During the pandemic, whole genome sequencing was critical to characterize SARS-CoV-2 for surveillance, clinical and therapeutical purposes. However, low viral loads in specimens often led to ...suboptimal sequencing, making lineage assignment and phylogenetic analysis difficult. We propose an alternative approach to sequencing these specimens that involves sequencing in triplicate and concatenation of the reads obtained using bioinformatics. This proposal is based on the hypothesis that the uncovered regions in each replicate differ and that concatenation would compensate for these gaps and recover a larger percentage of the sequenced genome.
Whole genome sequencing was performed in triplicate on 30 samples with Ct > 32 and the benefit of replicate read concatenation was assessed. After concatenation: i) 28% of samples reached the standard quality coverage threshold (> 90% genome covered > 30x); ii) 39% of samples did not reach the coverage quality thresholds but coverage improved by more than 40%; and iii) SARS-CoV-2 lineage assignment was possible in 68.7% of samples where it had been impaired.
Concatenation of reads from replicate sequencing reactions provides a simple way to access hidden information in the large proportion of SARS-CoV-2-positive specimens eliminated from analysis in standard sequencing schemes. This approach will enhance our potential to rule out involvement in outbreaks, to characterize reinfections and to identify lineages of concern for surveillance or therapeutical purposes.
COVID-19 diagnosis lies on the detection of SARS-CoV-2 on nasopharyngeal specimens by RT-PCR. The Xpert-Xpress SARS-CoV-2 assay provides results in less than one hour from specimen reception, which ...makes it suitable for clinical/epidemiological circumstances that require faster responses. The analysis of a COVID-19 outbreak suspected in the neonatology ward from our institution showed that the Ct values obtained for the targeted genes in the Xpert assay were markedly different within each specimen (N Ct value > 20 cycles above the E Ct value).
We identified the mutation C29200T in the N gene as responsible for an impairment in the N gene amplification by performing whole genome sequencing of the specimens involved in the outbreak (Omicron variant). Subsequently, a retrospective analysis of all specimens sequenced in our institution allowed us to identify the same SNP as responsible for similar impairments in another 12 cases (42% of the total cases reported in the literature). Finally, we found that the same SNP emerged in five different lineages independently, throughout almost all the COVID-19 pandemic.
We demonstrated for the first time the impact of this SNP on the Xpert assay, when harbored by new Omicron variants. We extend our observation period throughout almost all the COVID-19 pandemic, offering the most updated observations of this phenomenon, including sequences from the seventh pandemic wave, until now absent in the reports related to this issue. Continuous monitoring of emerging SNPs that could affect the performance of the most commonly used diagnostic tests, is required to redesign the tests to restore their correct performance.
We present clinical, genomic and epidemiological data on the first 106 cases with the SARS-CoV-2 B.1.1.7 variant in Madrid. Even from the start, the increase of this variant was due to transmission ...events within the community, some causing extensive clusters, rather than further imports. Most cases developed non-severe disease.
Few cases of avulsion fractures of the tibial tuberosity with simultaneous rupture of the patellar tendon have been reported in the literature. Therefore, its mechanism and incidence have not been ...determined conclusively. This type of fracture is considered a serious injury that requires prompt diagnosis and early surgical repair. There is no therapeutic algorithm or standard method of treatment due to the infrequency of the injury. In this case report, we conducted an exhaustive review and synthesis of the existing literature including all previously reported cases.
We present a 16-year-old male soccer player with a case of a tibial tuberosity fracture with distal avulsion of the patellar tendon 5 d prior to surgical treatment. The patient presented with a loss of the extensor mechanism of the knee, edema, the inability to walk, and pain. X-rays showed a high patella and a 180-degree avulsion of the tibial tuberosity. The diagnosis was confirmed by magnetic resonance imaging and computed tomography. The patient underwent open reduction and internal fixation of the fracture with a cannulated screw and washer as well as patellar tendon repair with two metallic anchors. The rehabilitation protocol consisted of initial immobilization in extension followed by passive mobility and muscle strengthening exercises. The patient demonstrated excellent postoperative outcomes and returned to regular activity without complications.
This case presentation and literature review comprise the most relevant clinical, radiographic, and treatment details described in the international literature to date, providing the reader with an overview of this rare condition.
to present an interventional radiology standard of practice on the use of inferior vena cava filters (IVCFs) in patients with or at risk to develop venous thromboembolism (VTE) from the Iberoamerican ...Interventional Society (SIDI) and Spanish Vascular and Interventional Radiology Society (SERVEI).
a group of twenty-two interventional radiologist experts, from the SIDI and SERVEI societies, attended online meetings to develop a current clinical practice guideline on the proper indication for the placement and retrieval of IVCFs. A broad review was undertaken to determine the participation of interventional radiologists in the current guidelines and a consensus on inferior vena cava filters. Twenty-two experts from both societies worked on a common draft and received a questionnaire where they had to assess, for IVCF placement, the absolute, relative, and prophylactic indications. The experts voted on the different indications and reasoned their decision.
a total of two-hundred-thirty-three articles were reviewed. Interventional radiologists participated in the development of just two of the eight guidelines. The threshold for inclusion was 100% agreement. Three absolute and four relative indications for the IVCF placement were identified. No indications for the prophylactic filter placement reached the threshold.
interventional radiologists are highly involved in the management of IVCFs but have limited participation in the development of multidisciplinary clinical practice guidelines.
