In New York City Sewage, a Mysterious Coronavirus Signal

Last January (https://nyti.ms/3onY7zm), a team of researchers
searching for the coronavirus in New York City’s wastewater
spotted something strange in their samples. The viral fragments
they found had a unique constellation of mutations that had never
been reported before in human patients — a potential sign of a
new, previously undetected variant.
For the past year, these oddball sequences, or what the scientists
call “cryptic lineages,” have continued to pop up in the city’s
wastewater.
There is no evidence that the lineages, which have been circulating
for at least a year without overtaking Delta or Omicron, pose an
elevated health risk to humans. But the researchers, whose findings
were published in Nature Communications on Thursday, still have
no idea where they came from.
“At this point, what we can say is that we haven’t found the cryptic
lineages in human databases, and we have looked all over,” said
Monica Trujillo, a microbiologist at Queensborough Community
College and an author of the new paper.
The researchers themselves are torn about the lineages’ origins.
Some lean toward the explanation that the virus is coming from
people whose infections aren’t being captured by sequencing. But
others suspect that the lineages may be coming from virus-infected
animals, possibly the city’s enormous population of rats. Even
then, the favored theory can change from day-to-day or hour-to-hour.
Answers remain elusive.
“I think it’s really important that we find the source, and we have
not been able to pin that down,” said John Dennehy, a virologist
at Queens College and an author of the paper.
Strange sequences
The researchers - who also include Marc Johnson, a virologist at
the University of Missouri, Davida Smyth, a microbiologist at Texas
A&M University and others — have been sampling wastewater from
14 treatment plants in New York City since June 2020. In January
of 2021, they began doing targeted sequencing of the samples,
focusing on part of the gene for the virus’s all-important spike
protein.
Although this approach provides a limited look at the viral genome,
it allows researchers to extract a lot of data from wastewater, in
which the virus is typically fragmented.
Viral fragments with novel patterns of mutations appeared repeatedly
at a handful of treatment plants, the researchers found. (They could
not disclose the specific plants or areas of the city, they said.)