Viral pathogen discovery.pdf

Viral pathogen discovery Charles Y Chiu1,2 Available online at Viral pathogen discovery is of critical importance to clinical microbiology, infectious diseases, and public health. Genomic approaches for pathogen discovery, including consensus polymerase chain reaction (PCR), microarrays, and unbiased next-generation sequencing (NGS), have the capacity to comprehensively identify novel microbes present in clinical samples. Although numerous challenges remain to be addressed, including the bioinformatics analysis and interpretation of large datasets, these technologies have been successful in rapidly identifying emerging outbreak threats, screening vaccines and other biological products for microbial contamination, and discovering novel viruses associated with both acute and chronic illnesses. Downstream studies such as genome assembly, epidemiologic screening, and a culture system or animal model of infection are necessary to establish an association of a candidate pathogen with disease. Addresses 1 Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA 2 UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA Corresponding author: Chiu, Charles Y (charles.chiu@) Current Opinion in Microbiology 2013, 16:468–478 This review comes from a themed issue on Host–microbe interactions: viruses Edited by Carlos F Arias For a complete overview see the Issue and the Editorial Available online 29th May 2013 1369-5274 # 2013 The Author. Published by Elsevier Ltd. /10.1016/j.mib.2013.05.001 Introduction The identification of novel pathogens has a tremendous impact on infectious diseases, microbiology, and human health. Nearly all of the outbreaks of clinical and public health importance over the past two decades have been caused by novel emerging viruses, including Severe Acute Respiratory Syndrome (SARS) coronavirus [1], Sin Nombre hantavirus [2], 2009 pandemic influenza H1N1 [3,4], and the recently described cor