Pan-genomics of virus and its applications

Advances in DNA sequencing technology have ushered in a new era of pan-genomics and genomic surveillance, in which traditional molecular diagnostics and genotyping methods are being enhanced and even replaced by genomics-based methods to aid epidemiologic investigations of communicable diseases. The ability to compare and analyze the entire pathogen's genomes has allowed unprecedented resolution into how and why infectious diseases spread. The rapid development of sequencing technologies has made sequencing routine of viral genomes possible. As these genomics-based methods continue to improve regarding speed, costs, and accuracy, they will increasingly be used to inform and guide infection control and public health practices. There are currently two major ways in which high-throughput sequencing technologies are used in public health and diagnostic applications, (i) to track outbreaks and epidemics in order to call public health responses and (ii) to characterize individual infections to tailor treatment decisions. Focusing on these aims, genome sequencing has been successfully used to describe unique and detailed insights into the transmission, biology, and epidemiology of many health-care-associated viral pathogens. Considering the improvements on portability and quality of sequencing, and the acceleration and standardization of analytical pipelines, the applicable routine of genome sequencing may soon become the common de facto method for infectious diseases control. Using genomic analysis tools to complement existing genotyping and epidemiologic methods, the future of infection control and prevention will lead to more targeted and successful interventions for outbreaks, which will ultimately result in the reduction of infectious diseases impact.