Surveillance for SARS-CoV-2 in Norway Rats (Rattus norvegicus) from Southern Ontario

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from wildlife has raised concerns about spillover from humans to animals, the establishment of novel wildlife reservoirs, and the potential for future outbreaks caused by variants of wildlife origin. Norway rats (Rattus norvegicus) are abundant in urban areas and live in close proximity to humans, providing the opportunity for spillover of SARS-CoV-2. Evidence of SARS-CoV-2 infection and exposure has been reported in Norway rats. We investigated SARS-CoV-2 infection and exposure in Norway rats from Southern Ontario, Canada. From October 2019 to June 2021, 224 rats were submitted by collaborating pest control companies. The majority of samples were collected in Windsor (79.9%;n = 179), Hamilton (13.8%;n = 31), and the Greater Toronto Area (5.8%;n = 13). Overall, 50.0% (n = 112) were female and most rats were sexually mature (55.8%;n = 125). Notably, 202 samples were collected prior to the emergence of variants of concern (VOC) and 22 were collected while the Alpha variant (B.1.1.7) was the predominant circulating VOC in humans. Nasal turbinate (n = 164) and small intestinal (n = 213) tissue samples were analyzed for SARS-CoV-2 RNA by RT-PCR. Thoracic cavity fluid samples (n = 213) were tested for neutralizing antibodies using a surrogate virus neutralization test (sVNT) (GenScript cPass);confirmatory plaque reduction neutralization test (PRNT) was conducted on presumptive positive samples. We did not detect SARS-CoV-2 RNA in any samples tested. Two out of eleven samples positive on sVNT had neutralizing antibodies confirmed positive by PRNT (1 : 40 and 1 : 320 PRNT70);both were collected prior to the emergence of VOC. It is imperative that efforts to control and monitor SARS-CoV-2 include surveillance of rats and other relevant wildlife species as novel variants continue to emerge.

Game meat procurement market in Poland in 2009-2021

Procurement of game animals is a major source of revenue for hunting clubs in Poland. For several years, the game meat buying market has been showing an upward trend, but this situation is also influenced by random factors that negatively affect the value of the game meat buying market. For several years in our country we have been struggling with the ASF virus, and since 2020, negative effects in the economy related to the occurrence of the SARS-CoV virus have been observed, also affecting the hunting sector with its activities. The aim of the study was to analyze the dynamics of game meat procurement in Poland in the years 2009-2021. The data concerned the three most important species, namely deer, roe deer and wild boar. The analysis covered the quantity of game meat, procurement value and the average price of game meat depending on animal species. The conducted research confirmed an upward trend in the volume and value of game meat procurement for all the analysed game species. Similarly, the average procurement prices of roe dee and wild boar meat with the exception of red deer, showed an upward trend. The study confirmed the negative impact of the ASF virus and the SARS-CoV-2 virus on the game meat buying market in Poland.

The effect of COVID-19 confinement on the activity behaviour of red deer.

The COVID-19 pandemic has drastically affected people's social habits, especially those related to outdoor activities. We intended to understand the effects of the two national lockdowns in Portugal on the presence and activity of a wild population of red deer (Cervus elaphus) by analysing data from camera traps installed at Lousã mountain, in the central part of Portugal. The cameras were set between 2019 and 2021, and a total of 2434 individual contacts of red deer and 182 contacts of people were recorded. Results showed a higher human presence in the mountain area during the COVID-19 outbreak, especially during the first lockdown in 2020 (0.05 ± 0.17 individuals/day), compared to the same period of the year before the pandemic (0.02 ± 0.05 individuals/day), which resulted in an increase of people by 150%. The increase in human presence did not have a significant direct effect on the presence of red deer. Despite the low overlap of activity patterns between people and red deer, deer showed avoidance behaviour in the 24 h after the detection of human presence on camera traps, as well as an increase in daily activity during the 2020 lockdown, showing red deer's awareness of human visitation. These results showed that people's increased search for cultural services in wild environments during COVID-19 lockdowns, such as hiking and biking, seemed to influence the population of red deer, albeit momentarily.

