Michael Coston
Editor, Senior Moderator
PLoS Path.: Will Animal Reservoirs Give Us The Next SARS-CoV-2 variant?
#19,088
As we discussed on Monday in Nature Comms Med.: Interactions of SARS-CoV-2, Influenza and RSV Influence Epidemic Timing and Risk, a strong flu season can briefly inhibit SARS-CoV-2 transmission at the population level, but that impact is short-lived.
Which suggests our recent lull in COVID cases is probably temporary, and another spring or summer COVID surge likely awaits.
Surveillance and reporting on SARS-CoV-2 has deteriorated badly around the world (90% of countries no longer report COVID hospitalizations or deaths), and the WHO published their last comprehensive COVID-19 epidemiological update more than a year ago.
While much remains hidden from view, the SARS-CoV-2 virus continues to circulate, and evolve, around the globe. And not just in humans.
Over the years we've looked at the spillover - and onward transmission - of the SARS-CoV-2 virus in a growing number of non-human hosts; including:
PrePrint: Anthropozoonotic Spillovers Reveal Sustained Long-Term Cryptic Circulation of SARS-CoV-2 Within and Between Lithuanian Mink Farms
SARS-CoV-2 Exposure in Norway Rats in New York City
PNAS: White-Tailed Deer as a Wildlife Reservoir for Nearly Extinct SARS-CoV-2 Variants
While some of these were likely limited `dead-end' spillovers, in some species we've seen evidence of vigorous onward transmission, and continued evolution of the virus. And from at least two of these - white-tailed deer and mink - we've seen evidence of a spillback into humans.
Nature: Divergent SARS-CoV-2 Variant Emerges in White-tailed Deer with Deer-to-Human Transmission (Revisited)
WHO 2nd Update: SARS-CoV-2 mink-associated variant strain – Denmark
While none of these spill backs has taken hold in humans (unless you accept the theory that the Omicron variant had a mouse origin), they serve as a proof-of-concept. Unfortunately, our surveillance of non-human hosts for the SARS virus is extremely limited.
Which brings us to a brief, and refreshingly plain-language `Pearls' article in PLoS Pathogens, which provides a 9-point review of what we know about the threat from cryptic lineages of SARS-CoV-2 spreading in non-human reservoir hosts.
I've provided the link and a brief excerpt, but this is one you'll definitely want to read in its entirety. I'll have a bit more after the break.
Will animal reservoirs give us the next SARS-CoV-2 variant?
Davey Smith
Published: March 3, 2026
https://doi.org/10.1371/journal.ppat.1014008
1. What does it mean that SARS-CoV-2 is now a virus with multiple natural hosts?
Like all known human coronaviruses, SARS-CoV-2 originated from animals, most likely through wildlife sold at the Huanan Seafood Market, with bats serving as the deeper evolutionary reservoir [1]. Since its emergence in humans, SARS-CoV-2 has repeatedly crossed into non-human hosts. Over five years of widespread circulation, the virus has been detected in a surprising array of animals, including white-tailed deer, mink, rats, hamsters, horses, cats, zoo animals and dogs, though sustained transmission is clearly documented only in deer and farmed mink, with other species showing limited or no onward spread. For white-tailed deer and mink, the virus has achieved sustained animal-to-animal transmission and spillback to humans [2–6].
This shift transforms SARS-CoV-2 from a purely human epidemic into a network of linked epidemics across species. Humans remain their largest host, but no longer its only long-term home. When a virus gains multiple such homes, it also gains more ecological space and evolutionary possibilities. This article does not address the original zoonotic emergence of coronaviruses broadly; instead, it focuses on the less explored problem: how sustained circulation of SARS-CoV-2 in animal reservoirs may shape future human disease.
(SNIP)
9. Why should pathogen researchers care, even if they do not work on coronaviruses?
Animal reservoirs slow down viral extinction. They expand the virus’s evolutionary playground. They give SARS-CoV-2 places to mutate where human immunity has little influence. For virologists and pathogenesis researchers of any specialty, these reservoirs show how quickly an emerging virus can become an ecological resident [3]. Ignoring the animal side of SARS-CoV-2 means accepting surprise when spillback occurs. Paying attention gives us a chance to see the next jump coming, and maybe even prevent it.
(Continue . . . )
Several studies (see BMJ Global: Historical Trends Demonstrate a Pattern of Increasingly Frequent & Severe Zoonotic Spillover Events and PNAS Research: Intensity and Frequency of Extreme Novel Epidemics), suggest the number, frequency, and intensity of pandemics is only expected to increase in the years ahead.
But even if SARS-CoV-2 is unable to fully reinvent itself in a human or non-human host, there are plenty of other coronaviruses circulating in the wild with pandemic potential.
A few (of many) recent blogs include:
All of which makes it highly unlikely we've seen our last coronavirus threat.
https://afludiary.blogspot.com/2026/03/plos-path-will-animal-reservoirs-give.html
#19,088
As we discussed on Monday in Nature Comms Med.: Interactions of SARS-CoV-2, Influenza and RSV Influence Epidemic Timing and Risk, a strong flu season can briefly inhibit SARS-CoV-2 transmission at the population level, but that impact is short-lived.
