And the Next Variant Is….The need to build equitable global capacity for genomic surveillance

By Shipra Srihari and Zamira Baydulloeva

By now, much has been written about the egregious global inequities in COVID-19 vaccine distribution. But less has been said about another inequity that holds serious implications for global health: the disparities in the distribution of genomic sequencing capacities and capabilities worldwide. 

What is genomic surveillance?

The genome of a virus encodes instructions (sectioned into genes) to build the virus. As viruses spread, their genomes are naturally and constantly changing or mutating. Genomic sequencing of viral genomes allows scientists to monitor these mutations in the genome of new variants of a virus, so that we can understand how these changes affect the virus and therefore if and how they might have an impact on public health. This monitoring of variants is called genomic surveillance.

In the two years that COVID-19 has been a part of our lives, we’ve encountered numerous variants of the virus, underscoring the need for both science and societies to adapt long-term. Omicron BA.2, a sub-variant of the dominant Omicron strain, is just the latest evolution in what is likely to be an ongoing dance between public health measures and viral mutation.

Genomic sequencing technologies allow scientists to decode the characteristics of viruses, compare different viral strains, and understand which viruses and variants are spreading and where. Genomic surveillance is a critical component in country and global responses to COVID-19 and other infectious disease threats, both now and in the future.

Yet today, over 60 percent of sequences submitted to the GISAID database, the online platform for open sharing of COVID-19 viral genome sequences, are from just two countries: the UK and the United States.¹ And only 1 percent of over 3.5 million COVID-19 sequences generated as of late 2021 were from the African continent.²  

This imbalance in global coverage for genomic sequencing and surveillance threatens the cohesion of a global response. Indeed, despite a historic high burden of tuberculosis compared to other countries, many Asian and African countries lack the skills and infrastructure required to conduct genomic sequencing of the pathogen that causes this disease. As a result, these countries are unable to participate fully in the surveillance and research efforts that have implications for their populations.³ 

In December 2021, at a special session of the World Health Assembly, WHO member states began a global consultative process aimed at drafting an international instrument to strengthen pandemic prevention, preparedness, and response. WHO Director General Tedros Adhanom Ghebreyesus pointed to weaknesses in the global architecture for pandemic preparedness and response as a key challenge.

The Global Health Security Agenda and WHO have also long highlighted the need for “better systems and tools to predict, prevent, detect and respond rapidly to outbreaks with epidemic and pandemic potential.” ⁴ Genomic sequencing and surveillance⁵  will be necessary long-term to guide informed public health decisions, such as deciding on lockdowns or preparing for surges that may require increased supplies and staffing. Genomic surveillance can also guide countries in selecting the most appropriate vaccines for their population,⁶ by helping them understand which variants are circulating within their borders.

The global health security community and individual countries worldwide should also direct efforts  toward ensuring that countries have the capacity to rapidly conduct genomic sequencing or can outsource it to regional laboratories. This is critical in order to quickly detect new sequences and immediately share findings with the global community. In South Africa, researchers were quick to share details of the Omicron variant with GISAID and the global community, giving countries and global organizations time to react and prepare.  The transparency with which South Africa offered this data undoubtedly aided in preparing the rest of the world for Omicron's spread -- despite the controversial response of many countries to impose flight restrictions to and from South Africa.

To address the lack of capacity for sequencing for COVID-19, the WHO and Africa Center for Disease Control have established a laboratory network which has produced 43,000 sequences⁷ from countries in Africa. A regional center of excellence in southern Africa supports 14 countries in COVID-19 sequencing. In Asia, the WHO supports countries without sequencing capacity by linking them with collaborating laboratories.  The Rockefeller Foundation has recently announced $20 million in grants,⁸ in collaboration with organizations and initiatives such as GISAID and Oxford Nanopore, to build country and regional capacity for genomic sequencing in sub-Saharan Africa, India, and the United States.

The foundation’s pandemic prevention institute will collaborate with the WHO’s Hub for Pandemic and Epidemic Intelligence. This new WHO hub focuses on strengthening pandemic and epidemic intelligence through better data, better analytics, and better decisions across all aspects of managing public health emergencies. A similar hub to serve as a global clearinghouse or coordinating mechanism that links countries to support for building their capability for genomic sequencing and surveillance could help strengthen the global response to COVID-19 and other future threats.

As a USAID partner focused on health system strengthening, the Local Health System Sustainability Project (LHSS) has been supporting COVID-19 responses in more than 10 low- and middle-income countries since the outset of the pandemic. Foreseeing that the pandemic would evolve and that health systems would need to be prepared for variants and other viral threats, we have worked with countries to increase their capacity for genomic surveillance.

• In Tajikistan, LHSS is supporting government efforts to implement the Tajikistan COVID-19 Preparedness and Response Plan. Since March 2020, the project has been a key partner to the Ministry of Health in strengthening the capacity of microbiological and virology laboratories to detect COVID-19, and has contributed to negotiations and coordination with USAID and key international partners such as WHO and the global diagnostics technology firm ThermoFisher Scientific. LHSS has supported efforts to assess sequencing needs, procure needed materials, calibrate equipment for sequencing, improve biosafety and biosecurity measurements, and build capacity of local laboratory staff through training and technical support.
• In Laos, at the start of the pandemic, few personnel were trained to perform genomic sequencing and analyze the sequence results. LHSS, through the Pasteur Institute in Laos, trained lab technicians and junior scientists on the science behind viral variants, how to perform genomic sequencing, and how to analyze the results to identify different variants in circulation. These efforts proved immensely important, providing the Ministry of Health with crucial data to adapt the response and reduce the transmission of COVID -19.
• LHSS is also supporting USAID, ministries of health, and academic partners in Jamaica, Jordan, and Kazakhstan as they seek to scale immediate and long-term capacity for genomic sequencing.

As the pandemic continues to evolve, LHSS is focused more than ever on ensuring that our project countries and partners are better-positioned to identify COVID-19 variants through genomic sequencing as well as to detect other pathogens in the future.

About the authors:

Shipra Srihari is a health systems strengthening specialist on the LHSS Project.

Zamira Baydulloeva is the regional laboratory expert for LHSS COVID-19 activities in Central Asia.

Additional contributors:

Somphavanh Somlor is a scientist with the Arbovirus and Emerging Viral Diseases Laboratory at the Pasteur Institute in Laos.

James White is the LHSS Project Senior Technical Advisor for Health System Resilience.

[1] https://www.sciencedirect.com/science/article/pii/S1201971220325571

[2] https://www.afro.who.int/news/scaling-genomic-sequencing-africa

[3] https://academic.oup.com/bib/article/22/4/bbaa246/5917386

[4] https://www.who.int/director-general/speeches/detail/who-director-gener…

[5] https://www.cdc.gov/coronavirus/2019-ncov/variants/genomic-surveillance…

[6] https://www.afro.who.int/news/why-genomic-sequencing-crucial-covid-19-r…

[7] https://www.afro.who.int/news/scaling-genomic-sequencing-africa

[8] https://www.rockefellerfoundation.org/news/the-rockefeller-foundation-a…