Genetic information derived from pathogens is an increasingly essential input for infectious disease control, public health and research. While the technical developments of sequencing technology are being implemented at a rapid pace, the non-technical aspects of implementing this technology are still being broadly discussed. The successful implementation of this rapidly developing technology will, for example, require sharing of samples and metadata, interdisciplinary global collaborative partnerships, and will need to offer useful evidence for public health decision-making. Importantly, appropriately addressing these challenges will require the systematic identification, and analysis of a number of complex ethical, legal and social issues. A number of factors will contribute to the types of ethical issues that arise in different instances. These are likely to include characteristics of the disease, the environmental, political and geographical context, existing laws and policies, public attitudes, and cultural differences. This talk will identify the emerging ethical challenges; assess the gaps in ethical frameworks or thinking, and consider how ethics can help to solve practical challenges.