The growing understanding of how sequence information can contribute to improved public health is driving global investments in sequencing facilities and programmes. The falling cost and complexity of generating GSD provides opportunities for expanding sequencing capacity; however, challenges to widespread implementation remain. This document provides policy-makers and stakeholders with guidance on how to maximize the public health benefit of SARS-CoV-2 genomic sequencing activities in the short and long term as the pandemic continues to unfold. Practical considerations for the implementation of a virus genomic sequencing programme and an overview of the public health objectives of genomic sequencing are covered. This guidance focuses on SARS-CoV-2 but is applicable to other pathogens of public health concern.