Next generation sequencing (NGS) and bioinformatics are being increasingly used in infectious disease surveillance. Genomic surveillance leverages NGS and bioinformatic analysis in identifying outbreak origins, tracking transmission dynamics and pathogen evolution, and developing countermeasures such as vaccines. The emergence of SARS-CoV-2, including its many variants has reiterated the prominent role NGS and bioinformatics play in pathogen genomic surveillance.
Genomic sequencing and bioinformatics remain complex technologies, and as with most new and evolving technologies, implementation can prove challenging. Those challenges range from access to appropriate tools (sequencing platform, computation and information technology infrastructure), use of suitable methodologies (sequencing approach and choice of bioinformatics methodologies), to the availability of adequately trained workforce (supply and retention of specialists).
Prior to the COVID-19 pandemic, NGS was being used for TB surveillance in the National TB Reference Laboratory, National TB Center, Bishkek City. This capability was leveraged in response to the COVID-19 pandemic with the support of WHO Regional Office for Europe (WHO/EURO) and German Epidemic Preparedness Team (SEEG) of Deutsche Gesellschaft für Internationale Zusammenarbeit GmbH. This was in addition to the implementation of the multisectoral contingency plan to strengthen the country's laboratory capacity for COVID-19. In collaboration with the Ministry of Health and Department of Disease Prevention and State Sanitary and Epidemiological Surveillance (DDP&SSES), laboratory specialists from the National TB Center commenced sequencing for SARS-CoV-2 in 2021. The National TB Reference Laboratory serves as a learning hub for laboratory specialists from the National Influenza Center, the High Threat Pathogens and HIV Center to increase country capacity on genomic sequencing. However, one major implementation challenge was the lack of experts in bioinformatics. Recognizing the need to build an adequate workforce to accelerate and sustain capability for genomic surveillance, Kyrgyzstan prioritized specialized training for NGS and bioinformatics.
With the support of WHO/EURO, a training on Bioinformatics for Molecular Epidemiology of SARS-CoV-2 was conducted for laboratory specialists involved in SARS-CoV-2 diagnostics in April 2022. The training aimed to strengthen the NGS and bioinformatics capacity for SARS-CoV-2 surveillance and its application to other emerging and re-emerging pathogens of epidemic and pandemic potential. In June 2022, beneficiaries of the training in the National TB Reference Laboratory shared sharing the SARS-CoV-2 genomic sequence data on GISAID. As of August 2022, over 300 SARS-CoV-2 sequences have been generated and shared, largely by national experts in Kyrgyzstan.
"Sharing the genomic sequence data on GISAID is a result of great partnership with national and international partners. Continuous support and fruitful collaboration with the WHO Europe Regional Office played a key role in this accomplishment."
- Altyn Iskakova, Microbiologist, National Tuberculosis Reference Laboratory, Kyrgyzstan
Kyrgyzstan is committed to scaling up genomic sequencing and bioinformatics for public health at the national level.
"With the aim of supporting the use of genomic epidemiology in decision-making for public health, and openly and rapidly sharing the genomic sequence data in the collective effort of public health surveillance, Kyrgyzstan is committed to scaling up its genomics capabilities by bridging the workforce gap (laboratory specialists, public health practitioners and policy experts) and providing adequate infrastructure".
- Aigul Djumakanova, Head of Department of Disease Prevention and State Sanitary and Epidemiological Surveillance Laboratory Service, Kyrgyzstan
One of the objectives of the Global Genomic Surveillance Strategy for Pathogens with Pandemic and Epidemic Potential 2022–2032is to "strengthen the workforce to deliver at speed, scale and quality." This can be achieved through the implementation of training packages in genomic sequencing and bioinformatics. Outputs from workforce strengthening for genomic surveillance will enable the country to prepare and respond to effectively to the COVID-19 pandemic and other pathogens with pandemic and epidemic potential.