SARS-CoV-2 recombinants involving the divergent Delta and Omicron lineages have been described, and one of them, "Kraken" (XBB.1.5), has recently been a matter of concern. Recombination requires the ...coexistence of two SARS-CoV-2 strains in the same individual. Only a limited number of studies have focused on the identification of co-infections and are restricted to co-infections involving the Delta/Omicron lineages.
We performed a systematic identification of SARS-CoV-2 co-infections throughout the pandemic (7609 different patients sequenced), not biassed towards the involvement of highly divergent lineages. Through a comprehensive set of validations based on the distribution of allelic frequencies, phylogenetic consistency, re-sequencing, host genetic analysis and contextual epidemiological analysis, these co-infections were robustly assigned.
Fourteen (0.18%) co-infections with ≥ 8 heterozygous calls (8-85 HZs) were identified. Co-infections were identified throughout the pandemic and involved an equal proportion of strains from different lineages/sublineages (including pre-Alpha variants, Delta and Omicron) or strains from the same lineage. Co-infected cases were mainly unvaccinated, with mild or asymptomatic clinical presentation, and most were at risk of overexposure associated with the healthcare environment. Strain segregation enabled integration of sequences to clarify nosocomial outbreaks where analysis had been impaired due to co-infection.
Co-infection cases were identified throughout the pandemic, not just in the time periods when highly divergent lineages were co-circulating. Co-infections involving different lineages or strains from the same lineage were occurring in the same proportion. Most cases were mild, did not require medical assistance and were not vaccinated, and a large proportion were associated with the hospital environment.
Abstract The aim of this paper is to provide a computational study of migration forces of a retrievable filter (Günther Tulip inferior vena cava filter). Using an experimental setup and finite ...element simulation, the migration forces and stress at the end of the anchored hooks in the struts were estimated. After that, the estimation value of migration stress ( τ rup ) was used to analyze the effect of different mechanical factors (strut thickness, vena cava diameter) in the migration of the IVC filter. Our results show that the migration stress is τ rup = 4.37 N/mm2 . Using this value we obtain that the filter with higher strut diameter ( strut = 0.45 mm) shows the maximal migration forces in every cava diameter. On the other hand, the value of the migration force decreases when the cava diameter increases. In addition, the finite element simulations also show that there are contact between the struts of the filter and the vein in regions close to the anchors.
Since SAR-COV-2 infection emerged and spread worldwide, little is known about its impact on people living with human immunodeficiency virus (HIV). We performed a single-center retrospective study to ...describe the potential particularities and risk factors for respiratory failure (RF) in that population. This single-center retrospective study included patients infected with HIV, whose current follow-up is run in this center, above18 years of age, with diagnosis of SARS-CoV-2 infection between March 5, 2020 and April 15, 2021. We collected data regarding HIV immunological and virological status, main epidemiological characteristics, as well as those conditions considered to potentially influence in SARS-CoV-2 evolution; and clinical, microbiological, radiological, respiratory status, and survival concerning coronavirus disease 2019 (COVID-19). We compared all that, for patients with and without RF and performed a logistic regression for suspected risk factors for RF. One hundred seventy-seven HIV patients were diagnosed from COVID-19 (mean age 53.8 years, 81.3% male). At diagnosis, 95.5% were receiving ART and 91.3% had undetectable viral load, with median CD4 count of 569 cells/μL. One hundred thirty-eight patients (78.4%) had symptoms, 44 (25%) developed RF and 53 (31%) developed bilateral pneumonia. The most commonly used treatments were: steroids (26.7%) and hydroxychloroquine (13.1%). When comparing patients with and without RF, we found statistically significant differences for 20 of the analyzed variables such as age (
< .001) and CD4 (
0.002), and route of HIV transmission by intravenous drug users IVDU (
0.002) were determined. In multivariate analysis, age odds ratio (OR) 1.095 and CD4 count less than 350 cells/μL (OR 3.36) emerged as risk factor for RF. People living with HIV whose CD4 count is <350 cells are at higher risk of developing RF when infected by SARS-CoV-2.
La hiponatremia es un trastorno multifactorial definido como una disminución en la concentración plasmática de sodio. Su diagnóstico diferencial requiere una evaluación adecuada del volumen ...extracelular. Sin embargo, la determinación del volumen extracelular, simplemente basada en la historia clínica, las constantes vitales, el examen físico y los hallazgos de laboratorio, conducen en ocasiones a un diagnóstico erróneo por lo que el enfoque terapéutico puede ser equivocado. El empleo de ecografía a pie de cama (Point-of-Care Ultrasound PoCUS), mediante la combinación de ecografía pulmonar (Lung Ultrasound LUS), Venous Excess UltraSound (VExUS) y la ecocardioscopia (Focused Cardiac Ultrasound FoCUS) permiten, en combinación con el resto de los parámetros, una valoración holística mucho más precisa del estado del volumen extracelular del paciente.
Hyponatremia is a multifactorial disorder defined as a decrease in plasma sodium concentration. Its differential diagnosis requires an adequate evaluation of the extracellular volume. However, extracellular volume determination, simply based on the clinical history, vital signs, physical examination, and laboratory findings can leads to misdiagnosis and inappropriate treatment. The use of Point-of-Care Ultrasound (PoCUS), through the combination of Lung Ultrasound (LUS), Venous Excess UltraSound (VExUS) and Focused Cardiac Ultrasound (FoCUS), allows a much more accurate holistic assessment of the patient's extracellular volume status in combination with the other parameters.
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