The crucial role of effective genomic surveillance
With the COVID-19 pandemic progressing, genomic surveillance, conducted in an efficient way, is essential to inform us of circulating viruses and response measures required. The sequencing of representative samples continuously collected in a standardized approach from patients meeting influenza-like illness, acute respiratory infection, and severe acute respiratory infection case definitions, allows us to monitor the evolving trends and relative proportions of existing and emerging genetic variants circulating in the community.
GISRS has monitored influenza viruses since 1952, and since March 2020, SARS-CoV-2 was added to GISRS. In February 2021, the Global Influenza Programme (GIP) published Operational considerations to expedite genomic sequencing component of GISRS surveillance of SARS-CoV-2, to improve the geographic, demographic and temporal representativeness of data, monitor the trends and prevalence of genetic variants, and better understand the associations among the genetic characteristics, transmission fitness and disease profiles of SARS-CoV-2. In October 2021, GIP hosted an e-consultation to update the Operational Considerations and incorporate them with the previously published guidance document Maintaining surveillance of influenza and monitoring SARS-CoV-2: adapting Global Influenza Surveillance and Response System (GISRS) and sentinel systems during COVID-19 pandemic. This new publication is due for publication soon.
GISAID has been an important partner of GISRS, and its EpiFlu database has been a key component of influenza surveillance since 2008. At the start of COVID-19 pandemic GISAID rapidly launched the EpiCoV platform, where the first complete genome of SARS-CoV-2 was shared globally, and various analytical tools were developed to support the rapid sharing and interpreting of SARS-CoV-2 data.
GISRS-GISAID collaboration on influenza has been expanded to other respiratory viruses including SARS-CoV-2 and Respiratory Syncytial Virus (RSV). A joint bioinformatics training programme was developed to support WHO Member States to expedite the effective genomic surveillance of SARS-CoV-2 using influenza surveillance systems.
Training workshops organized
To further strengthen GISRS genomic surveillance capacity, the WHO Global Influenza Programme and GISAID jointly organized a series of workshops with experts from National Influenza Centres (NICs) and National COVID-19 laboratories. The objectives of the training includes:
- Scaling up GISRS SARS-CoV-2 genomic surveillance, data sharing and interpretation of SARS-CoV-2 bioinformatics; and
- Equipping NICs with the skills to access, use and contribute to GISAID databases, platforms and tools, from SARS-CoV-2 to influenza and RSV.
The course is divided into three modules, from basic to advanced levels.
Module 1 (Introductory) was recently completed. It was attended by more than 110 experts from over 40 countries across the world, from Algeria and Australia to the United States and Venezuela. It comprised online lectures with real-time demonstrations followed by offline exercises. The training was held over a period of several months and grouped into five small groups according to their time zone and language spoken.
The module 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 (Intermediate) and Module 3 (Advanced) will be launched in the coming months.
As we have learnt from the COVID-19 pandemic, an effective genomic surveillance system using GISRS to monitor SARS-CoV-2, as well as for influenza, is a critical component of pandemic and post-pandemic response. WHO will continue to strengthen the global network of laboratories of GISRS.
