Genome sequencing of coronavirus in sewage can help detect local variants: Study

As reports of new strains of the novel coronavirus, including those with more transmissibility, emerge from different parts of the world, a new study says viral genome sequencing of wastewater can help discover variants before they are detected by local clinical tests.

According to the research, published in the peer-reviewed journal mBio, the ability to track SARS-CoV-2 mutations in wastewater could be particularly useful to track new variants like the B.1.17 strain which is now widespread in the UK and has already been introduced in several countries, including India.

Also read: Smokers, vegetarians at lower risk of contracting Covid-19: Study

“SARS CoV-2 virus is excreted by individuals that are infected by Covid-19 and the fecal waste ends up in the wastewater systems. By sampling wastewater, we can get information on infections for a whole population,” explained study co-author Kara Nelson from the University of California (UC)-Berkeley in the US.

Nelson believes sampling wastewater is a very efficient and less biased way to get information on the evolution of the virus.

“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,” Nelson added.

Sampling wastewater

In the current study, Nelson and her team developed and used a novel method for sampling wastewater.

When scientists sequence genetic material concentrated and extracted from wastewater samples, the study noted that there may be many different strains present as there are many individuals contributing to the sample.

Also read: Covid-19 spread can be traced in wastewater solids: Study

However, the scientists said distinguishing the SARS-CoV-2 genetic signal, its RNA, from the billions of bacteria and viruses people excrete every day is a difficult task.

“The way that we need to process the sequence information is complex. One contribution of this paper is the ability to prepare samples for sequencing from wastewater,” Nelson said.

Instead of directly sequencing everything present, the researchers used a new approach in which they first tried to enrich the viral RNA.

“Then 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,” Nelson said.

In the study, the scientists sequenced RNA directly from sewage collected by municipal utility districts in the San Francisco Bay Area to generate whole and nearly complete SARS-CoV-2 genomes.

SARS-CoV-2 genotypes

They found that the common SARS-CoV-2 genotypes detected in the sewage were identical to clinical genomes from the region.

The researchers also detected variants with very small differences in the genetic material that had only been reported from elsewhere in the US or globally.

Based on the study findings, the scientists believe wastewater sequencing can provide evidence for recent introductions of viral lineages before they are detected by local clinical sequencing.

By understanding which strains of SARS-CoV-2 are present in populations over time, they said researchers across the globe can gain insight into whether new variants, such as the one which emerged in the UK, are dominating transmission.

“Of everyone who gets tested, only a fraction of those samples even get sequenced. When you are sampling the wastewater, you get a more comprehensive and less biased data on your population,” Nelson said.

Early signal

According to the researchers, the new approach may provide 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,” Nelson said.