Mysterious "cryptic lineages" of SARS-CoV-2 have been found in the wastewater beneath New York City (NYC), according to a new study. These lineages of the virus that causes COVID-19 have never been documented in humans, leaving the researchers to wonder how they managed to spring up, not least in the sewers of NYC.
As reported in the journal Nature Communications, scientists studied wastewater samples from NYC and detected an increased number of “novel cryptic” SARS-CoV-2 lineages that had not been reported in humans. The study notes that the newly discovered lineages contain mutations that had been rarely observed in other clinical samples.
"The mutations that we were observing in our sample weren't typical among any of the known sequences circulating at that time," John Dennehy, study author and professor of biology at Queens College, City University of New York, said in a statement.
Between 40 and 80 percent of people infected with COVID-19 shed viral RNA in their poop, so monitoring sewage can be a useful tool for understanding the outbreak at a population-wide scale. Taking advantage of this fact, the US Centers for Disease Control and Prevention (CDC) launched the National Wastewater Surveillance System in September 2020, a program to search wastewater and sewage for the genetic material of viruses with the aim of gaining knowledge about the COVID-19 outbreak. There are currently 400 testing sites spread across the US, with the CDC working with 37 states, four cities, and two territories to boost their wastewater surveillance systems.
Back to NYC, it's uncertain where these cryptic lineages are coming from. Viruses require another host's cells to replicate. Through errors in their replication process, viruses can pick up mutations in their genetics, which can eventually accumulate to form new variants. But if these lineages have not been reported in humans, what are they being fostered by?
The researchers believe there are two main options. Firstly, they could be derived from unsampled human COVID-19 infections. Since these samples essentially came from human poop, perhaps viruses of these lineages predominantly replicate in the cells of the gut and aren’t picked up by the standard nose-and-throat swabbing techniques.
Secondly, other animals may be acting as a hidden reservoir for the virus. It’s known that SARS-CoV-2 can infect a number of mammals, including cats, dogs, tigers, mink, and deer, to name just a few. Although it’s yet to be proven, it’s possible that the virus could be infecting animals lurking in the sewer, like mice and rats (not alligators), and mutating into these new cryptic lineages.
Alternatively, another piece of research released this week offers another explanation. The study, published in ACS ES&T Water, found that sewer slime can accumulate on the genetic material of SARS-CoV-2, potentially damaging the accuracy of wastewater COVID-19 tests. This could suggest the detection of the mysterious lineages is simply an error.
For now, it remains a bit of a mystery. At a recent media conference, the CDC said it's in contact with the researchers that published the NYC sewage paper and is watching this avenue of research very closely.