Informatics for Genomics-informed Surveillance of RNA Viruses

NLM Informatics and Data Science Lecture Series Genomics-informed surveillance is now recognized as an important extension to the monitoring of rapidly evolving pathogens. Next generation sequencing has the ability to produce large amounts of data for tracking viruses of public health importance. Biomedical informatics approaches are able to facilitate the translation of these data into information for public health surveillance. Thus, epidemiologists can identify new outbreaks or monitor the course of a known epidemic by leveraging pathogen sequences (and corresponding metadata) generated from the clinical specimens of sick patients. In this presentation, Dr. Scotch will discuss NLM-funded projects related to the development and evaluation of a surveillance system that uses virus sequences to study the evolution, spread, and population size of viruses across geographic areas. This includes the development of a pipeline for virus phylogeography and spread and its utilization as part of a newly funded project on metagenomics of wastewater for outbreak detection and epidemic monitoring including seasonal influenza. This work aims to highlight the value of using biomedical informatics to translate viral genetic data into valuable information for surveillance of both known and novel viruses. Brief Bio: Matthew Scotch is Associate Professor of Biomedical Informatics at Arizona State University (ASU). He is also Assistant Director of ASU ’ s Biodesign Center for Environment...
Source: Videocast - All Events - Category: General Medicine Tags: Upcoming Events Source Type: video

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Over the past few years, Professor Zhang Yongzhen has made it his business to sequence thousands of previously unknown viruses. But he knew straight away that this one was particularly nasty. It was about 1:30 p.m. on Jan. 3 that a metal box arrived at the drab, beige buildings that house the Shanghai Public Health Clinical Center. Inside was a test tube packed in dry ice that contained swabs from a patient suffering from a peculiar pneumonia sweeping China’s central city of Wuhan. But little did Zhang know that that box would also unleash a vicious squall of blame and geopolitical acrimony worthy of Pandora herself....
Source: TIME: Health - Category: Consumer Health News Authors: Tags: Uncategorized COVID-19 overnight Source Type: news
Over the past few years, Professor Zhang Yongzhen has made it his business to sequence thousands of previously unknown viruses. But he knew straight away that this one was particularly nasty. It was about 1:30 p.m. on Jan. 3 that a metal box arrived at the drab, beige buildings that house the Shanghai Public Health Clinical Center. Inside was a test tube packed in dry ice that contained swabs from a patient suffering from a peculiar pneumonia sweeping China’s central city of Wuhan. But little did Zhang know that that box would also unleash a vicious squall of blame and geopolitical acrimony worthy of Pandora herself....
Source: TIME: Health - Category: Consumer Health News Authors: Tags: Uncategorized COVID-19 overnight Source Type: news
In this study, the pathogenesis of H5N8 HPAIV in comparison with H7N1 HPAIV and the role of domestic geese in the epidemiology of these viruses were evaluated. Local and commercial geese (Anser anser var. domesticus) were intranasally inoculated with 105 ELD50 of A/goose/Spain/IA17CR02699/2017 (H5N8) or A/Chicken/Italy/5093/1999 (H7N1) and monitored daily during 15 days. H5N8 was highly virulent to domestic geese, reaching 100% mortality by day 10 post-infection. Systemic microscopic necrotizing lesions associated to widespread AIV-antigen by IHC techniques were detected, being the most severely-affected the central nervou...
Source: Avian Pathology - Category: Pathology Authors: Tags: Avian Pathol Source Type: research
by Elisa Beninc à, Thomas Hagenaars, Gert Jan Boender, Jan van de Kassteele, Michiel van Boven Transmission of infectious diseases between immobile hosts (e.g., plants, farms) is strongly dependent on the spatial distribution of hosts and the distance-dependent probability of transmission. As the interplay between these factors is poorly understood, we use spatial process and transmission m odelling to investigate how epidemic size is shaped by host clustering and spatial range of transmission. We find that for a given degree of clustering and individual-level infectivity, the probability that an epidemic occurs af...
Source: PLoS Computational Biology - Category: Biology Authors: Source Type: research
In this study we used genomic and traditional epidemiological analyses to trace the origin and subsequent spread of these outbreaks within Bulgaria. Both methods indicate two separate incursions, one restricted to the northeastern region of Dobrich, and another largely restricted to Central and Eastern Bulgaria including places such as Plovdiv, Sliven and Stara Zagora, as well as one virus from the Western region of Vidin. Both outbreaks likely originate from different European 2.3.4.4b virus ancestors circulating in 2017. The viruses were likely introduced by wild birds or poultry trade links in 2017 and have continued to...
Source: Viruses - Category: Virology Authors: Tags: Article Source Type: research
In addition to causing the pandemic influenza outbreaks of 1918 and 2009, subtype H1N1 influenza A viruses (IAVs) have caused seasonal epidemics since 1977. Antigenic property of influenza viruses are determin...
Source: BMC Bioinformatics - Category: Bioinformatics Authors: Tags: Methodology article Source Type: research
CONCLUSIONThe pre ‐​COVID‐​19 research is unanimous that governments cannot expect to rely on travel restrictions to prevent the spread of pandemics similar to influenza. Travel restrictions do not prevent the spread of disease and may only delay it for a few days or weeks if implemented prior to the interna tional transmission of the disease. The Trump administration’s travel restrictions waited until after the virus had already entered the United States, and they exempted many travelers from China, not to mention the rest of the world.[30]The research shows that the Trump administration should have kno...
Source: Cato-at-liberty - Category: American Health Authors: Source Type: blogs
(BOISE, Idaho) — They are two disasters that require opposite responses: To save lives and reduce the spread of COVID-19, people are being told to remain isolated. But in a wildfire, thousands of firefighters must work in close quarters for weeks at a time. Wildfires have already broken out in Texas and Florida, and agencies are scrambling to finish plans for a new approach. They are considering waivers for some training requirements to previously-certified crew members, and moving some training online. Other proposals include limiting fire engines to a driver and one passenger, requiring other crew members to ride i...
Source: TIME: Science - Category: Science Authors: Tags: Uncategorized COVID-19 Environment News Desk wire Source Type: news
Source: World Health Organization (WHO). Published: 4/9/2020. This 196-page toolkit is intended for clinicians working in intensive care units in low- and middle-income countries, managing adult and pediatric patients with severe forms of acute respiratory infection, including severe pneumonia, acute respiratory distress syndrome, sepsis, and septic shock. It is a hands-on practical guide to be used by healthcare professionals involved in critical care management during the COVID-19 pandemic and outbreaks of influenza (seasonal or avian influenza), Middle East respiratory syndrome coronavirus (MERS-CoV), or other emerging...
Source: Disaster Lit: Resource Guide for Disaster Medicine and Public Health - Category: International Medicine & Public Health Source Type: news
The recent WHO decision to declare the novel coronavirus outbreak a Public Health Emergency of International Concern (PHEIC), while both appropriate and hardly surprising, offers the opportunity to reflect on the previous PHEIC which was declared, namely the Ebola epidemic in Kivu region, Democratic Republic of the Congo (DRC). And you should really say the ongoing Ebola epidemic, as during the time since the declaration in July 2019 through to the present day (March 2020), a total of 3,453 cases have been reported [1]. The nCoV-2019 outbreak is still ballooning; as of today, over 400,000 confirmed cases worldwide with no ...
Source: GIDEON blog - Category: Databases & Libraries Authors: Tags: Ebooks Epidemiology Outbreaks Source Type: blogs
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