Background: The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatics tools and resources, and advocate for greater openness, interoperability, accessibility, and reproducibility in public health microbial bioinformatics. In the face of the current pandemic, PHA4GE has identified a need for a fit-for-purpose, open-source SARS-CoV-2 contextual data standard. Results: As such, we have developed a SARS-CoV-2 contextual data specification package based on harmonizable, publicly available community standards. The specification can be implemented via a collection template, as well as an array of protocols and tools to support both the harmonization and submission of sequence data and contextual information to public biorepositories. Conclusions: Well-structured, rich contextual data add value, promote reuse, and enable aggregation and integration of disparate datasets. Adoption of the proposed standard and practices will better enable interoperability between datasets and systems, improve the consistency and utility of generated data, and ultimately facilitate novel insights and discoveries in SARS-CoV-2 and COVID-19. The package is now supported by the NCBI’s BioSample database.

The Protection of Personal Information Act (POPIA) [No.4 of 2013] is the first comprehensive data protection regulation to be passed in South Africa and it gives effect to the right to informational privacy derived from the constitutional right to privacy It is due to come into force in 2020, and seeks to regulate the processing of personal information in South Africa, regulate the flow of personal information across South Africa’s borders, and ensure that any limitations on the right to privacy are justified and aimed at protecting other important rights and interests. Although it was not drafted with health research in mind, POPIA will have an impact on the sharing of health data for research, in particular biorepositories. It is now timely to consider the impact of POPIA on biorepositories, and the necessary changes to their access and sharing arrangements prior to POPIA coming into force.

Antarctic biota evolved under the influence of a suite of geological and climatic factors, including geographic isolation of the landmass and continental shelves, extremely low temperatures and seasonality. Current warming trends in the continent and surrounding oceans may trigger substantial shifts in community composition and biodiversity, impacting the dominance of cold-adapted over more generalist species. Until recently, the diversity of microorganisms in cold environments was investigated only in terms of distribution, with little attention to their functional roles in important environmental processes. The ‘omic’ methodologies now offer effective tools to investigate the relationships between biodiversity and ecosystem functioning and to understand the evolutionary principles of adaptation and tolerance/resistance to extreme conditions. In this review we summarise how cold temperatures affect the physiology of microorganisms and focus on the molecular mechanisms of cold adaptation revealed by recent biochemical and genetic studies.

The POPIA Code of Conduct for Research, as it is currently being considered, pertains to research conducted in South Africa, which, as part of the research process, uses personal information as defined under POPIA. This Discussion Document outlines the main areas relating to the processing of personal information for research purposes which the proposed Code will address, including what consent models would be permissible under POPIA; the issues in relation to genetic research and the processing of personal information contained in inherited characteristics; the use of information matching programmes by researchers; and the use of personal information obtained from social media platforms for research. With ongoing and wide consultation with the scientific community in South Africa and all relevant stakeholders, it is hoped that the Code will provide guidance in supporting the lawful and responsible use of personal information while conducting scientific research in South Africa. The purpose and scope of the Code of Conduct for Research are set out in the accompanying Commentary available at https://doi.org/10.17159/sajs.2021/10935