FOCUS | feature Methods for fighting emerging pathogens We asked scientists around the globe for their views on the basic research methods, tools and resources needed to fight future emerging pathogenic threats. Luiz Carlos Junior Alcantara: The COVID-19 pandemic has reshaped the world in a variety of ways, leading to millions of cases and deaths globally, economic decline, disruption to the social fabric and many other hardships. This emphasized that country-level strategies for pandemic preparedness need to be put in place throughout the world. Recently we have established a mobile national network in Brazil, called VigECoV-2, for real-time genomic sequencing, genomic epidemiology and data analysis in public health laboratories. We believe that this methodology can be a powerful toolkit for quickly identifying emerging viral threats, monitoring the evolution of their genomes, understanding the origins of outbreaks and epidemics, predicting future outbreaks and helping to maintain updated diagnostic methods through the generation of data that can inform outbreak control responses. Lucas Amenga-Etego: Nanopore sequencing technology has been critical in tracking SARS-CoV-2 spread and identifying and classifying variants. Key challenges have been to increase the sensitivity for samples containing low concentrations of RNA (with C t values >25), and to innovate and develop robust assembly tools to understand how these samples, which currently fail to be detected through sequencing, may influence viral evolution and spread. It may also be useful to attempt primer-free sequencing approaches with Nanopore sequencing methodology to make experiments cheaper and faster. Additionally, mitigating the effects of future pandemics will require robust, high-throughput model systems and organisms to use to fully understand host immune response and identify viral entry inhibitors and neutralizing agents. Robin Andersson: Enhancers play a key role in activating and maintaining functional phenotypes for controlling disease. Better understanding of the mechanisms through which enhancers regulate gene activity may therefore provide crucial insights into disease pathogenesis and, ultimately, prevention or treatment. For this, new assays are needed that can capture regulatory activities in single cells, at large scale and with high sensitivity, allowing the establishment of probabilistic models of transcriptional regulation based on the stochasticity of regulatory events. From there, interpretable and generalizable computational models need to be devised that allow inference of the determinants of regulatory activity of individual enhancers and the functional interplay of multiple enhancers within regulatory domains. Moumita Bhaumik: Much progress has been made in the field of vaccine research during the COVID-19 pandemic. However, the efficacy of these vaccines in immunocom- promised individuals remains uncertain. Therefore, there is a need to develop delivery systems that will better serve immunocompromised subjects. Use of trained immunity or innate immune memory can be exploited to cause such individuals to mount more robust immune response. Expressing the antigen of interest in a trained-immunity-based vector, such as Bacillus Calmette–Guérin (BCG), will help to stimulate both innate and adaptive immune memory and will enhance the efficiency of vaccines. With the addition of cytokines as adjuvants and with delivery by liposomes or nanoparticles, BCG-based vaccines will open up new avenues of exploration for the generation of vaccines against pandemic pathogens. Young Ki Choi: Following the flu and COVID-19 pandemics, the continuous outbreaks of novel viral infections underscore the threats of the next potential pandemic, the so-called ‘Disease X’. However, a vast number of viruses cannot be studied well in vitro due to the lack of readily available culture systems for predicting viral infectivity. Organoids, which mainly represent cultured tissue derived from stem cells, could be a valuable tool for studying viruses that are difficult to culture in vitro. The physiological and structural similarities of organoids to specific tissues or organs provide also better resolution of virus–host interaction dynamics that are invisible in two-dimensional systems. Given these advantages, organoid-based culture systems will be invaluable for studying the as-yet-unknown new pandemic candidates that will succeed SARS-CoV-2. Hélène Decaluwe: The past decade has seen an extraordinary burst of knowledge about T-cell-mediated immune responses to pathogens, thanks to the development of powerful flow and mass cytometry approaches combined with single-cell transcriptomic pipelines and T cell receptor (TCR) sequencing approaches. These technological advances have revealed the diversity and heterogeneity of the T cell pool following infections and have shed light on the cellular and molecular parameters shaping effective and long-lasting immune responses in the host. Developing high-throughput technologies to assess T cell responses to viruses of pandemic potential in large cohorts of subjects efficiently will be essential for the effective assessment of the next pandemic. Further, we will need to develop accessible bioinformatic pipelines to efficiently and reliably identify immunogenic epitopes based on identified TCR sequences. Credit: CHU Sainte-Justine – Stéphane Dedelis FOCUS | FEATURE NATURE METHODS | www.nature.com/naturemethods