Funding unlocked during the COVID-19 pandemic allowed many countries in Asia and Africa to perform in-house genome sequencing, resulting in faster results and action that can help stem the spread of disease. Previously, samples would be sent to distant labs for analysis. Now, many countries are using the increased capacity to analyze samples from other outbreaks, including cholera, Ebola, polio, and malaria. However, researchers warn that continued funding is necessary to maintain the surveillance equipment, purchase supplies, and provide necessary training for sequencing samples other than SARS-CoV-2.
Sequencing data provides a powerful tool in public health. When combined with other clinical information, it can be used to diagnose diseases, identify chains of transmission, accelerate the public health response, and advance vaccine development. The benefits of having labs located closer to outbreaks was evident during the pandemic as it accelerated tracing and increased efficiency.
Benefits of In-House Analysis
The Pasteur Institute of Cambodia in Phnom Penh, for example, used the genome-sequencing technology it purchased during the pandemic to quickly confirm that a three-year-old boy had avian influenza. They were able to sequence samples of the virus from a chicken living in the boy’s house and thereby determine that the virus was unlikely to spread. This source was identified in a single day, compared to what would have been a much longer timeline before the pandemic. The lab is now looking to use this technology for other pathogens. The shift to expand the technology’s use is happening across the region.
In Africa, 38 countries now own next-generation sequencing equipment. Labs across those countries sequenced more than 140,000 SARS-CoV-2 genomes since 2020. “Since early 2022, we’ve been thinking about how to utilize this capacity for other pathogens,” Sofonias Tessema, who leads the pathogen genomics initiative at the Africa Centers for Disease Control and Prevention in Addis Ababa, reported to Nature. For example, when case of Ebola was identified in the Democratic Republic of Congo, samples were analyzed at a lab in Goma which could provide results much faster than the facility across the country in Kinshasa.
Opportunities and Challenges
The shift from studying SARS-CoV-2 to endemic pathogens provides new opportunities for research and collaboration across the laboratories but also creates challenges as lab personnel require additional training on how to interpret the data for other diseases. Organizations including the Bill and Melinda Gates Foundation in Seattle, Washington have announced grants to support sequencing pathogens other than SARS-CoV-2.
Despite these grants, researchers are concerned that increased costs and diminished pandemic funding will cut off testing capacity. Philanthropic funding does not typically go toward the maintenance costs that would be needed to continue the surveillance efforts. Without money to purchase supplies, maintain the equipment, and train the staff, the sequencing technology could go unused. However, standardizing processes for sequencing pathogens other than SARS-CoV-2 could help reduce the costs.
The Asia Pathogen Genomics Initiative (PGI), among others, will support the ongoing surveillance efforts. As Paul Pronyk, an infectious disease physician and global health specialist at Duke-NUS medical school, which supports the PGI, reported to Nature, “The days of sending your specimens overseas for analysis are numbered.” He notes that finding funds to support the continued surveillance will be a priority for the PGI moving forward.
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