Covid-19: A Multi-Host Pandemic

SARS-CoV-2, the causal agent of the COVID-19 pandemic, is related to a group of viruses (Sarbecovirus) that circulate in horseshoe bats. Its origin is still uncertain, as there is lack of an identifiable intermediate host species for the proximal animal ancestor of SARS-CoV-2. Irrespective of its origin, SARS-CoV-2 has been shown to replicate in many mammalian species. So far, over forty species have been found to be susceptible to SARS-CoV-2 infection, and natural infections have been documented in at least 23 species of distant mammalian orders, including Primata, Rodentia, Carnivora, and Arthiodactyla. In two of those species, minks and white tailed deer, continued transmission among conspecifics occurred following introduction of SARS-CoV-2 from humans, at a rate which makes mink farms and deer populations suitable compartments where the virus may be maintained and evolve, and then perhaps spill back to humans or other animals as a new variant, as suggested by molecular evidence. Considering the above, what is truly unique about this pandemic, and adds a major obstacle to attain its control, is its multi-host nature. This is another compelling example of the relevance of the 'One Health' approach. This approach recognizes the inextricable links between people and nature, and visualizes the health and disease phenomenon from an integrative perspective. The COVID-19 pandemic urges us to acknowledge the interconnection between people and the remaining forms of life, and with the environments they share, and demonstrates that the improvement of global health needs a collaborative, multisectoral, and transdisciplinary approach, acting at the local, regional and global levels. This concept becomes paramount when taking into account that most diseases affecting humans in the last decades -not only COVID-19 - have been caused by pathogens originated in animals.Copyright © 2023

Serosurveillance for Severe Acute Respiratory Syndrome Coronavirus 2 Antibody in Feral Swine and White-Tailed Deer in Texas.

Background: Serological evidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has been reported in white-tailed deer (WTD) in the United States and Canada. Even though WTD are susceptible to SARS-CoV-2 infection, there is no evidence of infection by this virus in other mammalian species that might interact with WTD in nature. Similar to WTD, feral swine are widely distributed and generally occupy the same range as WTD in Texas. The objective of this study was to determine the prevalence of SARS-CoV-2 neutralizing antibody in WTD during 2020 and 2021 and determine the prevalence of SARS-CoV-2 neutralizing antibody in feral swine during 2018 (prepandemic period) and from March 2020 to February 2021 (pandemic period) in Travis County, Texas. Materials and Methods: Sera samples were collected from hunter-killed WTD and feral swine during the prepandemic and pandemic period and tested for SARS-CoV-2 antibody by a plaque reduction neutralization assay in Vero cells. Results: SARS-CoV-2 antibody was not detected in any of the 166 feral swine sera samples, including 24 samples collected during the prepandemic and 142 samples collected during the pandemic period. Furthermore, SARS-CoV-2 antibody was not detected in the 115 WTD samples collected during late 2020, but antibody was detected in WTD in early 2021. Conclusions: The results indicated that SARS-CoV-2 infection of WTD occurred during early 2021 in Travis County, Texas, but serological evidence of SARS-CoV-2 infection was not detected in the feral swine samples collected from the same locality and during the same time period of the collection of WTD samples.

Cervids ACE2 Residues that Bind the Spike Protein can Provide Susceptibility to SARS-CoV-2.

The susceptibility of the white-tailed deer (WTD; Odocoileus virginianus) to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted cervids as coronavirus reservoirs. This study aimed to evaluate the angiotensin-converting enzyme 2 (ACE2) residues which bind the spike protein of SARS-CoV-2 from 16 cervids to predict their potential susceptibility to SARS-CoV-2 infection. Eleven out of 16 species presented identical ACE2 key residues to WTD ACE2. Four cervids presented K31N, a variant associated with low SARS-CoV-2 susceptibility. Large herding of cervids with ACE2 key residues identical to that of the WTD can result in extensive reservoirs of SARS-CoV-2. Cervids as potential reservoirs could favor SARS-CoV-2 adaptation and the emergence of new coronavirus strains.

Identifying Potential Super-Spreaders and Disease Transmission Hotspots Using White-Tailed Deer Scraping Networks.

