health.

Genetic Analysis of SARS-CoV-2 Variants in Mexico during the First Year of the COVID-19 Pandemic.

During the first year of the SARS-CoV-2 pandemic in Mexico, more than two million people were infected. In this study, we analyzed full genome sequences from 27 February 2020 to 28 February 2021 to characterize the geographical and temporal distribution of SARS-CoV-2 lineages and identify the most common circulating lineages during this period. We defined six different geographical regions with particular dynamics of lineage circulation. The Northeast and Northwest regions were the ones that exhibited the highest lineage diversity, while the Central south and South/Southeast regions presented less diversity with predominance of a certain lineage. Additionally, by late February 2021, lineage B.1.1.519 represented more than 89% of all circulating lineages in the country.

Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico.

SARS-CoV-2 variants emerged in late 2020, and at least three variants of concern (B.1.1.7, B.1.351, and P1) have been reported by WHO. These variants have several substitutions in the spike protein that affect receptor binding; they exhibit increased transmissibility and may be associated with reduced vaccine effectiveness. In the present work, we report the identification of a potential variant of interest, harboring the mutations T478K, P681H, and T732A in the spike protein, within the newly named lineage B.1.1.519, that rapidly outcompeted the preexisting variants in Mexico and has been the dominant virus in the country during the first trimester of 2021.

Genomic Analysis of Early SARS-CoV-2 Variants Introduced in Mexico.

The coronavirus disease 2019 (COVID-19) pandemic has affected most countries in the world. Studying the evolution and transmission patterns in different countries is crucial to enabling implementation of effective strategies for disease control and prevention. In this work, we present the full genome sequence for 17 SARS-CoV-2 isolates corresponding to the earliest sampled cases in Mexico. Global and local phylogenomics, coupled with mutational analysis, consistently revealed that these viral sequences are distributed within 2 known lineages, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage A/G, containing mostly sequences from North America, and lineage B/S, containing mainly sequences from Europe. Based on the exposure history of the cases and on the phylogenomic analysis, we characterized 14 independent introduction events. Additionally, three cases with no travel history were identified. We found evidence that two of these cases represented local transmission cases occurring in Mexico during mid-March 2020, denoting the earliest events described for the country. Within this local transmission cluster, we also identified an H49Y amino acid change in the Spike protein. This mutation represents a homoplasy occurring independently through time and space and may function as a molecular marker to follow any further spread of these viral variants throughout the country. Our results provide a general picture of the SARS-CoV-2 variants introduced at the beginning of the outbreak in Mexico, setting the foundation for future surveillance efforts.IMPORTANCE Understanding the introduction, spread, and establishment of SARS-CoV-2 within distinct human populations as well as the evolution of the pandemics is crucial to implement effective control strategies. In this work, we report that the initial virus strains introduced in Mexico came from Europe and the United States and that the virus was circulating locally in the country as early as mid-March. We also found evidence for early local transmission of strains with a H49Y mutation in the Spike protein, which could be further used as a molecular marker to follow viral spread within the country and the region.

Full genome sequence of the first SARS-CoV-2 detected in Mexico.

SARS-CoV-2 was first detected in the city of Wuhan, Hubei Province, China. In this report, we describe the complete genome sequence of the first imported SARS-CoV-2, detected in a Mexican patient who had traveled to Bergamo, Italy. Phylogenetic analysis showed that this isolate belongs to subclade A2a (lineage G) and is closely related to isolates from Finland, Germany and Brazil, all of which were from patients with a history of travel to Italy. This is the first report of the complete genome sequence of this virus in Mexico.

Complete genome sequence of a coxsackievirus type A24 variant causing an outbreak of acute haemorrhagic conjunctivitis in southeastern Mexico in 2017.

Cases of acute haemorrhagic conjunctivitis (AHC) caused by a coxsackie virus A24 variant (CV-A24v) in Mexico have been reported since 1987; however, no molecular data on the causative strains have been available. Here, we report the identification of the etiological agent responsible for the most recent AHC outbreak in southeastern Mexico (at the end of 2017) as well as the complete genome sequences of seven isolates, using next-generation sequencing (NGS). Phylogenomic analysis of the CV-A24v sequences reported here showed similarity to contemporary strains causing AHC outbreaks in French Guiana and Uganda, forming a novel clade related to genotype IV. Moreover, a specific mutational pattern in the non-structural proteins was identified in the 2017 isolates. This is the first report of genetic characterization of CV-A24v isolates obtained in Mexico.

Full genome and phylogenetic analysis of hepatitis B virus genotype F in Mexican isolates.

Hepatitis B virus genotype F (HBV/F) is endemic in Central and South America with a minor proportion in Mexico and North America. HBV/F is divided into subgenotypes and subtypes with particular geographic circulation patterns. Here, we report the complete genome sequence and molecular characterization of HBV/F from three isolates. Phylogenetic analysis with all available HBV/F sequences showed that our sequences belonged to the F1b subtype and, in addition, the absence of the previously reported F1a subtype in Mexican isolates. Our findings suggest the circulation of HBV/F1b, the first phylogenomic study of HBV/F in Mexico.

Genotypic variability analysis of DENV-1 in Mexico reveals the presence of a novel Mexican lineage.

Here, we report for the first time the circulation of dengue virus type 1 (DENV-1) belonging to the lineage IV of genotype V (African American genotype) based on phylogenetic analysis of nucleotide sequences from 10 DENV-1-positive samples obtained in Mexico between 2012 and 2014. Our data revealed that the lineages III and IV of DENV-1 genotype V were found circulating during the same period, probably explaining the rise in the number of cases of severe dengue during that period.

Genome Sequence of a Rabies Virus Isolated from a Dog in Chiapas, Mexico, 2013.

Rabies virus (RABV), a member of the genus Lyssavirus, causes encephalitis that is almost always fatal following the onset of clinical signs. Here, we report the complete codifying sequence of an RABV isolated from a dog in Mexico. Molecular data showed that this strain belongs to the Chiapas lineage.

Nontuberculous mycobacteria in clinical samples with negative acid-fast bacilli.

BACKGROUND: There is a progressive increase in nontuberculous mycobacteria (NTM) in pulmonary and extrapulmonary infections that might cause confusion with the Mycobacterium tuberculosis complex. To determine the frequency of finding NTM in clinical samples from patients diagnosed with active tuberculosis, with negative acid-alcohol-resistant bacilli (acid-fast bacillus [AFB]) in a third-level specialty hospital's mycobacterial laboratory between January 2013 and December 2014. METHODS: This is a prospective, descriptive study where isolated strains of biological material were studied in Lowenstein-Jensen and BACTEC MGIT 960 cultures. RESULTS: Clinical samples of 120 patients were studied, with pulmonary samples of 99/120 (82%) and extrapulmonary samples of 21/120 (18%). We identified NTM in 37/120 samples (30.8%), of which 16 in pulmonary, 13 in genitourinary, 3 in bone marrow, and 5 in various specimens. Mycobacterium avium was isolated in 20 samples, Mycobacterium intracellulare in seven samples, and various other species of NTM in the other 10 samples. CONCLUSION: To establish adequate treatment, we point out the importance of identifying the presence of NTM in the clinical samples of active tuberculosis patients with negative AFB, as possibly becoming confused with M. tuberculosis and which is essential in deciding which treatment is the most adequate.