Comparison of Nanopore and Synthesis-Based Next-Generation Sequencing Platforms for SARS-CoV-2 Variant Monitoring in Wastewater.

Shortly after the beginning of the SARS-CoV-2 pandemic, many countries implemented sewage sentinel systems to monitor the circulation of the virus in the population. A fundamental part of these surveillance programs is the variant tracking through sequencing approaches to monitor and identify new variants or mutations that may be of importance. Two of the main sequencing platforms are Illumina and Oxford Nanopore Technologies. Here, we compare the performance of MiSeq (Illumina) and MinION (Oxford Nanopore Technologies), as well as two different data processing pipelines, to determine the effect they may have on the results. MiSeq showed higher sequencing coverage, lower error rate, and better capacity to detect and accurately estimate variant abundances than MinION R9.4.1 flow cell data. The use of different variant callers (LoFreq and iVar) and approaches to calculate the variant proportions had a remarkable impact on the results generated from wastewater samples. Freyja, coupled with iVar, may be more sensitive and accurate than LoFreq, especially with MinION data, but it comes at the cost of having a higher error rate. The analysis of MinION R10.4.1 flow cell data using Freyja combined with iVar narrows the gap with MiSeq performance in terms of read quality, accuracy, sensitivity, and number of detected mutations. Although MiSeq should still be considered as the standard method for SARS-CoV-2 variant tracking, MinION's versatility and rapid turnaround time may represent a clear advantage during the ongoing pandemic.

Dynamic and Seasonal Distribution of Enteric Viruses in Surface and Well Water in Riyadh (Saudi Arabia).

Enteric viruses are the major cause of gastroenteritis and enteric hepatitis worldwide, but in some areas like Saudi Arabia, little is known about their presence in water sources. The available information from clinical samples is not enough to figure out their actual prevalence. The aim of this study was to gather information for the first time in Saudi Arabia on the presence of the Norovirus (NoV) genogroup GI and GII, hepatitis A virus (HAV), and hepatitis E virus (HEV) in water. For this purpose, thirteen monthly samples were collected from Lake Wadi Hanifa and surrounding wells from December 2014 to November 2015. Viruses were detected and quantified using real-time RT-qPCR. Despite HEV findings being anecdotic, our results highlight interesting behaviors of the other viruses. There was a higher prevalence of noroviruses in Wadi Hanifa samples than in well water samples (46.43% vs. 12.5% of NoV GI; 66.67% vs. 8.33% of NoV GII). On the contrary, similar levels of HAV positivity were observed (40.48% in surface water vs. 43.06% in well water). Also, a strong influence of flooding events on HAV and NoV GI occurrence was observed in both surface and well water samples, with NoV GII apparently not affected.

El reto educativo de El buen quehacer del médico / The educational challenge of The Good Physician housework

No disponible

El médico del futuro / Physician for the future

No disponible

No disponible

Resultados de la cirugía tiroidea limitada a un lóbulo en régimen ambulatorio. Estudio preliminar / Results of ambulatory unilateral thyroid surgery. A preliminary study

Introducción. La cirugía del tiroides en régimen ambulatorio ha demostrado ser eficaz, pero su implementación no ha sido la esperada. La probabilidad de hemorragia en las primeras 24 h del postoperatorio y el desarrollo posterior de hematoma sofocante planean sobre los cirujanos endocrinos y promueven la desconfianza en esta indicación. El advenimiento de nuevas tecnologías aplicadas a la cirugía tiroidea y la especialización del cirujano endocrino pueden revertir esta situación de transición que vive la cirugía tiroidea en régimen ambulatorio. Presentamos nuestros resultados preliminares en cirugía tiroidea limitada a un lóbulo en régimen ambulatorio. Métodos. Los pacientes han sido intervenidos en el período febrero de 2005-julio de 2006 por un único cirujano dedicado a la cirugía endocrina desde el año 2000, que aplicó a la mayoría los criterios de cirugía mínimamente invasiva (incisión < 3 cm). Resultados. El 79,1% (53/67) de los pacientes sometidos a intervenciones de cirugía tiroidea limitada han sido considerados candidatos a cirugía mayor ambulatoria (CMA). El índice de sustitución (IS) y el índice de ingresos no deseados (IND) han sido del 90,5 (48/53) y el 9,4% (5/53), respectivamente; 2 pacientes han presentado complicaciones menores (3,8%) y ninguno presentó hemorragia ni reingresó en el postoperatorio inmediato. Conclusiones. Estos resultados, aunque preliminares, deberían por lo menos replantear la posibilidad de realizar la tiroidectomía en régimen ambulatorio e incluir este proceso en la rutina de la CMA de algunos hospitales. Todo ello, eso sí, realizado por cirujanos con un mínimo de experiencia acumulada en cirugía tiroidea y con un número de casos de cirugía tiroidea asegurados a lo largo del año (AU)

