Choice of assemblers has a critical impact on de novo assembly of SARS-CoV-2 genome and characterizing variants.

BACKGROUND: Coronavirus Disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a global pandemic following its initial emergence in China. SARS-CoV-2 has a positive-sense single-stranded RNA virus genome of around 30Kb. Using next-generation sequencing technologies, a large number of SARS-CoV-2 genomes are being sequenced at an unprecedented rate and being deposited in public repositories. For the de novo assembly of the SARS-CoV-2 genomes, a myriad of assemblers is being used, although their impact on the assembly quality has not been characterized for this virus. In this study, we aim to understand the variabilities on assembly qualities due to the choice of the assemblers. RESULTS: We performed 6648 de novo assemblies of 416 SARS-CoV-2 samples using eight different assemblers with different k-mer lengths. We used Illumina paired-end sequencing reads and compared the assembly quality of those assemblers. We showed that the choice of assembler plays a significant role in reconstructing the SARS-CoV-2 genome. Two metagenomic assemblers, e.g. MEGAHIT and metaSPAdes, performed better compared with others in most of the assembly quality metrics including, recovery of a larger fraction of the genome, constructing larger contigs and higher N50, NA50 values, etc. We showed that at least 09% (259/2873) of the variants present in the assemblies between MEGAHIT and metaSPAdes are unique to one of the assembly methods. CONCLUSION: Our analyses indicate the critical role of assembly methods for assembling SARS-CoV-2 genome using short reads and their impact on variant characterization. This study could help guide future studies to determine the best-suited assembler for the de novo assembly of virus genomes.

A novel paper-based lysis strip for SARS-CoV-2 RNA detection at low resource settings.

Infectious respiratory diseases such as COVID-19 are serious and global concerns from the past to the present. To isolate the spread of infectious diseases even in the absence of a health system, a simple, inexpensive, reliable, sensitive, and selective molecular diagnosis platform for Point of Care Test (POCT) is required. Especially, the nucleic acid extraction step is difficult to perform out of laboratory. Here, we propose a paper-based lysis (PBL) strip for nucleic acid extraction, especially in low-resource settings (LRS). PBL strips are suitable for isolating RNA from viruses with biological interference and inhibitors. We optimized the buffer compositions and membranes of the strip. A simple preparation method using a PBL strip could obtain an eluent for downstream inspection within 20 min. Overall, 104 copies/swaps were detected for 20 min for amplification in combination with Reverse Transcription Loop-Mediated Amplification (RT-LAMP).

Performance analysis of portable HEPA filters and temporary plastic anterooms on the spread of surrogate coronavirus.

The outbreak of COVID-19, and its current resurgence in the United States has resulted in a shortage of isolation rooms within many U.S. hospitals admitting COVID-19-positive cases. As a result, hospital systems, especially those at an epicenter of this outbreak, have initiated task forces to identify and implement various approaches to increase their isolation capacities. This paper describes an innovative temporary anteroom in addition to a portable air purifier unit to turn a general patient room into an isolation space. Using an aerosolization system with a surrogate oil-based substance, we evaluated the effectiveness of the temporary plastic anteroom and the portable air purifier unit. Moreover, the optimal location of the portable unit, as well as the effect of negative pressurization and door opening on the containment of surrogate aerosols were assessed. Results suggested that the temporary anteroom alone could prevent the migration of nearly 98% of the surrogate aerosols into the adjacent corridor. Also, it was shown that the best location of a single portable air purifier unit is inside the isolation room and near the patient's bed. The outcome of this paper can be widely used by hospital facilities managers when attempting to retrofit a general patient room into an airborne infection isolation room.

Molecules targeting a novel homotrimer cavity of Spike protein attenuate replication of SARS-CoV-2.

