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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This article reviews the risk factors of nosocomial influenza outbreaks and discusses clinical, diagnostic, and treatment aspects of seasonal and avian influenza to facilitate hospital preparations for future influenza outbreaks. Literature search was conducted through PubMed of relevant peer-reviewed full papers in English journals with inclusion of relevant publications by the WHO and US CDC. Expert opinion: Accurate and rapid identification of an influenza outbreak is important to facilitate patient care and prevent nosocomial transmission. Timely treatment with a neuraminidase inhibitor (NAI) for adults hospitalized wi...
Source: Expert Review of Respiratory Medicine - Category: Respiratory Medicine Tags: Expert Rev Respir Med Source Type: research
A recent study in this journal compared codon usage among NA subtypes (N1, N2, N6, and N8)  of H5Nx highly pathogenic avian influenza A viruses (HPAIVs) and suggested that codon usage in N1 subtype is better adapted to its host than the epidemic NA subtypes (N6 and N8), which had fewer number of human cases compared to the N1 subtype.1 To date, there are 18 known HA subtypes (H1-H18) and 11 known NA subtypes (N1-N11)2. However, only N1 and N2 subtypes have been reported to cause pandemics (H1N1 for the 1918 and 2009 pandemics; H2N2 for the 1957 pandemic; and H3N2 for the 1968 pandemic) or seasonal outbreaks in humans3.
Source: Journal of Infection - Category: Infectious Diseases Authors: Tags: Letter to the Editor Source Type: research
This study is the first full genome characterization H5N8 HPAIV in Iran. The data complete the puzzle of molecular epidemiology of H5N8 HPAIV in Iran and the region. Our study provides evidence for fast and continuing reassortment of H5 clade 2.3.4.4 viruses, that might lead to changes in virus structural and functional characteristics such as the route and method of transmission of the virus and virus infective, pathogenic and zoonotic potential. PMID: 31174704 [PubMed - in process]
Source: Comparative immunology, microbiology and infectious diseases. - Category: Allergy & Immunology Authors: Tags: Comp Immunol Microbiol Infect Dis Source Type: research
AbstractIn recent decades, exceeding 60% of infectious cases in human beings are originated from pathogenic agents related to feral or companion animals. This figure continues to swiftly increase due to excessive exposure between human and contaminated hosts by means of applying unhygienic farming practices throughout society. In Asia countries —renowned for lax regulation towards animal-trading markets—have experienced tremendous outbreaks of zoonotic diseases every year. Meanwhile, various epidemic surges were first reported in the residential area of China—one of the largest distributor of all animal p...
Source: European Journal of Clinical Microbiology and Infectious Diseases - Category: Microbiology Source Type: research
We read with interest the recent communication by Guo et al. concerning avian influenza virus pathogenicity.1 Swine has been considered an intermediate host for avian influenza viruses to adapt to humans. Cross-species transmissions caused by novel reassortant swine-originate influenza A virus (S-OIV) are of particular concern after the 2009 pandemic caused by pdH1N1 virus and epidemic outbreaks caused by H3N2v.2,3 The genesis of these viruses shows that reassortant is the major driving force for producing highly infectious variants.
Source: Journal of Infection - Category: Infectious Diseases Authors: Tags: Letter to the Editor Source Type: research
Conclusions: Human challenge studies and systems biology approaches are important tools that should be used in concert to advance our understanding of influenza infection and provide targets for novel therapeutics and immunizations. Introduction Although influenza virus was recognized as an important pathogen over a century ago, influenza continues to cause a significant burden of disease. In the United States alone, it's estimated that in the 2017–2018 season there were 959,000 hospitalizations related to influenza illness, and 79,400 deaths (CDC, 2018). Worldwide, WHO estimates that annual influenza...
Source: Frontiers in cellular and infection microbiology - Category: Microbiology Source Type: research
In conclusion, road transport and socioeconomic status had significant impacts and should be considered for the prevention and control of future pandemics.
Source: International Journal of Environmental Research and Public Health - Category: Environmental Health Authors: Tags: Article Source Type: research
Two different influenza A viruses have infected and spread among dogs since 2000, and both have been widespread in dogs in North America. The H3N8 canine influenza virus arose in the United States as a variant of equine influenza virus. The H3N2 canine influenza virus arose in Asia by transfer of an avian influenza virus to dogs. Both viruses cause mild respiratory disease and are associated with outbreaks in densely housed dogs or those with frequent connections to other dogs. The 2 canine influenza viruses each caused widespread epidemics over at least several years that were associated with localized outbreaks.
Source: Veterinary Clinics of North America: Small Animal Practice - Category: Veterinary Research Authors: Source Type: research
This study showcases the possible contribution of modeling to inform and optimize control strategies during an outbreak.
Source: Epidemics - Category: Epidemiology Source Type: research
Since H7N9 influenza A virus (H7N9) was first reported in 2013, five waves of outbreaks have occurred, posing a huge threat to human health. In preparation for a potential H7N9 epidemic, it is essential to eva...
Source: Virology Journal - Category: Virology Authors: Tags: Research Source Type: research
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