A Lack of COVID-19 Genomes Could Prolong the Pandemic Quanta Magazine – Quanta Magazine

More variants will undoubtedly emerge over time, and it is unclear how much these variants will complicate, or even set back, efforts to bring the pandemic to an end. Ongoing genomic sequencing is key in identifying the emergence of vaccine escape variants, Moi said. This makes it all the more troubling that most nations have failed to even come close to the levels of genome sequencing that may be needed.

The state of the genomic surveillance situation is grimmest in 38 countries with reported COVID-19 infections but no sequencing data shared with Gisaid. These make up some of the poorest countries in the world, such as Chad and Burundi. The African continent, as of June 27, has reported more than 5.3 million infections (3.9 million of these are confirmed), but its countries have sequenced and released only about 22,700 genomes, or at best only 0.6% of its cases. More than 40% of those genome sequences (about 9,600) come from just one country, South Africa.

The consequences of the paucity of data on Africa could be serious for people everywhere. Africa, given its human population variation, is a candidate to becoming the source of ever more pathogenic and refractory strains, said Muntasar Ibrahim, a Sudanese geneticist and professor of molecular biology at the University of Khartoum, where he leads its Institute of Endemic Diseases.

Shortfalls in sequencing cannot be blamed simply on a lack of money. (Sequencing costs about $120 per SARS-CoV-2 genome, but the costs can be significantly lowered by sequencing the genomes in large batches, according to Haussler.) Some of the poorest countries have sequenced more of their cases than some of the richest countries, so wealth cannot be the only determining factor. Gambia, for instance, at 7.8%, has sequenced more than Germany (3.6%), a country with 60 times its gross domestic product per capita.

Nor do low rates merely reflect how hard countries have been hit by the pandemic. About 10% of the U.S. population has had COVID-19, resulting in a low sequencing rate (1.7%) even though the U.S. has sequenced the most SARS-CoV-2 genomes. But the U.K., where about 7% of the population has had the disease, has sequenced more than 10% of its caseload: It has only the 13th-highest rate of sequencing in the world, but it has sequenced more virus genomes than all the countries ahead of it put together.

What really seems to have determined the genome-sequencing performance of countries during the pandemic is a combination of their strategic choices and biomedical infrastructure.

Tom Maniatis, chief executive officer of the New York Genome Center (NYGC), noted that COVID-19 surveillance in the U.S. has been compromised by a systemic lack of connections between facilities that have samples of the virus hospitals, public health laboratories and commercial testing facilities and facilities with the capacity to sequence them. Though the situation has improved, there have been persistent logistical challenges, he said.

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 countrys 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.

OGrady 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.

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 weve made are fragile and could be upended by viral variants, OConnor 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.

Had the pandemic happened even five years ago, it would have been a lot more difficult to implement genomic surveillance programs at scale, OConnor said. The technologies to democratize sequencing and make it available to small laboratories and public health authorities simply werent 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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A Lack of COVID-19 Genomes Could Prolong the Pandemic Quanta Magazine - Quanta Magazine