White-tailed deer (Odocoileus virginianus, WTD) spread communicable diseases such the zoonotic coronavirus SARS-CoV-2, which is a major public health concern, and chronic wasting disease (CWD), a fatal, highly contagious prion disease occurring in cervids. Currently, it is not well understood how WTD are spreading these diseases. In this paper, we speculate that "super-spreaders" mediate disease transmission via direct social interactions and indirectly via body fluids exchanged at scrape sites. Super-spreaders are infected individuals that infect more contacts than other infectious individuals within a population. In this study, we used network analysis from scrape visitation data to identify potential super-spreaders among multiple communities of a rural WTD herd. We combined local network communities to form a large region-wide social network consisting of 96 male WTD. Analysis of WTD bachelor groups and random network modeling demonstrated that scraping networks depict real social networks, allowing detection of direct and indirect contacts, which could spread diseases. Using this regional network, we model three major types of potential super-spreaders of communicable disease: in-degree, out-degree, and betweenness potential super-spreaders. We found out-degree and betweenness potential super-spreaders to be critical for disease transmission across multiple communities. Analysis of age structure revealed that potential super-spreaders were mostly young males, less than 2.5 years of age. We also used social network analysis to measure the outbreak potential across the landscape using a new technique to locate disease transmission hotspots. To model indirect transmission risk, we developed the first scrape-to-scrape network model demonstrating connectivity of scrape sites. Comparing scrape betweenness scores allowed us to locate high-risk transmission crossroads between communities. We also monitored predator activity, hunting activity, and hunter harvests to better understand how predation influences social networks and potential disease transmission. We found that predator activity significantly influenced the age structure of scraping communities. We assessed disease-management strategies by social-network modeling using hunter harvests or removal of potential super-spreaders, which fragmented WTD social networks reducing the potential spread of disease. Overall, this study demonstrates a model capable of predicting potential super-spreaders of diseases, outlines methods to locate transmission hotspots and community crossroads, and provides new insight for disease management and outbreak prevention strategies.

SRC: Superior Robustness of COVID-19 Detection from Noisy Cough Data Using GFCC

This research is focused on a highly effective and untapped feature called gammatone frequency cepstral coefficients (GFCC) for the detection of COVID-19 by using the nature-inspired meta-heuristic algorithm of deer hunting optimization and artificial neural network (DHO-ANN). The noisy crowdsourced cough datasets were collected from the public domain. This research work claimed that the GFCC yielded better results in terms of COVID-19 detection as compared to the widely used Mel-frequency cepstral coefficient in noisy crowdsourced speech corpora. The proposed algorithm's performance for detecting COVID-19 disease is rigorously validated using statistical measures, F1 score, confusion matrix, specificity, and sensitivity parameters. Besides, it is found that the proposed algorithm using GFCC performs well in terms of detecting the COVID-19 disease from the noisy crowdsourced cough dataset, COUGHVID. Moreover, the proposed algorithm and undertaken feature parameters have improved the detection of COVID-19 by 5% compared to the existing methods. © 2023 CRL Publishing. All rights reserved.

Stability of SARS-CoV-2 in Biological Fluids of Animals.

Since its first emergence in 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to evolve genetically, jump species barriers, and expand its host range. There is growing evidence of interspecies transmission including infection of domestic animals and widespread circulation in wildlife. However, knowledge of SARS-CoV-2 stability in animal biological fluids and their role in transmission is still limited as previous studies focused on human biological fluids. Therefore, this study aimed to determine the SARS-CoV-2 stability in biological fluids from three animal species, cats, sheep and white-tailed deer (WTD). Saliva, feces, 10% fecal suspensions, and urine of cats, sheep, and WTD were mixed with a known concentration of virus and incubated under indoor and three different climatic conditions. Our results show that the virus was stable for up to 1 day in the saliva of cats, sheep, and WTD regardless of the environmental conditions. The virus remained infectious for up to 6 days in feces and 15 days in fecal suspension of WTD, whereas the virus was rather unstable in cat and sheep feces and fecal suspensions. We found the longest survival of SARS-CoV-2 in the urine of cats, sheep, and WTD. Furthermore, side-by-side comparison with different SARS-CoV-2 strains showed that the Alpha, Delta, and Omicron variants of concern were less stable than the ancestral Wuhan-like strain in WTD fecal suspension. The results of our study provide valuable information for assessing the potential role of various animal biological fluids in SARS-CoV-2 transmission.

