Zoonotic Disease Pathways
#17,875
After emerging in 2019, SARS-CoV-2 quickly evolved into an overwhelmingly `humanized' pathogen, but the virus has also found refuge in a large number of non-human hosts, including mink, deer, dogs, cats, and even rodents (see Nature: Comparative Susceptibility of SARS-CoV-2, SARS-CoV, and MERS-CoV Across Mammals).
This is not just a theoretical concern, as we've already seen it happen several times.
The first big event was reported from Denmark in 2020, when farmed mink were exposed (via a human) to the SARS-CoV-2 virus - which spread rapidly and evolved into a novel strain - which eventually spilled back into humans (see EID Journal: SARS-CoV-2 Transmission between Mink (Neovison vison) and Humans, Denmark).
Seven million mink were destroyed in order to stop this variant, and for a time Denmark locked down North Jutland, where most of the human cases had been identified, and the UK banned travel to and from Denmark.
Similar outbreaks have been documented other non-human species, resulting in a `spill back' into humans, including:
CDC: Investigating Possible Mink-To-Human Transmission Of SARS-CoV-2 In The United States
Nature: Divergent SARS-CoV-2 Variant Emerges in White-tailed Deer with Deer-to-Human Transmission (Revisited)
Hong Kong: Compulsory Quarantine For Those Exposed To COVID-Positive Hamsters
EID Journal: Suspected Cat-to-Human Transmission of SARS-CoV-2 - Thailand
While unproven, in late 2021 a new and highly divergent Omicron virus emerged in South Africa, and there is plausible scientific evidence to suggest it may have first evolved in rodents (see Evidence for a mouse origin of the SARS-CoV-2 Omicron variant).
SARS-CoV-2 has been found in literally dozens of non-human species around the world, including Norway Rats from New York City, in poultry, cattle, goats, and even lizards in Nigeria, Wild Coatis in Brazil, and many more (see USDA chart below).
In September of 2021, China's Xinhuanet carried a brief report describing a spillover into farmed beavers in Mongolia (see Mongolia reports first COVID-19 cases in animals).
A few weeks later we saw the first of several high profile cautionary reports from Chinese health officials (see CCDC Weekly Perspectives: COVID-19 Expands Its Territories from Humans to Animals) warning of the risks of SARS-CoV-2 spilling over into non-human populations.
Thirty months have now passed, but last week the CDC's EID Journal published a research letter describing the outbreak in beavers in Mongolia.
Volume 30, Number 2—February 2024
Abstract
Research Letter
SARS-CoV-2 Infection in Beaver Farm, Mongolia, 2021
Taichiro Takemura1, Ulaankhuu Ankhanbaatar1, Tirumala Bharani K. Settypalli, Dulam Purevtseren, Gansukh Shura, Batchuluun Damdinjav, Hatem Ouled Ahmed Ben Ali, William G Dundon, Giovanni Cattoli, and Charles E. Lamien
We report an outbreak of COVID-19 in a beaver farm in Mongolia in 2021. Genomic characterization revealed a unique combination of mutations in the SARS-CoV-2 of the infected beavers. Based on these findings, increased surveillance of farmed beavers should be encouraged.(SNIP)We identified SARS-CoV-2 infection in beavers (Castor fiber) farmed for conservation reasons in Mongolia and report on serologic and whole genome sequence data from this outbreak. The beaver farm, located in the Bayanzurkh district in Ulaanbaatar, Mongolia, reared 32 adults and 16 kits in 2021. They were housed indoors in a large area separated by waist-high walls, with space for multiple animals. One of the 7 employees of the farm had influenza-like symptoms for several days and was diagnosed with COVID-19 on August 6, 2021. On August 9, the beaver farm reported the death of 2 beavers (one 6 months of age and one 2 years of age) after signs of coughing, nasal discharge, rasping on auscultation of the lungs and chest cavity, sluggish movement, and aversion to food. On August 13, research investigators collected nasal swabs, saliva, and 7 tissue samples (lung, kidney, liver, heart, spleen, larynx, and tongue from the 2 dead animals. Researchers also collected nasal swab specimens, saliva, and blood from 7 other beavers with notable clinical signs of coughing and purulent nasal discharge. Follow-up investigation on August 18 or 19 and on September 12 included collection of additional nasal swab specimens, saliva, and blood samples from the same animals as well as from 2 healthy animals (September 12 only).(SNIP)
We shipped 5 randomly selected quantitative reverse transcription PCR–confirmed SARS-CoV-2–positive RNA samples to the Animal Production and Health Laboratory (Seibersdorf, Austria), a joint program of the International Atomic Energy Agency and the Food and Agriculture Organization of the United Nations, and subjected them to whole-genome sequencing (Appendix 1; Appendix 2). Based on genotype analysis, all 5 genome sequences were assigned to the B.1.617.2 lineage, commonly referred to as the Delta variant. At the time of sampling, Alpha and Delta variants of SARS-CoV-2 were being identified in humans in Mongolia.The closest related sequences to those we identified in the beavers studied were from human SARS-CoV-2 in Mongolia (GenBank accession nos. ON008302, OM190617, and OM961234) identified during April–September 2021 (Figure). In addition to 4 mutations in the spike region, the sequences shared 7 amino acid substitutions in open reading frame [ORF] 1a, 4 amino acid substitutions in ORF1b, and 1 amino acid substitution in nucleocapsid genes. In the beaver sequences, 4 amino acid substitutions identified were not in the human isolates from Mongolia: S2500F, A3657V in ORF1a and H604Y, T1404M in ORF1b. Although those substitutions have been identified individually in SARS-CoV-2 sequences in GenBank and the GISAID database (https://www.gisaid.orgExternal Link), there are no records of sequences with all 4 mutations.
Several cases of SARS-CoV-2 transmission between humans and animals have already been reported (5–8). An alarming aspect of SARS-CoV-2 infection in animals is that host animals can maintain the virus and contribute to the emergence in humans of new variants that have accumulated multiple mutations (7–10). Indeed, the specific combination of mutations observed in the beavers we studied has not been found in other SARS-CoV-2 sequences in public databases (as of November 2023).This finding suggests that the mutations might have occurred or accumulated after the introduction of the virus into the beaver population. Because the emergence of viruses with mutations not targeted by current SARS-CoV-2 vaccines is a credible possibility, more active surveillance of SARS-CoV-2 infection in animals should be encouraged to identify the appearance of mutated viruses. In intensively farmed animals, species–species and species–humans contact is more frequent than in animals dwelling in other environments, which might increase the risk for zoonotic pathogen transmission (2). Thus, implementing more active surveillance and infection control strategies is critical to disease prevention and containment.
Dr Takemura is a technical expert for the ZODIAC project, Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture. His main research interests are in the biology of infectious pathogens.
Which means it is always possible that a new, radically different COVID variant could eventually emerge and spark another global health crisis.
Nature: Transmission of SARS-CoV-2 in Free-ranging White-tailed Deer in the United States
Eurosurveillance: Cryptic SARS-CoV-2 Lineage Identified on Two Mink Farms In Poland
The Lancet Microbe: Ecology of SARS-CoV-2 in the Post-Pandemic Era
Preprint: Wildlife Exposure to SARS-CoV-2 Across a Human Use Gradient
