Ebola Outbreak Prevention: Scientists Use First-Ever Large Scale Genomic Sequencing

Amidst the political stability and conflict that coincided with the 2018-2020 Ebola outbreak in the Democratic Republic of the Congo (DRC), scientists performed genomic sequencing of the pathogen on an unprecedented scale.

These scientists, Eddy Kinganda-Lusamaki at the National Institute of Biomedical Research in Kinshasa, Trevor Bedford at the Fred Hutchinson Cancer Research Center in Seattle, Washington, and their colleagues report that they sequenced viral samples that represented about 24 percent of validated Ebola infections, despite facing shipping woes, Internet connection problems, and worse physical violence. Findings show the outbreak started around a month prior to the first diagnosed case.

How the Latest Ebola Outbreak Began

The study, "Integration of genomic sequencing into the response to the Ebola virus outbreak in Nord Kivu, Democratic Republic of the Congo" also confirmed that a taxi driver transmitted the virus to several people, and other cases were connected to a pastor's funeral. Because of this, the Ebola vaccination policy was altered to include members of the clergy and taxi drivers.

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Congolese scientists also carried out the sequencing in the DRC during the West African Ebola outbreak from 2013 to 2016 with research done in the US and Europe. This comes as Ebola would persist in a person's body leading to new outbreaks, such as the 2018-2020 spread.

An end-to-end genomic surveillance system was used, and this included sequencing, bioinformatic analysis, and the distribution of genomic epidemiologic results to frontline public health workers, thus preventing a spread. This system provided viral whole-genome sequencing, bioinformatic analysis, and dissemination of genomic epidemiologic results to frontline public health workers. Genomic surveillance data were also used to broadly describe epidemic dynamics.

744 New Genomes Sampled

Findings show 744 new genomes that were sampled from July 27, 2018, and April 27, 2020, that were generated by the surveillance system. Inclusive of past sequence data, the current surveillance data represent about 24 percent of laboratory-confirmed Ebola virus infections in DRC in the said period.

"Our findings suggest that the frequent movement of viral lineages between health zones sustained the epidemic, with only a small number of lineages circulating locally within a health zone over longer periods of time," researchers penned in the study.

Researchers inferred spatiotemporal transmission dynamics from the genomic data with the generated new sequences and disseminated the findings to back epidemiological response efforts.

Their work on the 2018-2020 Ebola outbreak shows how genomic surveillance for outbreak response has progressed.

"The value of building capacity within a country is demonstrated not only by our work here but also by the sustainability of a system that can be shifted to other surveillance efforts. Indeed, using this same genomic surveillance system we are now providing much-needed epidemiologic support for understanding SARS-CoV-2 epidemiology in the DRC," the researchers said.