How genomic epidemiology is tracking the spread of COVID-19 locally and globally

Auhors: Claire Jarvis, special to C&EN

n early April, a paper published in the journal Proceedings of the National Academy of Sciences of the United States of America (PNAS) raised the eyebrows of a number of genomic epidemiologists. It suggested that there were three distinct variants of the novel coronavirus, SARS-CoV-2, spreading in different regions of the world—one predominantly in Australia and North America, one in China, and one in Europe. It also suggested that the variant circulating in North America and Australia was older than the one that appeared in Wuhan, China, at the end of December (Proc. Natl. Acad. Sci. USA 2020, DOI: 10.1073/pnas.2004999117).

If this were true, the outbreak of COVID-19, the disease caused by the virus, would have started outside Wuhan, which contradicts scientific consensus.Credit: TwitterMolecular evolution expert and University of Edinburgh professor Andrew Rambaut took to Twitter on April 9 to point out problems with a recently published PNAS paper.

Some genomic epidemiologists, who track the genomes of pathogens to understand how diseases spread, thought that although the data the PNAS paper used were sound, the paper’s analytical approach led to a false conclusion. PNAS says it has received letters about the paper and is currently reviewing them.

The incident illustrates the challenges that the COVID-19 pandemic has been presenting to these scientists: technology for sequencing, tracking, and mapping genes has never been stronger nor the results shared so publicly, but the field of genomic epidemiology has also never been deployed on such a large scale before nor against such a fast-moving foe.

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