The SARS-CoV-2 Spike glycoprotein (S) utilizes a unique trimeric conformation to interact with the ACE2 receptor on host cells, making it a prime target for inhibitors that block viral entry. We have previously identified a novel proteinaceous cavity within the Spike protein homotrimer that could serve as a binding site for small molecules. However, it is not known whether these molecules would inhibit, stimulate, or have no effect on viral replication. To address this, we employed structural-based screening to identify small molecules that dock into the trimer cavity and assessed their impact on viral replication. Our findings show that a cohort of identified small molecules binding to the Spike trimer cavity effectively reduces the replication of various SARS-CoV-2 variants. These molecules exhibited inhibitory effects on B.1 (European original, D614G, EDB2) and B.1.617.2 (δ) variants, while showing moderate activity against the B.1.1.7 (α) variant. We further categorized these molecules into distinct groups based on their structural similarities. Our experiments demonstrated a dose-dependent viral replication inhibitory activity of these compounds, with some, like BCC0040453 exhibiting no adverse effects on cell viability even at high concentrations. Further investigation revealed that pre-incubating virions with compounds like BCC0031216 at different temperatures significantly inhibited viral replication, suggesting their specificity towards the S protein. Overall, our study highlights the inhibitory impact of a diverse set of chemical molecules on the biological activity of the Spike protein. These findings provide valuable insights into the role of the trimer cavity in the viral replication cycle and aid drug discovery programs aimed at targeting the coronavirus family.

Role of Vitamin D, ACE2 and the Proteases as TMPRSS2 and Furin on SARS-CoV-2 Pathogenesis and COVID-19 Severity.

BACKGROUND: COVID-19, the 21st century pandemic disease caused by SARS-CoV-2, has shown a wide clinical spectrum ranging from asymptomatic to deadly serious pneumonia. OBJECTIVE: In our study, the relationship between the pathogenesis and clinical severity of COVID-19 and vitamin D, ACE2, Furin and TMPRSS2 was investigated. METHODS: Serum 25(OH)D, 1,25(OH)2D and ACE2 protein were measured in 85 COVID-19 cases, divided into 5 groups, according to disease severity, from asymptomatic to severe and including a healthy control group. Expression levels of ACE2, VDR, TMPRSS2 and Furin mRNAs in PBMC were also measured. The relationship of the parameters within each group, the severity of the disease and the effect on the patients' fate were investigated. RESULTS: Statistically significant differences were found between the severity of COVID-19 and all study parameters, except for serum 25(OH)D. A strong negative correlation was found between serum ACE2 protein, 1,25(OH)2D, and ACE2 mRNA, and disease severity, length of hospital stay and death/survival rate. Vitamin D deficiency increased the death risk by 5.6-fold (95% CI 0.75-41.47), and the levels of 1,25(OH)2D lower than 1 ng/mL increased the risk of death by 3.8-fold (95% CI 1.07-13.30). CONCLUSION: This study suggests that vitamin D supplementation could be beneficial in the treatment and/or prevention of COVID-19.

Modelling SARS-CoV-2 unreported cases in Italy: Analysis of serological survey and vaccination scenarios.

OBJECTIVES: Aim of the present paper is the study of the large unreported component, characterizing the SARS-CoV-2 epidemic event in Italy, taking advantage of the Istat survey. Particular attention is devoted to the sensitivity and specificity of the serological test and their effects. METHODS: The model satisfactory reproduces the data of the Italian survey showing a relevant predictive power and relegating in a secondary position models which do not include, in the simulation, the presence of asymptomatic groups. The corrections due to the serological test sensitivity (in particular those ones depending on the symptoms onset) are crucial for a realistic analysis of the unreported (and asymptomatic) components. RESULTS: The relevant presence of an unreported component during the second pandemic wave in Italy is confirmed and the ratio of reported to unreported cases is predicted to be roughly 1:4 in the last months of year 2020. A method to correct the serological data on the basis of the antibody sensitivity is suggested and systematically applied. The asymptomatic component is also studied in some detail and its amount quantified. A model analyses of the vaccination scenarios is performed confirming the relevance of a massive campaign (at least 80000 immunized per day) during the first six months of the year 2021, to obtain important immunization effects within August/September 2021.

Acompanyament parental als nounats de les unitats neonatals i plantes de maternitat durant la pandèmia per SARS-CoV-2 / Acompañamiento parental a recién nacidos en las unidades neonatales y plantas de maternidad en relación A lA pandemia por sars-coV-2 / Policies on parental Access restriction in neonatal units And maternity wards during the sars-cov-2 pandemic

