Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are free to use and available online, either through web applications or public code repositories. Contact:evbc@unj-jena.de.

Epidemiología, clínica y distribución temporal de los casos confirmados y sospechosos de Covid-19 atendidos por un Centro de Salud urbano (Cáceres)

Resumen Objetivo: Describir la experiencia de la atención sanitaria a pacientes con sospecha de COVID-19 en un centro de salud tipo durante el periodo de alarma. Diseño: Estudio observacional retrospectivo. Emplazamiento: Centro de salud “Zona Centro” de Cáceres. Participantes: Pacientes consecutivos atendidos por sospecha de infección COVID-19 del 2 de marzo al 21 de junio de 2020. Mediciones principals: Edad, sexo, síntomas más frecuentes atribuidos a la infección, duración de los síntomas, días hasta el alta epidemiológica, comorbilidades, tratamientos farmacológicos, método diagnóstico, derivaciones a urgencias hospitalarias, hospitalizados, afectados de neumonía, fallecidos, incapacidad temporal laboral, ámbito de diagnóstico y fase del periodo de alarma. Resultados: Se incluyeron 464 pacientes;53 fueron confirmados por PCR y 90 por serología. El 81,1% de los diagnósticos por PCR se produjo en las cuatro primeras semanas del periodo de confinamiento. Se derivaron 29 pacientes al hospital (6,2%). Fallecieron 7 (tasa 0,52/1.000). Los síntomas predominantes en los sospechosos fueron tos, fiebre, astenia y síntomas digestivos;en los confirmados tos, disnea y fiebre.  La enfermedad cardiovasculary la enfermedad renal crónica fueron más frecuentes en este último grupo (p<0.001). Conclusiones: La mortalidad fue similar a la española. Las variables epidemiológicas y clínicas se corresponden con las descritas en otros ámbitos. Los diagnosticados por PCR se concentraron en la primera mitad del periodo de confinamiento. Summary Objective: To describe the experience about healthcare provided to suspected COVID-19 patients in a typical primary healthcare center during the alarm period. Design: Retrospective observational study. Setting: Primary healthcare centre "Zona Centro" in Cáceres. Participants: Consecutive suspected COVID-19 patients attended from March 2 to June 21, 2020. Main measurements: Age, sex, most frequent symptoms attributed to the infection, duration of symptoms, days to epidemiological discharge, comorbidities, treatments, diagnostic methods, referrals to hospital emergencies, hospitalized patients, patients suffering from pneumonia, deaths, diagnostic setting and alarm period phase. Results: 464 patients were included;53 were confirmed by PCR and 90 by serology. A 81.1% of PCR diagnoses were made during the first 4 weeks of the confinement period. Twenty-nine patients were referred to hospital (6.2%). Seven died (rate 0.52/1,000). Cough, fever, asthenia and digestive symptomswerepredominant in suspected cases;cough, dyspnea and feverin those confirmed ones. Cardiovascular diseaseand chronic renal disease were more frequent in the latter group (p<0.001). Conclusions: The mortality rate was similar to the Spanish one. Epidemiological and clinical variables correspond to those described in other areas. Those diagnosed by PCR were concentrated in the first half of the confinement period.

Overall management of emergency general surgery patients during the surge of the COVID-19 pandemic: an analysis of procedures and outcomes from a teaching hospital at the worst hit area in Spain.

OBJECTIVE: To assess how the COVID-19 outbreak has affected emergency general surgery (EGS) care during the pandemic, indications for surgery, types of procedures, perioperative course, and final outcomes. METHODS: This is a retrospective study of EGS patients during the pandemic period. The main outcome was 30-day morbidity and mortality according to severity and COVID-19 infection status. Secondary outcomes were changes in overall management. A logistic regression analysis was done to assess factors predictive of mortality. RESULTS: One hundred and fifty-three patients were included. Half of the patients with an abdominal ultrasound and/or CT scan had signs of severity at diagnosis, four times higher than the previous year. Non-COVID patients underwent surgery more often than the COVID group. Over 1/3 of 100 operated patients had postoperative morbidity, versus only 15% the previous year. The most common complications were septic shock, pneumonia, and ARDS. ICU care was required in 17% of patients, and was most often required in the SARS-CoV-2-infected group, which also had a higher morbidity and mortality. The 30-day mortality in the surgical series was of 7%, with no differences with the previous year. The strongest independent predictors of overall mortality were age > 70 years, ASA III-IV, ESS > 9, and SARS-CoV-2 infection. CONCLUSIONS: Non-operative management (NOM) was undertaken in a third of patients, and only 14% of operated patients had a perioperative confirmation of -CoV-2 infection. The severity and morbidity of COVID-19-infected patients was much higher. Late presentations for medical care may have added to the high morbidity of the series.

CORDITE: The Curated CORona Drug InTERactions Database for SARS-CoV-2.

Since the outbreak in 2019, researchers are trying to find effective drugs against the SARS-CoV-2 virus based on de novo drug design and drug repurposing. The former approach is very time consuming and needs extensive testing in humans, whereas drug repurposing is more promising, as the drugs have already been tested for side effects, etc. At present, there is no treatment for COVID-19 that is clinically effective, but there is a huge amount of data from studies that analyze potential drugs. We developed CORDITE to efficiently combine state-of-the-art knowledge on potential drugs and make it accessible to scientists and clinicians. The web interface also provides access to an easy-to-use API that allows a wide use for other software and applications, e.g., for meta-analysis, design of new clinical studies, or simple literature search. CORDITE is currently empowering many scientists across all continents and accelerates research in the knowledge domains of virology and drug design.