Finding COVID variants in sewage

As we emerge from lockdown, keeping tabs on where COVID-19 might be about to rear its ugly head again, as well as watching for the appearance of viral variants that might be able to sidestep our vaccines, is going to be key to keeping the country moving. And most scientists agree that mass testing in one form or another is crucial. But how do we do this in a way that's not inconvenient, onerous and costly? Well, researchers at the UK's National Institute for Biological Standards and Control, have found that they can use...what we put down the drain...as a sensitive way to track the activity of COVID in the population and also spot the early emergence of variants we're worried about. It stemmed from an existing project to use sewage to screen for polio; Chris Smith spoke with Javier Martin, one of the brains behind it...

Javier - There was early evidence that there was high concentration of the virus genetic material in stool samples from infected people. So since we have been carrying out surveillance for polio virus in wastewater samples, we thought that we could adapt our techniques to detect the virus causing COVID.

Chris - So you were already doing this for polio?

Javier - Yes. For many years now, yes.

Chris - Does this involve, then - not to put too fine a point on it - just going into the sewage farm and saying, "can I have a sample of what's coming down the sewer pipe, please?"

Javier - We were lucky because we've been doing this for many years now, so we regular samples supplied by the sewage plant every month. So we had samples from before and during the pandemic to look at.

Chris - Presumably, then, this bottle arrives, which is wastewater from different parts of the country; how do you process it?

Javier - Yes - you clear it up from any solids that might be there, by using filters to concentrate particles such as viruses.

Chris -
What, is it whole viruses that you're collecting, or will there just be bits of genetic information from these viruses in there?

Javier - We are not sure what if they are viable virus. We think they are not infectious, they're probably particles that are somehow damaged, but they contain genetic material that's sufficient to detect it.

Chris - And you can get that genetic material out and read it, can you?

Javier - Yes.

Chris - And can you detect things like variants doing this? If you can read genetic code, does that mean you can basically spot a variant, or spot the rate of change, how a variant is increasing its population as the infection spreads through the country, or a variant emerges, for example?

Javier - Yes. We're trying to quantify the amount of genetic material in wastewater; also sequencing so we can identify those mutations that correspond to variants, and therefore monitor them.

Chris - What's the point of doing this? Why do you think this would be useful?

Javier - I think it would be useful to help understand how these viruses meet between people, and also to possibly establish early alert systems for such variants becoming predominant in a population. Also, what you find as water is obviously what people are excreting, so you are not biased by the sampling of clinical samples; and they represent also asymptomatic infection, so a more detailed picture of what's happening.

Chris - I suppose one constraint, though, is how sensitive this is. Because if you only end up seeing it after, arguably, the virological horse has bolted, and there's already a rip roaring outbreak in a particular town, it's not going to really add anything; whereas if this could be an early warning sign - the canary in the coal mine almost - and you get early warning of a variant coming or an outbreak about to erupt, then that would be really powerful.

Javier - Yes, you're right. Sensitivity is the key. You could increase it by looking at a higher volume of your sample, by increasing the frequency, and also by maybe doing a more targeted community surveillance in areas that, for example, you have detected new concerning variants. So you can go to smaller surveillance areas to increase the sensitivity of your sampling.

Chris - You obviously straddle the time when we've seen the emergence of things like the Kent variant. So have you been able to see that appear as a blip on your radar, and then begin to dominate - as it has done - during the course of doing these experiments?

Javier - Yeah, we have seen the variant very clearly appearing in our wastewater samples since early November. So at that time, this was not obvious from clinical samples yet. And then, the proportion of this variant increased really nicely - exponentially, actually, since then - to become almost a hundred percent by the end of January.

Chris - So it does look like there is the prospect to use this, and it could provide advanced warning of a threat that's coming.

Javier - Yes, indeed. And in fact, the way we've designed the processes would also detect those variants that have been firstly detected in Brazil and South Africa, which are quite worrying, including some mutations that we know seem to affect vaccine efficacy.