As SARS-CoV-2 continues to rip through the human population, we’re getting more information about downstream impacts, including transmission to animals. One of my talking points since the start of the pandemic has been that we want to keep this virus in the human population. If we spread it to animals, it will be much harder to control in the longterm. That sentiment hasn’t changed.

While control of the pandemic at this stage is pretty much still solely dependent on addressing human-to-human transmission, as things slowly get more controlled in people, other sources of infection and other sources of variants become more relevant.  The potential for animals to be sources of variants is a realistic concern. It’s a potential (but unlikely) explanation for how Omicron emerged.  If the virus spreads widely and continuously in animals, it creates a situation amenable to new variant development, as I’ve previously explained. We’ve seen variants emerge in mink and spread into people, and widespread infection in deer adds another potential source, though we’ve yet to identify new variants in deer or deer-to-human transmission.

A report about a wastewater study from New York (Smyth et al. Nature Communications 2022) adds another twist to the story. Wastewater was collected from treatment plants in New York City, from January to June 2021. Researchers sequenced parts of the SARS-CoV-2 genome found in the water samples to look for mutations. They couldn’t look at specific strains since samples like wastewater are a complex soup of RNA pieces from lots of different strains, but they targeted the spike protein region, which we know is important for virulence (and it’s the region of the viral genome in which we see significant mutations in variants of concern).

Not surprisingly, a range of mutations were detected over the study period. That’s expected, since we’ve gone through serial waves of variants, and we know that a range of mutations are present in different strains of SARS-CoV-2. The trends in strain variation in wastewater over time largely mimicked those in people, since what’s circulating in people should be roughly the same as what’s in their waste.

But… there were some other sequences present in samples from 3 of the 14 wastewater treatment plants that were not consistent with what’s commonly found in people, and which did not correspond to any lineages in GISAID (an international genetic sequence depository).  These “cryptic lineages” also seemed to change a bit over time, acquiring other mutations. There were also differences in viral lineages that were found only at specific wastewater treatment plants, suggesting that the source of the virus was geographically constrained in these cases.

What does these study results suggest?

The study suggests that there is an unknown source of SARS-CoV-2 that’s not captured by routine clinical testing of people. That could be from virus circulating in people who aren’t getting sick and therefore aren’t being tested for surveillance purposes, or in people who are getting sick but are not tested for any reason. In either of these scenarios, there would have to be ongoing transmission between people to keep the specific viral strain in circulation in a relatively small area, and allow it to continue to evolve.  Longterm care facilities are a possible source, with a high risk and relatively immobile population (although it’s presumably also one where testing is still pretty common, so that doesn’t fit with the “unknown” component).

The other potential explanation (and one that fits better in some ways) is movement of SARS-CoV-2 into an animal reservoir that lives in the urban environment, is susceptible to the virus, and is present in large enough numbers to both sustain transmission and to produce enough virus that it’s detectable in wastewater.

What’s the leading candidate for a potential animal source in this situation?

Rats. There are lots of them in New York, and rats have been shown to be susceptible to some SARS-CoV-2 strains.

Adding more to the potential rat story is the nature of some of the genetic mutations in the spike protein, as some of the mutations that were detected have been previously associated with increased infectivity of the virus in rodents.

Another interesting finding was as the concentrations of overall SARS-CoV-2 genetic material decreased over time (consistent with the decrease in human infections), the concentration of these cryptic strains did not show the same trend, providing more reason to think these lineages may not be directly associated with humans.

Is this proof of an animal reservoir in NYC?

  • No. There’s no smoking gun here, but these are very interesting data that provide yet more support for the need to consider transmission of SARS-CoV-2 from people to animals, and the potential for mutation and spill-back into humans. More study of rats is indicated, but we also need to know more about other urban (and non-urban) wildlife, as there could be alternative or additional sources.

No reason to panic, but another reason to investigate.