Which suggests our recent lull in COVID cases is probably temporary, and another spring or summer COVID surge likely awaits.
Surveillance and reporting on SARS-CoV-2 has deteriorated badly around the world (90% of countries no longer report COVID hospitalizations or deaths), and the WHO published their last comprehensive COVID-19 epidemiological update more than a year ago.
While much remains hidden from view, the SARS-CoV-2 virus continues to circulate, and evolve, around the globe. And not just in humans.
Over the years we've looked at the spillover - and onward transmission - of the SARS-CoV-2 virus in a growing number of non-human hosts; including:
PrePrint: Anthropozoonotic Spillovers Reveal Sustained Long-Term Cryptic Circulation of SARS-CoV-2 Within and Between Lithuanian Mink Farms
SARS-CoV-2 Exposure in Norway Rats in New York City
PNAS: White-Tailed Deer as a Wildlife Reservoir for Nearly Extinct SARS-CoV-2 Variants
While some of these were likely limited `dead-end' spillovers, in some species we've seen evidence of vigorous onward transmission, and continued evolution of the virus. And from at least two of these - white-tailed deer and mink - we've seen evidence of a spillback into humans.
Nature: Divergent SARS-CoV-2 Variant Emerges in White-tailed Deer with Deer-to-Human Transmission (Revisited)
WHO 2nd Update: SARS-CoV-2 mink-associated variant strain – Denmark
Which brings us to a brief, and refreshingly plain-language `Pearls' article in PLoS Pathogens, which provides a 9-point review of what we know about the threat from cryptic lineages of SARS-CoV-2 spreading in non-human reservoir hosts.
I've provided the link and a brief excerpt, but this is one you'll definitely want to read in its entirety. I'll have a bit more after the break.
Will animal reservoirs give us the next SARS-CoV-2 variant?
Davey Smith
Published: March 3, 2026
https://doi.org/10.1371/journal.ppat.1014008
1. What does it mean that SARS-CoV-2 is now a virus with multiple natural hosts?
Like all known human coronaviruses, SARS-CoV-2 originated from animals, most likely through wildlife sold at the Huanan Seafood Market, with bats serving as the deeper evolutionary reservoir [1]. Since its emergence in humans, SARS-CoV-2 has repeatedly crossed into non-human hosts. Over five years of widespread circulation, the virus has been detected in a surprising array of animals, including white-tailed deer, mink, rats, hamsters, horses, cats, zoo animals and dogs, though sustained transmission is clearly documented only in deer and farmed mink, with other species showing limited or no onward spread. For white-tailed deer and mink, the virus has achieved sustained animal-to-animal transmission and spillback to humans [2–6].
This shift transforms SARS-CoV-2 from a purely human epidemic into a network of linked epidemics across species. Humans remain their largest host, but no longer its only long-term home. When a virus gains multiple such homes, it also gains more ecological space and evolutionary possibilities. This article does not address the original zoonotic emergence of coronaviruses broadly; instead, it focuses on the less explored problem: how sustained circulation of SARS-CoV-2 in animal reservoirs may shape future human disease.
(SNIP)
9. Why should pathogen researchers care, even if they do not work on coronaviruses?
Animal reservoirs slow down viral extinction. They expand the virus’s evolutionary playground. They give SARS-CoV-2 places to mutate where human immunity has little influence. For virologists and pathogenesis researchers of any specialty, these reservoirs show how quickly an emerging virus can become an ecological resident [3]. Ignoring the animal side of SARS-CoV-2 means accepting surprise when spillback occurs. Paying attention gives us a chance to see the next jump coming, and maybe even prevent it.
(Continue . . . )
Several studies (see BMJ Global: Historical Trends Demonstrate a Pattern of Increasingly Frequent & Severe Zoonotic Spillover Events and PNAS Research: Intensity and Frequency of Extreme Novel Epidemics), suggest the number, frequency, and intensity of pandemics is only expected to increase in the years ahead.
But even if SARS-CoV-2 is unable to fully reinvent itself in a human or non-human host, there are plenty of other coronaviruses circulating in the wild with pandemic potential.
A few (of many) recent blogs include:
- Last January (see EID Journal (Perspective): Emerging Respiratory Virus Threats from Influenza D and Canine Coronavirus HuPn-2018) we looked at 2 emerging threats, including a canine coronavirus which has spilled over into humans in Malaysia.
- Three months ago, in The Lancet: The Threat of Another Coronavirus Pandemic, we looked at somewhat technical commentary on recently identified ACE2-using merbecoviruses - like HKU5-CoV-2 - which may represent potential future coronavirus pandemic threats.
- And exactly a year-ago today, in Viruses: Novel Rodent Coronavirus-like Virus Detected Among Beef Cattle with Respiratory Disease in Mexico, we looked at a novel coronavirus that closely resembled a rodent-coronavirus isolated in China in 2021 (see Nature: Virus Diversity, Wildlife-Domestic Animal Circulation and Potential Zoonotic Viruses of Small Mammals, Pangolins and Zoo Animals).
All of which makes it highly unlikely we've seen our last coronavirus threat.
https://afludiary.blogspot.com/2026/03/plos-path-will-animal-reservoirs-give.html