The genetic technique that finds (almost) every infection

It identified Covid-19. Now this genetic technique is helping doctors to make life-or-death decisions.

In late December 2019, a team of virologists from three major Chinese cities began analysing swabs taken from patients hospitalised with mysterious cases of severe pneumonia. 

All had been present at the Huanan Seafood Market, Wuhan, before rapidly falling unwell. But when the virologists ran the samples, they drew a blank: the genetic material did not match any previously discovered pathogen.

The doctors turned to a new screening method known as metagenomic testing. Instead of checking for known microbes, the test could reveal all the microorganisms present in the samples – previously identified or not. 

It enabled them to see that the pathogen in the patients' samples bore a close resemblance to the coronavirus family, a group that included viruses which had previously caused outbreaks of severe pneumonia in humans, such as Middle East Respiratory Syndrome (Mers). The scientists had just discovered Covid-19. 

"It was a gamechanger compared with previous pandemics," says Niranjan Nagarajan, an associate professor at the National University of Singapore. Knowing what the pathogen was made it possible to rapidly develop Covid diagnostics to try to curb the spread, and kickstarted the frantic search for treatments and vaccines around the globe. 

This remains the best-known use of metagenomics to date. But the test is now increasingly being used in hospitals. And from quickly diagnosing sepsis to identifying the causes of unexplained ailments, it's already saving lives.  

Revealing the unknown

Whenever a patient arrives in a neurological ward displaying signs of confusion and drowsiness, and complaining of fever, headache and weakness, doctors are acutely aware that it could be a life-or-death emergency.

How metagenomic testing works

Metagenomics, the study of all the DNA and RNA found in a particular environment, is seen as an increasingly important clinical approach. Metagenomic testing involves extracting genetic material from a sample, then using advanced sequencing methods to identify the genetic codes of everything that's there. These results can be analysed by computers with reference to large databases, allowing doctors to pinpoint the exact organisms present, such as bacteria or viruses.

This constellation of symptoms can indicate meningitis or encephalitis – deadly conditions affecting the brain and spinal cord. Yet doctors often face a critical dilemma. The most suitable treatment would depend on whether the patient's condition was due to a virus or bacteria, or an overreaction from the brain's immune system. With limited tests and time, however, doctors are often forced to hedge their bets.

"You need to make a decision immediately," says Charles Chiu, a professorand infectious diseases expertat the University of California San Francisco Department of Medicine in the US, who has been carrying out new studies into the use of metagenomic tests. "Currently, with patients who are critically ill, doctors treat them for........

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