Pathogen Genomics in Public Health

Abstract

Rapid advances in DNA sequencing technology ("next-generation sequencing") have inspired optimism about the future potential of human genomics for "precision medicine." Meanwhile, pathogen genomics is already delivering "precision public health" via more effective foodborne illness outbreak investigations, better targeted tuberculosis control, and more timely and granular influenza surveillance to inform vaccine strain selection. In this article, we describe how public health agencies are rapidly adopting pathogen genomics to improve their effectiveness in almost all domains of infectious disease. This momentum is likely to continue, given ongoing development in sequencing and sequencing-related technologies. An important transformation is underway in public health. Next-generation sequencing (NGS, also called "high-throughput sequencing") is reshaping communicable disease surveillance, allowing for earlier detection and more precise investigation of outbreaks. NGS helps characterize microbes more effectively and offers new insights into their ecology and

Improving epidemic surveillance and response: big data is dead, long live big data

“…Despite the challenges above, ongoing advances in computational power, methods, and new data streams offer genuine hope for better surveillance and useful forecasting systems. New data sources at our disposal include not only the passively observed big data streams from mobile phones but also detailed environmental data and local sensor information from distributed devices, internet search information, pathogen genomic data that can be generated rapidly during an outbreak to inform the response, 7 and crowd-sourced approaches to monitoring rapidly evolving emergencies. 8 Data sharing platforms and standardised aggregation approaches that protect the privacy of personal data are being developed, 9 and increasing internet connectivity allows for rapid data transfer and communication between geographically disparate teams of responders.…”

Global transmission network of SARS-CoV-2: from outbreak to pandemic

“…First of all, the genomic analyses do not necessarily replace traditional epidemiology methods that aim to investigate sources of transmission based on traditional surveillance systems that keeps track of the trajectory of the epidemic. Rather, genomic analyses complement and confirm other epidemiological findings using the sequencing data as an independent source of information that is not subject to the biases associated with the traditional epidemiological data [27,2]. Second, it is important to understand that the edges in the estimated global transmission network may not be synonymous with actual transmission events, but rather link infected hosts from the same epidemiological transmission clusters.…”

“…It also demonstrates the importance of internationally coordinated public health measures and highlights how epidemiological and molecular surveillance analyses complement each other to characterize the spatial-temporal spread of epidemics. 2…”

Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia

“…Instead of being limited to consensus Sanger sequencing, which may not detect high risk quasispecies, metagenomics is a powerful approach to detect variants of both novel and known species as epidemics evolve. 11 The clear limitation in an mNGS approach is that low viral titers or high levels of host material demand greater read depth than may be available on instruments such as the iSeq100. To overcome this barrier, our follow-up steps included a target enrichment of SARS-CoV-2 while keeping the comprehensiveness of our mNGS pipeline intact.…”