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Genomic outbreak surveillance in resource-poor settings

Viral disease outbreaks are common in Africa, often starting in remote areas at the animal–human interface, with the potential to reach epidemic proportions. For example, the West African Ebola outbreak of 2014–2016 received significant international attention owing to its scale (~28,000 infected, ~11,000 dead) and international cases. Coincidentally, 2014 saw the development of an affordable, highly portable sequencing device that measures the disruption of ion charges caused by the different nucleic acid bases when a DNA strand passes through a nanopore. This palm-sized device was unlike conventional whole-genome sequencing platforms, which were large and non-portable, required a steady power supply and, if moved, needed extensive calibration. A paper by Quick et al., who were part of the swift international response to the Ebola outbreak, demonstrates how leveraging a novel sequencing technology challenged the notion that genomic surveillance could not be carried out in resource-poor field settings.

Quick et al. elegantly describe their steps to surmount all previous barriers to conducting on-site Ebola virus genome sequencing in remote settings using this new mobile nanopore sequencing technology. First, to generate enough material for sequencing from patient samples, they optimized a targeted reverse transcriptase PCR protocol using 38 primers sets to amplify the RNA genome of the Ebola virus and identified a minimal 11-amplicon set to cover 97% of the 19 kb Ebola virus genome.

Second, they deployed a 50 kg sequencing tool kit, including the nanopore device, laptops, supplies and reagents, on a commercial airline to Guinea and set it up in an Ebola treatment unit at the heart of the epidemic. The nanopore was unaffected by the power surges and outages, confirming its field readiness.

Third, a well-validated bioinformatics analysis workflow yielded sequence alignment results, assigned genotypes, identified variants and phylogenetic clusters comparable to Illumina sequencing reads. The few exceptions were due to the masked primer binding domains, gaps in primer coverage and challenges in sequencing homopolymer stretches. The investigators noted that the limitations of nanopore sequencing did not significantly alter the key outcomes.

The study demonstrated that the team could get from patient samples to genomic analysis within 24–48 hours. They analysed 142 Ebola viruses over 6 months but, already within 10 days of analysis, could determine that two distinct lineages of strains — the endemic Guinean GN1 strain and a strain from Sierra Leone SL3 — caused the Guinea outbreak, with evidence of cross-country transmission.

Previous strategies, where patient samples were shipped to other countries for testing, had delayed information required to take appropriate treatment and control measures. The extensive network of collaborations and open genomic data sharing by Quick et al. promoted rapid epidemiological analysis and contributed to public health action.

Although the paper emphasizes the deployed genome sequencing capability, it is worth noting that the computational whole-genome sequence analysis was conducted overseas. The authors cite a lack of internet access as the reason and major limitation to running genomic analyses in the field. However, genomic sequencing capacity is incomplete without deploying analysis capacity. Moreover, the exportation of data to other countries for genomic analysis raises problematic ethical issues regarding the ownership of data and creates a dependency on the international community’s interest and goodwill, which does not promote genomic equity.

…leveraging a novel sequencing technology challenged the notion that genomic surveillance could not be carried out in resource-poor field settings

Many epidemics only affect populations in under-resourced environments, which lack the genomic epidemiology capability to control the outbreaks. The paper by Quick et al. demonstrates how the adoption of a new technology in a pandemic can cause paradigm shifts in how and where genome sequencing is conducted. The SARS-CoV-2 pandemic fueled massive growth in sequencing capability, with more countries beginning to conduct routine genomic epidemiological surveillance, mainly because of the accessibility and ease of use of portable nanopore sequencers. But we should not wait for the next pandemic to achieve full genomic equity, enabled by the end-to-end capability to sequence and analyse genomic data for public health in under-resourced settings!


Original article

  • Quick, J. et al. Real-time, portable genome sequencing for Ebola surveillance. Nature 530, 228–232 (2016)

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Related article

  • Deamer, D. et al. Three decades of nanopore sequencing. Nat. Biotechnol. 34, 518–524 (2016)

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Correspondence to Lillian Musila.

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Musila, L. Genomic outbreak surveillance in resource-poor settings. Nat Rev Genet (2022).

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