Know Thine Enemy: Viral Genome Sequencing in Outbreaks

Abstract

CONTAINING a viral outbreak with public health measures firstly requires identification of the causative virus, followed by more detailed understanding of viral features. Genomic sequencing provides exhaustive insight into viral features that may help predict outbreak behaviours, assist in diagnosis and tracking, and shape treatment and vaccination strategies. When coupled with epidemiologic study of outbreak data, viral genomic sequencing can be used to direct public health measures and increase the speed of understanding compared to epidemiology alone. Community spread of cases can be used to guide mathematic models and contact tracing of viral outbreaks for public health response. However, epidemiologic data alone better suits responses to low-prevalence and less-widespread outbreaks. Where pathogens have a longer latency period or spread affects rural and remote communities, features of the virus itself must be considered in determining the response. Genotypic and phenotypic characteristics, identified using molecular biology tools, can clarify the type and strain of a virus responsible for an outbreak, and inform and improve case diagnosis, treatment options, and vaccine development, as well as improve tracing accuracy.1