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Understanding pathogen emergence in new host species is fundamental for developing prevention and response plans for human and animal health. We leveraged a large-scale surveillance dataset coordinated by United States Department of Agriculture, Animal and Plant Health Inspection Service and State Natural Resources Agencies to quantify the outbreak dynamics of SARS-CoV-2 in North American white-tailed deer (Odocoileus virginianus; WTD) throughout its range in the United States. Local epidemics in WTD were well approximated by a single-outbreak peak followed by fade out. Outbreaks peaked early in the northeast and mid-Atlantic. Local effective reproduction ratios of SARS-CoV-2 were between 1 and 2.5. Ten percent of variability in peak prevalence was explained by human infection pressure. This, together with the similar peak infection prevalence times across many counties and single-peak outbreak dynamics followed by fade out, suggest that widespread transmission via human-to-deer spillover may have been an important driver of the patterns and persistence. We provide a framework for inferring population-level epidemiological processes through joint analysis of many sparsely observed local outbreaks (landscape-scale surveillance data) and linking epidemiological parameters to ecological risk factors. The framework combines mechanistic and statistical models that can identify and track local outbreaks in long-term infection surveillance monitoring data. [ABSTRACT FROM AUTHOR]

The epidemiological situation of SARS‐CoV‐2 in humans and animals is continually evolving. To date, animal species known to transmit SARS‐CoV‐2 are American mink, raccoon dog, cat, ferret, hamster, house mouse, Egyptian fruit bat, deer mouse and white‐tailed deer. Among farmed animals, American mink have the highest likelihood to become infected from humans or animals and further transmit SARS‐CoV‐2. In the EU, 44 outbreaks were reported in 2021 in mink farms in seven MSs, while only six in 2022 in two MSs, thus representing a decreasing trend. The introduction of SARS‐CoV‐2 into mink farms is usually via infected humans; this can be controlled by systematically testing people entering farms and adequate biosecurity. The current most appropriate monitoring approach for mink is the outbreak confirmation based on suspicion, testing dead or clinically sick animals in case of increased mortality or positive farm personnel and the genomic surveillance of virus variants. The genomic analysis of SARS‐CoV‐2 showed mink‐specific clusters with a potential to spill back into the human population. Among companion animals, cats, ferrets and hamsters are those at highest risk of SARS‐CoV‐2 infection, which most likely originates from an infected human, and which has no or very low impact on virus circulation in the human population. Among wild animals (including zoo animals), mostly carnivores, great apes and white‐tailed deer have been reported to be naturally infected by SARS‐CoV‐2. In the EU, no cases of infected wildlife have been reported so far. Proper disposal of human waste is advised to reduce the risks of spill‐over of SARS‐CoV‐2 to wildlife. Furthermore, contact with wildlife, especially if sick or dead, should be minimised. No specific monitoring for wildlife is recommended apart from testing hunter‐harvested animals with clinical signs or found‐dead. Bats should be monitored as a natural host of many coronaviruses. [ABSTRACT FROM AUTHOR]

Many countries have reported severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infections in mink, and transmission back to humans has raised the concern of novel variants emerging in these animals. The monitoring system on Polish mink farms detected SARS-CoV-2 infection first in January 2021 and has been kept in place since then. Oral swab samples collected between February 2021 and March 2022 from 11,853 mink from 594 farms in different regions of Poland were screened molecularly for SARS-CoV-2. Isolates from those with the highest loads of viral genetic material from positive farms were sequenced and phylogenetically analysed. Serological studies were also carried out for one positive farm in order to follow the antibody response after infection. SARS-CoV-2 RNA was detected in mink on 11 farms in 8 out of 16 Polish administrative regions. Whole genome sequences were obtained for 19 SARS-CoV-2 strains from 10 out of 11 positive farms. These genomes belonged to four different variants of concern (VOC) – VOC-Gamma (20B), VOC-Delta (21J), VOC-Alpha (20I) and VOC-Omicron (21L) – and seven different Pango lineages – B.1.1.464, B.1.1.7, AY.43, AY.122, AY.126, B.1.617.2 and BA.2. One of the nucleotide and amino acid mutations specific for persistent strains found in the analysed samples was the Y453F host adaptation mutation. Serological testing of blood samples revealed a high rate of seroprevalence on the single mink farm studied. Farmed mink are highly susceptible to infection with SARS-CoV-2 of different lineages, including Omicron BA.2 VOC. As these infections were asymptomatic, mink may become an unnoticeable virus reservoir generating new variants potentially threatening human health. Therefore, real-time monitoring of mink is extremely important in the context of the One Health approach. [ABSTRACT FROM AUTHOR]