White-tailed deer (Odocoileus virginianus) may serve as a wildlife reservoir for nearly extinct SARS-CoV-2 variants of concern.

The spillover of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from humans to white-tailed deer (WTD) and its ability to transmit from deer to deer raised concerns about the role of WTD in the epidemiology and ecology of the virus. Here, we present a comprehensive cross-sectional study assessing the prevalence, genetic diversity, and evolution of SARS-CoV-2 in WTD in the State of New York (NY). A total of 5,462 retropharyngeal lymph node samples collected from free-ranging hunter-harvested WTD during the hunting seasons of 2020 (Season 1, September to December 2020, n = 2,700) and 2021 (Season 2, September to December 2021, n = 2,762) were tested by SARS-CoV-2 real-time RT-PCR (rRT-PCR). SARS-CoV-2 RNA was detected in 17 samples (0.6%) from Season 1 and in 583 samples (21.1%) from Season 2. Hotspots of infection were identified in multiple confined geographic areas of NY. Sequence analysis of SARS-CoV-2 genomes from 164 samples demonstrated the presence of multiple SARS-CoV-2 lineages and the cocirculation of three major variants of concern (VOCs) (Alpha, Gamma, and Delta) in WTD. Our analysis suggests the occurrence of multiple spillover events (human to deer) of the Alpha and Delta lineages with subsequent deer-to-deer transmission and adaptation of the viruses. Detection of Alpha and Gamma variants in WTD long after their broad circulation in humans in NY suggests that WTD may serve as a wildlife reservoir for VOCs no longer circulating in humans. Thus, implementation of continuous surveillance programs to monitor SARS-CoV-2 dynamics in WTD is warranted, and measures to minimize virus transmission between humans and animals are urgently needed.

Parainfluenza and corona viruses in a fallow deer (Dama dama) with fatal respiratory disease.

Parainfluenza virus type 3 (PIV-3) and coronaviruses (CoV) are commonly found in respiratory tracts of ruminants and capable of causing clinical disease. Here, we investigated the cause of ill-thrift and sudden death in a five-month-old male fallow deer which occurred in December 2019. The calf was one of the five calves in a herd of 170 deer that, along with three adult hinds, died during a 2-week period. The deer calves were in a shed, sharing airspace with young cattle that had been reported to be coughing. Significant gross pathology was observed in the respiratory and alimentary tracts of the deer calf and histopathology of the lung and trachea was suggestive of likely involvement of PIV-3. Strong and specific cytoplasmic labeling of bronchiolar epithelium and terminal airway, alike those seen with PIV-3 pneumonia in cattle, was observed using a polyclonal bovine PIV-3 antibody. Metagenomic analysis detected a PIV-3 and a CoV in the lung tissue. The PIV-3 L protein gene had the highest sequence identity with those of bovine PIV-3 (83.1 to 98.4%) and phylogenetically clustered with bovine PIV-3 in the genotype C. The CoV spike protein gene shared 96.7% to 97.9% sequence identity with those of bovine CoVs, but only 53.1% identity with SARS-CoV-2 reference virus. We believe this is the first report of PIV-3 and CoV co-infection in fallow deer and their association with fatal pneumonia; major pathology caused by PIV-3.

SARS-CoV-2 Omicron (B.1.1.529) Infection of Wild White-Tailed Deer in New York City.

There is mounting evidence of SARS-CoV-2 spillover from humans into many domestic, companion, and wild animal species. Research indicates that humans have infected white-tailed deer, and that deer-to-deer transmission has occurred, indicating that deer could be a wildlife reservoir and a source of novel SARS-CoV-2 variants. We examined the hypothesis that the Omicron variant is actively and asymptomatically infecting the free-ranging deer of New York City. Between December 2021 and February 2022, 155 deer on Staten Island, New York, were anesthetized and examined for gross abnormalities and illnesses. Paired nasopharyngeal swabs and blood samples were collected and analyzed for the presence of SARS-CoV-2 RNA and antibodies. Of 135 serum samples, 19 (14.1%) indicated SARS-CoV-2 exposure, and 11 reacted most strongly to the wild-type B.1 lineage. Of the 71 swabs, 8 were positive for SARS-CoV-2 RNA (4 Omicron and 4 Delta). Two of the animals had active infections and robust neutralizing antibodies, revealing evidence of reinfection or early seroconversion in deer. Variants of concern continue to circulate among and may reinfect US deer populations, and establish enzootic transmission cycles in the wild: this warrants a coordinated One Health response, to proactively surveil, identify, and curtail variants of concern before they can spill back into humans.

