On December 18, 2019, Wuhan Central Hospital admitted a affected person with signs widespread for the winter flu season: a 65-year-old man with fever and pneumonia. Ai Fen, director of the emergency division, oversaw a typical therapy plan, together with antibiotics and anti-influenza medicine.
Six days later, the affected person was nonetheless sick, and Ai was puzzled, in accordance with information studies and an in depth reconstruction of this era by evolutionary biologist Michael Worobey. The respiratory division determined to attempt to determine the responsible pathogen by studying its genetic code, a course of referred to as sequencing. They rinsed a part of the affected person’s lungs with saline, collected the liquid, and despatched the pattern to a biotech firm. On December 27, the hospital received the outcomes: The person had contracted a brand new coronavirus intently associated to the one which brought on the SARS outbreak that started 17 years earlier than.
The unique SARS virus was sequenced 5 months after the primary circumstances have been recorded. Such a conventional sequencing reads the total genetic code, or genome, of only one organism at a time, which first must be rigorously remoted from a pattern. The researchers employed by Wuhan Central Hospital have been capable of map the brand new virus so shortly utilizing a extra demanding method referred to as metagenomic sequencing, which reads the genomes of each organism in a pattern without delay — with out such time-intensive preparation. If the standard strategy is like finding a single e book on a shelf and copying it, metagenomic sequencing is like grabbing the entire books off the shelf and scanning them suddenly.
This skill to shortly learn a spread of genomes has confirmed helpful in fields from ecology to most cancers therapy. And the COVID-19 pandemic has pushed some researchers to make use of metagenomics to attempt to spot new illnesses and reply to them earlier — earlier than they turn into epidemics, and doubtlessly earlier than they even infect individuals. A few of these specialists say the early unfold of COVID-19 in the US may have been curbed extra shortly if the medical group had utilized this know-how.
“If metagenomic sequencing was achieved extra routinely, possibly we might’ve recognized what it was when there have been solely 20 infections,” within the US, mentioned Joe DeRisi, a professor of biochemistry and biophysics on the College of California San Francisco and president of the Chan Zuckerberg Biohub, a nonprofit analysis heart.
However whereas the uncooked energy of metagenomics is evident, there are challenges to utilizing it to squelch potential pandemics. The method requires intensive laptop processing, making it costlier than some others, and requires better experience to interpret the outcomes. Utilizing the copious information metagenomics produce to information therapy additionally raises quandaries about medical decision-making when, as an example, it’s not clear whether or not a sure pathogen is inflicting a sure sickness.
Nonetheless, advocates say the prices are value it. “Metagenomics performs a vital function in pandemic preparedness, by searching for the issues we don’t know to search for,” mentioned Jessica Manning, an infectious illness researcher on the Nationwide Institute of Allergy and Infectious Illnesses.
The rise of metagenomics over the previous couple of a long time is due partly to advances in genome sequencing. To learn the contents of the genome, researchers first isolate the molecules that retailer genetic info, DNA and RNA, that are lengthy chains of nucleotides, the letters of the genetic library. Then they minimize the lengthy molecules into shorter chunks and skim the order of letters in every chunk. Lastly, they mix the shorter “reads” to reconstruct the total genome.
Over the previous 40 years, innovation, particularly automation, dramatically improved each a part of this course of. The Human Genome Mission, launched in 1990, took greater than a decade of labor coordinated between 20 analysis teams and value round a billion {dollars}. Right now a human genome may be sequenced extra precisely, for lower than one-millionth the associated fee, by one scientist in at some point.
Because the know-how received higher, researchers began attempting to sequence many organisms without delay, a posh process that requires determining how hundreds of thousands of quick reads match collectively to make any variety of genomes. Ultimately researchers wrote refined software program that may kind out the sequences utilizing networks of highly effective computer systems.
