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Recent advances have allowed the genomes of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) – the causative agent of COVID-19 – to be sequenced within hours or days of a case being identified. As a result, for the first time, genomic sequencing in real time has been able to inform the public health response to a pandemic. Metagenomic sequencing was fundamental to the detection and characterization of the novel pathogen. Early sharing of SARS- CoV-2 genome sequences allowed molecular diagnostic assays to be developed rapidly, which improved global preparedness, and contributed to the design of countermeasures. Rapid, large- scale virus genome sequencing is contributing to understanding the dynamics of viral epidemics and to evaluating the efficacy of control measures. Increased recognition that viral genome sequencing can contribute to improving public health is driving more laboratories to invest in this area. However, the cost and work involved in gene sequencing are substantial, and laboratories need to have a clear idea of the expected public health returns on this investment. This document provides guidance for laboratories on maximizing the impact of SARS-CoV-2 sequencing activities now and in the future.



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public health, viruses, whole-genome sequencing, SARS-CoV-2, COVID-19