SARS-CoV-2 variants of concerns in animals: An unmonitored rising health threat.

Recent findings have highlighted the urgency for rapidly detecting and characterizing SARS-CoV-2 variants of concern in companion and wild animals. The significance of active surveillance and genomic investigation on these animals could pave the way for more understanding of the viral circulation and how the variants emerge. It enables us to predict the next viral challenges and prepare for or prevent these challenges. Horrible neglect of this issue could make the COVID-19 pandemic a continuous threat. Continuing to monitor the animal-origin SARS-CoV-2, and tailoring prevention and control measures to avoid large-scale community transmission in the future caused by the virus leaping from animals to humans, is essential. The reliance on only developing vaccines with ignoring this strategy could cost us many lives. Here, we discuss the most recent data about the transmissibility of SARS-CoV-2 variants of concern (VOCs) among animals and humans.

SARS-CoV-2 as a Zooanthroponotic Infection: Spillbacks, Secondary Spillovers, and Their Importance.

In the midst of a persistent pandemic of a probable zoonotic origin, one needs to constantly evaluate the interplay of SARS-CoV-2 (severe acute respiratory syndrome-related coronavirus-2) with animal populations. Animals can get infected from humans, and certain species, including mink and white-tailed deer, exhibit considerable animal-to-animal transmission resulting in potential endemicity, mutation pressure, and possible secondary spillover to humans. We attempt a comprehensive review of the available data on animal species infected by SARS-CoV-2, as presented in the scientific literature and official reports of relevant organizations. We further evaluate the lessons humans should learn from mink outbreaks, white-tailed deer endemicity, zoo outbreaks, the threat for certain species conservation, the possible implication of rodents in the evolution of novel variants such as Omicron, and the potential role of pets as animal reservoirs of the virus. Finally, we outline the need for a broader approach to the pandemic and epidemics, in general, incorporating the principles of One Health and Planetary Health.

Wild Red Deer (Cervus elaphus) Do Not Play a Role as Vectors or Reservoirs of SARS-CoV-2 in North-Eastern Poland.

Several studies reported a high prevalence of SARS-CoV-2 among white-tailed deer in North America. Monitoring cervids in all regions to better understand SARS-CoV-2 infection and circulation in other deer populations has been urged. To evaluate deer exposure and/or infection to/by SARS-CoV-2 in Poland, we sampled 90 red deer shot by hunters in five hunting districts in north-eastern Poland. Serum and nasopharyngeal swabs were collected, and then an immunofluorescent assay (IFA) to detect anti-SARS-CoV-2 antibodies was performed as well as real-time PCR with reverse transcription for direct virus detection. No positive samples were detected. There is no evidence of spillover of SARS-CoV-2 from the human to deer population in Poland.

A meta heuristic approach for reliable capacitated facility joint inventory-location problem with round-trip transportation under imperfect information of disruption in a Fuzzy environment

In today’s systems and networks, disruption is inevitable. Designing a reliable system to overcome probable facility disruptions plays a crucial role in planning and management. This article proposes a reliable capacitated facility joint inventory-location problem where location-independent disruption may occur in facilities. The system tries to satisfy customer’s demands and considers penalty costs for unmet customer demand. The article aims to minimize total costs such as establishing inventory, uncovered demand’s penalty, and transportation costs. While many articles in this area only use exact methods to solve the problem, this article uses a metaheuristic algorithm, the red deer algorithm, and the exact methods. Various numerical examples have shown the outstanding performance of the red deer algorithm compared to exact methods. Sensitivity analyses show the impacts of various parameters on the objective function and the optimal facility layouts. Lastly, managerial insights will be proposed based on sensitivity analysis.

