Future mutant strains of coronavirus could be detected faster by studying SEWAGE for new variants, study finds
- Sewage analysis has been shown to be effective at spotting Covid outbreaks
- New technique allows researchers to also study the genetic code of each virus
- Would expand the scope for spotting mutated viruses from only lab tests to thousands of asymptomatic people
Scanning sewage for new coronavirus variants is a viable strategy for speeding up detection of new strains which may be more infectious, a study has found.
Wastewater analysis has previously been identified as a good way of spotting signs of local infection, but now Covid is rife around the world the focus has shifted towards using sewage to spot new variants.
Currently, emerging variants are spotted when coronavirus swabs are sent to a special lab for genomic analysis.
However, only around one in ten swabs are sent for this analysis in the UK, and many people who have the virus are asymptomatic and do not receive a test.
To get a bigger sample size the researchers turned to sewage, which catches waste from thousands of people at a time.
US-based academics from the University of California-Berkeley devised a way to spot trace amounts of SARS-CoV-2, the virus which causes Covid-19, amplify it and then scan its genetic code to spot any mutations.
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Wastewater analysis was previously been identified as a good way of spotting signs of local infection but now Covid is rife around the world, the focus has shifted towards using sewage to spot new variants
The new variants of the coronavirus have mutations on the spike protein, which are key for the immune system’s antibodies to latch onto and destroy it. Changing the shape of them makes it harder for the body to catch the virus
The discovery means scientists can catch variants without the need to screen people individually.
‘SARS CoV-2 virus is excreted by individuals that are infected by Covid-19 and the faecal waste ends up in the wastewater systems,’ explains Professor Kara Nelson, who led the investigation.
‘By sampling wastewater, we can get information on infections for a whole population.
‘Some wastewater systems serve several thousand people. Some serve hundreds of thousands of people.
The South African coronavirus variant may slip past parts of the immune system in as many as half of people infected with different versions in the past, scientists fear.
Researchers say that a mutation on a specific part of the virus’s outer spike protein appears to make it able to ‘escape’ antibodies. Antibodies are substances made by the immune system that are key to destroying viruses or marking them for destruction by white blood cells.
South African academics found that 48 per cent of blood samples from people who had been infected in the past did not show an immune response to the new variant. One researcher said it was ‘clear that we have a problem’.
Professor Penny Moore, the researcher behind the project, claimed people who were sicker with coronavirus the first time and had a stronger immune response appeared less likely to get reinfected.
Antibodies are a major part of the immunity that is created by vaccines – although not the only part – so if the virus continues evolving to escape from them it could mean that vaccines have to be redesigned and given out again.
But experts so far say they have no reason to believe vaccines won’t work, which may be because they produce a stronger immune response than a very mild infection, and because they produce various different types of immune cells.
At least 54 people in the UK have already been confirmed to have had the South African Covid variant, although these were picked up by random sampling so the true number is likely much higher.
‘Sampling wastewater is a very efficient way to get information. It is also a less biased source of information, because we can get information from all individuals in the sewershed, whether or not they are being tested in a clinic.
‘We know that there are individuals that have asymptomatic infections that may never get tested.’
New coronavirus variants are increasingly causing concern among the scientific community.
In the spring, the D614G mutation swiftly became dominant, and then the so-called Kent strain (B.1.1.7), was announced in December and has since spread internationally.
There is also growing concern over another mutant from South Africa, labelled B.1.351, which may be able to reinfect people who have previously been infected with and recovered from Covid-19. At least 54 Britons are believed to have caught this strain.
The latest variants of concern to emerge are from Brazil, where there are two closely-related versions, P.1 and P.2.
P.1 drove a surge in cases in Manau, Brazil and has been spotted in Japan, whereas P.2. has infected 11 Britons.
All of these variants contain the N501Y mutation, which is believed to improve the virus’s ability to bind to human cells, and all except the Kent strain have E484K, which is believed to play a role in avoiding detection by antibodies.
Three other variants have been spotted in the US, with one also being spotted in Nigeria.
Professor Nelson adds: ‘It appears that we might be able to get an earlier signal in the wastewater if a new variant shows up compared to only relying on the sequencing of clinical samples.
‘Just knowing that SARS-CoV-2 is present in a population is the first step in providing information to help control the spread of the virus, but knowing which variants are present provides additional but very useful information.’
Dr Nelson and her team developed a new approach to analysing the genetic constitution of new Covid mutations.
‘We developed a novel bioinformatic analysis approach which was sensitive enough to detect a single nucleotide difference. You can’t get any more sensitive than that.’
The findings were published in the journal mBio.
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