Concerted effort among different collaborators is required to generate a public health response for the control of disease outbreaks. Among the collaborators, public health laboratories play a major role as they answer the “What is causing this disease?” question. This is through sequencing samples to detect pathogens of concern. However, sequencing laboratories use different bioinformatics platforms to get this data. This creates a common data sharing challenge – the lack of interoperability of datasets and databases.
To minimize such a challenge, our consortium’s Data Structure Working Group developed two standardized open-source tools: “hAMRonization” a gene detection output for anti-microbial resistance [(AMR) – quick facts] and a contextual data specification for severe acute respiratory syndrome coronavirus 2 [(SARS-CoV-2) -quick facts]. With support from other Working Groups in the consortium, there is uptake and utilization of these specifications across different public health laboratories globally.
Notably, in select low to middle income countries (LMICs), funds from the Bill and Melinda Gates Foundation have become instrumental to further utilization of this specification and other advancements in bioinformatics for public health. Ten research teams will be partnering with national public health laboratories to implement standardized bioinformatics practices, pipelines, and data structures in either AMR or SARS-CoV-2 sequencing.
In this edition, we share the profiles of the recipients of these sub-awards.
AMR theme recipients are from Cambodia, Malaysia and Nigeria. Teams will build genomic AMR surveillance capacity in their countries and regionally through: 1) developing data structures for AMR pathogens relevant to their region 2) implementing bioinformatic pipelines to analyse genomic AMR data, where required 3) AMR data exchange and comparison across partner laboratories and beyond 4) conducting training sessions coupled with support visits to each sentinel site on next-generation sequencing (NGS)- (applicable to Nigerian context only).
For the SARS-CoV-2 theme, the recipients are from Fiji, Kenya, Malawi, Nigeria, Pakistan, The Gambia and Zambia. Teams will focus on strengthening SARS-CoV-2 disease surveillance and where possible, identification of variants of concern in their regions and globally through: 1) establishing sequencing protocols that can generate high-quality SARS-CoV-2 sequence data 2) training and capacity development in bioinformatics -protocol and automated bioinformatics pipeline development, sequencing and data analysis of bioinformatics workflows 3) presenting analysed data among partners in a form suitable for public health utility and inform public health policy 4) uploading SARS-CoV-2 sequence data and relevant metadata onto international genomic databases 5) growing regional scientific capacity to tackle the ongoing and future pandemics by establishing new and strengthen existing partnerships.