Fonament: Des de l’inici de la pandèmia per SARS-CoV-2,la majoria d’unitats neonatals d’arreu del món han aplicatprotocols de restricció de la presència de mares i pares,amb l’objectiu de protegir el personal sanitari i els nounats.Objectiu. Avaluar els efectes col·laterals derivats de la pocapresència de mares i pares al costat dels seus nadons a lesunitats neonatals, i els relacionats amb les restriccions ales plantes de maternitat. Mètode: Revisió de la literatura. S’ha consultat Pubmed iGoogle Scholar utilitzant com a paraules clau ‘SARS-CoV-2’i ‘covid-19’ combinades amb ‘neonatal’, ‘NICU’ i ‘parents’,‘family centered care’ i ‘neurodevelopmental care’. S’hanconsultat dominis en què es recullen resums actualitzatsde l’evidència científica disponible sobre la pandèmia perSARS-CoV-2: www.dontforgetthebubles.com i el web de laSocietat Espanyola de Neonatologia (www.seneo.es). Laveu de les famílies s’ha cercat mitjançant les pàgines deles associacions que els representen i a les xarxes socials.Resultats. El model de cures centrades en el desenvolupa-ment i la família, que ha demostrat efectes positius sobre lasalut dels nadons ingressats i el neurodesenvolupament delsprematurs, es veu amenaçat si es limita la presència paren-tal. La restricció també ha demostrat tenir efectes adversossobre la lactància materna i la salut psicològica dels pares imares. Les dades disponibles fins ara posen de manifest uncomportament benigne de la infecció covid-19 en nadons.Conclusions: En un moment crucial per a la implantació delmodel de cures centrades en el desenvolupament a les uni-tats neonatals catalanes, i amb les dades disponibles, ésimprescindible redissenyar les polítiques d’acompanyamentparental als nadons ingressats.(AU)

Fundamento: Desde el inicio de la pandemia por SARS-CoV-2, lamayoría de unidades neonatales de todo el mundo han aplicadoprotocolos de restricción de la presencia parental, con el objetivode proteger al personal sanitario y a los propios recién nacidos. Objetivo: Evaluar los efectos colaterales derivados de la menor pre-sencia de los padres junto a sus bebés en las unidades neonatales,y los relacionados con las restricciones en las plantas de maternidad.Método: Revisión de la literatura. Se ha realizado búsqueda enPubmed i Google Scholar utilizando como palabras clave ‘SARS-CoV-2’ y ‘covid-19’ en combinación con ‘neonatal’, ‘NICU’ y ‘pa-rents’, ‘family centered care’ y ‘neurodevelopmental care’. Se hanconsultado dominios donde se recogen resúmenes actualizados dela evidencia científica disponible sobre la pandemia por SARS-CoV-2: www.dontforgetthebubles.com y la web de la Sociedad Es-pañola de Neonatología (www.seneo.es). La opinión de las familiasse ha buscado en las páginas web de las asociaciones que las re-presentan y en las redes sociales. Resultados: El modelo de cuidados centrados en el desarrollo y lafamilia, que ha demostrado efectos positivos sobre la salud de losrecién nacidos ingresados y el neurodesarrollo de los prematuros,se ve amenazado si se limita la presencia parental. La restriccióntambién ha demostrado tener efectos adversos sobre la lactanciamaterna y la salud psicológica de los progenitores. Los datos dis-ponibles hasta ahora ponen de manifiesto un comportamiento be-nigno de la infección por covid-19 en recién nacidos. Conclusiones: En un momento crucial para la implantación del mo-delo de cuidados centrados en el desarrollo en las unidades neo-natales catalanas, y con los datos disponibles, es imprescindiblerediseñar las políticas de acompañamiento de los padres a sushijos recién nacidos ingresados.(AU)

Objective: To evaluate the side effects of the limitation of parentspresence with their babies in neonatal units and those related torestrictions on maternity wards access. Method: Literature review. A search using ‘SARS-CoV-2’ and ‘CO-VID-19’ as keywords combined to ‘neonatal’, ‘NICU’, ‘parents’,‘family centered care’ and ‘neurodevelopmental care’. Consulta-tion of websites containing updated and summarized scientific li-terature about the pandemic and its consequences in newbornshas also been performed: www.dontforgetthebubles.com andwww.seneo.es. The voice of the families has been mainly obtainedthrough the websites of their associations and the social networks. Results. The family-centered care model has shown positive effectson the health of sick newborns and on premature infants’ neuro-development. This model of care is under threat if parental accessis limited. It has been shown that these restrictions have also ad-verse effects on breastfeeding and on caregivers’ psychologicalwellbeing. Data from different neonatal series report a benigncourse of COVID-19 infection in neonates and preterm babies. Conclusions: At a crucial moment for the implementation of thedevelopmental centered care model in Catalan neonatal units, andwith the available data, it is essential to redesign the policies regar-ding parents who accompany their babies admitted to the units.(AU)

