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.