Bioinformatics training workshops to strengthen genomic surveillance successfully completed

The WHO Global Influenza Programme in collaboration with GISAID has successfully completed a series of three-module bioinformatics workshops to support Member States to expedite the genomic surveillance of SARS-CoV-2 using existing influenza surveillance systems.

The course was attended by a total of 486 laboratory experts from National Influenza Centres (NICs) or National COVID-19 laboratories from 105 different countries, across all six WHO regions. It was designed to: scale-up Global Influenza Surveillance and Response System (GISRS) SARS-CoV-2 genomic surveillance and data sharing; equip NICs with the skills to access, use and contribute to GISAID databases, platforms, and tools; and enable NICs to transfer sequencing and bioinformatics skills from SARS-CoV-2 to influenza and RSV.

GISRS is currently being expanded to GISRS Plus, an integrated surveillance network for influenza, SARS-CoV-2, respiratory syncytial virus (RSV), and other future respiratory viruses of pandemic and epidemic potential. Robust genomic sequencing surveillance, for which GISAID has proved to be an extensive data sharing and analysis platform, is essential to monitor the continuous evolution and transmission of circulating and newly emerging variants. The platform aids with risk assessments and with the timely development of interventions. In line with this objective, GISRS and GISAID successfully completed a series of joint bioinformatics training workshops in 2022 to support GISRS laboratories.

The course was divided into three modules (beginner-intermediate-advanced). It comprised webinars, online demonstrations, and offline exercises. Participants were divided into groups based on time zone and language spoken (interpretation of French, Spanish, and Russian was made available as required). Module one aimed to improve genomic surveillance coverage by targeting laboratories not yet submitting data to GISAID and was attended by more than 110 specialists from 40 countries. It covered the basics of virus sequencing; considerations for the genomic sequencing component of GISRS surveillance of SARS-CoV-2; and the submission, curation, annotation, and basic interpretation of data using GISAID tools.

Module 2 targeted laboratories already generating sequence data and submitting to GISAID, but with little in-house expertise for sequence analysis. This module was attended by more than 270 individuals from 80 countries. Participants learned how to use GISAID tools to monitor specificity of primer sequences for amplification of circulating virus strains, identify specific mutations of concern, and to track emerging variant viruses. The fundamentals of phylogenetics and phylogenetic tree interpretation were also covered.

Module three aimed to engage those laboratories with bioinformatics expertise to use GISAID data and analysis tools to create reports for publication and national surveillance, and to demonstrate the versatility of GISAID for genomic surveillance of multiple pathogens. It was attended by 200 participants from over 70 countries. Participants learned how to upload large numbers of SARS-CoV-2 sequences using a command line interface and how to visualise their own data using the GISAID tool, Augur. Common sequencing and bioinformatics challenges were discussed, and tips to create a situation report with phylogenetic data, interpretations and conclusions were shared.

Increased and improved genomic surveillance and data sharing to GISAID will continue to aid GISRS plus in its objective to provide a global mechanism for preparedness and response for epidemics, pandemics, and zoonotic outbreaks and continue to act as a global alert mechanism.

/Public Release. View in full here.