Opinion | We Are Still in a Race Against the Coronavirus – The New York Times

Hardware tools are important to such work. Software is also crucial. During the first year of the Covid-19 pandemic, a young graduate student named ine OToole, along with other members of Andrew Rambauts lab at the University of Edinburgh, developed a tool called PANGOLIN (Phylogenetic Assignment of Named Global Outbreak Lineages). It became one of the go-to systems for placing new genomes on the SARS-CoV-2 family tree, assigning them rational if unmemorable labels (such as B.1.1.7), and contextualizing new variants of the virus when they emerged.

It was Dr. Rambaut, Dr. OToole and their lab colleagues who helped spot and track the first major variant, now called Alpha, when it appeared in southeastern England, moving toward London, in autumn of 2020. One year later, scientists in South Africa and Botswana, sequencing samples from travelers, detected another rising variant, named Omicron.

Such quick detection of variants is enormously valuable, but only if the data are transformed promptly into clear, actionable guidance. We still have the important gaps in getting it into the clinic, Dr. Peacock said. These gaps include making it easy for public health and medical personnel not trained in sequencing to use the data and the willingness of health care providers like hospitals to finance such work. At the moment, the majority of sequencing beyond Covid-19 is funded by public health agencies and research funding, she said.

That hasnt changed since 2014, when Pardis Sabeti, a computational geneticist at Harvard University, led a team of genomic scientists responding to the horrific Ebola virus outbreak in West Africa. They sequenced 99 genomes of the virus, sampled from patients at a hospital in Sierra Leone. Comparing sequences revealed that all those cases most likely resulted from human-to-human transmission, rather than from spillovers from a wildlife host.

The West Africa outbreak ended after more than 28,000 Ebola cases and 11,000 deaths, by which point genomic epidemiology had proved its value by revealing how the virus was spreading. With Covid-19, there have been 589 million known cases and more than six million deaths so far. The new discipline is scarcely able to keep up, let alone get ahead of the virus. Sarah Cobey, an evolutionary biologist at the University of Chicago who works at the juncture of immunology, viral evolution and epidemiology, sees gaping holes in the genetic surveillance of Covid-19.

Even though we do have lots and lots of sequences, they are disproportionally from a few locations, Dr. Cobey told me. During the first year of the pandemic, Britain, New Zealand, Australia and Iceland were among the countries that sequenced a high share of cases. The Netherlands and the Democratic Republic of Congo were also notable for prompt sequencing. As the pandemic progressed, scientists in South Africa mounted an important sequencing effort (as reflected in the detection first of the Beta variant, then of the Omicron), and coverage improved also in Canada and Scandinavia. Other parts of the world remain blind spots, Dr. Cobey said.

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Opinion | We Are Still in a Race Against the Coronavirus - The New York Times