On December 18, 2019, Wuhan Central Hospital admitted a patient with symptoms common during the winter flu season. He is a 65-year-old man with fever and pneumonia. Emergency department director Ai Fen oversaw a typical treatment regimen that included antibiotics and anti-influenza drugs.
Six days later, the patient was still sick, leaving Ai baffled. This is a process called sequencing. They rinsed part of the patient’s lung with saline, took the fluid, and sent the sample to a biotech company. On December 27, the hospital got the results. The man had been infected with a new coronavirus closely related to the one that caused the SARS outbreak that began 17 years ago.
The original SARS virus was sequenced five months after the first case was documented. In this type of conventional sequencing, he reads the complete genetic code or genome of one organism at a time, which must first be carefully separated from the sample. Researchers hired by Wuhan Central Hospital are able to map new viruses very quickly using a more demanding technique called metagenomic sequencing, which reads the genomes of all organisms in a sample at once. I was. No such time-consuming preparation is required. If the traditional approach is like finding one of her books on the shelf and copying it, metagenomic sequencing is like taking all the books off the shelf and scanning them all at once.
This ability to quickly read different genomes has proven useful in fields ranging from ecology to cancer therapy. And with the COVID-19 pandemic, some researchers are using metagenomics to try to detect new diseases early and respond to them before they become epidemics or even infect humans. Some of these experts say his early spread of COVID-19 in the United States could have been contained more quickly if the medical community had applied the technology.
Chan Zuckerberg Biohub, a nonprofit research center and professor of biochemistry and biophysics at the University of California, San Francisco.
However, while the inherent power of metagenomics is clear, there are challenges in using metagenomics to quell a potential pandemic. This technique requires intensive computer processing, is more expensive than other techniques, and requires a higher degree of expertise to interpret the results. Using the large amount of data generated by metagenomics to guide treatment poses confusion regarding medical decision-making, for example when it is not clear whether a particular pathogen is causing a particular disease.
Still, proponents say the cost is worth it. Jessica Manning, an infectious disease researcher at the National Institute of Allergy and Infectious Diseases, said:
The rise of metagenomics over the last few decades is due in part to advances in genome sequencing. To read the contents of the genome, researchers first isolate the molecules that store the genetic information: DNA and RNA, the long strands of nucleotides that are the letters of the gene library. Then cut the long molecule into short chunks and read the order of the characters in each chunk. Finally, the short ‘reads’ are combined to reconstruct the complete genome.
Over the last 40 years, innovation, especially automation, has dramatically improved every part of this process. The Human Genome Project, launched in 1990, took him more than a decade of coordinated work among 20 research groups and cost about $1 billion. Today, one scientist can more accurately sequence the human genome in her day at less than a millionth of her cost.
As technology improved, researchers began trying to sequence many organisms at once. This is a complex task that requires understanding how millions of short reads can be combined to create an arbitrary number of genomes. Ultimately, researchers created sophisticated software that could classify sequences using a network of powerful computers.