El 31 de diciembre de 2019 las autoridades de la República Popular China comunicaron a la OMS varios casos de neumonía de etiología desconocida en Wuhan, una ciudad situada en la provincia China de Hubei. [Editorial] / On December 31, 2019, the authorities of the People's Republic of China reported to the WHO several cases of pneumonia of unknown etiology in Wuhan, a city located in the Chinese province of Hubei. [Editorial]

Resumen El 31 de diciembre de 2019 las autoridades de la República Popular China comunicaron a la OMS varios casos de neumonía de etiología desconocida en Wuhan, una ciudad situada en la provincia China de Hubei. Una semana más tarde confirmaron que se trataba de un nuevo coronavirus que ha sido denominado SARS-CoV-2 (coronavirus de tipo 2 causante del síndrome respiratorio agudo severo, del inglés, Severe acute respiratory syndrome coronavirus. Este nuevo virus causa diversos cuadros clínicos englobados bajo el término COVID-19 (enfermedad por coronavirus 2019, del inglés, coronavirus disease 2019), e incluyen desde infección asintomática, a cuadros respiratorios leves con tos, malestar general y fiebre hasta cuadros de neumonía grave con síndrome de distrés respiratorio agudo, shock séptico y fallo multi-orgánico y muerte. La mayoría de los casos de COVID-19 notificados hasta el momento cursan con cuadros leves; no obstante, tanto el pronóstico de la enfermedad como el conocimiento actual, basado en los datos más ecientes publicados y los pacientes ya tratados, indican que un porcentaje significativo de pacientes cursaran con insuficiencia respiratoria aguda, neumonía intersticial e hipoxemia grave que requieren ventilación mecánica prolongada y presentan una mortalidad elevada. La expansión del virus a todo el planeta, su capacidad de difusión y su infectividad, el elevado número de afectados en crecimiento exponencial, una mortalidad creciente con la edad y la comorbilidad de los afectados, así como su impacto sobre la vida de las personas y el sistema de asistencia sanitaria han provocado una emergencia sanitaria mundial de grandes proporciones. La Coordinación General de Docencia, conjuntamente con los diferentes servicios de esta casa de salud, participó de una manera activa y actualizada con información referente al COVID-19, destacamos los siguientes temas: Imagenología en tiempos de pandemia; embarazo y covid-19; miocardiopatía y COVID-19; planificación de una unidad de reanimación ante una pandemia y experiencia clínica; utilidad del ultrasonido en unidades críticas COVID-19; recomendaciones y experiencias para ecocardiografía y eco pulmonar en tiempos de COVID-19; cirugía plástica y quemaduras durante la pandemia; Kawasaki-like y COVID-19; VIH y COVID-19 historia natural; hemodiálisis en tiempos de COVID-19; plasma convaleciente e inmunidad en pacientes COVID-19; prevención y vacuna en COVID-19; abordaje del recién nacido con mal formación cardiaca: tratamiento sin cirugía por cateterismo; soporte nutricional en el paciente COVID-19 crítico; eventos trombo-embolicos en pacientes COVID-19, rescate vascular cerebral en tiempos COVID-19; desafíos actuales en el manejo de infarto agudo de miocardio en tiempos de pandemia; salud mental en tiempos de COVID-19; desde la fisiopatología y Medicina Basada en Evidencias (MBE) a la práctica clínica; mensajes clave para el manejo integral del paciente grave con Insuficiencia Renal Aguda (IRA) por COVID-19; experiencias y manejo del malestar emocional durante la pandemia COVID-19; Hipertensión Arterial: análisis de las últimas Felicitamos a todos los participantes y expresamos nuestro profundo reconocimiento por su vocación de servicio y entrega para enfrentar la crisis sanitaria, asumir su rol social y constituirse en sujeto social y político, que interpreta adecuadamente la realidad y plantea soluciones que contribuyen significativamente a la resolución de los problemas sociales; cada detalle cuenta para buscar una forma de contribuir como empresa cuya misión es la Salud. La Pandemia por COVID-19 ha ocasionado grandes impactos en nuestra sociedad y nos ha entristecido en lo más profundo la partida de innumerables colegas que nos dejan huella de bondad, lealtad, solidaridad y amistad, nuestro sentido pésame a sus distinguidas familias. (au)