Introduction. Ambulatory thyroid surgery has been demonstrated to be effective but this technique has been less widely implemented than expected. Because of the probability of hemorrhage in the first 24 hours after the intervention and the subsequent development of a suffocating hematoma, endocrine surgeons are reluctant to perform this procedure. The advent of new technologies applied to thyroid surgery and specialization of thyroid surgeons could reverse this impasse in ambulatory thyroid surgery. We present our preliminary results of ambulatory unilateral thyroid surgery. Methods. The patients underwent surgery between February 2005 and June 2006 carried out by the same surgeon performing endocrine surgery exclusively since 2000. In most patients, the criteria of minimally invasive surgery (incision < 3 cm) were applied. Results. A total of 79.1% (53/67) of the patients undergoing unilateral thyroid surgery were considered candidates for ambulatory surgery. The substitution index and the unplanned admission rate was 90.5% (48/53) and 9.4% (5/53), respectively. Two patients had minor complications (3.8%). None of the patients developed hemorrhage or required readmission in the immediate postoperative period. Conclusions. Although preliminary, these results should at least lead to reconsideration of the possibility of performing thyroidectomy in the ambulatory setting and of including this process in the routine activity of ambulatory units in certain hospitals. However, this type of surgery should be performed by surgeons experienced in thyroid surgery and there should be a sufficient number of patients requiring thyroid surgery throughout the year (AU)

Cribado neonatal de hemoglobinopatías y déficit de glucosa-6-fosfato deshidrogenasa (G6PD) en Cataluña. Estudio molecular de la anemia falciforme asociada a alfatalasemia y déficit de G6PD / Neonatal screening of hemoglobinopathies and G6PD deficiency in Catalonia (Spain). Molecular study of sickle cell disease associated with alpha thalassemia and G6PD deficiency

Fundamento y objetivo: Con los flujos inmigratorios se ha elevado la prevalencia de hemoglobinopatías y déficit de glucosa-6-fosfato deshidrogenasa (G6PD) en nuestra población. La probabilidad de encontrar en un individuo más de un defecto del eritrocito es elevada, lo que comporta una mayor heterogeneidad clínica y dificultades diagnósticas. El objetivo de este trabajo ha sido realizar el diagnóstico precoz de la anemia falciforme mediante cribado neonatal, analizar la prevalencia de herencia conjunta de alfatalasemia, déficit de G6PD y hemoglobina S e identificar los genotipos asociados. Pacientes y método: Se ha estudiado a 4.020 recién nacidos (RN) de población de riesgo y autóctona. El cribado neonatal de hemoglobinopatías se realizó mediante cromatografía líquida de alta resolución y el de déficit de G6PD mediante la técnica de la mancha fluorescente. Se analizó molecularmente la asociación entre el gen ßS y alfatalasemia con deleción ­3.7 Kb. Finalmente se estableció el genotipo de los casos de déficit de G6PD. Resultados: La prevalencia de anemia falciforme en población de riesgo fue de 1/475 RN, y la de déficit de G6PD, de 1/43 RN en población de riesgo y de 1/527 RN en población autóctona. La hemoglobina S se confirmó mediante ARMS (amplification refractory mutation system). La asociación entre el gen ßS y la alfatalasemia con deleción ­3.7 Kb fue de un 32,2%, y entre el gen ßS y el déficit de G6PD, de un 7%. Conclusiones: Se confirma la elevada prevalencia de la anemia falciforme y del déficit de G6PD en población de riesgo, así como la elevada heterogeneidad molecular de ambos defectos. El conocimiento de los genotipos asociados y su relación con la expresión clínica es de gran utilidad para establecer criterios adecuados de diagnóstico y pronóstico

Background and objective: The prevalence of hemoglobinopathies and glucose-6-phosphate dehidrogenase (G6PD) deficiency in the Catalan neonatal population is increasing due to immigration. Coinheritance of more than a single RBC genetic defect is becoming more frequent and diagnostic pitfalls are also increasing. We intended to demonstrate the need to perform an early diagnosis of sickle cell disease (SCD) by means of neonatal screening, to establish the prevalence of SCD associated with alpha thalassemia and G6PD deficiency and to identify genotypes associated with sickle cell disease and G6PD deficiency. Patients and method: 4,020 blood samples from newborns were screened. For the screening of hemoglobinopathies the high performance liquid chromatography method was used and for G6PD deficiency the fluorescent spot test was employed. We studied the association between ßS gene and alpha thalassaemia del-3.7 Kb. SCD and G6PD deficiency genotypes were established. Results: Prevalence of SCD in population at risk was 1/475 newborns. Prevalence of G6PD deficiency in population at risk was 1/43, and in autochthonous population was 1/527 newborns. In all the cases, sickle hemoglobin was confirmed by ARMS (amplification refractory mutation system). Association between ßS gene and alpha thalassaemia del-3.7 Kb was found in 32.2% of the samples, and an association between ßS gene and G6PD deficiency was observed in 7% of the samples. Conclusions: This study confirms the high prevalence of SCD and G6PD deficiency in population at risk as well as their genetic and clinical heterogeneity. The study of genotype/phenotype relationships allows a better knowledge of molecular mechanism and is useful to establish suitable criteria of diagnosis

De la medicina del “Gran Patrón” a la medicina en equipos multidisciplinarios / From the medicine of the “Big Boss” to the medicine done by multidisciplinary teams

No disponible

¿Especialización o áreas de capacitación? / Specialization or capacitation areas?

No disponible

Calidad y simulaciones / Quality and simulation

No disponible