Strengthening genomic sequencing and bioinformatics in SEAR

The COVID-19 pandemic has seen widespread application of genomic approaches to understand the epidemiology and evolution of SARS-CoV-2 virus. The accelerated efforts to sequence SARS-CoV-2 genomes picked up pace following the initial genome sequencing of the virus from a patient in Wuhan, the epicenter for the pandemic with substantial increases at the emergence of variants of the SARS-CoV-2 virus.

WHO interim guidance on “SARS-CoV-2 genomic sequencing for public health goals” provides the basis and guidance for implementing such efforts globally. The availability of the genome sequences in the public domain has provided a unique view of the introduction, evolution, and dynamics of SARS-CoV-2 virus  in different parts of the world.

Among the most important yields of such work contributing to outbreak monitoring and response is the detection of variants of concern (VoC).  These VoCs are associated with pathogenicity of the virus and/or changes in the transmissibility, disease severity or host immunity. Furthermore, they have the potential to reduce effectiveness of medical countermeasures (diagnostics, vaccines and therapeutics).

Enhancing access to high throughput sequencing facilities and analysis capacities

The Infectious Hazard Management (IHM)  Unit of the WHO South-East Asia Regional Office in collaboration with the Public Health Laboratory scientist at the health emergencies department  is providing genome sequencing support to increase the access with quick turnaround time, as well as technical assistance in bioinformatics analysis and scientific interpretation of genomic data to its Member States.

Considering the demands that the ongoing pandemic has caused, the health emergencies department of SEARO mapped potential institutes with high scale genomic sequencing and analysis capacities within and beyond the South East Asia region.

After  the mapping exercise, the Council of Scientific and Industrial Research Institute of Genomics & Integrative Biology (CSIR-IGIB), India was identified to support  SEARO by offering  volume testing, conducting downstream bioinformatic analyses and technical capacity building in the region. The Council for Scientific and Industrial Research, Government of India (IGIB) has been one of the early laboratories globally to clinically validate the COVIDSeq approach (Bhoyar et al 2020). The institute pioneered state-wide genomic surveillance programmes in India that are working closely with the states of Kerala and Maharashtra. The institute is one of the key and founding members of the Indian SARS-CoV-2 Genomics Consortium (INSACOG) initiative for genome sequencing and surveillance of SARS-CoV-2 in India and maintains the central analysis of genomic surveillance data  as well as data repositories in the country.

As far as   CSIR-IGIB support to Member States  is concerned, so far nearly 1600 specimens have been sequenced at the CSIR-IGIB for Maldives and Nepal with appropriate material transfer agreements being signed between these countries and CSIR-IGIB. Further CSIR-IGIB has also assisted these countries to submit their data on global databases.

SEARO with the support of  IGIB has organized one onsite training for Maldives in New Delhi. More online/offline training sessions will be conducted to help Member States establish better understanding of how to apply genomic surveillance for SARS-CoV-2.

As part of WHO’s agreement  with IGIB,  SEARO with the assistance of IGIB is  finalizing laboratory standard operating procedures (SoP) for sequencing and bioinformatic analysis (country specific). Once all countries have completed their SoPs, a regional publication will be curated in the form of a handbook.

With this effort, it is envisioned that the Member States of SEAR will have timely access to genomic characterization facilities to better handle the ongoing COVID-19  pandemic and also build domestic capacity  for  genomic surveillance with  sequencing as a part of  preparing for any future outbreaks.