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On December 18, 2019, Wuhan Central Hospital admitted a patient with symptoms common for the winter flu season: a 65-year-old man with fever and pneumonia. Ai Fen, director of the emergency department, oversaw a typical treatment plan, including antibiotics and anti-influenza drugs.
Six days later, the patient was still sick, and Ai was puzzled, according to news reports and a detailed reconstruction of this period by evolutionary biologist Michael Worobey. The respiratory department decided to try to identify the guilty pathogen by reading its genetic code, a process called sequencing. They rinsed part of the patient’s lungs with saline, collected the liquid, and sent the sample to a biotech company. On December 27, the hospital got the results: The man had contracted a new coronavirus closely related to the one that caused the SARS outbreak that began 17 years before.
The original SARS virus was sequenced five months after the first cases were recorded. This type of traditional sequencing reads the full genetic code, or genome, of just one organism at a time, which first needs to be carefully isolated from a sample. The researchers hired by Wuhan Central Hospital were able to map the new virus so quickly using a more demanding technique called metagenomic sequencing, which reads the genomes of every organism in a sample at once — without such time-intensive preparation. If the traditional approach is like locating a single book on a shelf and copying it, metagenomic sequencing is like grabbing all of the books off the shelf and scanning them all at once.
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