Multiple Introductions of SARS-CoV-2 Alpha and Delta Variants into White-Tailed Deer in Pennsylvania.

The SARS-CoV-2 pandemic began by viral spillover from animals to humans; today multiple animal species are known to be susceptible to infection. White-tailed deer, Odocoileus virginianus, are infected in North America at substantial levels, and genomic data suggests that a variant in deer may have spilled back to humans. Here, we characterize SARS-CoV-2 in deer from Pennsylvania (PA) sampled during fall and winter 2021. Of 123 nasal swab samples analyzed by RT-qPCR, 20 (16.3%) were positive for SARS-CoV-2. Seven whole genome sequences were obtained, together with six more partial spike gene sequences. These annotated as alpha and delta variants, the first reported observations of these lineages in deer, documenting multiple new jumps from humans to deer. The alpha lineage persisted in deer after its displacement by delta in humans, and deer-derived alpha variants diverged significantly from those in humans, consistent with a distinctive evolutionary trajectory in deer. IMPORTANCE Coronaviruses have been documented to replicate in numerous species of vertebrates, and multiple spillovers of coronaviruses from animals into humans have founded human epidemics. The COVID-19 epidemic likely derived from a spillover of SARS-CoV-2 from bats into humans, possibly via an intermediate host. There are now several examples of SARS-CoV-2 jumping from humans into other mammals, including mink and deer, creating the potential for new animal reservoirs from which spillback into humans could occur. For this reason, data on formation of new animal reservoirs is of great importance for understanding possible sources of future infection. Here, we identify extensive infection in white-tailed deer in Pennsylvania, including what appear to be multiple independent transmissions. Data further suggests possible transmission among deer. These data thus help identify a potential new animal reservoir and provide background information relevant to its management.

Persistence of SARS-CoV-2 neutralizing antibodies longer than 13 months in naturally infected, captive white-tailed deer (Odocoileus virginianus), Texas.

After identifying a captive herd of white-tailed deer in central Texas with >94% seroprevalence with SARS-CoV-2 neutralizing antibodies in September 2021, we worked retrospectively through archived serum samples of 21 deer and detected seroconversion of all animals between December 2020 and January 2021. We then collected prospective samples to conclude that the duration of persistence of neutralizing antibodies is at least 13 months for 19 (90.5%) of the animals, with two animals converting to seronegative after six and eight months. Antibody titres generally waned over this time frame, but three deer had a temporary 4- to 8-fold increases in plaque reduction neutralization test titres over a month after seroconversion; anamnestic response cannot be ruled out.

Upper Midwest tribal natural resource managers' perspectives on chronic wasting disease outreach, surveillance, and management

Management strategies for chronic wasting disease (CWD) across tribal lands have varied in response to changing dynamics of CWD risk. As CWD continues to spread across the United States, concerns associated with the disease are increasing. We interviewed 19 natural resource managers representing Anishinaabe and Dakota tribes in Minnesota, Michigan, and Wisconsin with goals of understanding needs and opportunities for CWD engagement, surveillance, and outreach on tribal lands;the implementation of natural resources policy and management across tribal nations;and opportunities for tribal partnership‐development to control CWD. Qualitative data analyses of interview responses revealed substantial variation in the number of tribal hunters, hunter regulation, and huntable tribal lands across our study area. Proximity of tribal lands in relation to CWD detections impacted tribal agency management strategies for CWD. Our results indicate a desire for CWD outreach and surveillance, mutually beneficial collaborations, and a need for incorporating cultural knowledge into CWD management strategies. We conclude that tribal CWD management and surveillance plans will be enhanced through strategic and thoughtful CWD outreach methods. Moreover, partnerships must recognize tribal sovereignty and respectfully integrate tribal values, knowledge, and worldview.

Quarterly report of investigations of suspected exotic diseases: July to September 2021

Exotic pest and disease investigations are managed and reported by the Ministry for Primary Industries' (MPI's) Diagnostic and Surveillance Directorate. This article presents a summary of investigations of suspect exotic and emerging pests and diseases in New Zealand during the period from July to September 2021.