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Global health authorities have recommended sequencing the viral genomes of 5% or more of all confirmed COVID-19 cases, but most countries are lagging far behind that goal. Choose a dataset for a map of the sequencing progress, caseload or number of genomes sequenced in each nation.




Percentage of COVID-19 genomes that have been sequenced

Number of confirmed COVID-19 cases


Under 1%
10 million or more

1%-4.9%
1 million-9,999,999


To see the data for a specific nation, select from the drop-down menu or place your cursor over the map.

Maniatis and Soren Germer, who leads the sequencing and analytics teams at NYGC, said that obtaining samples had been the biggest challenge in the U.S. “During the early days of the pandemic when New York was particularly hard hit, even the most research-focused hospitals often did not have the resources to collect samples for research,” they explained by email. “We have heard stories of truly heroic efforts to save some of these samples for research and surveillance,” but the severely strained hospitals had to prioritize treating patients and protecting staff. Maniatis and Germer also pointed to a lack of coordinated funding in the U.S., which has been uneven at the state and local level and has only recently begun at the federal level.

Rolf Apweiler, director of the European Bioinformatics Institute, says that the nations depositing SARS-CoV-2 sequences into the dedicated genome data platform that his organization operates also vary substantially in their ambitions. While some countries aim low or have no genomic surveillance of SARS-CoV-2, he said, “countries like Denmark, Iceland, Australia and the U.K. aim to sequence between 10% of all positive samples in times of high infection rates and all positive samples technically feasible in times of low infection rates.”

The genome sequencing effort may already be bearing fruit for some of the countries engaging in it most vigorously. COG-UK is a consortium of genomic experts working to track, trace and control the SARS-CoV-2 virus in the U.K. It formed when the country’s scientists took steps early in the pandemic to ensure genomic sequencing at scale, aided by £20 million from the government. Within weeks of its formation in March 2020, the consortium had made the first sampled genomes publicly available; it has now sequenced more than 450,000 virus genomes.

O’Grady credits that work with helping to contain the pandemic in the U.K. “Genome sequencing identified the B.1.1.7 variant, providing us with an answer as to why case numbers were increasing dramatically towards the end of 2020 and enabling us to implement successful control measures,” he said. When other variants were discovered in South Africa and elsewhere, U.K. authorities increased the testing and contract tracing efforts and curtailed the spread of the variants into the country.

Preparing to Fight On

Many countries are now working to scale up their sequencing programs. In February, the CDC pledged $200 million as a “down payment” for genome surveillance. In April, the Biden administration dedicated $1.7 billion to boosting sequencing efforts and fighting variants of SARS-CoV-2. “The U.S. is now investing heavily in sequencing with the realization that the gains we’ve made are fragile and could be upended by viral variants,” O’Connor said.

In January, the Indian government set up the Indian SARS-CoV-2 Genomics Consortium to expedite the gene sequencing effort through a growing network of institutions. The nationally coordinated genome-sequencing program has sequenced more than 15,000 genomes in about three months, said Anurag Agrawal, a senior scientist with the consortium and director of the CSIR-Institute of Genomics and Integrative Biology in New Delhi, one of the participating institutions. “I expect the numbers to keep getting better,” he said.

The situation is improving in Africa, too. Segun Fatumo, an assistant professor of genetic epidemiology and bioinformatics at the Medical Research Council/Uganda Virus Research Institute, said that African governments urgently need to provide funding for relevant research and infrastructure. But he also noted that Africa has been moderately successful in the fight against the coronavirus, and genome sequencing has greatly contributed to this.

“The WHO has established a network of COVID-19 genomic sequencing laboratories across Africa” in 18 countries, he said. “Africa is central to human origin and disease susceptibility, so large-scale genomic study in populations of African descent might yield potential therapeutic strategies.”

Apweiler feels that a pandemic can be successfully managed only if it is tackled at a global level with as much coordination and collaboration as possible. “A problematic new lineage of SARS-CoV-2 in one country may become a worldwide problem very quickly,” he said. “Our response to the pandemic will be globally only as strong as the weakest part of the global efforts.”

Moi agrees about the importance of sequencing, but also suggests that it will always be necessary to balance that effort against other local priorities to ensure the best public health impact. “Particularly during large outbreaks, sequencing large numbers of virus [genomes] may not be practical” and could increase the burdens on laboratories and medical facilities that are already under pressure, she said. But she is also confident that “with optimal sequencing strategies in place, powerful insights can still be achieved with well-planned sampling and testing.”

Preventing Future Pandemics

“Had the pandemic happened even five years ago, it would have been a lot more difficult to implement genomic surveillance programs at scale,” O’Connor said.  “The technologies to democratize sequencing and make it available to small laboratories and public health authorities simply weren’t available.”

The infrastructure and technology developed to map the virus could also be beneficial beyond COVID-19. “Our next hope is that the detailed observation of viral evolution during the pandemic and the research will help with the more rapid development of targeted therapeutics in future pandemics,” Maniatis said.

To him, the real question is whether the informational networks and infrastructure will enable viral surveillance to become routine, so that the discovery of the next potential pandemic virus can be a normal part of the public health system. The WHO has called the integration of genome sequencing into the regular practices of the global health community “a must” in preparations for future threats.

Haussler agreed that building global pathogen sequencing and genome sharing capability could help prevent future viral outbreaks. “It is one of the most important investments the world can make at this point,” he said. “It is likely to save many lives and many trillions of dollars in the long run.”

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