The Genomics of Emerging Pathogens

Abstract

Globalization and industrialization have dramatically altered the vulnerability of human and animal populations to emerging and reemerging infectious diseases while shifting both the scale and pace of disease outbreaks. Fortunately, the advent of high-throughput DNA sequencing platforms has also increased the speed with which such pathogens can be detected and characterized as part of an outbreak response effort. It is now possible to sequence the genome of a pathogen rapidly, inexpensively, and with high sensitivity, transforming the fields of diagnostics, surveillance, forensic analysis, and pathogenesis. Here, we review advances in methods for microbial discovery and characterization, as well as strategies for testing the clinical and public health significance of microbe-disease associations. Finally, we discuss how genetic data can inform our understanding of the general process of pathogen emergence.

Feasibility of Using the Mosquito Blood Meal for Rapid and Efficient Human and Animal Virus Surveillance and Discovery

“…22 In contrast, NGS is still relatively new for diagnostics use. 23 Sequencing-based diagnosis has attracted more and more attention and is believed to be broadly and routinely used in clinical and public health areas in the near future. 24,25 However, the comparison of results clearly suggested the complexity of NGS data and the technical challenges and potential risks that need to be recognized and addressed carefully.…”

Negeviruses found in multiple species of mosquitoes from southern Portugal: Isolation, genetic diversity, and replication in insect cell culture

“…Since nextgeneration sequencing (NGS) approaches have not yet been fully exploited for the unbiased analysis of mosquito viromes, the characterization of new mosquito-associated viruses has been based on the amplification of their genomes by RT-PCR, frequently preceded by their isolation in cell culture (Firth and Lipkin, 2013;Junglen and Drosten, 2013). Despite the limited sensitivity/specificity these experimental approaches entail, they have allowed the identification and/or characterization of multiple viruses over time, many of which have been shown to replicate exclusively in insect cells.…”

Metagenomic analysis of the shrew enteric virome reveals novel viruses related to human stool-associated viruses

“…Therefore, to predict and manage future outbreaks, it is helpful to investigate the baseline level of viruses in animals and virus-host relationships (Mokili et al, 2012;Morse et al, 2012). The advent of highthroughput sequencing technology has enabled comprehensive approaches for the simultaneous detection of many viral genomes and the identification of unknown viral genomes without viral isolation (Firth & Lipkin, 2013). Using high-throughput sequencing, viral metagenomics approaches have elucidated whole enteric viromes, resulting in the discovery of unknown viruses in a variety of mammals, including non-human primates, bats, pigs, rodents, cats, sea lions, martens, badgers, foxes, ferrets and pigeons (Baker et al, 2013;Bodewes et al, 2013;Dacheux et al, 2014;Donaldson et al, 2010;Ge et al, 2012;Handley et al, 2012;Li et al, 2010bLi et al, , 2011bNg et al, 2014;Phan et al, 2011Phan et al, , 2013aShan et al, 2011;Smits et al, 2013a;van den Brand et al, 2012;Wu et al, 2012).…”